Cue identification in phenology: A case study of the predictive performance of current statistical tools.
Changes in the timing of life-history events (phenology) are a widespread consequence of climate change. Predicting population resilience requires knowledge of how phenology is likely to change over time, which can be gained by identifying the specific environmental cues that drive phenological events. Cue identification is often achieved with statistical testing of candidate cues. As the number of methods used to generate predictions increases, assessing the predictive accuracy of different approaches has become necessary. This study aims to (a) provide an empirical illustration of the predictive ability of five commonly applied statistical methods for cue identification (absolute and relative sliding time window analyses, penalized signal regression, climate sensitivity profiles and a growing degree-day model) and (b) discuss approaches for implementing cue identification methods in different systems. Using a dataset of mean clutch initiation timing in wild great tits (Parus major), we explored how the days of the year identified as most important, and the aggregate statistic identified as a cue, differed between statistical methods and with respect to the time span of data used. Each method's predictive capacity was tested using cross-validation and assessed for robustness to varying sample size. We show that the identified critical time window of cue sensitivity was consistent across four of the five methods. The accuracy and precision of predictions differed by method with penalized signal regression resulting in the most accurate and most precise predictions in our case. Accuracy was maximal for near-future predictions and showed a relationship with time. The difference between predictions and observations systematically shifted across the study from preceding observations to lagging. This temporal trend in prediction error suggests that the current statistical tools either fail to capture a key component of the cue-phenology relationship, or the relationship itself is changing through time in our system. These two influences need to be teased apart if we are to generate realistic predictions of phenological change. We recommend future phenological studies to challenge the idea of a static cue-phenology relationship and should cross-validate results across multiple time periods.


Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations.
Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole-genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms showed a substantial reduction of heterozygosity in freshwater populations compared with marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X chromosomes compared with autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared with marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X chromosomes than on autosomes. The interpopulation comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole-genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.


Microclimate and Larval Habitat Density Predict Adult Aedes albopictus Abundance in Urban Areas.
The Asian tiger mosquito, Aedes albopictus, transmits several arboviruses of public health importance, including chikungunya and dengue. Since its introduction to the United States in 1985, the species has invaded more than 40 states, including temperate areas not previously at risk of Aedes-transmitted arboviruses. Mathematical models incorporate climatic variables in predictions of site-specific Ae. albopictus abundances to identify human populations at risk of disease. However, these models rely on coarse resolutions of environmental data that may not accurately represent the climatic profile experienced by mosquitoes in the field, particularly in climatically heterogeneous urban areas. In this study, we pair field surveys of larval and adult Ae. albopictus mosquitoes with site-specific microclimate data across a range of land use types to investigate the relationships between microclimate, density of larval habitat, and adult mosquito abundance and determine whether these relationships change across an urban gradient. We find no evidence for a difference in larval habitat density or adult abundance between rural, suburban, and urban land classes. Adult abundance increases with increasing larval habitat density, which itself is dependent on microclimate. Adult abundance is strongly explained by microclimate variables, demonstrating that theoretically derived, laboratory-parameterized relationships in ectotherm physiology apply to the field. Our results support the continued use of temperature-dependent models to predict Ae. albopictus abundance in urban areas.


Extended analysis of benchmark datasets for Agilent two-color microarrays.
As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consideration of different methods for processing the data from the Agilent two-color platform. While this omission is understandable given the scale of the project, it can create the false impression that there is consensus about the best way to process Agilent two-color data. It is also important to consider whether ERCs are representative of all the probes on a microarray. A comparison of different methods of processing Agilent two-color data shows substantial differences among methods for low-intensity genes. The sensitivity and specificity for detecting differentially expressed genes varies substantially for different methods. Analysis also reveals that the ERCs in the MAQC data only span the upper half of the intensity range, and therefore cannot be representative of all genes on the microarray. Although ERCs demonstrate good agreement between observed and expected log-ratios on the Agilent two-color platform, such an analysis is incomplete. Simple loess normalization outperformed data processing with Agilent's Feature Extraction software for accurate identification of differentially expressed genes. Results from studies using ERCs should not be over-generalized when ERCs are not representative of all probes on a microarray.


