Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray.
We have performed microarray hybridization studies on 40 clinical isolates from 12 common serovars within Salmonella enterica subspecies I to identify the conserved chromosomal gene pool. We were able to separate the core invariant portion of the genome by a novel mathematical approach using a decision tree based on genes ranked by increasing variance. All genes within the core component were confirmed using available sequence and microarray information for S. enterica subspecies I strains. The majority of genes within the core component had conserved homologues in Escherichia coli K-12 strain MG1655. However, many genes present in the conserved set which were absent or highly divergent in K-12 had close homologues in pathogenic bacteria such as Shigella flexneri and Pseudomonas aeruginosa. Genes within previously established virulence determinants such as SPI1 to SPI5 were conserved. In addition several genes within SPI6, all of SPI9, and three fimbrial operons (fim, bcf, and stb) were conserved within all S. enterica strains included in this study. Although many phage and insertion sequence elements were missing from the core component, approximately half the pseudogenes present in S. enterica serovar Typhi were conserved. Furthermore, approximately half the genes conserved in the core set encoded hypothetical proteins. Separation of the core and variant gene sets within S.enterica subspecies I has offered fundamental biological insight into the genetic basis of phenotypic similarity and diversity across S. enterica subspecies I and shown how the core genome of these pathogens differs from the closely related E. coli K-12 laboratory strain.


Radiotherapy for node positive penile cancer: experience of the Leeds teaching hospitals.
We studied the outcomes in patients with node positive penile cancer who received radiotherapy to inguinal and pelvic nodes. Although half of node positive cases are cured by lymphadenectomy, little data are available on the potential further benefits and toxicities of postoperative radiotherapy. We retrospectively audited the clinical notes and electronic records of 23 patients referred to a specialist center from 2002 to 2008 who received radiotherapy to the inguinal/pelvic nodes as adjuvant treatment after lymphadenectomy (14), or as high grade palliation for extensive/fixed nodes (8) or extensive local tumor (1). The primary outcome measure was overall survival. Secondary end points were locoregional recurrence-free survival and toxicity. All 13 deaths were due to penile cancer. Patients with adjuvant therapy had better overall survival (66% vs 11%, p<0.001) and locoregional relapse-free survival (56% vs 22%, p=0.03) than those with high grade palliation. Six of 14 adjuvant cases and 7 of 9 with high grade palliation relapsed locoregionally. Of patients with adjuvant therapy and extracapsular spread 1 of 6 with N1, 1 of 4 with N2 and 3 of 4 with N3 disease relapsed (p=0.31). No life threatening toxicity was observed. It was difficult to determine the relative contributions of radiotherapy and surgery to leg/scrotal lymphedema. The study was limited by its small size, which reflects the rarity of this tumor. Adjuvant radiotherapy appears to have a role after inguinal lymphadenectomy, particularly in patients with extracapsular nodal spread, in whom historically survival rates have been poor. Our findings warrant further investigation in larger series of patients.


[Junk food consumption and child nutrition. Nutritional anthropological analysis].
The increasing consumption of junk food and snacks in Chile in recent years and its association with marketing strategies and prevalent diseases, is reviewed. In the context of world economy, junk food is a global phenomenon. The availability of junk food and snacks at low prices and marketing has triggered an evolution of consumption of foods that require neither the structure nor the preparation of a formal meal. Many studies have suggested that the increase in snack consumption is associated with an increase in obesity, tooth decay and other chronic diseases among children and adolescents. The hypothesis suggests a link between the pattern of snack consumption and an increase increase in the energy density of food consumed, a decrease in satiety, passive over consumption, and an increase in obesity. Between 1977 and 1996, the contribution: of snacks to daily energy intake among children between 2 and 5 years increased by 30% in the United States. In each age group in Chile the frequency of non-transmissible chronic diseases is increasing due primarily to a westernized diet that is high in fat, cholesterol, sodium, and sugar and a sedentary lifestyle. Education about junk food consumption and healthy eating habits in the family, starling since childbirth and public policies about healthy lifestyles should be strengthened.


Age Modulates the Association of Caffeine Intake With Cognition and With Gray Matter in Elderly Diabetics.
The association between caffeine and cognitive performance has not been tested in older individuals with type 2 diabetes (T2D). Its association with brain volume in T2D has been tested only in animals. We examined the association of caffeine with cognitive function and brain volume in a sample of elderly diabetics participating in the Israel Diabetes and Cognitive Decline Study (n = 638) and the moderating effect of age on this association. In a subsample (n = 185) with magnetic resonance imaging, we also examined these associations with gray and white matter volumes (GM/WM). Using linear regression adjusting for cognition-related covariates, we found that higher caffeine intake was associated with better function in overall cognition (p = .018), attention/working memory (p = .002), executive functioning (p = .047), and semantic categorization (p = .026). Interaction analyses of caffeine intake with age were significant for semantic categorization (p = .025), and approached significance for overall cognition (p = .066). This association was driven by the older group (above-median) for whom the association of caffeine intake with semantic categorization (p = .001), attention/working memory (p = .007), executive functioning (p = .005), and overall cognition (p = .002) were significant. In the magnetic resonance imaging subsample, there was an interaction (p = .034) of caffeine intake with age for GM volume; in the older group, higher caffeine intake was associated with greater GM volume (β = .198, p = .033). Caffeine intake may have a beneficial role in cognitive functioning of elderly adults with T2D, which may be moderated by age. Greater GM volume may be a mechanism underlying the association of higher caffeine intake with better cognitive function.


The Association Between Mild Cognitive Impairment and Self-care in Adults With Chronic Heart Failure: A Systematic Review and Narrative Synthesis.
Emerging evidence suggests that heart failure (HF) patients who have mild cognitive impairment (MCI) may experience greater difficulty with self-care. This article reports a systematic review that addressed the objective "What is the evidence for an association between MCI and self-care, measured in 1 or more of the self-care domains related to HF, in adults who have a diagnosis of chronic HF?" We adopted Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for the review and synthesis of quantitative research studies that formally measured both cognitive function and self-care in HF patients and sought to describe the relationship between these factors. Ninety-one potentially relevant studies were located; 10 studies (2006-2014) were included. Because of heterogeneity in the retrieved studies, meta-analysis was not possible. Narrative synthesis found growing evidence regarding the association between MCI and adverse effects on self-care in HF. Nine studies reported significant positive associations between MCI and self-care in HF, either specifically in relation to medication adherence or more generic measures of self-care activity. One study reported a significant, negative correlation between cognitive function and self-care, suggesting that worse cognitive function was associated with better self-care; however, this is partially explained by a small sample size and mixed methodology. These findings have implications for clinical practice. It is known that HF patients have difficulty with self-care, and the influence of cognitive function needs to be considered when providing professional support. Further research to determine the feasibility and acceptability of cognitive assessment in routine clinical care is recommended.


Poor tolerance and limited effects of isosorbide-5-mononitrate in microvascular angina.
To assess the effects of isosorbide-5-mononitrate (ISMN) in patients with microvascular angina (MVA). We randomized 20 MVA patients, treated with a β-blocker or a calcium antagonist, to 60 mg slow-release ISMN (halved to 30 mg if not tolerated) or placebo once a day for 4 weeks; the patients were then switched to the other treatment for another 4 weeks. Their clinical status was assessed with the Seattle Angina Questionnaire (SAQ) and the EuroQoL score for quality of life. The exercise stress test (EST), coronary blood flow (CBF) response to nitrate and the cold pressor test (CPT), brachial artery flow-mediated dilation (FMD) and nitrate-mediated dilation (NMD) were also assessed. Nine patients (45%) did not complete the ISMN phase due to side effects; 2 patients refused a follow-up. Nine patients completed the study. The SAQ and EuroQoL scores were significantly better with ISMN than with placebo, although the differences were small. No differences were found between the treatments in the EST results, CBF response to nitroglycerin (p = 0.55) and the CPT (p = 0.54), FMD (p = 0.26) and NMD (p = 0.35). In this study, a high proportion of MVA patients showed an intolerance to ISMN; in those tolerating the drug, significant effects on their angina status were observed, but the benefit appeared to be modest and independent of effects on coronary microvascular function.


Antimicrobial susceptibility of Brachyspira spp. isolated from commercial laying hens and free-living wild mallards (Anas platyrhynchos).
In vitro antimicrobial susceptibility to tylosin, valnemulin, tiamulin, doxycycline, lincomycin and ampicillin was investigated by broth dilution in 48 Brachyspira spp. isolates from commercial laying hens (n=30) and free-living wild mallards (Anas platyrhynchos) (n=18). Presumed pathogens (Brachyspira alvinipulli, Brachyspira intermedia, Brachyspira pilosicoli), commensals (Brachyspira murdochii, Brachyspira innocens, "Brachyspira pulli"), and isolates of undetermined species affiliation were included. The laying hens had not been exposed to therapeutic levels of antimicrobials for at least 50 weeks before sampling, and low levels of environmental antimicrobial exposure were presumed in mallards. No isolates with decreased susceptibility to tylosin, valnemulin, tiamulin or doxycycline were found. Decreased susceptibility to lincomycin (minimum inhibitory concentration 16 µg/ml) was detected in two isolates (Brachyspira sp.) from laying hens. Five isolates showed decreased susceptibility to ampicillin (minimum inhibitory concentration 16 to >32 µg/ml), including two "B. pulli" and one B. alvinipulli from laying hens, and isolates of B. pilosicoli and "B. pulli" from mallards. Decreased susceptibility to ampicillin was associated with β-lactamase activity in four isolates. A new variant of a class D β-lactamase gene designated bla (oxa-192) was identified in a B. pilosicoli isolate of mallard origin. This is the first time the genetic basis for antimicrobial resistance is described in Brachyspira spp. from a free-living wild bird. Isolates displaying decreased susceptibility to ampicillin were accompanied by fully susceptible isolates of the same species or other genotypes within three laying hen flocks. This underlines the need for performing antimicrobial susceptibility tests on single clones/genotypes, and to analyse multiple isolates from the same flock.


