Transient information flow in a network of excitatory and inhibitory model neurons: role of noise and signal autocorrelation.
We investigate the performance of sparsely-connected networks of integrate-and-fire neurons for ultra-short term information processing. We exploit the fact that the population activity of networks with balanced excitation and inhibition can switch from an oscillatory firing regime to a state of asynchronous irregular firing or quiescence depending on the rate of external background spikes. We find that in terms of information buffering the network performs best for a moderate, non-zero, amount of noise. Analogous to the phenomenon of stochastic resonance the performance decreases for higher and lower noise levels. The optimal amount of noise corresponds to the transition zone between a quiescent state and a regime of stochastic dynamics. This provides a potential explanation of the role of non-oscillatory population activity in a simplified model of cortical micro-circuits.


Prostate cancer clinical trials of the Southwest Oncology Group.
The changing clinical dynamics of prostate cancer have resulted in a broadening of the research focus of the Genitourinary (GU) Cancer Committee of the Southwest Oncology Group (SWOG). Beginning with an emphasis on hormone-refractory disease in its early years, SWOG prostate cancer trials now cover the entire spectrum of the disease: localized, locally advanced, metastatic and hormone-refractory disease. As the world's largest GU cancer research group, the GU committee of SWOG has pioneered studies in combined androgen therapy for metastatic disease, quality-of-life (QOL) assessments for patients with localized and advanced disease, adjuvant therapy models, and prostate cancer chemoprevention. The committee has also formed the GU Global Group, whose purpose is to convene the chairs of the GU committees of all the major national and international oncology cooperative groups. Meeting semiannually, this group discusses activities within their respective organizations, plans collaborative strategies and protocols, and establishes global strategy in prostate cancer clinical research. The future directions of national and international prostate cancer trials will build on this broad foundation of well-conceived, logically sequenced studies.


Electroporation Method for In Vivo Delivery of Plasmid DNA in the Adult Zebrafish Telencephalon.
Electroporation is a transfection method in which an electrical field is applied to cells to create temporary pores in a cell membrane and increase its permeability, thereby allowing different molecules to be introduced to the cell. In this paper, electroporation is used to introduce plasmids to ependymoglial cells, which line the ventricular zone of the adult zebrafish telencephalon. A fraction of these cells shows stem cell properties and generates new neurons in the zebrafish brain; therefore, studying their behavior is essential to determine their roles in neurogenesis and regeneration. The introduction of plasmids via electroporation enables long-term labeling and tracking of a single ependymoglial cell. Furthermore, plasmids such as Cre recombinase or Cas9 can be delivered to single ependymoglial cells, which enables gene recombination or gene editing and provides a unique opportunity to assess the cell's autonomous gene function in a controlled, natural environment. Finally, this detailed, step-by-step electroporation protocol is used to obtain successful introduction of plasmids into a large number of single ependymoglial cells.


Genetic dissection of sympatric populations of brown planthopper, Nilaparvata lugens (Stål), using DALP-PCR molecular markers.
Direct amplified length polymorphism (DALP) combines the advantages of a high-resolution fingerprint method and also characterizing the genetic polymorphisms. This molecular method was also found to be useful in brown planthopper, Nilaparvata lugens species complex for the analysis of genetic polymorphisms. A total of 11 populations of Nilaparvata spp. were collected from 6 locations from Malaysia. Two sympatric populations of brown planthopper, N. lugens, one from rice and the other from a weed grass (Leersia hexandra), were collected from each of five locations. N. bakeri was used as an out group. Three oligonucleotide primer pairs, DALP231/DALPR'5, DALP234/DALPR'5, and DALP235/DALPR'5 were applied in this study. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on genetic distances for the 11 populations of Nilaparvata spp. revealed that populations belonging to the same species and the same host type clustered together irrespective of their geographical localities of capture. The populations of N. lugens formed into two distinct clusters, one was insects with high esterase activities usually captured from rice and the other was with low esterase activities usually captured from L. hexandra. N. bakeri, an out group, was the most isolated group. Analyses of principal components, molecular variance, and robustness also supported greatly to the findings of cluster analysis.


Experimental Multicenter and Multivendor Evaluation of the Performance of PET Radiomic Features Using 3-Dimensionally Printed Phantom Inserts.
The sensitivity of radiomic features to several confounding factors, such as reconstruction settings, makes clinical use challenging. To investigate the impact of harmonized image reconstructions on feature consistency, a multicenter phantom study was performed using 3-dimensionally printed phantom inserts reflecting realistic tumor shapes and heterogeneity uptakes. Methods: Tumors extracted from real PET/CT scans of patients with non-small cell lung cancer served as model for three 3-dimensionally printed inserts. Different heterogeneity pattern were realized by printing separate compartments that could be filled with different activity solutions. The inserts were placed in the National Electrical Manufacturers Association image-quality phantom and scanned various times. First, a list-mode scan was acquired and 5 statistically equal replicates were reconstructed. Second, the phantom was scanned 4 times on the same scanner. Third, the phantom was scanned on 6 PET/CT systems. All images were reconstructed using EANM Research Ltd. (EARL)-compliant and locally clinically preferred reconstructions. EARL-compliant reconstructions were performed without (EARL1) or with (EARL2) point-spread function. Images were analyzed with and without resampling to 2-mm cubic voxels. Images were discretized with a fixed bin width (FBW) of 0.25 and a fixed bin number (FBN) of 64. The intraclass correlation coefficient (ICC) of each scan setup was calculated and compared across reconstruction settings. An ICC above 0.75 was regarded as high. Results: The percentage of features yielding a high ICC was largest for the statistically equal replicates (70%-91% for FBN; 90%-96% for FBW discretization). For scans acquired on the same system, the percentage decreased, but most features still resulted in a high ICC (FBN, 52%-63%; FBW, 75%-85%). The percentage of features yielding a high ICC decreased more in the multicenter setting. In this case, the percentage of features yielding a high ICC was larger for images reconstructed with EARL-compliant reconstructions: for example, 40% for EARL1 and 60% for EARL2 versus 21% for the clinically preferred setting for FBW discretization. When discretized with FBW and resampled to isotropic voxels, this benefit was more pronounced. Conclusion: EARL-compliant reconstructions harmonize a wide range of radiomic features. FBW discretization and a sampling to isotropic voxels enhances the benefits of EARL-compliant reconstructions.


Selective anticancer effects and protection from chemotherapy by the botanical compound LCS101: Implications for cancer treatment.
There is a need for new options for reducing the side effects of cancer treatment, without compromising efficacy, enabling patients to complete treatment regimens. The botanical compound LCS101 exhibits inhibitory effects on cancer cell growth, and reduces chemotherapy-induced hematological toxicities. The aim of the present study is to examine the selectivity of the effects of the compound, alone and in conjunction with conventional chemotherapy agents, on cancer cell proliferation. The effects of LCS101 were tested on a number of cancer cell lines (breast, MCF7, MDA-MB‑231; colorectal, HCT116; prostate, PC-3, DU-145) and on non-tumorigenic normal human epithelial cells (breast, MCF10A; prostate, EP#2). Cell viability was analyzed using an XTT assay and observed by light microscopy. Necrosis and apoptosis were examined using FACS analysis and immunoblotting. LCS101 selectively induced cell death in breast, colon and prostate cancer cell lines, as measured by XTT assay. Light microscopy and FACS analysis showed changes indicative of a necrotic process. LCS101 was also found to induce PARP-1 reduction in breast cancer cells, with no effect on non-tumorigenic breast epithelial cells. While LCS101 increased cell death in cancer cells exposed to doxorubicin and 5-FU, it showed a protective effect on non-tumorigenic human epithelial cells from chemotherapy-induced cell death. A similar selective effect was observed with apoptosis-associated PARP-1 cleavage. The findings demonstrate that the anti-proliferative effects exhibited by the botanical compound LCS101 are selective to cancer cells, and offer protection to non-tumorigenic normal epithelial cells from chemotherapy agents.


You don't bring me anything but down: adolescent romance and depression.
What accounts for the sex difference in depression that emerges during the period of adolescence? We propose that females become more depressed than males in adolescence partly as a consequence of their involvement in romantic relationships. Using two waves of data from the National Longitudinal Study of Adolescent Health (N = 8,181), a study which began interviewing respondents in 1994, we compare change in levels of depression for adolescents with and without romantic involvement between interviews. Our results suggest that males and females who become romantically involved between interviews experience a larger increase in depression than their counterparts who do not; however, females experience a larger increase in depression than males in response to romantic involvement. Our results suggest that females' greater vulnerability to romantic involvement explains a large part of the emerging sex difference in depression during adolescence.


Cohesin: a catenase with separate entry and exit gates?
Cohesin confers both intrachromatid and interchromatid cohesion through formation of a tripartite ring within which DNA is thought to be entrapped. Here, I discuss what is known about the four stages of the cohesin ring cycle using the ring model as an intellectual framework. I postulate that cohesin loading onto chromosomes, catalysed by a separate complex called kollerin, is mediated by the entry of DNA into cohesin rings, whereas dissociation, catalysed by Wapl and several other cohesin subunits (an activity that will be called releasin here), is mediated by the subsequent exit of DNA. I suggest that the ring's entry and exit gates may be separate, with the former and latter taking place at Smc1-Smc3 and Smc3-kleisin interfaces, respectively. Establishment of cohesion during S phase involves neutralization of releasin through acetylation of Smc3 at a site close to the putative exit gate of DNA, which locks rings shut until opened irreversibly by kleisin cleavage through the action of separase, an event that triggers the metaphase to anaphase transition.