Increased heat shock protein 90 (hsp90) expression leads to increased apoptosis in the monoblastoid cell line U937 following induction with TNF-alpha and cycloheximide: a possible role in immunopathology.
In this study, we examined the hypothesis that heat shock proteins (hsp) (such as hsp72 and hsp90) are implicated in the regulation of forms of cell injury that lead to programmed cell death. The monoblastoid cell line U937 has been used as a model system. For hsp90, which is not heat inducible in this cell line, we used stable U937 transfectants that either hyperexpress or hypoexpress the protein. For hsp72 (which is reproducibly induced in all three cell lines to relatively high levels of expression), we studied U937 cells before and after heat shock. We showed that apoptosis does occur in the monoblast/mononuclear phagocyte lineage, and that it could be induced in vitro by serum deprivation, UV light, or TNF-alpha in combination with cycloheximide (cx). However, an excess of hsp90 is associated with increased apoptosis when the cells are treated with a combination of TNF-alpha and cx but not when they are exposed to UV B radiation. This was complemented by the finding that reduced hsp90 levels correlate with protection against apoptosis in the TNF-alpha- and cx-treated cells. Furthermore, new synthesis of hsp72 does not protect against apoptosis. Thus, hsp90 levels may play a role in controlling the part played by mononuclear phagocytes in immunopathology.


Cutaneous anthrax in eastern Turkey.
Anthrax, caused by the spore-forming bacterium Bacillus anthracis, is rarely seen in industrial nations but is common in developing countries. Cutaneous anthrax (CA), the most common form of the disease, accounts for 95% of cases and usually develops on exposed sites. This study reviews the clinical and laboratory findings of 21 patients diagnosed with CA during 2 separate epidemics in the Van region of Turkey. All patients had a history of direct contact with infected cattle. The patients, aged 1.5 to 64 years, included 13 females and 8 males. Of the patients, 9 were 15 years or younger. Skin lesions were localized on the hands and fingers in 15 patients, on the face in 3 patients, on the face and finger in 1 patient, on the chest and finger in 1 patient, and on the eyelid in 1 patient. Gram-positive bacillus were noted on Gram stains of material obtained from skin lesions in 2 patients. All but one patient was successfully treated with penicillin; the unresponsive patient was treated with cefuroxime and required plastic reconstructive surgery because of a skin defect on the eyelid.


Infectious risk moments: a novel, human factors-informed approach to infection prevention.
We pilot tested a novel human factors-informed concept to identify infectious risk moments (IRMs) that occur with high frequency during routine intensive care. Following 30 observation-hours, 28 potential IRMs related to hand hygiene, gloves, and objects were expert rated. A comprehensive IRM inventory may provide valuable taxonomy for research, training, and intervention.


Recycling the CoMo/Al2O3 catalyst for effectively hydro-upgrading shale oil with high sulfur content and viscosity.
Hydrotreatment is an effective upgrading technology for removing contaminants and saturating double bonds. Still, few studies have reported the hydro-upgrading of shale oil, with unusually high sulfur (13200 ppm) content, using the CoMo/Al2O3 catalyst. Here we report an extensive study on the upgrading of shale oil by hydrotreatment in a stirred batch autoclave reactor (500 ml) for sulfur removal and viscosity reduction. From a preliminary optimization of the reaction factors, the best-operating conditions were 400 °C, an initial H2-pressure of 5 MPa, and an agitation rate of 800 rpm, a catalyst-to-oil ratio of 0.1, and a reaction time of 1 h. We could achieve a sulfur removal efficiency of 87.1% and 88.2% viscosity reduction under the optimal conditions. After that, the spent CoMo/Al2O3 was repeatedly used for subsequent upgrading tests without any form of pre-treatment. The results showed an increase in the sulfur removal efficiency with an increase in the number of catalyst runs. Ultimately, 99.5-99.9% sulfur removal from the shale oil was achieved by recycling the spent material. Both the fresh and the spent CoMo/Al2O3 were characterized and analyzed to ascertain their transformation levels by XRD, TEM, TG, XPS, TPD and N2 adsorption analysis. The increasing HDS efficiency is attributed to the continuing rise in the sulfidation degree of the catalyst in the sulfur-rich shale oil. The light fraction component in the liquid products (IBP-180 °C) was 30-37 vol% higher than in the fresh shale oil. The product oil can meet the sulfur content requirement of the national standard marine fuel (GB17411-2015/XG1-2018) of China.