Recent developments in MAS DNP-NMR of materials.
Solid-state NMR spectroscopy is a powerful technique for the characterization of the atomic-level structure and dynamics of materials. Nevertheless, the use of this technique is often limited by its lack of sensitivity, which can prevent the observation of surfaces, defects or insensitive isotopes. Dynamic Nuclear Polarization (DNP) has been shown to improve by one to three orders of magnitude the sensitivity of NMR experiments on materials under Magic-Angle Spinning (MAS), at static magnetic field B0 ≥ 5 T, conditions allowing for the acquisition of high-resolution spectra. The field of DNP-NMR spectroscopy of materials has undergone a rapid development in the last ten years, spurred notably by the availability of commercial DNP-NMR systems. We provide here an in-depth overview of MAS DNP-NMR studies of materials at high B0 field. After a historical perspective of DNP of materials, we describe the DNP transfers under MAS, the transport of polarization by spin diffusion and the various contributions to the overall sensitivity of DNP-NMR experiments. We discuss the design of tailored polarizing agents and the sample preparation in the case of materials. We present the DNP-NMR hardware and the influence of key experimental parameters, such as microwave power, magnetic field, temperature and MAS frequency. We give an overview of the isotopes that have been detected by this technique, and the NMR methods that have been combined with DNP. Finally, we show how MAS DNP-NMR has been applied to gain new insights into the structure of organic, hybrid and inorganic materials with applications in fields, such as health, energy, catalysis, optoelectronics etc.


MHYT, a new integral membrane sensor domain.
MHYT, a new conserved protein domain with a likely signaling function, is described. This domain consists of six transmembrane segments, three of which contain conserved methionine, histidine, and tyrosine residues that are projected to lie near the outer face of the cytoplasmic membrane. In Synechocystis sp. PCC6803, this domain forms the N-terminus of the sensor histidine kinase Slr2098. In Pseudomonas aeruginosa and several other organisms, the MHYT domain forms the N-terminal part of a three-domain protein together with previously described GGDEF and EAL domains, both of which have been associated with signal transduction due to their presence in likely signaling proteins. In Bacillus subtilis YkoW protein, an additional PAS domain is found between the MHYT and GGDEF domains. A ykoW null mutant of B. subtilis did not exhibit any growth alterations, consistent with a non-essential, signaling role of this protein. A model of the membrane topology of the MHYT domain indicates that its conserved residues could coordinate one or two copper ions, suggesting a role in sensing oxygen, CO, or NO.


CXCL12 induces connective tissue growth factor expression in human lung fibroblasts through the Rac1/ERK, JNK, and AP-1 pathways.
CXCL12 (stromal cell-derived factor-1, SDF-1) is a potent chemokine for homing of CXCR4+ fibrocytes to injury sites of lung tissue, which contributes to pulmonary fibrosis. Overexpression of connective tissue growth factor (CTGF) plays a critical role in pulmonary fibrosis. In this study, we investigated the roles of Rac1, extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and activator protein-1 (AP-1) in CXCL12-induced CTGF expression in human lung fibroblasts. CXCL12 caused concentration- and time-dependent increases in CTGF expression and CTGF-luciferase activity. CXCL12-induced CTGF expression was inhibited by a CXCR4 antagonist (AMD3100), small interfering RNA of CXCR4 (CXCR4 siRNA), a dominant negative mutant of Rac1 (RacN17), a mitogen-activated protein kinase (MAPK) kinase (MEK) inhibitor (PD98059), a JNK inhibitor (SP600125), a p21-activated kinase inhibitor (PAK18), c-Jun siRNA, and an AP-1 inhibitor (curcumin). Treatment of cells with CXCL12 caused activations of Rac1, Rho, ERK, and c-Jun. The CXCL12-induced increase in ERK phosphorylation was inhibited by RacN17. Treatment of cells with PD98059 and SP600125 both inhibited CXCL12-induced c-Jun phosphorylation. CXCL12 caused the recruitment of c-Jun and c-Fos binding to the CTGF promoter. Furthermore, CXCL12 induced an increase in α-smooth muscle actin (α-SMA) expression, a myofibroblastic phenotype, and actin stress fiber formation. CXCL12-induced actin stress fiber formation and α-SMA expression were respectively inhibited by AMD3100 and CTGF siRNA. Taken together, our results suggest that CXCL12, acting through CXCR4, activates the Rac/ERK and JNK signaling pathways, which in turn initiates c-Jun phosphorylation, and recruits c-Jun and c-Fos to the CTGF promoter and ultimately induces CTGF expression in human lung fibroblasts. Moreover, overexpression of CTGF mediates CXCL12-induced α-SMA expression.


In vivo evidence for reduced binding of low density lipoproteins to receptors as a cause of primary moderate hypercholesterolemia.
The causes of primary moderate hypercholesterolemia are not understood, but some patients have reduced fractional clearance rates (FCRs) for low density lipoproteins (LDL). This could be due to either decreased activity of LDL receptors or to a defect in structure (or composition) of LDL that reduces its affinity for receptors. To distinguish between these causes, simultaneous turnover rates of autologous and normal homologous LDL were determined in 15 patients with primary moderate hypercholesterolemia. In 10, turnover rates of both types of LDL were indistinguishable, which indicated that autologous LDL was cleared as efficiently as normal homologous LDL. In five others, FCRs for autologous LDL were significantly lower than for homologous LDL. Two of the latter five were treated with mevinolin, and although FCRs for both types of LDL rose during treatment, differences in FCRs between the two types of LDL persisted. In these five patients, autologous LDL appeared to be a poor ligand for LDL receptors.


Piezoelectrically Actuated Robotic System for MRI-Guided Prostate Percutaneous Therapy.
This paper presents a fully-actuated robotic system for percutaneous prostate therapy under continuously acquired live magnetic resonance imaging (MRI) guidance. The system is composed of modular hardware and software to support the surgical workflow of intra-operative MRI-guided surgical procedures. We present the development of a 6-degree-of-freedom (DOF) needle placement robot for transperineal prostate interventions. The robot consists of a 3-DOF needle driver module and a 3-DOF Cartesian motion module. The needle driver provides needle cannula translation and rotation (2-DOF) and stylet translation (1-DOF). A custom robot controller consisting of multiple piezoelectric motor drivers provides precision closed-loop control of piezoelectric motors and enables simultaneous robot motion and MR imaging. The developed modular robot control interface software performs image-based registration, kinematics calculation, and exchanges robot commands and coordinates between the navigation software and the robot controller with a new implementation of the open network communication protocol OpenIGTLink. Comprehensive compatibility of the robot is evaluated inside a 3-Tesla MRI scanner using standard imaging sequences and the signal-to-noise ratio (SNR) loss is limited to 15%. The image deterioration due to the present and motion of robot demonstrates unobservable image interference. Twenty-five targeted needle placements inside gelatin phantoms utilizing an 18-gauge ceramic needle demonstrated 0.87 mm root mean square (RMS) error in 3D Euclidean distance based on MRI volume segmentation of the image-guided robotic needle placement procedure.


Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
Single-cell CRISPR screens enable the exploration of mammalian gene function and genetic regulatory networks. However, use of this technology has been limited by reliance on indirect indexing of single-guide RNAs (sgRNAs). Here we present direct-capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct-capture Perturb-seq enables detection of multiple distinct sgRNA sequences from individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries that contain dual-guide expression vectors. We demonstrate the utility of this approach for high-throughput investigations of genetic interactions and, leveraging this ability, dissect epistatic interactions between cholesterol biogenesis and DNA repair. Using direct capture Perturb-seq, we also show that targeting individual genes with multiple sgRNAs per cell improves efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Last, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.


Mathematical modeling of tumor therapy with oncolytic viruses: regimes with complete tumor elimination within the framework of deterministic models.
Oncolytic viruses that specifically target tumor cells are promising anti-cancer therapeutic agents. The interaction between an oncolytic virus and tumor cells is amenable to mathematical modeling using adaptations of techniques employed previously for modeling other types of virus-cell interaction. A complete parametric analysis of dynamic regimes of a conceptual model of anti-tumor virus therapy is presented. The role and limitations of mass-action kinetics are discussed. A functional response, which is a function of the ratio of uninfected to infected tumor cells, is proposed to describe the spread of the virus infection in the tumor. One of the main mathematical features of ratio-dependent models is that the origin is a complicated equilibrium point whose characteristics determine the main properties of the model. It is shown that, in a certain area of parameter values, the trajectories of the model form a family of homoclinics to the origin (so-called elliptic sector). Biologically, this means that both infected and uninfected tumor cells can be eliminated with time, and complete recovery is possible as a result of the virus therapy within the framework of deterministic models. Our model, in contrast to the previously published models of oncolytic virus-tumor interaction, exhibits all possible outcomes of oncolytic virus infection, i.e., no effect on the tumor, stabilization or reduction of the tumor load, and complete elimination of the tumor. The parameter values that result in tumor elimination, which is, obviously, the desired outcome, are compatible with some of the available experimental data. This article was reviewed by Mikhail Blagosklonny, David Krakauer, Erik Van Nimwegen, and Ned Wingreen. Reviewed by Mikhail Blagosklonny, David Krakauer, Erik Van Nimwegen, and Ned Wingreen. For the full reviews, please go to the Reviewers' comments section.