High Expression of p62 Protein Is Associated with Poor Prognosis and Aggressive Phenotypes in Endometrial Cancer.
High expression of SQSTM1/p62 (p62) protein, which functions as a hub of oncogenic signaling pathways, has been detected in several human cancers. However, the clinicopathological and functional contribution of p62 expression is largely unknown in endometrial cancers (ECs). In this study, we assessed the expression status of p62 in primary ECs (n = 194) by immunohistochemistry and analyzed its clinical significance. Although p62 was expressed in the cytoplasm and/or nucleus in primary ECs, we observed that an expression subtype, high expression of cytoplasmic p62 but low expression of nuclear p62 (cytoplasm(High)/nucleus(Low)), significantly correlated with nonendometrioid types (P = 0.002), high grade (P < 0.001), deep myometrial invasion (P = 0.025), vascular invasion (P = 0.012), and poor prognosis (P < 0.001), and may be an independent prognostic marker of ECs (P = 0.011). Furthermore, RNA interference-mediated inhibition of p62 expression in the HEC-1A EC cell line led to the reduction of invasiveness and resistance to oxidative stress in vitro, as well as the suppression of in vivo tumor growth in an orthotopic mouse model of ECs. High expression of cytoplasmic p62 is a novel prognostic biomarker of ECs, and excess p62 expression may functionally contribute to the acquirement of malignant phenotypes in EC cells.


Chemistry in second life.
This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.


Spatially-resolved profiling of carbon nanotube uptake across cell lines.
The internalisation and intra-cellular distribution of carbon nanotubes (CNT) has been quantitatively assessed using imaging flow cytometry. Spatial analysis of the bright field images indicates the presence of a small sub-population (5% of cells) in which the internalised CNTs are packed into pronounced clusters, visible as dark spots due to strong optical scattering by the nanotubes. The area of these spots can be used as a label-free metric of CNT dose and we assess the relative uptake of charge-neutral CNTs, over a 24 hours exposure period across four cell types: J774 mouse macrophage cells, A549 and Calu-6 human lung cancer cells, and MCF-7 human breast cells. The relative dose as indicated by the spot-area metric closely correlates to results using the same CNT preparation, conjugated to a FITC-label and shows pronounced uptake by the J774 cells leading to a mean dose that is >60% higher than for the other cell types. Spatial evaluation of dosing clusters is also used to quantify differences in uptake by J774 cells of CNTs with different surface functionalisation. While the percentage of CNT-cluster positive cells increases from 5% to 19% when switching from charge-neutral CNTs to poly-cationic, dendron functionalised CNTs, the single cell level analysis of internalised clusters indicates a lower dose per cell of poly-cationic CNTs relative to the charge-neutral CNTs. We concluded that there is dose homeostasis i.e., the population-averaged cellular dose of CNTs remained unchanged.


Confocal microscopy with a high numerical aperture parabolic mirror.
A novel high-resolution stage scanning confocal microscope for fluorescence microscopy and spatially resolved spectroscopy with a high numerical aperture (NA 1) parabolic mirror objective is investigated. A spatial resolution close to the diffraction limit is achieved. As microscopic fluorescent test objects, dye-loaded zeolite microcrystals (diameter approx. 0.4 microm) and single fluorescent molecules were used. Confocal fluorescence images show a spatial resolution of .x = 0.8 . both at room temperature and at 1.8 K. Imaging of a quasi-point light source and focusing by the parabolic mirror were investigated experimentally and theoretically. Deviations between the theoretical results for a perfect parabolic mirror and the experimental results can be attributed to small deviations of the mirror profile from an ideal parabola.


The T cell repertoire in infection and vaccination: implications for control of persistent viruses.
Most currently available vaccines target acute infectious agents such as polio, smallpox and influenza virus. The development of vaccines to persistent infectious agents has proven much more difficult. Although it is possible to generate T cell responses to such viruses, these responses are currently unable to prevent the establishment of infection, and immune control may be lost during the chronic phase. Recent advances have increased our understanding of the interactions between persistent viruses and the available T cell repertoire, and will guide approaches to the generation and maintenance of an 'ideal' T cell response.


Impact of Migration and Acculturation on Turkish Men Who Have Sex with Men in Germany: Results from the 2010 European MSM Internet Survey.
To examine the impact of migration and acculturation of Turkish men who have sex with men (MSM) to Germany, using data from the European MSM Internet Survey (EMIS-2010), on measures of acculturation including circumcision status, internalized homonegativity (IH), HIV/STI knowledge, sexual orientation, outness, HIV-testing, and sexual behaviors. We compared four groups of MSM: MSM born and residing in Germany who had completed the questionnaire in German (n = 38,915), MSM born and residing in Germany, with a father or mother born in Turkey (n = 97), MSM residing in Germany who were born in Turkey or whose parents were born in Turkey (n = 262), and MSM who were born and residing in Turkey and who completed the questionnaire in Turkish (n = 1,717). Data showed that there were significant dose-response curves between level of migration and several outcome variables. As exposure to Germany increased, MSM had lower IH, higher HIV/STI knowledge, increased outness, and were less likely to be circumcised. There were similar significant findings with regard to sexual HIV risk behavior (condomless anal intercourse with partners of unknown (or sero-discordant) HIV status). Data were consistent with acculturation over generations in immigrant groups in MSM migrating from Turkey to Germany. Integration includes both cultural aspects (circumcision) and integration into a more homopositive gay environment (IH, outness, increased HIV/STI knowledge), and sexual HIV risk behavior. Migration and associated acculturation may constitute a risk change for HIV/STI and mental health issues associated with IH and outness.


Tibia and rearfoot motion and ground reaction forces in subjects with patellofemoral pain syndrome during walking.
Abnormal subtalar joint function and the consequent rotation of the tibia during walking are thought to contribute to patellofemoral pain syndrome (PFPS). The purpose of this study was to measure rearfoot and tibia motion, and the ground reaction force (GRF) during the stance phase of walking in subjects with PFPS and compare them to healthy subjects. A four camera motion analysis system with a single force plate was used to investigate rearfoot motion relative to the tibia in three planes, the tibial transverse plane rotation and the GRF during the stance phase of walking in 13 female subjects diagnosed with PFPS and 14 healthy females. Analysis showed significantly delayed peak rearfoot eversion (p=0.02), and earlier occurrence of peak dorsiflexion (p=0.02) for the PFPS group. Furthermore, significantly lower peak medial GRF (p=0.03), minimum vertical GRF trough (p=0.02) and the second vertical GRF peak (p=0.01) were found in the PFPS group. Tibial transverse rotation was not shown to be different in PFPS subjects. However, there was prolonged rearfoot eversion during the stance phase of walking. The earlier appearance of rearfoot dorsiflexion as well as the lower GRFs indicate altered propulsive function of the foot during supination.


Thoracic gas compression during forced expiration is greater in men than women.
Intrapleural pressure during a forced vital capacity (VC) maneuver is often in excess of that required to generate maximal expiratory airflow. This excess pressure compresses alveolar gas (i.e., thoracic gas compression [TGC]), resulting in underestimated forced expiratory flows (FEFs) at a given lung volume. It is unknown if TGC is influenced by sex; however, because men have larger lungs and stronger respiratory muscles, we hypothesized that men would have greater TGC. We examined TGC across the "effort-dependent" region of VC in healthy young men (n = 11) and women (n = 12). Subjects performed VC maneuvers at varying efforts while airflow, volume, and esophageal pressure (POES ) were measured. Quasistatic expiratory deflation curves were used to obtain lung recoil (PLUNG ) and alveolar pressures (i.e., PALV = POES -PLUNG ). The raw maximal expiratory flow-volume (MEFVraw ) curve was obtained from the "maximum effort" VC maneuver. The TGC-corrected curve was obtained by constructing a "maximal perimeter" curve from all VC efforts (MEFVcorr ). TGC was examined via differences between curves in FEFs (∆FEF), area under the expiratory curves (∆AEX ), and estimated compressed gas volume (∆VGC) across the VC range. Men displayed greater total ∆AEX (5.4 ± 2.0 vs. 2.0 ± 1.5 L2 ·s-1 ; p < .001). ∆FEF was greater in men at 25% of exhaled volume only (p < .05), whereas ∆VGC was systematically greater in men across the entire VC (main effect; p < .05). PALV was also greater in men throughout forced expiration (p < .01). Taken together, these findings demonstrate that men display more TGC, occurring early in forced expiration, likely due to greater expiratory pressures throughout the forced VC maneuver.


The butterfly - a well-defined constant-current topography pattern on Si(001):H and Ge(001):H resulting from current-induced defect fluctuations.
Dangling bond (DB) arrays on Si(001):H and Ge(001):H surfaces can be patterned with atomic precision and they exhibit complex and rich physics making them interesting from both technological and fundamental perspectives. But their complex behavior often makes scanning tunneling microscopy (STM) images difficult to interpret and simulate. Recently it was shown that low-temperature imaging of unoccupied states of an unpassivated dimer on Ge(001):H results in a symmetric butterfly-like STM pattern, despite the fact that the equilibrium dimer configuration is expected to be a bistable, buckled geometry. Here, based on a thorough characterization of the low-bias switching events on Ge(001):H, we propose a new imaging model featuring a dynamical two-state rate equation. On both Si(001):H and Ge(001):H, this model allows us to reproduce the features of the observed symmetric empty-state images which strongly corroborates the idea that the patterns arise due to fast switching events and provides an insight into the relationship between the tunneling current and switching rates. We envision that our new imaging model can be applied to simulate other bistable systems where fluctuations arise from transiently charged electronic states.


A simple visual assessment technique to discriminate between menorrhagia and normal menstrual blood loss.
To validate a simple, highly predictive test to discriminate between menorrhagia and normal menstrual blood loss. The sanitary wear of 489 menstrual bleeding episodes was collected by 288 women for objective measurement of menstrual blood loss (alkaline hematin method); the women made a subjective assessment of the volume and, based on a pictorial chart, recorded the amount of and the degree to which their sanitary wear was soiled. Based on that degree, a score was calculated for each episode and a suitable cutoff point was chosen, above which the presence of menorrhagia was likely and below which it was unlikely. Using a score of 185 as the cutoff point, the predictive values of positive and negative tests were almost equally high, 85.9 and 84.8%, respectively. Whether or not the presence of clots was recorded, these values did not change. The predictive value of a woman's complaint of heavy bleeding for the presence of menorrhagia was 55.9% and that of anemia (hemoglobin less than 12.0 g/dL) was 74.4%. We validated and refined a new, simple, visual assessment technique and demonstrated that it is superior to a woman's subjective assessment of menstrual blood loss and the occurrence of anemia for predicting menorrhagia, even if it is performed only once. We also demonstrated that the volume that clots contribute to menstruation is not as large as many clinicians believe. With this technique, the quality of therapy can be enhanced by making it more adequate and rational.