Mutagenesis of the cyclic AMP receptor protein of Escherichia coli: targeting positions 83, 127 and 128 of the cyclic nucleotide binding pocket.
The cyclic 3', 5' adenosine monophosphate (cAMP) binding pocket of the cAMP receptor protein (CRP) of Escherichia coli was mutagenized to substitute cysteine or glycine for serine 83; cysteine, glycine, isoleucine, or serine for threonine 127; and threonine or alanine for serine 128. Cells that expressed the binding pocket residue-substituted forms of CRP were characterized by measurements of beta-galactosidase activity. Purified wild-type and mutant CRP preparations were characterized by measurement of cAMP binding activity and by their capacity to support lacP activation in vitro. CRP structure was assessed by measurement of sensitivity to protease and DTNB-mediated subunit crosslinking. The results of this study show that cAMP interactions with serine 83, threonine 127 and serine 128 contribute to CRP activation and have little effect on cAMP binding. Amino acid substitutions that introduce hydrophobic amino acid side chain constituents at either position 127 or 128 decrease CRP discrimination of cAMP and cGMP. Finally, cAMP-induced CRP structural change(s) that occur in or near the CRP hinge region result from cAMP interaction with threonine 127; substitution of threonine 127 by cysteine, glycine, isoleucine, or serine produced forms of CRP that contained, independently of cAMP binding, structural changes similar to those of the wild-type CRP:cAMP complex.


Peak bone mineral density in Vietnamese women.
SUMMARY: This cross-sectional study showed that peak bone mineral density in Vietnamese women is comparable to that in Caucasian women; however, the prevalence of osteoporosis in post-menopausal Vietnamese women was slightly higher than in Caucasian women. The age of achieving peak bone mass in Vietnamese women was between 26 and 30 years. INTRODUCTION: While peak bone mass and its determinants have been well-documented in Caucasian populations, little has been studied in Asian populations. The present study was designed to estimate the peak bone mineral density (BMD), age of its attainment, and to examine the prevalence of osteoporosis in Vietnamese women aged 50+. METHODS: The study was designed as a cross-sectional study with 328 women aged between 10 and 65 years (average age: 41) who were randomly selected from two districts around Hanoi city according to a stratified sampling scheme. BMD at the lumbar spine, femoral neck and total hip was measured by a DXA instrument (GE Lunar Prodigy, WI, USA). BMD was modeled as a cubic function of age, from which peak BMD and age at peak BMD were estimated. Bootstrap method was utilized to estimate the 95% confidence interval of peak BMD and age at peak BMD. From the peak BMD, T-score was calculated for each woman, and using the World Health Organization criteria, any woman with femoral neck BMD T-score </= -2.5 was classified as having osteoporosis. RESULTS: Peak BMD was estimated at 1.16 g/cm(2) (standard deviation [SD]: 0.13 g/cm(2)) at the lumbar spine, 1.02 g/cm(2) (SD 0.12) at the total hip, and 0.94 g/cm(2) (SD 0.11) at the femoral neck. In the cubic polynomial model, the age at peak BMD was estimated to range between 27 and 29 years. The prevalence of osteoporosis among those aged between 50 and 65 years was 23%. This prevalence was higher than in Chinese, Japanese, Korean and Caucasian populations. CONCLUSION: These data suggest that although the peak BMD in Vietnamese women is comparable to, the prevalence of osteoporosis is higher than, in some other Asian and Caucasian women. It seems that osteoporosis is an important public health burden in Vietnam.


Cross-evaluation of metrics to estimate the significance of creative works.
In a world overflowing with creative works, it is useful to be able to filter out the unimportant works so that the significant ones can be identified and thereby absorbed. An automated method could provide an objective approach for evaluating the significance of works on a universal scale. However, there have been few attempts at creating such a measure, and there are few "ground truths" for validating the effectiveness of potential metrics for significance. For movies, the US Library of Congress's National Film Registry (NFR) contains American films that are "culturally, historically, or aesthetically significant" as chosen through a careful evaluation and deliberation process. By analyzing a network of citations between 15,425 United States-produced films procured from the Internet Movie Database (IMDb), we obtain several automated metrics for significance. The best of these metrics is able to indicate a film's presence in the NFR at least as well or better than metrics based on aggregated expert opinions or large population surveys. Importantly, automated metrics can easily be applied to older films for which no other rating may be available. Our results may have implications for the evaluation of other creative works such as scientific research.


Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4.
DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors. It is not clear what factors determine the genome-wide pattern of binding or regulation for a given transcription factor. We used an integrated approach to study how trans influences shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor activated in response to phosphate limitation. We find that nucleosomes significantly restrict Pho4 binding. At nucleosome-depleted sites, competition from another transcription factor, Cbf1, determines Pho4 occupancy, raising the threshold for transcriptional activation in phosphate replete conditions and preventing Pho4 activation of genes outside the phosphate regulon during phosphate starvation. Pho4 binding is not sufficient for transcriptional activation-a cooperative interaction between Pho2 and Pho4 specifies genes that are activated. Combining these experimental observations, we are able to globally predict Pho4 binding and its functionality.