Vaccine Induced Herd Immunity for Control of Respiratory Syncytial Virus Disease in a Low-Income Country Setting.
Respiratory syncytial virus (RSV) is globally ubiquitous, and infection during the first six months of life is a major risk for severe disease and hospital admission; consequently RSV is the most important viral cause of respiratory morbidity and mortality in young children. Development of vaccines for young infants is complicated by the presence of maternal antibodies and immunological immaturity, but vaccines targeted at older children avoid these problems. Vaccine development for young infants has been unsuccessful, but this is not the case for older children (> 6 m). Would vaccinating older children have a significant public health impact? We developed a mathematical model to explore the benefits of a vaccine against RSV. We have used a deterministic age structured model capturing the key epidemiological characteristics of RSV and performed a statistical maximum-likelihood fit to age-specific hospitalization data from a developing country setting. To explore the effects of vaccination under different mixing assumptions, we included two versions of contact matrices: one from a social contact diary study, and the second a synthesised construction based on demographic data. Vaccination is assumed to elicit an immune response equivalent to primary infection. Our results show that immunisation of young children (5-10 m) is likely to be a highly effective method of protection of infants (<6 m) against hospitalisation. The majority benefit is derived from indirect protection (herd immunity). A full sensitivity and uncertainty analysis using Latin Hypercube Sampling of the parameter space shows that our results are robust to model structure and model parameters. This result suggests that vaccinating older infants and children against RSV can have a major public health benefit.


Torque and buckling in stretched intertwined double-helix DNAs.
We present a statistical-mechanical model for the behavior of intertwined DNAs, with a focus on their torque and extension as a function of their catenation (linking) number and applied force, as studied in magnetic tweezers experiments. Our model produces results in good agreement with available experimental data and predicts a catenation-dependent effective twist modulus distinct from what is observed for twisted individual double-helix DNAs. We find that buckling occurs near the point where experiments have observed a kink in the extension versus linking number, and that the subsequent "supercoiled braid" state corresponds to a proliferation of multiple small plectoneme structures. We predict a discontinuity in extension at the buckling transition corresponding to nucleation of the first plectoneme domain. We also find that buckling occurs for lower linking number at lower salt; the opposite trend is observed for supercoiled single DNAs.


In Toto Imaging of Dynamic Osteoblast Behaviors in Regenerating Skeletal Bone.
Osteoblasts are matrix-depositing cells that can divide and heal bone injuries. Their deep-tissue location and the slow progression of bone regeneration challenge attempts to capture osteoblast behaviors in live tissue at high spatiotemporal resolution. Here, we have developed an imaging platform to monitor and quantify individual and collective behaviors of osteoblasts in adult zebrafish scales, skeletal body armor discs that regenerate rapidly after loss. Using a panel of transgenic lines that visualize and manipulate osteoblasts, we find that a founder pool of osteoblasts emerges through de novo differentiation within one day of scale plucking. These osteoblasts undergo division events that are largely uniform in frequency and orientation to establish a primordium. Osteoblast proliferation dynamics diversify across the primordium by two days after injury, with cell divisions focused near, and with orientations parallel to, the scale periphery, occurring coincident with dynamic localization of fgf20a gene expression. In posterior scale regions, cell elongation events initiate in areas soon occupied by mineralized grooves called radii, beginning approximately 2 days post injury, with patterned osteoblast death events accompanying maturation of these radii. By imaging at single-cell resolution, we detail acquisition of spatiotemporally distinct cell division, motility, and death dynamics within a founder osteoblast pool as bone regenerates.


Evidence of a coupled electron-phonon liquid in NbGe2.
Whereas electron-phonon scattering relaxes the electron's momentum in metals, a perpetual exchange of momentum between phonons and electrons may conserve total momentum and lead to a coupled electron-phonon liquid. Such a phase of matter could be a platform for observing electron hydrodynamics. Here we present evidence of an electron-phonon liquid in the transition metal ditetrelide, NbGe2, from three different experiments. First, quantum oscillations reveal an enhanced quasiparticle mass, which is unexpected in NbGe2 with weak electron-electron correlations, hence pointing at electron-phonon interactions. Second, resistivity measurements exhibit a discrepancy between the experimental data and standard Fermi liquid calculations. Third, Raman scattering shows anomalous temperature dependences of the phonon linewidths that fit an empirical model based on phonon-electron coupling. We discuss structural factors, such as chiral symmetry, short metallic bonds, and a low-symmetry coordination environment as potential design principles for materials with coupled electron-phonon liquid.


Comparison of muscle metabolomics between two Chinese horse breeds.
With their enormous muscle mass and athletic ability, horses are well-positioned as model organisms for understanding muscle metabolism. There are two different types of horse breeds-Guanzhong (GZ) horses, an athletic breed with a larger body height (~148.7 cm), and the Ningqiang pony (NQ) horses, a lower height breed generally used for ornamental purposes-both inhabited in the same region of China with obvious differences in muscle content. The main objective of this study was to evaluate the breed-specific mechanisms controlling muscle metabolism. In this study, we observed muscle glycogen, enzyme activities, and LC-MS/MS untargeted metabolomics in the gluteus medius muscle of six, each of GZ and NQ horses, to explore differentiated metabolites that are related to the development of two muscles. As expected, the glycogen content, citrate synthase, and hexokinase activity of muscle were significantly higher in GZ horses. To alleviate the false positive rate, we used both MS1 and MS2 ions for metabolite classification and differential analysis. As a result, a total of 51,535 MS1 and 541 MS2 metabolites were identified, and these metabolites can separate these two groups from each other. Notably, 40% of these metabolites were clustered into lipids and lipid-like molecules. Furthermore, 13 significant metabolites were differentially detected between GZ and NQ horses (fold change [FC] value ≥ 2, variable important in projection value ≥1, and Q value ≤ 0.05). They are primarily clustered into glutathione metabolism (GSH, p = 0.01), taurine, and hypotaurine metabolism (p < 0.05) pathways. Seven of the 13 metabolites were also found in thoroughbred racing horses, suggesting that metabolites related to antioxidants, amino acids, and lipids played a key role in the development of skeleton muscle in horses. Those metabolites related to muscle development shed a light on racing horses' routine maintenance and improvement of athletic performance.


Susceptibility of channel catfish fry to Channel Catfish Virus (CCV) challenge increases with age.
Susceptibility of channel catfish to Channel Catfish Virus Disease (CCVD) has been generally considered to be inversely related to age. However, in experimental immersion challenges, we found that channel catfish fry, 3 to 8 d post hatch (dph), are most resistant to CCV and susceptibility increases with age. Initial studies involved 2 spawns that had high CCV carrier percentage. To determine if the resistance seen in the fry was related to the CCV carrier status of the parents, we selected 4 spawns from CCV negative parents and 2 spawns from CCV positive parents and immersion challenged them at 8, 23, 36 and 60 dph with 0, 2.5 x 10(4) or 2.5 x 10(6) plaque forming units (PFU) of CCV l(-1). Survivors of the low-dose exposed groups were rechallenged at 120 dph with 2.5 x 10(6) PFU CCV l(-1). Each brood demonstrated increasing susceptibility to CCVD with age and only the fish that were initially exposed at 60 dph developed protective immunity. Time course assays evaluating tissue levels of virus in channel catfish exposed to CCV at 7, 21 and 42 dph suggested that the resistance was an early event in the infection process. The resistance in fry was most pronounced in fish from CCV positive spawns and was correlated to neutralizing antibody titers in the maternal parent in the 8 dph challenge. However, other factors may be involved because all groups displayed the initial resistance and subsequent susceptibility to CCVD. The age effect may be an important influence on the progression of CCVD outbreaks and indicates the need to consider age for experimental challenges. Additionally, we documented the level of vertical transmission of CCV. Fry from the 4 positive spawns had a CCV prevalence of 40 to 75 %.


Evidence for attenuation of myo-inositol uptake, phosphoinositide turnover and inositol phosphate production in aortic vasculature of rats during pregnancy.
We postulated that vascular phosphoinositide metabolism is attenuated during pregnancy, and thereby could contribute to maternal vasodilation and reduced vascular reactivity. The basal rate of incorporation of [3H]myo-inositol and [3H]glycerol into phosphoinositides of aortae from pregnant rats in vitro was significantly reduced, when compared with vessels from virgin animals. After injection of [3H]myo-inositol intravenously into chronically instrumented conscious pregnant and virgin rats, the incorporation of the label by phosphatidylinositol was 66 +/- 4% less in aortae of gravid versus virgin animals (P less than 0.001), despite comparable plasma concentrations of radioactivity. Fold stimulation of total [3H]inositol phosphates by arginine vasopressin, norepinephrine, and angiotensin II over a 15-min period was not different between aortic segments from virgin and gravid rats, although both absolute basal and stimulated levels were significantly less in vessels from pregnant animals. After 45 s of incubation with 10(-7) M arginine vasopressin, however, the fold-stimulation of [3H]inositol trisplus tetrakisphosphate was reduced in aortae from gravid rats, when compared with vessels from virgin animals (P less than 0.005). By HPLC, greater than 90% of the radioactivity in the [3H]inositol trisplus tetrakisphosphate column fraction after 30 and 60 s of agonist stimulation was [3H]inositol-1,4,5-trisphosphate. We further observed that the rate of uptake of [3H]myo-inositol by aortic vasculature obtained from gravid rats was significantly (24%) less than uptake by vessels from virgin animals. Plasma myo-inositol concentrations were not significantly different, but presumably as a consequence of reduced uptake, aortic segments freshly isolated from pregnant rats contained 22 +/- 6% less myo-inositol than vessels from virgin controls as measured by gas chromatography-mass spectrometry (P less than 0.03). We conclude that myo-inositol uptake and content, phosphoinositide turnover, and inositol phosphate production are reduced in aortic vasculature of gravid rats.