Tuberculosis in UK cities: workload and effectiveness of tuberculosis control programmes.
Tuberculosis (TB) has increased within the UK and, in response, targets for TB control have been set and interventions recommended. The question was whether these had been implemented and, if so, had they been effective in reducing TB cases. Epidemiological data were obtained from enhanced surveillance and clinics. Primary care trusts or TB clinics with an average of > 100 TB cases per year were identified and provided reflections on the reasons for any change in their local incidence, which was compared to an audit against the national TB plan. Access to data for planning varied (0-22 months). Sputum smear status was usually well recorded within the clinics. All cities had TB networks, a key worker for each case, free treatment and arrangements to treat HIV co-infection. Achievement of targets in the national plan correlated well with change in workload figures for the commissioning organizations (Spearman's rank correlation R = 0.8, P < 0.01) but not with clinic numbers. Four cities had not achieved the target of one nurse per 40 notifications (Birmingham, Bradford, Manchester and Sheffield). Compared to other cities, their loss to follow-up during treatment was usually > 6% (χ2 = 4.2, P < 0.05), there was less TB detected by screening and less outreach. Manchester was most poorly resourced and showed the highest rate of increase of TB. Direct referral from radiology, sputum from primary care and outreach workers were cited as important in TB control. TB control programmes depend on adequate numbers of specialist TB nurses for early detection and case-holding.Please see related article: http://www.biomedcentral.com/1741-7015/9/127.


Catalysis of ATP-dependent homologous DNA pairing and strand exchange by yeast RAD51 protein.
The RAD51 gene of Saccharomyces cerevisiae is required for genetic recombination and DNA double-strand break repair. Here it is demonstrated that RAD51 protein pairs circular viral single-stranded DNA from phi X 174 or M13 with its respective homologous linear double-stranded form. The product of synapsis between these DNA partners is further processed by RAD51 to yield nicked circular duplex DNA, which indicates that RAD51 can catalyze strand exchange. The pairing and strand exchange reaction requires adenosine triphosphate, a result consistent with the presence of a DNA-dependent adenosine triphosphatase activity in RAD51 protein. Thus, RAD51 is a eukaryotic recombination protein that can catalyze the strand exchange reaction.


Abiotic factors shape microbial diversity in Sonoran Desert soils.
High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.


Structural and redox requirements for the action of anti-diabetic vanadium compounds.
This study presents the first systematic investigation of the anti-diabetic properties of non-oxido V(IV) complexes. In particular, the insulin-mimetic activity of [V(IV)(taci)2](4+), [V(IV)(inoH-3)2](2-), [V(IV)(dhab)2], [V(IV)(hyph(Ph))2], [V(IV)(cat)3](2-) and [V(IV)(pdbh)2]--where taci is 1,3,5-triamino-1,3,5-trideoxy-cis-inositol, ino is cis-inositol, H2dhab is 2,2'-dihydroxyazobenzene, H2hyph(Ph) is 3,5-bis(2-hydroxyphenyl)-1H-1,2,4-triazole, H2cat is catechol and H2pdbh is pentan-2,4-dione benzoylhydrazone--was evaluated in terms of free fatty acid (FFA) release. Among the six compounds examined, only [V(IV)(pdbh)2], [V(IV)(cat)3](2-) and [V(IV)(hyph(Ph))2], which at the physiological pH convert to the corresponding V(IV)O complexes, were found to exhibit a significant insulin-mimetic activity compared to VOSO4. In contrast, [V(taci)2](4+), [V(inoH-3)2](2-) and [V(dhab)2], which at pH 7.4 keep their 'bare' non-oxido structure, did not cause any inhibition of FFA. The results, therefore, suggest that a V(IV)O functionality is necessary for vanadium complexes to exhibit anti-diabetic effects. This agrees with the notion that the biotransformations of V compounds in the organism are more important than the nature of the species.


Broad cytolytic specificity of myotoxin II, a lysine-49 phospholipase A2 of Bothrops asper snake venom.
The cytotoxic activity of Bothrops asper myotoxin II, a lysine-49 phospholipase A2 isoform, on different cell types in culture, was investigated. Myotoxin II caused a dose-dependent cytolytic effect on all cell types tested, characterized by rapid release of cytoplasmic lactic dehydrogenase and drastic morphological cell alterations. Quantitative differences in the susceptibility to myotoxin II among cell types fell within a relatively narrow range, and in general, the toxin was cytolytic at concentrations of 50-100 micrograms/ml (3-7 microM), when assays were performed using culture medium as a diluent. Toxin activity was markedly enhanced if phosphate-buffered saline was utilized instead of medium. The cytotoxic activity of myotoxin III, an aspartate-49 isoform from the same venom, on both endothelial cells and skeletal muscle myoblasts was higher than that of myotoxin II, suggesting that, although phospholipase A2 activity is clearly not required for the induction of cell damage, it may have an enhancing role. In contrast to B. asper myotoxins, other basic phospholipases A2 with myotoxic activity in vivo (notexin from Notechis scutatus, and two enzymes isolated from Vipera russelli venom) did not affect endothelial cells and myoblasts. Pretreatment of cells with neuraminidase, tunicamycin, or protamine, did not alter their susceptibility to myotoxin II. At low temperatures (2-4 degrees C) myotoxin II was devoid of cytolytic effect. Washing and neutralization experiments using heparin with low affinity for antithrombin or mouse monoclonal antibody MAb-3 suggest that at low temperatures myotoxin II binds very weakly to the cells, and that its normal interaction with the putative target is probably not only based on charge, but that a membrane penetration event may be required.


Free-breathing combined three-dimensional phase sensitive late gadolinium enhancement and T1 mapping for myocardial tissue characterization.
To develop a novel MR sequence for combined three-dimensional (3D) phase-sensitive (PS) late gadolinium enhancement (LGE) and T1 mapping to allow for simultaneous assessment of focal and diffuse myocardial fibrosis. In the proposed sequence, four 3D imaging volumes are acquired with different T1 weightings using a combined saturation and inversion preparation, after administration of a gadolinium contrast agent. One image is acquired fully sampled with the inversion time selected to null the healthy myocardial signal (the LGE image). The other three images are three-fold under-sampled and reconstructed using compressed sensing. An acquisition scheme with two interleaved imaging cycles and joint navigator-gating of those cycles ensures spatial registration of the imaging volumes. T1 maps are generated using all four imaging volumes. The signal-polarity in the LGE image is restored using supplementary information from the T1 fit to generate PS-LGE images. The accuracy of the proposed method was assessed with respect to a inversion-recovery spin-echo sequence. In vivo T1 maps and LGE images were acquired with the proposed sequence and quantitatively compared with 2D multislice Modified Look-Locker inversion recovery (MOLLI) T1 maps. Exemplary images in a patient with focal scar were compared with conventional LGE imaging. The deviation of the proposed method and the spin-echo reference was < 11 ms in phantom for T1 times between 250 and 600 ms, regardless of the inversion time selected in the LGE image. There was no significant difference in the in vivo T1 times of the proposed sequence and the 2D MOLLI technique (myocardium: 292 ± 75 ms versus 310 ± 49 ms, blood-pools: 191 ± 75 ms versus 182.0 ± 33). The LGE images showed proper nulling of the healthy myocardium in all subjects and clear depiction of scar in the patient. The proposed sequence enables simultaneous acquisition of 3D PS-LGE images and spatially registered 3D T1 maps in a single scan.


Modular organization of cellular networks.
We investigated the organization of interacting proteins and protein complexes into networks of modules. A network-clustering method was developed to identify modules. This method of network-structure determination was validated by clustering known signaling-protein modules and by identifying module rudiments in exclusively high-throughput protein-interaction data with high error frequencies and low coverage. The signaling network controlling the yeast developmental transition to a filamentous form was clustered. Abstraction of a modular network-structure model identified module-organizer proteins and module-connector proteins. The functions of these proteins suggest that they are important for module function and intermodule communication.


Evolution of antiretroviral phenotypic and genotypic drug resistance in antiretroviral-naive HIV-1-infected children treated with abacavir/lamivudine, zidovudine/lamivudine or abacavir/zidovudine, with or without nelfinavir (the PENTA 5 trial).
To describe the evolution of resistance to zidovudine (ZDV), lamivudine (3TC), abacavir (ABC) and nelfinavir (NFV), 113 previously untreated children in the PENTA 5 trial had resistance assayed at baseline, rebound and/or 24, 48, 72 weeks (VIRCO: phenotyping and genotyping with 'Virtual Phenotype' interpretation). At baseline, few reverse transcriptase mutations and no primary protease inhibitor mutations were observed. Time to detectable HIV-1 RNA with reduced phenotypic susceptibility to any drug was shortest in the ZDV+3TC arm (overall logrank P=0.02). Through a median follow-up of 55 weeks, at their last assessment 11 (28%), 16 (40%) and 13 (32%) children with detectable HIV-1 RNA and a resistance test available had mutations conferring resistance to none, one, or two or more trial drugs, respectively, according to the virtual phenotype. Reduced phenotypic susceptibility to ABC only occurred in the 3TC+ABC arm and required K65R and/or L74V in addition to M184V. NFV-resistant virus was selected slowly through D30N or L90M pathways, and selection of ZDV-resistant virus was rare. Selection of 3TC-resistant virus was most frequent, followed by NFV and/or ABC; selection of ZDV-resistant virus was rare. Importantly, although in vitro, ABC selects for M184V as the first mutation, ABC did not select for M184V when combined with ZDV without 3TC. The most sustained HIV-1 RNA response was in the 3TC+ABC arm, but mutations conferring reduced susceptibility to 3TC and/or ABC evolved more frequently if virological failure occurred with 3TC+ABC than with ZDV+ABC.