Cyclosporine A-resistant human immunodeficiency virus type 1 mutants demonstrate that Gag encodes the functional target of cyclophilin A.
The cellular peptidyl-prolyl isomerase cyclophilin A is incorporated into human immunodeficiency virus type 1 virions via contacts with the proline-rich domain of the Gag polyprotein. Cyclosporine A and nonimmunosuppressive analogs bind with high affinity to cyclophilin A, compete with Gag for binding to cyclophilin A, and prevent incorporation of cyclophilin A into virions; in parallel with the disruption of cyclophilin A incorporation into virions, there is a linear reduction in the initiation of reverse transcription after infection of a T cell. Passage of human immunodeficiency virus type 1 in the presence of the drug selects one of two mutations, either of which alters the proline-rich domain of Gag and is sufficient to confer drug resistance on the cloned wild-type provirus. Neither mutation alters Gag's cyclophilin A-binding properties in vitro, and cyclophilin A incorporation into drug-resistant virions is effectively disrupted by cyclosporine A, indicating that the drug-resistant mutants do not require virion-associated cyclophilin A to initiate infection. That Gag's functional dependence on cyclophilin A can be differentiated genetically from its ability to bind cyclophilin A is further demonstrated by the rescue of a mutation precluding cyclophilin A packaging by a mutation conferring cyclosporine A resistance. These experiments demonstrate that, in addition to its ability to package cyclophilin A into virions, gag encodes the functional target of cyclophilin A.


Combined thalidomide and temozolomide treatment in patients with glioblastoma multiforme.
Glioblastoma multiforme (GBM) may potentially be responsive to antiangiogenic therapies as these tumors are highly vascularized and overexpress angiogenic factors. Thalidomide exhibits antiangiogenic activity and may provide additive or synergistic antitumor effects when given concurrently with temozolomide, an alkylating agent. To further evaluate this new concept of combining an antiangiogenic with an alkylating agent, efficacy and tolerability of thalidomide alone and in combination with temozolomide were explored in a single-institution, nonrandomized open-label phase II study. Forty-four patients with GBMs, who received thalidomide for a period of at least three months, were evaluated for survival, time to tumor progression (TTP), and side effects. Microsurgical tumor extirpation and radiotherapy preceded chemotherapy. Nineteen patients (43%) received thalidomide only (T), and 25 patients (57%) had a combined chemotherapy of thalidomide and temozolomide (TT). Median thalidomide dosage was 200 mg/day. Median temozolomide dosage was 200 mg/m2/day for five days, in monthly cycles. Neuroradiological outcomes were assessed by a semiquantitative grading system. Median survival was 103 weeks (95% CI, 65-141 weeks) for TT-patients and 63 weeks (95% CI, 49-77 weeks) for T-patients (p < 0.01). Median TTP for the TT-group was 36 weeks (95% CI, 20-52 weeks) and 17 weeks (95% CI, 13-21 weeks) for the T-group (p < 0.06). Neuroradiologically, 14 patients (56%) of the TT-group and six (32%) of the T-group had evidence of stable disease on at least two successive neuroradiological follow-ups. Progressive disease was found in nine patients (36%) of the TT-group and in 13 (68%) of the T-group. In two patients (8%) of the TT-group, a response with tumor regression was found. Thalidomide and concurrent temozolomide were safe and well tolerated with mild to moderate toxicities. The combination of thalidomide and temozolomide in the treatment of GBM appears to be more effective than that of thalidomide alone with respect to survival, TTP, and neuroradiological documentation of progression, stable disease or response. Further concurrent prospective studies of these agents in a larger group of patients with GBM will be required to establish the soundness of these intriguing observations.


Spectral reflectance properties of hydrocarbons: remote-sensing implications.
The spectral reflectance properties of bituminous tar sands were examined in the wavelength range from 0.35 to 2.6 micrometers. Unique absorption features due to all the major phases, except quartz, appear in the spectra. The intensities of the absorption features correlate with the abundances of the various phases. The results of this study have applications to the remote sensing of many terrestrial and extraterrestrial targets because of potential similarities between tar sand and other hydrocarbon occurrences. For example, it is found that highly polymerized hydrocarbons are a plausible constituent of the dark material on one of Saturn's satellites, Iapetus.