Relationship between tooth loss and carotid intima-media thickness in Korean adults.
The aim of this study was to examine the relationship between tooth loss and sub-clinical atherosclerosis in Korean adults. The subjects were part of a cohort study conducted in Ansan city by the Korea University medical school as part of the Korean Genome project. 749 subjects over than 40 years old were evaluated. After taking panoramic radiography, the amount of tooth loss was calculated. The intima-media thickness (IMT) was assessed by using ultrasonography at the common carotid artery. Traditional cardiovascular risk factors for atherosclerosis were also evaluated. The relationship between tooth loss and the IMT was evaluated using ANOVA with Scheffe's multiple comparison method in univariate analysis. Multiple regression analysis was also performed to determine the significance between the IMT and tooth loss. With age, tooth loss increased, but there was no significant increase in other traditional cardiovascular risk factors. Univariate analysis revealed the IMT to be positively related with the amount of tooth loss. Regression analysis of the IMT in the anterior and posterior tooth loss revealed that only the posterior tooth loss was significantly related with the IMT at all sites of the common carotid artery (right far wall, P = .015; left far wall, P = .008; right near wall, P < .001; left near wall, P = .001). This study verified the positive relationship between the increased tooth loss at the posterior area and the accumulation of atheroma in arteries.


Tissue-protective effects of estrogen involve regulation of caspase gene expression.
Estrogen plays a critical role in the protection from apoptosis in several cell types because the withdrawal of estrogen leads to increased apoptosis in tissues such as the brain, endothelium, testes, and uterus. Our recent report demonstrated that the chick oviduct also regresses through apoptotic mechanisms during estrogen deficiency. Despite these observations, very little is known concerning the intracellular mechanisms by which estrogen opposes apoptosis. To better understand how estrogen exerts its antiapoptotic effects, several key apoptotic genes were examined for their regulation by estrogen. Our results show that mRNA expression levels of Bcl-2, hsp-70, c-myc, Bcl-X(l), caspase-3, and caspase-6 remain essentially constant when apoptosis is stimulated by estrogen withdrawal. However, the genes for caspase-1 and caspase-2 are rapidly stimulated, at least for the most part, at the transcriptional level after the withdrawal of estrogen. This increase in caspase-2 mRNA is followed by an increase in enzyme activity. Furthermore, although mRNA expression levels are unaffected, both caspase-3 and caspase-6 proenzymes are activated in the estrogen-withdrawn cells. Taken together, these results demonstrate that estrogen has the potential to oppose apoptosis by regulating caspase activity through both transcriptional and posttranscriptional mechanisms in reproductive tissues.


Digital traces of brain drain: developers during the Russian invasion of Ukraine.
The Russian invasion of Ukraine has caused large scale destruction, significant loss of life, and the displacement of millions of people. Besides those fleeing direct conflict in Ukraine, many individuals in Russia are also thought to have moved to third countries. In particular the exodus of skilled human capital, sometimes called brain drain, out of Russia may have a significant effect on the course of the war and the Russian economy in the long run. Yet quantifying brain drain, especially during crisis situations is generally difficult. This hinders our ability to understand its drivers and to anticipate its consequences. To address this gap, I draw on and extend a large scale dataset of the locations of highly active software developers collected in February 2021, one year before the invasion. Revisiting those developers that had been located in Russia in 2021, I confirm an ongoing exodus of developers from Russia in snapshots taken in June and November 2022. By November 11.1% of Russian developers list a new country, compared with 2.8% of developers from comparable countries in the region but not directly involved in the conflict. 13.2% of Russian developers have obscured their location (vs. 2.4% in the comparison set). Developers leaving Russia were significantly more active and central in the collaboration network than those who remain. This suggests that many of the most important developers have already left Russia. In some receiving countries the number of arrivals is significant: I estimate an increase in the number of local software developers of 42% in Armenia, 60% in Cyprus and 94% in Georgia. The online version contains supplementary material available at 10.1140/epjds/s13688-023-00389-3.


Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches.
Numerous processes across both the physical and biological sciences are driven by diffusion. Partial differential equations are a popular tool for modelling such phenomena deterministically, but it is often necessary to use stochastic models to accurately capture the behaviour of a system, especially when the number of diffusing particles is low. The stochastic models we consider in this paper are 'compartment-based': the domain is discretized into compartments, and particles can jump between these compartments. Volume-excluding effects (crowding) can be incorporated by blocking movement with some probability. Recent work has established the connection between fine- and coarse-grained models incorporating volume exclusion, but only for uniform lattices. In this paper, we consider non-uniform, hybrid lattices that incorporate both fine- and coarse-grained regions, and present two different approaches to describe the interface of the regions. We test both techniques in a range of scenarios to establish their accuracy, benchmarking against fine-grained models, and show that the hybrid models developed in this paper can be significantly faster to simulate than the fine-grained models in certain situations and are at least as fast otherwise.


Near vision examination in presbyopia patients: Do we need good homologated near vision charts?
Presbyopia correction is mainly concerned with the goal of regaining an uncorrected reading performance. Since historic reading charts do not provide a unique standard that is applicable for the analysis of clinical and scientific reading performance, new standardized reading charts have been developed, in order to provide reading performance analyses analogous to modern single-optotype distance acuity measurements: the Bailey-Lovie Word Reading Chart, the Colenbrander English Continuous Text Near Vision Cards, the MNREAD Charts, and the RADNER Reading Charts. The last three are also meant to measure reading speed, thus allowing detailed analysis of the reading capabilities of the patient's functional vision. Furthermore, these reading charts can be declared homologated, based on the standards that were published for reading charts by the Visual Function Committee of the International Council of Ophthalmology (ICO) in 1988. Many research studies have shown that by analyzing the reading performance with homologated reading charts, valuable insight into the reading performance of patients suffering from various diseases can be obtained. These reading charts have also been successfully used in presbyopia research. It therefore seems evident that homologated, standardized reading charts facilitate not only research concerning functional vision in many fields of ophthalmology but also international communication about near visual performance. Homologated reading charts are available in almost all languages and have become a valuable tool in analyzing reading performance. We argue in this review that homologated reading charts are clearly a necessity for presbyopia research.


High-volume hemofiltration for septic acute kidney injury: a systematic review and meta-analysis.
High-volume hemofiltration (HVHF) is an attractive therapy for the treatment of septic acute kidney injury (AKI). Small experimental and uncontrolled studies have suggested hemodynamic and survival benefits at higher doses of HVHF than those used for the high-intensity arms of the RENAL and ATN studies. Our aim was to evaluate the effects of high-volume hemofiltration (HVHF) compared with standard-volume hemofiltration (SVHF) for septic AKI. A systematic review and meta-analysis of publications between 1966 and 2013 was performed. The review was limited to randomized-controlled trials that compared HVHF (effluent rate greater than 50 ml/kg per hour) versus SVHF in the treatment of sepsis and septic shock. The primary outcome assessed was 28-day mortality. Other outcomes assessed were recovery of kidney function, lengths of ICU and hospital stays, vasopressor dose reduction, and adverse events. Four trials, including 470 total participants, were included. Pooled analysis for 28-day mortality did not show any meaningful difference between HVHF compared with SVHF (OR, 0.76; 95% CI, 0.45 to 1.29). No included studies reported statistically significant differences between groups for any of the secondary outcomes. Adverse events, including hypophosphatemia and hypokalemia, were more commonly observed in HVHF-treated patients, although reporting was inconsistent across studies. Insufficient evidence exists of a therapeutic benefit for routine use of HVHF for septic AKI, other than on an experimental basis. Given the logistic challenges related to patient recruitment along with an incomplete understanding of the biologic mechanisms by which HVHF may modify outcomes, further trials should focus on alternative extracorporeal therapies as an adjuvant therapy for septic AKI rather than HVHF.


Surrogate-Assisted Genetic Programming With Simplified Models for Automated Design of Dispatching Rules.
Automated design of dispatching rules for production systems has been an interesting research topic over the last several years. Machine learning, especially genetic programming (GP), has been a powerful approach to dealing with this design problem. However, intensive computational requirements, accuracy and interpretability are still its limitations. This paper aims at developing a new surrogate assisted GP to help improving the quality of the evolved rules without significant computational costs. The experiments have verified the effectiveness and efficiency of the proposed algorithms as compared to those in the literature. Furthermore, new simplification and visualisation approaches have also been developed to improve the interpretability of the evolved rules. These approaches have shown great potentials and proved to be a critical part of the automated design system.


Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.
Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?


'I Used to Fight with Them but Now I Have Stopped!': Conflict and Doctor-Nurse-Anaesthetists' Motivation in Maternal and Neonatal Care Provision in a Specialist Referral Hospital.
This paper analyses why and how conflicts occur and their influence on doctors and nurse-anaesthetists' motivation in the provision of maternal and neonatal health care in a specialist hospital. The study used ethnographic methods including participant observation, conversation and in-depth interviews over eleven months in a specialist referral hospital in Ghana. Qualitative analysis software Nvivo 8 was used for coding and analysis of data. Main themes identified in the analysis form the basis for interpreting and reporting study findings. Ethical clearance was obtained from the Ghana Health Service Ethics Review board (approval number GHS-ERC:06/01/12) and from the University of Wageningen. Written consent was obtained from interview participants, while verbal consent was obtained for conversations. To protect the identity of the hospital and research participants pseudonyms are used in the article and the part of Ghana in which the study was conducted is not mentioned. Individual characteristics, interpersonal and organisational factors contributed to conflicts. Unequal power relations and distrust relations among doctors and nurse-anaesthetists affected how they responded to conflicts. Responses to conflicts including forcing, avoiding, accommodating and compromising contributed to persistent conflicts, which frustrated and demotivated doctors and nurse-anaesthetists. Demotivated workers exhibited poor attitudes in collaborating with co-workers in the provision of maternal and neonatal care, which sometimes led to poor health worker response to client care, consequently compromising the hospital's goal of providing quality health care to clients. To improve health care delivery in health facilities in Ghana, health managers and supervisors need to identify conflicts as an important phenomenon that should be addressed whenever they occur. Effective mechanisms including training managers and health workers on conflict management should be put in place. Additionally promoting communication and interaction among health workers can foster team spirit. Also resolving conflicts using the collaborating response may help to create a conducive work environment that will promote healthy work relations, which can facilitate the delivery of quality maternal and neonatal health care. However, such an approach requires that unequal power relations, which is a root cause of the conflicts is addressed.