Prognostic markers and tumour growth kinetics in melanoma patients progressing on vemurafenib.
The BRAF inhibitor vemurafenib is an effective drug in patients with BRAF mutant metastatic melanoma, but resistance occurs after a median of 6 months. The anti-CTLA4-antibody, ipilimumab, is a standard first-line and second-line treatment option in Europe, with a median time to response of 2-3 months, but some patients show rapid clinical deterioration before that. The aim of this analysis was to identify prognostic markers for survival after failure of vemurafenib treatment to identify patients who have a sufficient life expectancy to respond to new immunotherapy treatments. We retrospectively analysed 101 consecutive unselected patients treated with vemurafenib for metastatic melanoma at a single institution. The association between clinical parameters and death within 3 months after cessation of vemurafenib (n=69) was assessed by binary logistic and Cox regression. Of the patients, 45% died within 3 months of progression on vemurafenib. Elevated baseline serum lactate dehydrogenase, absence of normalization of serum lactate dehydrogenase on vemurafenib therapy, performance status of at least 2 at progression and time from primary tumour to metastatic disease less than 5 years were identified as poor prognostic markers. In an exploratory tumour growth kinetics analysis (n=16), we found that following cessation of vemurafenib, approximately a third each showed a stable, decelerated or accelerated rate of tumour growth. Patients with these poor prognostic markers are unlikely to have sufficient life expectancy to complete ipilimumab treatment after failure with vemurafenib. Consideration needs to be given to the elective use of immunotherapy before patients become resistant to vemurafenib. This requires prospective randomized evaluation. Our tumour growth kinetics analysis requires confirmation; however, it may suggest that intermittent vemurafenib treatment should be investigated in clinical trials.


Transient and persistent experimental infection of nonhuman primates with Helicobacter pylori: implications for human disease.
Helicobacter pylori can establish chronic infection in the human gastric mucosa, and it is a major cause of peptic ulcer disease and a principal risk factor for gastric cancer. This creates a need for H. pylori infection models that mimic the human condition. To test the suitability of rhesus monkeys as infection models, H. pylori-free animals were inoculated intragastrically with mixtures of H. pylori strains, bacteria recovered from colonized animals were typed by arbitrarily primed PCR, and host inflammatory and immunologic responses were monitored. Among five H. pylori-free animals inoculated with a mixture of two human strains plus one monkey strain, one became persistently infected and one became only transiently infected. The recovered bacteria matched the monkey input strain in DNA fingerprint. A subsequent trial using two new human isolates and three animals that had resisted colonization by the monkey strain resulted in persistent infection in one animal and transient infection in two others. Antral gastritis, anti-H. pylori serum immunoglobulin G, and atrophy all increased, but with patterns that differed among animals. We conclude that (i) rhesus monkeys can be infected experimentally with H. pylori, (ii) individuals differ in susceptibility to particular bacterial strains, (iii) infections may be transient, and (iv) the fitness of a particular strain for a given host helps determine the consequences of exposure to that strain.


Hyaluronate in bronchoalveolar lavage fluid: a new marker in sarcoidosis reflecting pulmonary disease.
Hyaluronate (hyaluronic acid) was not detectable in bronchoalveolar lavage fluid from smoking or nonsmoking healthy volunteers but was present in fluid from 23 patients with sarcoidosis; the mean concentration was 16 micrograms/1 returned fluid (range less than or equal to 5-430) or, expressed in relation to the amount of albumin recovered, 0.22 micrograms/mg albumin (range less than or equal to 0.05-3.6). The serum hyaluronate concentrations in the patients with sarcoidosis were normal. There was a significant inverse correlation between vital lung capacity and hyaluronate concentrations in bronchoalveolar lavage fluid (p less than 0.001), and patients with abnormal lung volumes had hyaluronate concentrations that were on average six times higher than those in patients with normal vital capacity. Duration of disease, pulmonary radiological findings, and markers for macrophage activation (angiotensin converting enzyme) and lymphocyte activation (beta 2 microglobulin) were not correlated with bronchoalveolar lavage fluid hyaluronate. It was concluded that in sarcoidosis release of hyaluronate into the airways is related to lung volume and therefore to the course of the disease. Increased synthesis of hyaluronate in lung parenchyma may reflect activation of fibroblasts, and measurements of hyaluronate may have clinical value for prognosis and treatment.


ISG15 counteracts Listeria monocytogenes infection.
ISG15 is an interferon-stimulated, linear di-ubiquitin-like protein, with anti-viral activity. The role of ISG15 during bacterial infection remains elusive. We show that ISG15 expression in nonphagocytic cells is dramatically induced upon Listeria infection. Surprisingly this induction can be type I interferon independent and depends on the cytosolic surveillance pathway, which senses bacterial DNA and signals through STING, TBK1, IRF3 and IRF7. Most importantly, we observed that ISG15 expression restricts Listeria infection in vitro and in vivo. We made use of stable isotope labeling in tissue culture (SILAC) to identify ISGylated proteins that could be responsible for the protective effect. Strikingly, infection or overexpression of ISG15 leads to ISGylation of ER and Golgi proteins, which correlates with increased secretion of cytokines known to counteract infection. Together, our data reveal a previously uncharacterized ISG15-dependent restriction of Listeria infection, reinforcing the view that ISG15 is a key component of the innate immune response.


Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins.
Large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins. However, existing methods for estimating the probability of motif recurrence may be biased by the size and composition of the search dataset, such that p-value estimates from different datasets, or from motifs containing different numbers of non-wildcard positions, are not strictly comparable. Here, we develop more exact methods and explore the potential biases of computationally efficient approximations. A widely used heuristic for the calculation of motif over-representation approximates motif probability by assuming that all proteins have the same length and composition. We introduce pv, which calculates the probability exactly. Secondly, the recently introduced SLiMFinder statistic Sig, accounts for multiple testing (across all possible motifs) in motif discovery. However, it approximates the probability of all other possible motifs, occurring with a score of p or less, as being equal to p. Here, we show that the exhaustive calculation of the probability of all possible motif occurrences that are as rare or rarer than the motif of interest, Sig', may be carried out efficiently by grouping motifs of a common probability (i.e. those which have permuted orders of the same residues). Sig'v, which corrects both approximations, is shown to be uniformly distributed in a random dataset when searching for non-ambiguous motifs, indicating that it is a robust significance measure. A method is presented to compute exactly the true probability of a non-ambiguous short protein sequence motif, and the utility of an approximate approach for novel motif discovery across a large number of datasets is demonstrated.


Classical Conditioning Fails to Elicit Allodynia in an Experimental Study with Healthy Humans.
Associative learning has been proposed as a mechanism behind the persistence of pain after tissue healing. The simultaneous occurrence of nociceptive and non-nociceptive input during acute injury mimics the pairings thought to drive classical conditioning effects. However, empirical evidence for classically conditioned allodynia is lacking. We aimed to manipulate pain thresholds with a classical conditioning procedure that used non-nociceptive somatosensory stimuli as conditioned stimuli (CS) and nociceptive stimuli as unconditioned stimuli. We also explored the influence of gender, depression, anxiety, negative affect, and pain catastrophizing on the main manipulation. Thirty-four healthy humans participated in a differential classical conditioning procedure that used vibrotactile stimulations at two different locations as CS. In an acquisition phase, CS+ was paired with painful thermal stimulation, and CS- with nonpainful thermal stimulation. Heat pain threshold was assessed during paired heat-CS trials before and after acquisition. A 2 (time: 1 and 2) x 2 (condition: CS+ and CS-) repeated-measures analysis of variance compared pain thresholds before and after acquisition. Exploratory analyses explored the influence of gender, depression, anxiety, negative affect, and pain catastrophizing. Postexperiment questions investigated participants' awareness of the contingencies employed. The classical conditioning procedure did not alter pain thresholds. Exploratory analyses did not reveal any influence of individual differences. Thirty of the 34 participants were unaware of the contingencies between stimuli. The results of this study provide no evidence that allodynia can be induced in healthy humans using a classical conditioning procedure with simultaneous timing.


Bimanual, intra-operative, fluoroscopy-guided removal of nasopharyngeal migratory fish bone from carotid space.
We report a rare and unusual case of a patient with an ingested fishbone which migrated from the oropharynx to the anterior compartment of the retropharyngeal space and then to the deep neck space in the nasopharynx (i.e. the carotid space). This report aims to describe a successful, minimally invasive method of foreign body removal which avoided both major skull base surgery and any potential life-threatening complications. A secondary aim is to highlight the role of intra-operative fluoroscopy, an under-used tool. We present a 67-year-old man with a history of fish bone impaction but no fish bone visible on plain X-ray or flexible endoscopy. The diagnosis of fish bone lodged in the retropharyngeal space was confirmed by computed tomography. Surgical exploration of the anterior retropharyngeal space failed to locate the fish bone, as it had migrated to a new, unknown location. Intra-operative fluoroscopy was vital for the removal of the fish bone, as it was impossible to see with the naked eye and had migrated from its previously imaged position. The fish bone was finally retrieved bimanually using external pressure on the submandibular region, which displaced the fish bone, and fluoroscopic guidance, which assisted its removal from the nasopharyngeal lumen. To the best of our knowledge, this is the first reported case of bimanual, intra-operative, fluoroscopy-guided, intra-luminal removal of a migratory fish bone from the deep neck space in this region of the nasopharynx.


Altruism in social networks: evidence for a 'kinship premium'.
Why and under what conditions are individuals altruistic to family and friends in their social networks? Evolutionary psychology suggests that such behaviour is primarily the product of adaptations for kin- and reciprocal altruism, dependent on the degree of genetic relatedness and exchange of benefits, respectively. For this reason, individuals are expected to be more altruistic to family members than to friends: whereas family members can be the recipients of kin and reciprocal altruism, friends can be the recipients of reciprocal altruism only. However, there is a question about how the effect of kinship is implemented at the proximate psychological level. One possibility is that kinship contributes to some general measure of relationship quality (such as 'emotional closeness'), which in turn explains altruism. Another possibility is that the effect of kinship is independent of relationship quality. The present study tests between these two possibilities. Participants (N= 111) completed a self-report questionnaire about their willingness to be altruistic, and their emotional closeness, to 12 family members and friends at different positions in their extended social networks. As expected, altruism was greater for family than friends, and greater for more central layers of the network. Crucially, the results showed that kinship made a significant unique contribution to altruism, even when controlling for the effects of emotional closeness. Thus, participants were more altruistic towards kin than would be expected if altruism was dependent on emotional closeness alone - a phenomenon we label a 'kinship premium'. These results have implications for the ongoing debate about the extent to which kin relations and friendships are distinct kinds of social relationships, and how to measure the 'strength of ties' in social networks.