Responses of condensed tannins in poplar roots to fertilization and gypsy moth defoliation.
We examined the effects of fertilization and gypsy moth defoliation on condensed tannin concentration (%CT) of hybrid poplar (Populus x canadensis cv 'Eugeneii') fine roots in the summers of 1997 and 1998. This factorial experiment included two defoliation treatments (defoliated and a foliated control) and fertilization treatments (100 kg nitrogen (N) ha(-1) and an unfertilized control). Gypsy moth (Lymantria dispar L.) populations were experimentally increased to obtain defoliation in the summers of 1996, 1997 and 1998; fertilization subplots were supplemented with NH4NO3 (100 kg N ha(-1)) in the spring of each year. Despite the severity of defoliation, the effects were small, and significant on only two sampling dates: in May 1997, when fine root %CT was 23% lower in the defoliated trees, and in November 1997, when trees in the defoliated unfertilized plots had 35% higher root %CT than trees in all other plots. Defoliation effects on root %CT did not follow the same seasonal pattern as defoliation effects on root starch content, N uptake capacity or leaf %CT. Regulation of root condensed tannin concentration appeared to be partially uncoupled from these traits. The small transient effects on root defense reflect the resilience of this early successional tree to severe early season defoliation.


The structure-activity relationship of urea derivatives as anti-tuberculosis agents.
The treatment of tuberculosis is becoming more difficult due to the ever increasing prevalence of drug resistance. Thus, it is imperative that novel anti-tuberculosis agents, with unique mechanisms of action, be discovered and developed. The direct anti-tubercular testing of a small compound library led to discovery of adamantyl urea hit compound 1. In this study, the hit was followed up through the synthesis of an optimization library. This library was generated by systematically replacing each section of the molecule with a similar moiety until a clear structure-activity relationship was obtained with respect to anti-tubercular activity. The best compounds in this series contained a 1-adamantyl-3-phenyl urea core and had potent activity against Mycobacterium tuberculosis plus an acceptable therapeutic index. It was noted that the compounds identified and the pharmacophore developed is consistent with inhibitors of epoxide hydrolase family of enzymes. Consequently, the compounds were tested for inhibition of representative epoxide hydrolases: M. tuberculosis EphB and EphE; and human soluble epoxide hydrolase. Many of the optimized inhibitors showed both potent EphB and EphE inhibition suggesting the antitubercular activity is through inhibition of multiple epoxide hydrolase enzymes. The inhibitors also showed potent inhibition of humans soluble epoxide hydrolase, but limited cytotoxicity suggesting that future studies must be towards increasing the selectivity of epoxide hydrolase inhibition towards the M. tuberculosis enzymes.


NOD-Rag2null IL-2Rγnull mice: an alternative to NOG mice for generation of humanized mice.
We have developed NOD-Rag2(null) IL-2Rγ(null) (NR2G) mice similar to NOD-scidIL-2Rγ(null) (NOG) mice that are known as an excellent host to generate humanized mice. To evaluate the usefulness of NR2G mice as a host for humanized mice, the engraftment rates and differentiation of human cells after human hematopoietic stem cell (HSC) transplantation were compared among NR2G, NOG, and NOD-scid mice. For this purpose, the appropriate irradiation doses to expand the niche for human stem cells in the bone marrow were first determined. As a result, 8 and 2.5 Gy in adult, and 4 and 1 Gy in newborn NR2G and NOG mice, respectively, were found to be appropriate. Next, 5 × 10(4) human umbilical cord blood CD34(+) cells were intravenously inoculated into irradiated adult or newborn of the immunodeficient mice. These HSC transplantation experiments demonstrated that both NR2G and NOG mice showed high engraftment rates compared with NOD-scid mice, although NOG mice showed a slightly higher engraftment rate than that for NR2G mice. However, no difference was found in the human cell populations differentiated from HSCs between NR2G and NOG mice. The HSC transplantation experiments to adults and newborns of two immunodeficient mice also revealed that the HSC transplantation into newborn mice resulted in higher engraftment rate than those into adults. These results showed that NR2G mice could be used as an alternative host to NOG mice to generate humanized mice.


Is bacterial persistence a social trait?
The ability of bacteria to evolve resistance to antibiotics has been much reported in recent years. It is less well-known that within populations of bacteria there are cells which are resistant due to a non-inherited phenotypic switch to a slow-growing state. Although such 'persister' cells are receiving increasing attention, the evolutionary forces involved have been relatively ignored. Persistence has a direct benefit to cells because it allows survival during catastrophes-a form of bet-hedging. However, persistence can also provide an indirect benefit to other individuals, because the reduced growth rate can reduce competition for limiting resources. This raises the possibility that persistence is a social trait, which can be influenced by kin selection. We develop a theoretical model to investigate the social consequences of persistence. We predict that selection for persistence is increased when: (a) cells are related (e.g. a single, clonal lineage); and (b) resources are scarce. Our model allows us to predict how the level of persistence should vary with time, across populations, in response to intervention strategies and the level of competition. More generally, our results clarify the links between persistence and other bet-hedging or social behaviours.


Alanine to valine substitutions in the pore helix IIIP1 and linker-helix IIIL45 confer cockroach sodium channel resistance to DDT and pyrethroids.
Pyrethroid insecticides exert toxic effects by prolonging the opening of voltage-gated sodium channels. More than 20 sodium channel mutations from arthropod pests and disease vectors have been confirmed to confer pyrethroid resistance. These mutations have been valuable in elucidating the molecular interaction between pyrethroids and sodium channels, including identification of two pyrethroid receptor sites. Previously, two alanine to valine substitutions, one in the pore helix IIIP1 and the other in the linker-helix connecting S4 and S5 in domain III (IIIL45), were found in Drosophila melanogaster mutants that are resistant to DDT and deltamethrin (a type II pyrethroid with an α-cyano group at the phenylbenzyl alcohol position, which is lacking in type I pyrethroids), but their role in target-site-mediated insecticide resistance has not been functionally confirmed. In this study, we functionally examined the two mutations in cockroach sodium channels expressed in Xenopus laevis oocytes. Both mutations caused depolarizing shifts in the voltage dependence of activation, conferred DDT resistance and also resistance to two Type I pyrethroids by almost abolishing the tail currents induced by Type I pyrethroids. In contrast, neither mutation reduced the amplitude of tail currents induced by the Type II pyrethroids, deltamethrin or cypermethrin. However, both mutations accelerated the decay of Type II pyrethroid-induced tail currents, which normally decay extremely slowly. These results provided new insight into the molecular basis of different actions of Type I and Type II pyrethroids on sodium channels. Computer modeling predicts that both mutations may allosterically affect pyrethroid binding.


Increased susceptibility to induction of long-term depression and long-term potentiation reversal during aging.
Homosynaptic long-term depression (LTD) and reversal of long-term potentiation (LTP) were examined extracellularly at CA3-CA1 synapses in stratum radiatum of slices from adult (6-9 months) and aged (20-24 months) Fischer 344 rats. Prolonged low-frequency stimulation (LFS) (900 pulses/1 Hz) of the Schaffer collaterals depressed the initial slope of the excitatory postsynaptic potential (EPSP) in aged but not adult rats. LTD at aged synapses was pathway-specific, persistent, and sensitive to the NMDA receptor antagonist DL-2-amino-5-phosphonopentanoic acid (AP5). Adult slices exhibited AP5-sensitive LTD in high [Ca2+] medium, whereas LTD in aged slices was blocked by high [Mg2+], suggesting that differences in Ca2+ regulation may underlie susceptibility to LTD. Despite age-related differences in LTD induction, no age difference in LTP magnitude was revealed. Additionally, LFS delivered 60 min after LTP induction resulted in similar LTP reversal for both age groups. Susceptibility differences to LTP reversal were indicated after multiple short-duration LFS bursts (30 pulses/1 Hz), with each burst separated by 10 min. Aged synapses exhibited significant reversal after a single burst and complete reversal after three LFS episodes. In adult slices, LTP reversal appeared after the fourth burst, and at no time was LTP depressed to initial baseline levels. This study provides the first characterization of homosynaptic LTD/LTP reversal in the aged animal and demonstrates that one form of plasticity, depression attributable to LFS, is increased during aging.


How special is medical conscience?
The vigorous legal and ethical debates over conscientious objection have taken place largely within the domain of health care. Is this because conscience in medicine is of a special kind, or are there other reasons why it tends to dominate these debates? Beginning with an analysis of the analogy between medical conscience and conscientious objection in wartime, I go on to examine various possible grounds for distinguishing between medicine and other professional contexts (taking law and accountancy as examples). The conclusion is that no principled difference exists between the military and medical cases, nor between the health professions and other professions. Nevertheless, there are practical reasons why medical conscience has distinctive importance, mainly concerning the rapid advance of medical technology. Medical conscience will, for these reasons, continue to drive the debate over conscientious objection, even though legal protection should in principle extend to all professions.


The pigeon (Columba livia) model of spontaneous atherosclerosis.
Multiple animal models have been employed to study human atherosclerosis, the principal cause of mortality in the United States. Each model has individual advantages related to specific pathologies. Initiation, the earliest disease phase, is best modeled by the White Carneau (WC-As) pigeon. Atherosclerosis develops spontaneously in the WC-As without either external manipulation or known risk factors. Furthermore, susceptibility is caused by a single gene defect inherited in an autosomal recessive manner. The Show Racer (SR-Ar) pigeon is resistant to atherosclerosis. Breed differences in the biochemistry and metabolism of celiac foci cells have been described. For example, WC-As have lower oxidative metabolism but higher amounts of chondroitin-6-sulfate and nonesterified fatty acids compared with SR-Ar. Gene expression in aortic smooth muscle cells was compared between breeds using representational difference analysis and microarray analysis. Energy metabolism and cellular phenotype were the chief gene expression differences. Glycolysis and synthetic cell types were related to the WC-As but oxidative metabolism and contractile cell types were related to the SR-Ar. Rosiglitazone, a PPARγ agonist, blocked RNA binding motif (RBMS1) expression in WC-As cells. The drug may act through the c-myc oncogene as RBMS1 is a c-myc target. Proteomic tests of aortic smooth muscle cells supported greater glycosylation in the WC-As and a transforming growth factor β effect in SR-Ar. Unoxidized fatty acids build up in WC-As cells because of their metabolic deficiency, ultimately preventing the contractile phenotype in these cells. The single gene responsible for the disease is likely regulatory in nature.


Phase diagrams of nanoalloys: influence of size and morphology.
The size dependence of the phase diagram of nanoalloys with a tendency to phase separate is investigated. As the critical temperature may depend on both the size and the morphology of the nanoparticles, we consider nanowires with different cross-sections and also nanotubes with different circumferences. The variation of the critical temperature with the length of all these nanoparticles is systematically studied using Monte Carlo simulations based on an Ising model. A non-monotonic variation of the critical temperature is observed as a function of the length. The maximal value of the critical temperature is reached when the length and the circumference of the nanoparticles are similar. The phase diagrams obtained within two thermodynamic ensembles (the canonical ensemble and the pseudo grand canonical ensemble) are compared and discussed in terms of the behaviour of a single particle or an assembly of nanoparticles in mutual equilibrium with each other.


Levodopa-induced-dyskinesias clinical features, incidence, risk factors, management and impact on quality of life.
Levodopa-induced dyskinesias (LID) belong to the most common dose-limiting adverse effects of levodopa therapy. "Peak-dose" LID occur with the maximum effect of medication, 'diphasic dyskinesias' have a "beginning- and end-of-dose" pattern, and the, "off-period dyskinesia" occur during off-periods, most frequently in the early mornings and are typically dystonic in nature. The majority of patients will have developed dyskinesias after 10 years of treatment, and about 40-50% after 5 years. Occurrence of LID appears to be related to dose and duration of treatment with levodopa and severity and duration of disease. In addition, patients with younger age of onset have been reported to have an earlier onset and higher rate of LID. The important aetiological role of non-physiological pulsatile stimulation of dopaminergic receptors is increasingly recognized and more continuous dopaminergic stimulation with the longer acting dopamine agonists has been shown to reduce and delay the onset of dyskinesias. LID may not have a significant effect on quality of life in patients with early disease or in very advanced disease stages. when often other problems arise, but in other patients they may be severely disabling. Treatment strategies to overcome LID include adjustment of timing, type and amount of dopaminergic medication, treatment with amantadine and, in treatment resistant cases, stereotactic surgery involving deep brain stimulation or lesioning procedures. A number of other pharmacological options are also being explored. Several methods for the assessment of LID are available to attempt accurate assessment of efficacy, although all of these have limitations, and further evidence on their utility if needed.


Pond walls: inclined planes to improve pathogen removal in pond systems for wastewater treatment?
Attenuation of sunlight in wastewater treatment ponds reduces the depth of the water exposed to disinfecting irradiances. Shallow pond depth with paddlewheel rotation increases exposure of pathogens to sunlight in high rate algal ponds. Generation of thin films, using pond walls as inclined planes, may increase inactivation of pathogens by increasing sunlight exposure. The performance of a laboratory based model system incorporating an inclined plane (IP) was evaluated. F-RNA bacteriophage, in tap water or wastewater, was exposed to sunlight only on the IP with the bulk water incubated in the dark. MS2 inactivation was significantly higher when the IP was present (P < 0.05) with a 63% increase observed. Prolonged exposure increased MS2 die-off irrespective of IP presence. Versatility of the IP was also demonstrated with faster inactivation observed in both optically clear tap water and wastewaters. IPs of different surface areas produced similar inactivation rates when operated at similar hydraulic loading rates regardless of slope length.


Efficient coupling between dielectric waveguide modes and exterior plasmon whispering gallery modes.
Inefficient coupling between dielectric guided mode and plasmon mode has been overlooked in the past. The coupling mechanism is essentially different from the conventional coupling between dielectric modes. Based on qualitative theoretical analysis, we proposed two methods to strengthen the coupling between dielectric waveguide modes and exterior plasmon whispering gallery modes. One is using a U-shaped bent waveguide to break the adiabatic mode conversion process, and the other is to utilize higher-order dielectric mode to reach phase matching with plasmon mode. Both the transmission spectrum of waveguide and the energy spectrum of cavity demonstrate that the coupling efficiency can be greatly improved. These simple configurations are potential for wide applications, for example, tunable integrated optical devices and sensors.


Polarized laser oscillation of isotropic disordered Yb:Ca3(NbGa)(2-x)Ga3O12 crystal.
Linearly polarized laser oscillation is observed with the isotropic disordered Yb:Ca3(NbGa)(2-x)Ga3O12 crystal, resulting from stress-induced birefringence. At high pump levels, two orthogonal polarization states exist simultaneously. A continuous-wave output power of 2.0 W is obtained with an optical-to-optical efficiency of 32%, the slope efficiency amounts to 40%. In the passively Q-switched regime, the average output power reaches 1.35 W at a pulse repetition frequency of 16.7 kHz, with a slope efficiency of 37%; the laser pulse energy, duration, and peak power amount to 81 microJ, 25 ns, and 3.24 kW, respectively.


Thinking in spatial terms: decoupling spatial representation from sensorimotor control in monkey posterior parietal areas 7a and LIP.
Perhaps the simplest and most complete description of the cerebral cortex is that it is a sensorimotor controller whose primary purpose is to represent stimuli and movements, and adaptively control the mapping between them. However, in order to think, the cerebral cortex has to generate patterns of neuronal activity that encode abstract, generalized information independently of ongoing sensorimotor events. A critical question confronting cognitive systems neuroscience at present therefore is how neural signals encoding abstract information emerge within the sensorimotor control networks of the brain. In this review, we approach that question in the context of the neural representation of space in posterior parietal cortex of non-human primates. We describe evidence indicating that parietal cortex generates a hierarchy of spatial representations with three basic levels: including (1) sensorimotor signals that are tightly coupled to stimuli or movements, (2) sensorimotor signals modified in strength or timing to mediate cognition (examples include attention, working memory, and decision-processing), as well as (3) signals that encode frankly abstract spatial information (such as spatial relationships or categories) generalizing across a wide diversity of specific stimulus conditions. Here we summarize the evidence for this hierarchy, and consider data showing that signals at higher levels derive from signals at lower levels. That in turn could help characterize neural mechanisms that derive a capacity for abstraction from sensorimotor experience.


Host microbiota can facilitate pathogen infection.
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.


Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM).
We report on the implementation of a traveling wave (TW) based compression ratio ion mobility programming (CRIMP) approach within structures for lossless ion manipulations (SLIM) that enables both greatly enlarged trapped ion charge capacities and also efficient ion population compression for use in ion mobility (IM) separations. Ion accumulation is conducted in a SLIM serpentine ultralong path with extended routing (SUPER) region after which CRIMP compression allows the large ion populations to be "squeezed". The SLIM SUPER IM module has two regions, one operating with conventional traveling waves (i.e., traveling trap; TT region) and the second having an intermittently pausing or "stuttering" TW (i.e., stuttering trap; ST region). When a stationary voltage profile was used in the ST region, ions are blocked at the TT-ST interface and accumulated in the TT region and then can be released by resuming a conventional TW in the ST region. The population can also be compressed using CRIMP by the repetitive merging of ions distributed over multiple TW bins in the TT region into a single TW bin in the ST region. Ion accumulation followed by CRIMP compression provides the basis for the use of larger ion populations for IM separations. We show that over 109 ions can be accumulated with high efficiency in the present device and that the extent of subsequent compression is only limited by the space charge capacity of the trapping region. Approximately 5 × 109 charges introduced from an electrospray ionization source were trapped for a 40 s accumulation period, more than 2 orders of magnitude greater than the previously reported charge capacity of an ion funnel trap. Importantly, we show that extended ion accumulation in conjunction with CRIMP compression and multiple passes through the serpentine path provides the basis for a highly desirable combination of ultrahigh sensitivity and SLIM SUPER high-resolution IM separations.


Properties of the 120,000- and 95,000-dalton actin-binding proteins from Dictyostelium discoideum and their possible functions in assembling the cytoplasmic matrix.
The cell cortex of Dictyostelium amebae contains an actin-rich cytoplasmic matrix. Changes in geometry of this matrix are believed to regulate protrusive activity and motility of the cell cortex. Two actin-binding proteins (120,000 and 95,000 daltons [120K and 95K]) are present in the cell cortex, and their properties, many of which are described here for the first time, suggest that they regulate growth and organization of cortical microfilaments. The 120K protein is a flexible dimer 35 nm in length with a native molecular mass of 241,000. It nucleates the polymerization of actin and crosslinks the filaments to form branched networks like those seen in situ in the cell cortex. The production of a branched network of short crosslinked filaments results in a lattice that would theoretically generate the maximum rigidity with minimum amount of polymer. This sort of lattice would be very useful as a space-filling cytoskeleton capable of resisting deformation. The 120K protein inhibits the actin-stimulated Mg ATPase of myosin. Competition for actin binding between 120K and myosin, the impenetrability of the 120K-actin network to myosin, and the rigidity of actin filaments that are crosslinked by 120K could all contribute to the decrease in the actin-stimulated Mg ATPase of myosin. The properties of 120K are consistent with a role for this protein in regulating the site of actin filament growth and gelation in the cell but not the assembly of actin-containing structures that would participate in force generation by a sliding-filament mechanism involving myosin. The 95K protein is a rigid dimer 40 nm in length with a native molecular mass of between 190,000 and 210,000. Its physical and antigenic properties lead us to conclude that the 95K protein is Dictyostelium alpha-actinin. Unlike 120K, it crosslinks actin filaments into lateral arrays and increases the actin-stimulated Mg ATPase of myosin. Both activities are regulated by Ca2+. The properties of 95K are consistent with a role in organizing actin filaments in the cell into lateral arrays that are capable of efficient interaction with myosin to produce force for cell motility.