Therapeutic Clearance of Amyloid by Antibodies to Serum Amyloid P Component.
The amyloid fibril deposits that cause systemic amyloidosis always contain the nonfibrillar normal plasma protein, serum amyloid P component (SAP). The drug (R)-1-[6-[(R)-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl]pyrrolidine-2-carboxylic acid (CPHPC) efficiently depletes SAP from the plasma but leaves some SAP in amyloid deposits that can be specifically targeted by therapeutic IgG anti-SAP antibodies. In murine amyloid A type amyloidosis, the binding of these antibodies to the residual SAP in amyloid deposits activates complement and triggers the rapid clearance of amyloid by macrophage-derived multinucleated giant cells. We conducted an open-label, single-dose-escalation, phase 1 trial involving 15 patients with systemic amyloidosis. After first using CPHPC to deplete circulating SAP, we infused a fully humanized monoclonal IgG1 anti-SAP antibody. Patients with clinical evidence of cardiac involvement were not included for safety reasons. Organ function, inflammatory markers, and amyloid load were monitored. There were no serious adverse events. Infusion reactions occurred in some of the initial recipients of larger doses of antibody; reactions were reduced by slowing the infusion rate for later patients. At 6 weeks, patients who had received a sufficient dose of antibody in relation to their amyloid load had decreased liver stiffness, as measured with the use of transient elastography. These patients also had improvements in liver function in association with a substantial reduction in hepatic amyloid load, as shown by means of SAP scintigraphy and measurement of extracellular volume by magnetic resonance imaging. A reduction in kidney amyloid load and shrinkage of an amyloid-laden lymph node were also observed. Treatment with CPHPC followed by an anti-SAP antibody safely triggered clearance of amyloid deposits from the liver and some other tissues. (Funded by GlaxoSmithKline; ClinicalTrials.gov number, NCT01777243.).


The age-dependence of atrial arrhythmogenicity in Scn5a+/- murine hearts reflects alterations in action potential propagation and recovery.
1. In the present study, we investigated the effect of age on atrial electrophysiological properties in Scn5a(+/-) hearts used to model corresponding increases in atrial arrhythmic tendency in human Brugada syndrome. 2. Atrial action potential initiation, propagation and recovery were compared in young (3 month old) and aged (12 month old), wild-type (WT) and Scn5a(+/-) hearts. Multielectrode array recordings assessed the spatial propagation of intrinsic electrical activity in superfused atrial preparations, whereas bipolar electrogram recordings measured basic cycle lengths (BCL) in Langendorff preparations. The duration of electrogram activity (EGD) during regular and extrasystolic stimulation with programmed electrical stimulation provided EGD ratios and atrial effective refractory periods (AERP). Monophasic recordings measured action potential durations (APD). 3. Systematic statistical explorations for independent and interacting effects of age and the Scn5a(+/-) condition demonstrated that both young and aged Scn5a(+/-) mice exhibited slowed propagation of atrial excitation relative to corresponding WT mice, with the greatest effects in aged Scn5a(+/-) mice, which additionally exhibited increased intrinsic BCL. 4. Young Scn5a(+/-) mice exhibited greater EGD and EGD ratios, as well as APD/AERP ratios, suggesting increased arrhythmic tendency compared with WT mice. 5. Aged Scn5a(+/-) mice exhibited normal EGD, EGD ratios and APD compared to aged WT and young Scn5a(+/-), and increased AERP and smaller APD/AERP ratios compared with young Scn5a(+/-). 6. These electrophysiological findings indicate increased atrial arrhythmogenicity with maximal effects on both conduction and repolarization characteristics in young compared with aged Scn5a(+/-) mice.


Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation.
Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to reveal cis-regulatory mechanisms underlying phenotypic differences. In this study, we develop a new probabilistic model, called pGENMi, that integrates multi-omic data to investigate the transcriptional regulatory mechanisms underlying interindividual variation of a specific phenotype-that of cell line response to cytotoxic treatment. In particular, pGENMi simultaneously analyzes genotype, DNA methylation, gene expression, and transcription factor (TF)-DNA binding data, along with phenotypic measurements, to identify TFs regulating the phenotype. It does so by combining statistical information about expression quantitative trait loci (eQTLs) and expression-correlated methylation marks (eQTMs) located within TF binding sites, as well as observed correlations between gene expression and phenotype variation. Application of pGENMi to data from a panel of lymphoblastoid cell lines treated with 24 drugs, in conjunction with ENCODE TF ChIP data, yielded a number of known as well as novel (TF, Drug) associations. Experimental validations by TF knockdown confirmed 41% of the predicted and tested associations, compared to a 12% confirmation rate of tested nonassociations (controls). An extensive literature survey also corroborated 62% of the predicted associations above a stringent threshold. Moreover, associations predicted only when combining eQTL and eQTM data showed higher precision compared to an eQTL-only or eQTM-only analysis using pGENMi, further demonstrating the value of multi-omic integrative analysis.


Baroreceptor inputs to the nucleus tractus solitarius in the cat: modulation by the hypothalamus.
1. The effects of stimulation within the hypothalamic defence area (HDA) on the activity of neurones in the nucleus of the solitary tract (NTS) have been investigated in vivo. 2. HDA stimulation exerted marked influences on NTS neurones. Approximately two-thirds of units receiving a carotid sinus nerve (SN) input were inhibited by HDA stimulation. All units shown to receive an excitatory input from carotid sinus baroreceptors were inhibited by HDA stimulation. 3. The specificity of the HDA stimulation was investigated by generalized hypothalamic stimulation. In these experiments the number of units activated by SN stimulation that were inhibited was reduced considerably. A much smaller percentage (27%) of baroreceptive units were inhibited from hypothalamic stimulation outside the defence area. 4. Intracellular recordings revealed that HDA stimulation evoked a long-lasting hyperpolarization of membrane potential that resulted from postsynaptic inhibition (rather than disfacilitation). The HDA-evoked IPSP 'shunted' the SN-evoked EPSP when the SN stimulus was timed to occur during the initial peak hyperpolarizing phase of the HDA-evoked IPSP. 5. HDA stimulation disinhibited cells receiving an inhibitory input from the carotid sinus baroreceptors. 6. The effects of HDA stimulation were not limited to cells receiving SN afferent information or to cells within the NTS. 7. Our results explain, at the intracellular level, the mechanism for the central suppression of the baroreceptor reflex that forms an integral part of the defence response in the cat.


Chest compression-only CPR by lay rescuers and survival from out-of-hospital cardiac arrest.
Chest compression-only bystander cardiopulmonary resuscitation (CPR) may be as effective as conventional CPR with rescue breathing for out-of-hospital cardiac arrest. To investigate the survival of patients with out-of-hospital cardiac arrest using compression-only CPR (COCPR) compared with conventional CPR. A 5-year prospective observational cohort study of survival in patients at least 18 years old with out-of-hospital cardiac arrest between January 1, 2005, and December 31, 2009, in Arizona. The relationship between layperson bystander CPR and survival to hospital discharge was evaluated using multivariable logistic regression. Survival to hospital discharge. Among 5272 adults with out-of-hospital cardiac arrest of cardiac etiology not observed by responding emergency medical personnel, 779 were excluded because bystander CPR was provided by a health care professional or the arrest occurred in a medical facility. A total of 4415 met all inclusion criteria for analysis, including 2900 who received no bystander CPR, 666 who received conventional CPR, and 849 who received COCPR. Rates of survival to hospital discharge were 5.2% (95% confidence interval [CI], 4.4%-6.0%) for the no bystander CPR group, 7.8% (95% CI, 5.8%-9.8%) for conventional CPR, and 13.3% (95% CI, 11.0%-15.6%) for COCPR. The adjusted odds ratio (AOR) for survival for conventional CPR vs no CPR was 0.99 (95% CI, 0.69-1.43), for COCPR vs no CPR, 1.59 (95% CI, 1.18-2.13), and for COCPR vs conventional CPR, 1.60 (95% CI, 1.08-2.35). From 2005 to 2009, lay rescuer CPR increased from 28.2% (95% CI, 24.6%-31.8%) to 39.9% (95% CI, 36.8%-42.9%; P < .001); the proportion of CPR that was COCPR increased from 19.6% (95% CI, 13.6%-25.7%) to 75.9% (95% CI, 71.7%-80.1%; P < .001). Overall survival increased from 3.7% (95% CI, 2.2%-5.2%) to 9.8% (95% CI, 8.0%-11.6%; P < .001). Among patients with out-of-hospital cardiac arrest, layperson compression-only CPR was associated with increased survival compared with conventional CPR and no bystander CPR in this setting with public endorsement of chest compression-only CPR.


Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.
We have sequenced six overlapping clones from a library of bacterial artificial chromosome (BAC) clones derived from a laboratory strain of the mosquito, Anopheles gambiae, the major vector of human malaria in Africa. The resulting uninterrupted 528-kb sequence is from the 8C region of the mosquito 2R chromosome, at or very near the major refractoriness locus associated with melanotic encapsulation of parasites. This sequence represents the first extensive view of the mosquito genome structure encompassing 48 genes. Genomic comparison reveals that the majority of the orthologues are found in six microsyntenic clusters in Drosophila melanogaster. A BAC clone that is wholly contained within this region demonstrates the existence of a remarkable degree of local polymorphism in this species, which may prove important for its population structure and vectorial capacity.


The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model.
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. We fine-map one locus associated with D. magna resistance to P. ramosa and genetically characterize two haplotypes of the Pasteuria resistance (PR-) locus using de novo genome and transcriptome sequencing. Sequence comparison of PR-locus haplotypes finds dramatic structural polymorphisms between PR-locus haplotypes including a large portion of each haplotype being composed of non-homologous sequences resulting in haplotypes differing in size by 66 kb. The high divergence of PR-locus haplotypes suggest a history of multiple, diverse and repeated instances of structural mutation events and restricted recombination. Annotation of the haplotypes reveals striking differences in gene content. In particular, a group of glycosyltransferase genes that is present in the susceptible but absent in the resistant haplotype. Moreover, in natural populations, we find that the PR-locus polymorphism is associated with variation in resistance to different P. ramosa genotypes, pointing to the PR-locus polymorphism as being responsible for the matching-allele interactions that have been previously described for this system. Our results conclusively identify a genetic basis for the matching-allele interaction observed in a coevolving host-parasite system and provide a first insight into its molecular basis.


Reliability of telemetric electromyography and near-infrared spectroscopy during high-intensity resistance exercise.
This study quantified the inter- and intra-test reliability of telemetric surface electromyography (EMG) and near infrared spectroscopy (NIRS) during resistance exercise. Twelve well-trained young men performed high-intensity back squat exercise (12 sets at 70-90% 1-repetition maximum) on two occasions, during which EMG and NIRS continuously monitored muscle activation and oxygenation of the thigh muscles. Intra-test reliability for EMG and NIRS variables was generally higher than inter-test reliability. EMG median frequency variables were generally more reliable than amplitude-based variables. The reliability of EMG measures was not related to the intensity or number of repetitions performed during the set. No notable differences were evident in the reliability of EMG between different agonist muscles. NIRS-derived measures of oxyhaemoglobin, deoxyhaemoglobin and tissue saturation index were generally more reliable during single-repetition sets than multiple-repetition sets at the same intensity. Tissue saturation index was the most reliable NIRS variable. Although the reliability of the EMG and NIRS measures varied across the exercise protocol, the precise causes of this variability are not yet understood. However, it is likely that biological variation during multi-joint isotonic resistance exercise may account for some of the variation in the observed results.


Dynamic assessment of the right lateral frontal cortex response to painful stimulation.
The lateral surface of the right frontal lobe has a relevant role in modulating behavioral responses to aversive stimuli and may significantly influence pain experience. Imaging studies suggest that this modulatory role is multifaceted, but no studies have assessed the regional specialization of this cortex on the basis of its response dynamics during pain processing. We aimed to investigate functional specialization within the right lateral frontal cortex using a dynamic fMRI approach. Brain responses to a mechanical painful stimulus and a preceding anticipatory cue (auditory tone) were assessed in 25 healthy subjects. Functional data were decomposed into 15 sequential activation maps covering the full anticipation-painful stimulation cycle using a finite impulse response (FIR) analysis approach. Movie sequences showing the temporal evolution of brain activation illustrate the findings. A region involving premotor-prefrontal cortices was activated soon after the anticipatory cue and showed a significant correlation with both anterior cingulate cortex activation and subjective pain ratings. The frontal operculum also showed a significant anticipatory response, but the most robust activation followed painful stimulation onset and was strongly correlated with insula activation. The anterior prefrontal cortex showed full activation during late painful stimulation and was negatively correlated with pain unpleasantness. In conclusion, different elements within the right lateral frontal cortex showed distinct activation dynamics in response to painful stimulation, which would suggest relevant regional specialization during pain processing. These findings are congruent with the broad functional role of the right frontal cortex and its influence on crucial aspects of human behavior.


Deletion analysis and alternative splicing define a transactivation inhibitory domain in human oncoprotein REL.
Misregulation of REL, a nuclear factor-kappaB family transcription factor, has been implicated in several human lymphoid malignancies. REL has a conserved N-terminal DNA-binding/dimerization domain called the Rel homology domain (RHD) and a C-terminal transactivation domain (TAD). Here, we define the sequences (amino acids (aa) 323-422) between the RHD and TAD as a REL inhibitory domain (RID) because deletion of these sequences increases both REL transactivation and DNA binding. Furthermore, we have characterized two REL mRNA splice variants that encode proteins with alterations near RID: one lacking exon 9 sequences (aa 308-330; RELDelta9) and one with an exonized Alu fragment insertion of 32 aa after aa 307 (REL+Alu). Deletion of RID or exon 9-encoded sequences increases transactivation by GAL4-REL by approximately threefold. Moreover, deletion of RID or exon 9 sequences increases transactivation by full-length REL from certain kappaB site-containing promoters and increases DNA binding by REL. Deletion of RID does not affect REL's ability to transform chicken spleen cells. Reverse transcriptase-polymerase chain reaction analysis of mRNA from both primary lymphoma samples and several transformed tissue culture cell lines indicates that the RELDelta9 splice variant is preferentially expressed in lymphoma, suggesting that the REL transcript lacking exon 9 could serve as a marker for certain types of lymphoid tumors.


Use of insulin lispro in continuous subcutaneous insulin infusion treatment. Results of a multicenter trial. German Humalog-CSII Study Group.
Insulin lispro is an analog of human insulin with a faster onset and a shorter duration of action than regular human insulin. Efficacy and tolerability of insulin lispro in continuous subcutaneous insulin infusion (CSII) treatment were assessed in an open randomized crossover trial comparing insulin lispro and regular human insulin, both applied with insulin pumps. A total of 113 type 1 patients (60 male, 53 female, age [mean +/- SD] 37 +/- 12 years, duration of diabetes 19 +/- 9 years) participated in this open, randomized crossover study. Both insulins were applied for 4 months each with the appropriate intervals between the prandial insulin bolus and the meal (human insulin: 30 min; lispro: 0 min). Observation parameters were HbA1c, daily and postprandial blood glucose profiles, adverse events, rate of hypoglycemic and hyperglycemic events, number of catheter obstructions, and treatment satisfaction as assessed with an international validated questionnaire. The patients were well controlled with a mean HBA1c of 7.24 +/- 1.0% at baseline. HbA1c decreased in both treatment periods, but it was better during insulin lispro treatment (insulin lispro: 6.8 +/- 0.9%, regular human insulin: 6.9 +/- 1.0%, Friedman's rank-sum test: P < 0.02). In addition, the 1-h and 2-h postprandial rises in blood glucose were significantly lower (P < 0.001 for each meal) with insulin lispro, resulting in smoother daily glucose profiles as compared with regular human insulin. No significant differences were reported for the rate of hypoglycemia (mean +/- SD [median]: insulin lispro 12.4 +/- 13.9 [8], regular human insulin 11.0 +/- 11.2 [8]), for the rate of catheter obstructions (42 events in each treatment arm), and for the number and type of adverse events. No severe case of ketoacidosis was seen during insulin lispro treatment, whereas one case was reported during therapy with regular human insulin. Treatment satisfaction was better when patients were treated with insulin lispro. Insulin lispro is a suitable and very convenient pump insulin that may result in an improvement of long-term glucose control during CSII treatment. Its safety profile does not differ from that of regular human insulin.


Novel type of pilus associated with a Shiga-toxigenic E. coli hybrid pathovar conveys aggregative adherence and bacterial virulence.
A large German outbreak in 2011 was caused by a locus of enterocyte effacement (LEE)-negative enterohemorrhagic E. coli (EHEC) strain of the serotype O104:H4. This strain harbors markers that are characteristic of both EHEC and enteroaggregative E. coli (EAEC), including aggregative adhesion fimbriae (AAF) genes. Such rare EHEC/EAEC hybrids are highly pathogenic due to their possession of a combination of genes promoting severe toxicity and aggregative adhesion. We previously identified novel EHEC/EAEC hybrids and observed that one strain exhibited aggregative adherence but had no AAF genes. In this study, a genome sequence analysis showed that this strain belongs to the genoserotype O23:H8, MLST ST26, and harbors a 5.2 Mb chromosome and three plasmids. One plasmid carries some EAEC marker genes, such as aatA and genes with limited protein homology (11-61%) to those encoding the bundle-forming pilus (BFP) of enteropathogenic E. coli. Due to significant protein homology distance to known pili, we designated these as aggregate-forming pili (AFP)-encoding genes and the respective plasmid as pAFP. The afp operon was arranged similarly to the operon of BFP genes but contained an additional gene, afpA2, which is homologous to afpA. The deletion of the afp operon, afpA, or a nearby gene (afpR) encoding an AraC-like regulator, but not afpA2, led to a loss of pilin production, piliation, bacterial autoaggregation, and importantly, a >80% reduction in adhesion and cytotoxicity toward epithelial cells. Gene sets similar to the afp operon were identified in a variety of aatA-positive but AAF-negative intestinal pathogenic E. coli. In summary, we characterized widely distributed and novel fimbriae that are essential for aggregative adherence and cytotoxicity in a LEE-negative Shiga-toxigenic hybrid.


Nicotine depedence and salivary cotinine concentration in daily smokers.
There is scant information on nicotine dependence in smokers not seeking cessation treatment. This study analyses the relationship between nicotine dependence, measured by the Fagerström Test for Nicotine Dependence (FTND), and salivary cotinine concentration in a sample of smokers from the general population. We conducted a cross-sectional study (2004-2005) of a representative sample of the general population of Barcelona, Spain (n=1245). The analysis included 196 daily smokers aged more than 16 years. Information on smoking was obtained by questionnaire and cotinine concentration was determined in saliva. Geometric means of cotinine concentration by every single FTND item were computed, and multivariate linear regression was used to explore the relationship among these variables. Participants smoked a mean of 17.0 cigarettes per day, and the mean FTND score was 3.27 (95% confidence interval: 2.92-3.61). Around 17% of subjects (95% confidence interval: 12.0-22.5%) had high nicotine dependence. Cotinine concentration differed significantly by nicotine dependence levels. In a multiple linear regression model including the sum of the FTND items 2, 3, and 6, and the single FTND items 1, 4, and 5, adjusted for sex, the time to first cigarette after waking up (item 1), the number of cigarettes smoked daily (item 4), and smoking more in the first hours of the day (item 5) were significantly related to salivary cotinine concentration (R(2)=0.414). Salivary cotinine levels were associated with nicotine dependence as measured by the FTND, especially with the items on daily tobacco consumption, time to first cigarette after waking up, and smoking more in the first hours of the day.