Genetic mouse models of neurodegenerative diseases.
Neurodegenerative diseases are generally characterized by the selective degeneration of particular neuronal populations and the accumulation of abnormal or aggregated proteins within, but occasionally external to, neurons in affected brain regions. These diseases can be broadly classified as disorders of cognition and memory or movement, and both features can often coexist in a single disease. In recent years, the identification of genetic mutations that cause rare monogenic familial disease has revolutionized our understanding of the molecular basis of neurodegenerative disease and has provided new targets for the development of disease-modifying therapies. An essential part of this process has been the development of genetic animal models that accurately recapitulate the essential features of each disease, with particular emphasis on the use of mouse models. Such mouse models have provided unique insight into the molecular mechanism(s) through which genetic mutations precipitate neurodegeneration and produce associated clinical and pathological phenotypes. In this review, we provide an overview of the current status, uses and limitations of genetic mouse models for understanding major neurodegenerative diseases, including Alzheimer's, Parkinson's, and Huntington's disease and amyotrophic lateral sclerosis.


Dual-wavelength narrow-linewidth linearly polarized seed source and stimulated Brillouin scattering suppression in its high-power fiber amplification.
In this paper, we demonstrate a dual-wavelength narrow-linewidth linearly polarized all-fiber amplifier emitting 1035 and 1030 nm wavelengths with a high power of 80.0 W. The seed source features two sets of fiber Bragg gratings fabricated on polarization maintaining fibers and a ytterbium-doped fiber as the gain medium. Two wavelengths propagate in one overlapping cavity and the power ratio can be tuned by a coiling fiber setup. A master oscillator power amplifier system consisting of a two-stage amplifier is employed. Longitudinally varied strains are applied on the gain fiber to suppress the back-scattered Stokes light in the main amplifier stage. With an appropriate seed power ratio, we are able to generate amplification power to 80.0 W comprised of 1035 and 1030 nm light while achieving an increase of at least six times that of the stimulated Brillouin scattering threshold. Since both frequencies are propagating in one cavity and amplified in one gain medium, the 1035 and 1030 nm lasers have good temporal and spatial overlapping characteristics. This high-power MHz-level linearly polarized structure affords a compact, novel, and high-efficiency approach to different frequency generation of mid-infrared or terahertz emission.


Current principles and practice of ethics and law in perinatal medicine.
One of the most controversial discussion topics in modern bioethics, science or philosophy is represented by the beginning of the individual human life. It is ethically, medically and scientifically correct that the human conception product to be born, so to gain personality and individuality, to be treated as a patient since the intrauterine life. Intrauterine foetal interventions, performed in various therapeutic purposes are still in the experimental stage even in centres with rich experience in perinatal medicine. Progresses truly outstanding are present especially in the prenatal diagnostic methods. Non invasive prenatal testing represents without a doubt a great progress in prenatal diagnosis, but from this point of view, the role of practitioners in the field of perinatal medicine, on counselling and addressing the indication of this test becomes essential. Beyond cultural, national, social or related differences, in perinatal medicine practice is particularly important to respect and permanently reassess the ethical codes. Our paper is targeting to spotlight the essential principles and practice of ethics and law in perinatal medicine nowadays on one hand, and to bring an update review on a controversial topic on the other hand.


Shaping the oral microbiota through intimate kissing.
The variation of microbial communities associated with the human body can be the cause of many factors, including the human genetic makeup, diet, age, surroundings, and sexual behavior. In this study, we investigated the effects of intimate kissing on the oral microbiota of 21 couples by self-administered questionnaires about their past kissing behavior and by the evaluation of tongue and salivary microbiota samples in a controlled kissing experiment. In addition, we quantified the number of bacteria exchanged during intimate kissing by the use of marker bacteria introduced through the intake of a probiotic yoghurt drink by one of the partners prior to a second intimate kiss. Similarity indices of microbial communities show that average partners have a more similar oral microbiota composition compared to unrelated individuals, with by far most pronounced similarity for communities associated with the tongue surface. An intimate kiss did not lead to a significant additional increase of the average similarity of the oral microbiota between partners. However, clear correlations were observed between the similarity indices of the salivary microbiota of couples and self-reported kiss frequencies, and the reported time passed after the latest kiss. In control experiments for bacterial transfer, we identified the probiotic Lactobacillus and Bifidobacterium marker bacteria in most kiss receivers, corresponding to an average total bacterial transfer of 80 million bacteria per intimate kiss of 10 s. This study indicates that a shared salivary microbiota requires a frequent and recent bacterial exchange and is therefore most pronounced in couples with relatively high intimate kiss frequencies. The microbiota on the dorsal surface of the tongue is more similar among partners than unrelated individuals, but its similarity does not clearly correlate to kissing behavior, suggesting an important role for specific selection mechanisms resulting from a shared lifestyle, environment, or genetic factors from the host. Furthermore, our findings imply that some of the collective bacteria among partners are only transiently present, while others have found a true niche on the tongue's surface allowing long-term colonization.


Association between Adult Attention Deficit/Hyperactivity Disorder and Intravenous Misuse of Opioid and Benzodiazepine in Patients under Opioid Maintenance Treatment: A Cross-Sectional Multicentre Study.
Intravenous misuse and attention-deficit/hyperactivity disorder (ADHD) are common in patients under opioid maintenance treatment (OMT), who often misuse benzodiazepine (BZD). To explore the rate of adult ADHD among patients under OMT in Italy and whether screening positive for adult ADHD is associated with OMT and BZD misuse and emergency room (ER) admission because of misuse. We recruited 1,649 patients from 27 addiction units (AUs) in Italy and collected data on the self-reported rate of OMT intravenous misuse (prevalence, repeated misuse, main reason, temporal pattern in relation to AU access, experience), concurrent intravenous and intranasal BZD misuse (prevalence, type of misused BZD), ADHD and ER admissions because of misuse complications. Screening positive for adult ADHD was found in 11.2% patients (ADHD+), with a significant gender difference (women: 15.3%, men: 10.3%). OMT misuse was reported by 24.4 and 18.5% patients during lifetime and in the previous 6 months respectively. BZD misuse was reported by 20.0 and 8.6% patients for intravenous and intranasal route respectively. Misuse was significantly more common in ADHD+ (OMT 27.4-33.1%, BZD 14.5-31.5%) than ADHD- group (OMT 17.4-23.3%, BZD 7.9-18.3%). The multivariate logistic regression model showed positive screening for ADHD to be significantly associated with intravenous OMT misuse in the previous 6 months, and intravenous/intranasal BZD misuse, independently of age, gender and route of previous heroin administration. Screening positive for adult ADHD was associated with OMT and BZD misuse. AU physicians and medical personnel should focus on OMT patient's features that are associated with a higher likelihood of misuse, in particular ADHD.


Carbon dioxide addition to coral reef waters suppresses net community calcification.
Coral reefs feed millions of people worldwide, provide coastal protection and generate billions of dollars annually in tourism revenue. The underlying architecture of a reef is a biogenic carbonate structure that accretes over many years of active biomineralization by calcifying organisms, including corals and algae. Ocean acidification poses a chronic threat to coral reefs by reducing the saturation state of the aragonite mineral of which coral skeletons are primarily composed, and lowering the concentration of carbonate ions required to maintain the carbonate reef. Reduced calcification, coupled with increased bioerosion and dissolution, may drive reefs into a state of net loss this century. Our ability to predict changes in ecosystem function and associated services ultimately hinges on our understanding of community- and ecosystem-scale responses. Past research has primarily focused on the responses of individual species rather than evaluating more complex, community-level responses. Here we use an in situ carbon dioxide enrichment experiment to quantify the net calcification response of a coral reef flat to acidification. We present an estimate of community-scale calcification sensitivity to ocean acidification that is, to our knowledge, the first to be based on a controlled experiment in the natural environment. This estimate provides evidence that near-future reductions in the aragonite saturation state will compromise the ecosystem function of coral reefs.


Acute hospital costs after minimally invasive versus open lumbar interbody fusion: data from a US national database with 6106 patients.
Retrospective multi-institutional database review. To determine if minimally invasive interbody fusion is associated with cost savings when compared with open surgery. Minimally invasive spine (MIS) surgeries are increasingly recognized as equivalent to open procedures. Although these techniques have been advocated for reducing pain, disability, and length of hospitalization, to date there has been little data demonstrating these benefits. This study analyzed inpatient hospital records from the Premier Perspective database (2002 to 2009), including patients who underwent a posterior lumbar fusion with interbody cage placement by ICD-9 code, and had implant charge codes that allowed determination if MIS pedicle screws were utilized. Exclusion criteria included a refusion surgery, deformity, >2 levels, and anterior fusion. Total costs were adjusted for covariates (age, sex, race, hospital geography and setting, payor, and comorbidities) using an analysis of covariance model. A total of 6106 patients were identified (1667 MIS and 4439 open). Length of stay (LOS) for 1-level MIS surgery averaged of 3.35 days versus 3.6 days for open surgery (P≤0.006). For 2-level MIS surgery LOS averaged of 3.4 days versus 4.03 days for open surgery (P≤0.001). Total inflation-adjusted acute hospitalization cost averaged $29,187 for 1-level MIS procedures versus $29,947 for open surgery, a nonsignificant difference (P=0.55). Total inflation-adjusted acute hospitalization cost averaged $2106 lower for 2-level MIS surgery (total costs of $33,879 for MIS vs. $35,984 for open surgery, P=0.0023). Cost savings were attributable primarily to lower room and board ($857), operating room ($359), pharmacy ($304), and laboratory ($166) costs in the MIS group. High variances in the 2-level open surgery with prolonged hospital stay also accounted for overall cost differences. This data from a large nationwide sample of hospitalizations demonstrates that MIS lumbar interbody fusion results in a statistically significant reduction in hospital LOS and a reduction in total hospital costs with 2-level surgery after adjusting for significant covariates. The majority of cost savings from MIS surgery were due to more rapid mobilization and discharge, as well as a reduction in outliers with extended hospitalizations.


Enhancement of auditory cortical development by musical experience in children.
Auditory evoked potentials (AEPs) express the development of mature synaptic connections in the upper neocortical laminae known to occur between 4 and 15 years of age. AEPs evoked by piano, violin, and pure tones were measured twice in a group of 4- to 5-year-old children enrolled in Suzuki music lessons and in non-musician controls. P1 was larger in the Suzuki pupils for all tones whereas P2 was enhanced specifically for the instrument of practice (piano or violin). AEPs observed for the instrument of practice were comparable to those of non-musician children about 3 years older in chronological age. The findings set into relief a general process by which the neocortical synaptic matrix is shaped by an accumulation of specific auditory experiences.


Bone metabolism in postmenopausal women with lumbar spinal stenosis: analysis of bone mineral density and bone turnover markers.
A cross-sectional study. To investigate bone mineral density (BMD) and the change of bone turnover rate in postmenopausal women with lumbar spinal stenosis (LSS). Symptomatic LSS prevents elderly patients from performing daily activities because of back pain and neurogenic claudication. Walking intolerance due to neurologic claudication might have a negative effect on bone metabolism and BMD. However, there has been no study on the relationship between LSS and bone metabolism, especially on bone turnover rate. Sixty-seven patients were in the LSS group. As a control group, 67 age- and weight-matched subjects were selected. In both groups, BMD, bone turnover markers, vitamin D, severity of knee osteoarthritis, and demographic data were obtained. In the LSS group, walking distance without rest was also recorded. BMD, bone turnover markers, vitamin D, and severity of knee osteoarthritis were compared between the two groups. In the LSS group, the correlation between walking intolerance and bone turnover markers was also analyzed. In the LSS group, urinary N-terminal telopeptide of type I collagen (u-NTx) and alkaline phosphatase were significantly elevated when compared with those of the control group (P < 0.05). However, BMD was significantly low in the control group in all of the measured sites (P < 0.05). In the LSS group, neither bone markers nor BMD were correlated with the extent of walking difficulty. Our study highlights the fact that limited physical activity results in high bone turnover rate in patients with LSS.


A high-throughput pharmaceutical screen identifies compounds with specific toxicity against BRCA2-deficient tumors.
Hereditary breast cancer is partly explained by germline mutations in BRCA1 and BRCA2. Although patients carry heterozygous mutations, their tumors have typically lost the remaining wild-type allele. Selectively targeting BRCA deficiency may therefore constitute an important therapeutic approach. Clinical trials applying this principle are underway, but it is unknown whether the compounds tested are optimal. It is therefore important to identify alternative compounds that specifically target BRCA deficiency and to test new combination therapies to establish optimal treatment strategies. We did a high-throughput pharmaceutical screen on BRCA2-deficient mouse mammary tumor cells and isogenic controls with restored BRCA2 function. Subsequently, we validated positive hits in vitro and in vivo using mice carrying BRCA2-deficient mammary tumors. Three alkylators-chlorambucil, melphalan, and nimustine-displayed strong and specific toxicity against BRCA2-deficient cells. In vivo, these showed heterogeneous but generally strong BRCA2-deficient antitumor activity, with melphalan and nimustine doing better than cisplatin and the poly-(ADP-ribose)-polymerase inhibitor olaparib (AZD2281) in this small study. In vitro drug combination experiments showed synergistic interactions between the alkylators and olaparib. Tumor intervention studies combining nimustine and olaparib resulted in recurrence-free survival exceeding 330 days in 3 of 5 animals tested. We generated and validated a platform for identification of compounds with specific activity against BRCA2-deficient cells that translates well to the preclinical setting. Our data call for the re-evaluation of alkylators, especially melphalan and nimustine, alone or in combination with the poly-(ADP-ribose)-polymerase inhibitors, for the treatment of breast cancers with a defective BRCA pathway.


Looking Beyond Respiratory Cultures: Microbiome-Cytokine Signatures of Bacterial Pneumonia and Tracheobronchitis in Lung Transplant Recipients.
Bacterial pneumonia and tracheobronchitis are diagnosed frequently following lung transplantation. The diseases share clinical signs of inflammation and are often difficult to differentiate based on culture results. Microbiome and host immune-response signatures that distinguish between pneumonia and tracheobronchitis are undefined. Using a retrospective study design, we selected 49 bronchoalveolar lavage fluid samples from 16 lung transplant recipients associated with pneumonia (n = 8), tracheobronchitis (n = 12) or colonization without respiratory infection (n = 29). We ensured an even distribution of Pseudomonas aeruginosa or Staphylococcus aureus culture-positive samples across the groups. Bayesian regression analysis identified non-culture-based signatures comprising 16S ribosomal RNA microbiome profiles, cytokine levels and clinical variables that characterized the three diagnoses. Relative to samples associated with colonization, those from pneumonia had significantly lower microbial diversity, decreased levels of several bacterial genera and prominent multifunctional cytokine responses. In contrast, tracheobronchitis was characterized by high microbial diversity and multifunctional cytokine responses that differed from those of pneumonia-colonization comparisons. The dissimilar microbiomes and cytokine responses underlying bacterial pneumonia and tracheobronchitis following lung transplantation suggest that the diseases result from different pathogenic processes. Microbiomes and cytokine responses had complementary features, suggesting that they are closely interconnected in the pathogenesis of both diseases.


Synthetic molecular mimics of naturally occurring cyclopentenones exhibit antifungal activity towards pathogenic fungi.
The naturally occurring reactive electrophilic species 12-oxo-phytodienoic acid (12-oxo-PDA) is a potent antifungal agent, whereas the plant growth regulator jasmonic acid, which is synthesized from 12-oxo-PDA, is ineffective. To address what structural features of the molecule endow it with antifungal activity, we synthesized a series of molecular mimics of 12-oxo-PDA varying in the length of the alkyl chain at its C-4 ring position. The octyl analogue (4-octyl cyclopentenone) was the most effective at suppressing spore germination and subsequent mycelial growth of a range of fungal pathogens and was particularly effective against Cladosporium herbarum and Botrytis cinerea, with minimum fungicidal concentrations in the range 100-200 µM. Introduction of a carboxyl group to the end of the chain, mimicking natural fatty acids, markedly reduced antifungal efficacy. Electrolyte leakage, indicative of membrane perturbation, was evident in both C. herbarum and B. cinerea exposed to 4-octyl cyclopentenone. Lipid composition analysis of the fungal spores revealed that those species with a high oil content, namely Fusarium oxysporum and Alternaria brassicicola, were less sensitive to 4-octyl cyclopentenone. The comparable hydrophobicity of 4-octyl cyclopentenone and 12-oxo-PDA accounts for the similar spore suppression activity of these two compounds. The relative ease of synthesis of 4-octyl cyclopentenone makes it an attractive compound for potential use as an antifungal agent.


MEG3 noncoding RNA: a tumor suppressor.
Maternally expressed gene 3 (MEG3) is an imprinted gene belonging to the imprinted DLK1-MEG3 locus located at chromosome 14q32.3 in humans. Its mouse ortholog, Meg3, also known as gene trap locus 2 (Gtl2), is located at distal chromosome 12. The MEG3 gene encodes a long noncoding RNA (lncRNA) and is expressed in many normal tissues. MEG3 gene expression is lost in an expanding list of primary human tumors and tumor cell lines. Multiple mechanisms contribute to the loss of MEG3 expression in tumors, including gene deletion, promoter hypermethylation, and hypermethylation of the intergenic differentially methylated region. Re-expression of MEG3 inhibits tumor cell proliferation in culture and colony formation in soft agar. This growth inhibition is partly the result of apoptosis induced by MEG3. MEG3 induces accumulation of p53 (TP53) protein, stimulates transcription from a p53-dependent promoter, and selectively regulates p53 target gene expression. Maternal deletion of the Meg3 gene in mice results in skeletal muscle defects and perinatal death. Inactivation of Meg3 leads to a significant increase in expression of angiogenesis-promoting genes and microvessel formation in the brain. These lines of evidence strongly suggest that MEG3 functions as a novel lncRNA tumor suppressor.


Social learning of fear and safety is determined by the demonstrator's racial group.
Social learning offers an efficient route through which humans and other animals learn about potential dangers in the environment. Such learning inherently relies on the transmission of social information and should imply selectivity in what to learn from whom. Here, we conducted two observational learning experiments to assess how humans learn about danger and safety from members ('demonstrators') of an other social group than their own. We show that both fear and safety learning from a racial in-group demonstrator was more potent than learning from a racial out-group demonstrator.


Roles of dom34:hbs1 in nonstop protein clearance from translocators for normal organelle protein influx.
Because messenger RNAs without a stop codon (nonstop mRNAs) generate stalled ribosomes, cells have developed a mechanism allowing degradation of nonstop mRNAs and their translation products (nonstop proteins) in the cytosol. Here, we observe the fate of nonstop proteins destined for organelles such as the endoplasmic reticulum (ER) and mitochondria. Nonstop mRNAs for secretory-pathway proteins in yeast generate nonstop proteins that become stuck in the translocator, the Sec61 complex, in the ER membrane. These stuck nonstop secretory proteins avoid proteasomal degradation in the cytosol, but are instead released into the ER lumen through stalled ribosome and translocator channels by Dom34:Hbs1. We also found that nonstop mitochondrial proteins are cleared from the mitochondrial translocator, the TOM40 complex, by Dom34:Hbs1. Clearance of stuck nonstop proteins from organellar translocator channels is crucial for normal protein influx into organelles and for normal cell growth, especially when nonstop mRNA decay does not function efficiently.