The mediodorsal thalamus as a higher order thalamic relay nucleus important for learning and decision-making.
Recent evidence from monkey models of cognition shows that the magnocellular subdivision of the mediodorsal thalamus (MDmc) is more critical for learning new information than for retention of previously acquired information. Further, consistent evidence in animal models shows the mediodorsal thalamus (MD) contributes to adaptive decision-making. It is assumed that prefrontal cortex (PFC) and medial temporal lobes govern these cognitive processes so this evidence suggests that MD contributes a role in these cognitive processes too. Anatomically, the MD has extensive excitatory cortico-thalamo-cortical connections, especially with the PFC. MD also receives modulatory inputs from forebrain, midbrain and brainstem regions. It is suggested that the MD is a higher order thalamic relay of the PFC due to the dual cortico-thalamic inputs from layer V ('driver' inputs capable of transmitting a message) and layer VI ('modulator' inputs) of the PFC. Thus, the MD thalamic relay may support the transfer of information across the PFC via this indirect thalamic route. This review summarizes the current knowledge about the anatomy of MD as a higher order thalamic relay. It also reviews behavioral and electrophysiological studies in animals to consider how MD might support the transfer of information across the cortex during learning and decision-making. Current evidence suggests the MD is particularly important during rapid trial-by-trial associative learning and decision-making paradigms that involve multiple cognitive processes. Further studies need to consider the influence of the MD higher order relay to advance our knowledge about how the cortex processes higher order cognition.


A candidate reference measurement procedure for quantifying serum concentrations of 25-hydroxyvitamin D₃ and 25-hydroxyvitamin D₂ using isotope-dilution liquid chromatography-tandem mass spectrometry.
The inaccuracy of routine serum 25-hydroxyvitamin D measurements hampers the interpretation of data in patient care and public health research. We developed and validated a candidate reference measurement procedure (RMP) for highly accurate quantitation of two clinically important 25-hydroxyvitamin D metabolites in serum, 25-hydroxyvitamin D2 [25(OH)D2] and 25-hydroxyvitamin D3 [25(OH)D3]. The two compounds of interest together with spiked deuterium-labeled internal standards [d 3-25(OH)D2 and d 6-25(OH)D3] were extracted from serum via liquid-liquid extraction. The featured isotope-dilution LC-MS/MS method used reversed-phase chromatography and atmospheric pressure chemical ionization in positive ion mode. A pentafluorophenylpropyl-packed UHPLC column together with isocratic elution allowed for complete baseline resolution of 25(OH)D2 and 25(OH)D3 from their structural C-3 isomers within 12 min. We evaluated method trueness, precision, potential interferences, matrix effects, limits of quantitation, and measurement uncertainty. Calibration materials were, or were traceable to, NIST Standard Reference Materials 2972. Within-day and total imprecision (CV) averaged 1.9 and 2.0% for 25(OH)D3, respectively, and 2.4 and 3.5% for 25(OH)D2, respectively. Mean trueness was 100.3% for 25(OH)D3 and 25(OH)D2. The limits of quantitation/limits of detection were 4.61/1.38 nmol/L for 25(OH)D3 and 1.46/0.13 nmol/L for 25(OH)D2. When we compared our RMP results to an established RMP using 40 serum samples, we found a nonsignificant mean bias of 0.2% for total 25(OH)D. This candidate RMP for 25(OH)D metabolites meets predefined method performance specifications (≤5% total CV and ≤1.7% bias) and provides sufficient sample throughput to meet the needs of the Centers for Disease Control and Prevention Vitamin D Standardization Certification Program. Graphical abstract Bias assessment using NIST standard reference materials. Legend CDC mean mass fractions (ng/g) ± U 95 (6 replicates per mean). NIST-certified mass fractions (ng/g) ± U 95 from the Certificates of Analysis.


Sclerosing Mesenteritis: A Rare Cause of Small Bowel Obstruction.
Sclerosing mesenteritis falls within a spectrum of primary idiopathic inflammatory and fibrotic processes that affect the mesentery. The exact etiology has not been determined, although the following associations have been noted: abdominal surgery, trauma, autoimmunity, paraneoplastic syndrome, ischemia and infection. Progression of sclerosing mesentritis can lead to bowel obstruction, a rare complication of this uncommon condition. We report a case of a 66-year-old female with abdominal pain who was noted to have a small bowel obstruction requiring laparotomy and a partial small bowel resection. The pathology of the resected tissue was consistent with sclerosing mesenteritis, a rare cause of a small bowel obstruction. Sclerosing mesenteritis has variable rates of progression, and there is no consensus regarding the optimal treatment. Physicians should consider sclerosing mesenteritis in the differential diagnosis of a small bowel obstruction.


Trans fatty acids - A risk factor for cardiovascular disease.
Trans fatty acids (TFA) are produced either by hydrogenation of unsaturated oils or by biohydrogenation in the stomach of ruminant animals. Vanaspati ghee and margarine have high contents of TFA. A number of studies have shown an association of TFA consumption and increased risk of cardiovascular disease (CVD). This increased risk is because TFA increase the ratio of LDL cholesterol to HDL cholesterol. Food and Agriculture Organization of the United Nations and World Health Organization have come up with the recommendation that the contents of TFA in human dietary fat should be reduced to less than 4%. There is high prevalence of CVD in Pakistan. High consumption of vanaspati ghee which contains 14.2-34.3% of TFA could be one of the factors for this increased burden of CVD in Pakistan. Consumption of dietary fat low in TFA would be helpful in reducing the risk of CVD in South Asia. Denmark by banning the sale of food items with TFA has brought down the number of deaths due to coronary heart disease by nearly 50% over a period of 20 years. Public awareness about the adverse effects of TFA on human health would be extremely important. Media can play a very effective role in educating the masses and advocating the policy for the sale of only low TFA food items. Literature sources: Google and US National Library of Medicine, National Institute of Health were the sources of papers cited in this review article.


Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems.
The structural design of ATP and NADH producing systems, such as glycolysis and the citric acid cycle (TCA), is analysed using optimization principles. It is assumed that these pathways combined with oxidative phosphorylation have reached, during their evolution, a high efficiency with respect to ATP production rates. On the basis of kinetic and thermodynamic principles, conclusions are derived concerning the optimal stoichiometry of such pathways. Extending previous investigations, both the concentrations of adenine nucleotides as well as nicotinamide adenine dinucleotides are considered variable quantities. This implies the consideration of the interaction of an ATP and NADH producing system, an ATP consuming system, a system coupling NADH consumption with ATP production and a system consuming NADH decoupled from ATP production. It is examined in what respect real metabolic pathways can be considered optimal by studying a large number of alternative pathways. The kinetics of the individual reactions are described by linear or bilinear functions of reactant concentrations. In this manner, the steady-state ATP production rate can be calculated for any possible ATP and NADH producing pathway. It is shown that most of the possible pathways result in a very low ATP production rate and that the very efficient pathways share common structural properties. Optimization with respect to the ATP production rate is performed by an evolutionary algorithm. The following results of our analysis are in close correspondence to the real design of glycolysis and the TCA cycle. (1) In all efficient pathways the ATP consuming reactions are located near the beginning. (2) In all efficient pathways NADH producing reactions as well as ATP producing reactions are located near the end. (3) The number of NADH molecules produced by the consumption of one energy-rich molecule (glucose) amounts to four in all efficient pathways. A distance measure and a measure for the internal ordering of reactions are introduced to study differences and similarities in the stoichiometries of metabolic pathways.


Structural characterization and ecological roles of a novel exopolysaccharide from the deep-sea psychrotolerant bacterium Pseudoalteromonas sp. SM9913.
Pseudoalteromonas sp. SM9913 is a psychrotolerant bacterium isolated from deep-sea sediment. The structural characterization and ecological roles of the exopolysaccharide (EPS) secreted by this strain were studied in this work. The yield of the EPS increased as the culture temperature decreased in the range 30-10 degrees C, and it reached 5.25 g l(-1) (dry weight) under optimal growth conditions (15 degrees C, 52 h). EPS fraction was purified and its structure was identified by the combination of NMR spectra, high-resolution mass spectrometry (HRMS) analysis and methylation analysis. The ratio of the sugar units, the acetyl group and the ethoxyl group was close to 4 : 5 : 1. The major sugar unit of the EPS was 6-linked glucose (61.8 %); other sugar units present included terminal arabinofuranosyl (11.0 %) and glucopyranosyl (11.2 %) residues and a small amount of other sugar derivatives. Its structure was different from EPSs reported for other marine bacteria. Besides the structural elucidation of the EPS, its ecological roles were studied. This EPS could enhance the stability of the cold-adapted protease MCP-01 secreted by the same strain through preventing its autolysis. It could bind many metal ions, including Fe(2+), Zn(2+), Cu(2+), Co(2+). It was also a very good flocculating agent and could conglomerate colloidal and suspended particles. These results indicated that the EPS secreted by strain SM9913 might help this strain enrich the proteinaceous particles and the trace metals in the deep-sea environment, stabilize the secreted cold-adapted proteases and avoid its diffusion. This is believed to be the first report on the structure of the EPS secreted by a deep-sea psychrotolerant bacterium and its ecological roles. According to these results and other studies, a schematic diagram of the lifestyle of the deep-sea psychrotolerant strain SM9913 is suggested.


Algal Cell Factories: Approaches, Applications, and Potentials.
With the advent of modern biotechnology, microorganisms from diverse lineages have been used to produce bio-based feedstocks and bioactive compounds. Many of these compounds are currently commodities of interest, in a variety of markets and their utility warrants investigation into improving their production through strain development. In this review, we address the issue of strain improvement in a group of organisms with strong potential to be productive "cell factories": the photosynthetic microalgae. Microalgae are a diverse group of phytoplankton, involving polyphyletic lineage such as green algae and diatoms that are commonly used in the industry. The photosynthetic microalgae have been under intense investigation recently for their ability to produce commercial compounds using only light, CO₂, and basic nutrients. However, their strain improvement is still a relatively recent area of work that is under development. Importantly, it is only through appropriate engineering methods that we may see the full biotechnological potential of microalgae come to fruition. Thus, in this review, we address past and present endeavors towards the aim of creating productive algal cell factories and describe possible advantageous future directions for the field.


Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes.
Divergence within cis-regulatory sequences may contribute to the adaptive evolution of gene expression, but functional alleles in these regions are difficult to identify without abundant genomic resources. Among African cichlid fishes, the differential expression of seven opsin genes has produced adaptive differences in visual sensitivity. Quantitative genetic analysis suggests that cis-regulatory alleles near the SWS2-LWS opsins may contribute to this variation. Here, we sequence BACs containing the opsin genes of two cichlids, Oreochromis niloticus and Metriaclima zebra. We use phylogenetic footprinting and shadowing to examine divergence in conserved non-coding elements, promoter sequences, and 3'-UTRs surrounding each opsin in search of candidate cis-regulatory sequences that influence cichlid opsin expression. We identified 20 conserved non-coding elements surrounding the opsins of cichlids and other teleosts, including one known enhancer and a retinal microRNA. Most conserved elements contained computationally-predicted binding sites that correspond to transcription factors that function in vertebrate opsin expression; O. niloticus and M. zebra were significantly divergent in two of these. Similarly, we found a large number of relevant transcription factor binding sites within each opsin's proximal promoter, and identified five opsins that were considerably divergent in both expression and the number of transcription factor binding sites shared between O. niloticus and M. zebra. We also found several microRNA target sites within the 3'-UTR of each opsin, including two 3'-UTRs that differ significantly between O. niloticus and M. zebra. Finally, we examined interspecific divergence among 18 phenotypically diverse cichlids from Lake Malawi for one conserved non-coding element, two 3'-UTRs, and five opsin proximal promoters. We found that all regions were highly conserved with some evidence of CRX transcription factor binding site turnover. We also found three SNPs within two opsin promoters and one non-coding element that had weak association with cichlid opsin expression. This study is the first to systematically search the opsins of cichlids for putative cis-regulatory sequences. Although many putative regulatory regions are highly conserved across a large number of phenotypically diverse cichlids, we found at least nine divergent sequences that could contribute to opsin expression differences in cis and stand out as candidates for future functional analyses.


Research priorities to fill knowledge gaps on ASF seasonality that could improve the control of ASF.
The European Commission requested EFSA to provide study designs for the investigation of four research domains according to major gaps in knowledge identified by EFSA in a report published in 2019: i) the patterns of seasonality of ASF in wild boar and domestic pigs in the EU; ii) the ASF epidemiology in wild boar; iii) ASF virus (ASFV) survival in the environment and iv) ASF transmission by vectors. In this Scientific Opinion, the first research domain on ASF seasonality is addressed. Therefore, five research objectives were proposed by the working group and broader ASF expert networks, such as ASF stop, ENETWILD, VectorNet, AHAW network and the AHAW Panel Experts. Of the five research objectives, only two were prioritised and elaborated into a general protocol/study design research proposal, namely: 1) to monitor the herd incidence of ASF outbreaks in EU Member States (MS) and 2) to investigate potential (seasonal) risk factors for ASF incursion in domestic pig herds of different herd types and/or size. To monitor the incidence in different pig herd types, it is advised to collect, besides ASF surveillance data, pig population data describing at least the following parameters per farm from the first moment of incursion in an affected MS: the numbers of pigs (e.g. number of breeding pigs sows and boars, weaners and fatteners) and the location and the type of farm (including details on the level of biosecurity implemented on the farm and the outdoor/indoor production). We suggest collecting data from all ASF-affected MS through the SIGMA data model, which was developed for this purpose. To investigate potential risk factors for ASF incursion in domestic pig herds, we suggest a matched case-control design. Such a study design can be run either retrospectively or prospectively. The collected data on the pig herds and the ASF surveillance data in the SIGMA data model can be used to identify case and control farms.


Efficacy of "green" cleaning products with respect to common respiratory viruses and mold growth.
Some disinfectants have been demonstrated to be effective against surface mold growth and/or viruses responsible for the spread of common respiratory infections. Antimicrobial efficacy of green cleaning products has generally not been established in these areas. In this survey, the author found that out of 27 products approved by Green Seal as hard surface cleaners, 26 do not claim antimicrobial capability. While some contained hydrogen peroxide, a compound with limited spectrum disinfection capabilities, only one was registered with the U.S. Environmental Protection Agency as antimicrobial. The need for additional research and documentation is discussed.


Evaluation of the positional candidate gene CHRNA7 at the juvenile myoclonic epilepsy locus (EJM2) on chromosome 15q13-14.
A previous study of 34 nuclear pedigrees segregating juvenile myoclonic epilepsy (JME) gave significant evidence of linkage with heterogeneity to marker loci on chromosome 15q13-14 close to the candidate gene CHRNA7 (Hum. Mol. Genet. 6 (1997) 1329). The aim of this work was to further evaluate the putative aetiological role of CHRNA7 in JME within the 34 families originally described, and to assess the contribution of this locus to a broader phenotype of idiopathic generalised epilepsy (IGE). Multipoint linkage analysis and intrafamilial association studies were performed with microsatellite markers that encompass both CHRNA7 and its partial duplication (CHRFAM7A). A maximum HLOD of 3.45 [alpha=0.58; (Zall=2.88, P=0.0008)] was observed 8 cM distal to D15S1360, a CHRNA7 intragenic marker. Significant exclusion lod scores were obtained across the region in 12 mixed phenotype JME/IGE families. Mutation screening of the CHRNA7 gene (and consequently exons 5-10 of CHRFAM7A) and its putative promoter sequence identified a total of 13 sequence variants across 23 of 34 JME-affected families. Two variants (c.1354G>A and c.1466C>T) are predicted to result in amino acid changes and one (IVS9+5G>A) is predicted to result in aberrant transcript splicing. However, none of the variants alone appeared either necessary or sufficient to cause JME in the families in which they occurred. In conclusion, linkage analyses continue to support the existence of a locus on chromosome 15q13-14 that confers susceptibility to JME but not to a broader IGE phenotype. Causal sequence variants in the positional candidate CHRNA7 have not been identified but the presence of multiple segmental duplications in this region raises the possibility of undetected disease-causing genomic rearrangements.


Does anti-EGFR therapy improve outcome in advanced colorectal cancer? A systematic review and meta-analysis.
Randomised controlled trials (RCTs) of anti-EGFR monoclonal antibodies (MAb) in patients with advanced colorectal cancer (aCRC) have reported conflicting results. A systematic review of RCTs comparing standard treatments±anti-EGFR MAbs was conducted. Hazard ratios (HR) for progression-free (PFS) and overall survival (OS) were derived for patients with wild-type (WT) and mutant KRAS. Prespecified analyses were conducted for line of treatment, MAb used, chemotherapy regimen, and choice of fluouropyrimidine. Trials using bevacizumab on both arms were included in a sensitivity analysis. Fourteen eligible RCTs were identified, with results by KRAS status available for ten RCTs. For third line treatment, the effect of anti-EGFR MAbs depended on KRAS status (interaction p<0.00001), with a PFS benefit for patients with WT KRAS only (HR=0.43, 95% CI 0.35-0.52, p<0.00001). For first and second line treatment, the effect also appeared to depend on KRAS status (interaction p=0.0003), again with the PFS benefit only for patients with WT KRAS (HR=0.83, 95% CI 0.76-0.90, p<0.0001). Differences between trial results (heterogeneity p=0.02, I(2)=62%) were best explained by the fluouropyrimidine used, with PFS benefits confined to trials combining MAbs alongside 5FU-based chemotherapy (HR=0.77, 95% CI 0.70-0.85, p<0.00001). There was no evidence of a PFS benefit when MAbs were given with bevacizumab. For aCRC patients with WT KRAS, there are clear benefits of anti-EGFR MAbs in the third line and in the first and second line, when used alongside infusional 5FU-based regimens. However, there is no benefit for patients with KRAS mutations.


'Random coil' 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG.
Proton chemical shifts of a series of disordered linear peptides (H-Gly-Gly-X-Gly-Gly-OH, with X being one of the 20 naturally occurring amino acids) have been obtained using 1D and 2D 1H NMR at pH 5.0 as a function of temperature and solvent composition. The use of 2D methods has allowed some ambiguities in side-chain assignments in previous studies to be resolved. An additional benefit of the temperature data is that they can be used to obtain 'random coil' amide proton chemical shifts at any temperature between 278 and 318 K by interpolation. Changes of chemical shift as a function of trifluoroethanol concentration have also been determined at a variety of temperatures for a subset of peptides. Significant changes are found in backbone and side-chain amide proton chemical shifts in these 'random coil' peptides with increasing amounts of trifluoroethanol, suggesting that caution is required when interpreting chemical shift changes as a measure of helix formation in peptides in the presence of this solvent. Comparison of the proton chemical shifts obtained here for H-Gly-Gly-X-Gly-Gly-OH with those for H-Gly-Gly-X-Ala-OH [Bundi, A. and Wüthrich, K., (1979) Biopolymers, 18, 285-297] and for Ac-Gly-Gly-X-Ala-Gly-Gly-NH2 [Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67-81] generally shows good agreement for CH protons, but reveals significant variability for NH protons. Amide proton chemical shifts appear to be highly sensitive to local sequence variations and probably also to solution conditions. Caution must therefore be exercised in any structural interpretation based on amide proton chemical shifts.


Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort.
Esophageal squamous cell carcinoma (ESCC) is the most common histological subtype of esophageal cancer in India. Cigarette smoking and chewing tobacco are known risk factors associated with ESCC. However, genomic alterations associated with ESCC in India are not well-characterized. In this study, we carried out exome sequencing to characterize the mutational landscape of ESCC tumors from subjects with a varied history of tobacco usage. Whole exome sequence analysis of ESCC from an Indian cohort revealed several genes that were mutated or had copy number changes. ESCC from tobacco chewers had a higher frequency of C:G > A:T transversions and 2-fold enrichment for mutation signature 4 compared to smokers and non-users of tobacco. Genes, such as TP53, CSMD3, SYNE1, PIK3CA, and NOTCH1 were found to be frequently mutated in Indian cohort. Mutually exclusive mutation patterns were observed in PIK3CA-NOTCH1, DNAH5-ZFHX4, MUC16-FAT1, and ZFHX4-NOTCH1 gene pairs. Recurrent amplifications were observed in 3q22-3q29, 11q13.3-q13.4, 7q22.1-q31.1, and 8q24 regions. Approximately 53% of tumors had genomic alterations in PIK3CA making this pathway a promising candidate for targeted therapy. In conclusion, we observe enrichment of mutation signature 4 in ESCC tumors from patients with a history of tobacco chewing. This is likely due to direct exposure of esophagus to tobacco carcinogens when it is chewed and swallowed. Genomic alterations were frequently observed in PIK3CA-AKT pathway members independent of the history of tobacco usage. PIK3CA pathway can be potentially targeted in ESCC which currently has no effective targeted therapeutic options.