Pre-hypertension, pre-diabetes or both: which is best at predicting cardiovascular events in the long term?
The present study aimed to assess the value of pre-diabetes and pre-hypertension in predicting cardiovascular events. A population-based, cross-sectional survey was conducted, representing a large sample of the general Iranian population aged 35 years and older from the Isfahan Province and determined using a random, multistage cluster-sampling 10-year cohort. The five end points considered as study outcome were unstable angina (UA), acute occurrence of myocardial infarction (MI), sudden cardiac death (SCD), brain stroke and cardiovascular disease (CVD). Of the 6323 subjects scheduled for assessment of diabetes state 617 were diabetics and 712 were pre-diabetic. In addition, of these subjects, 1754 had hypertension and 2500 had pre-hypertension. Analysing only pre-hypertension, pre-diabetes and its combination and adjusted for gender and age variables, pre-hypertension and pre-diabetes status together, could only effectively predict occurrence of MI (hazard ratio (HR)=3.21, 95% confidence interval (CI): 1.06-9.76, P=0.04). In the same COX regression models, pre-hypertension status could predict UA and CVD occurrence (HR=2.94, 95% CI: 1.68-5.14, P<0.001 and HR=1.74, 95% CI: 1.23-2.47, P=0.002, respectively). However, pre-diabetes status could not predict any of these events after adjustment for gender and age. Our data provide valuable evidence of the triggering role of pre-hypertension and pre-diabetes together, on appearance and progression of MI even in healthy individuals and the significant predicting value of pre-hypertension on the occurrence of UA and CVD. In this regard, the value of pre-hypertension and pre-diabetes together, and the pre-hypertension state alone, are clearly superior to pre-diabetes state alone in predicting cardiovascular events.


Smoking restrictions on campus: changes and challenges at three Canadian universities, 1970-2010.
This article examines the restriction of smoking on university campuses in the Canadian context. Indoor smoking on campus is now completely prohibited by law, and universities are increasingly moving to restrict, or prohibit, outdoor smoking on their grounds. The research focuses on three case studies to identify changes in spatial restrictions on campus smoking over the last four decades (1970-2010), and to determine the challenges involved in establishing bans in outdoor areas of campus. The three universities were selected for their different approaches to the issue of outdoor smoking. Data collection involved semi-structured interviews with 36 key informants, conducted from September 2010 to January 2011, supplemented by documentary information. Interview data were analysed thematically. Protection against environmental tobacco smoke (ETS) on campus proceeded incrementally, via policy-making at the provincial, municipal and institutional levels. Historically, institutional bans on indoor smoking were particularly significant, but their health benefits could be limited by the presence of private property on campus. Universities continue to initiate smoking restrictions today, with respect to outdoor bans. However, respondents reported myriad challenges in developing, implementing and maintaining such bans. Five principal concerns were articulated: the need for ongoing policy communication; management of community relations as smokers are displaced from campus; enforcement to ensure that the policy has practical effect; safety concerns; and difficulties relating to campus layout. Because challenges are diverse and contextual, effective protection against outdoor ETS on campus is likely to require an ongoing commitment on the part of administrators.


Transferrin receptor 2: evidence for ligand-induced stabilization and redirection to a recycling pathway.
Transferrin receptor 2 (TfR2) is a homologue of transferrin receptor 1 (TfR1), the protein that delivers iron to cells through receptor-mediated endocytosis of diferric transferrin (Fe(2)Tf). TfR2 also binds Fe(2)Tf, but it seems to function primarily in the regulation of systemic iron homeostasis. In contrast to TfR1, the trafficking of TfR2 within the cell has not been extensively characterized. Previously, we showed that Fe(2)Tf increases TfR2 stability, suggesting that trafficking of TfR2 may be regulated by interaction with its ligand. In the present study, therefore, we sought to identify the mode of TfR2 degradation, to characterize TfR2 trafficking, and to determine how Fe(2)Tf stabilizes TfR2. Stabilization of TfR2 by bafilomycin implies that TfR2 traffics to the lysosome for degradation. Confocal microscopy reveals that treatment of cells with Fe(2)Tf increases the fraction of TfR2 localizing to recycling endosomes and decreases the fraction of TfR2 localizing to late endosomes. Mutational analysis of TfR2 shows that the mutation G679A, which blocks TfR2 binding to Fe(2)Tf, increases the rate of receptor turnover and prevents stabilization by Fe(2)Tf, indicating a direct role of Fe(2)Tf in TfR2 stabilization. The mutation Y23A in the cytoplasmic domain of TfR2 inhibits its internalization and degradation, implicating YQRV as an endocytic motif.


Ensemble approach to predict specificity determinants: benchmarking and validation.
It is extremely important and challenging to identify the sites that are responsible for functional specification or diversification in protein families. In this study, a rigorous comparative benchmarking protocol was employed to provide a reliable evaluation of methods which predict the specificity determining sites. Subsequently, three best performing methods were applied to identify new potential specificity determining sites through ensemble approach and common agreement of their prediction results. It was shown that the analysis of structural characteristics of predicted specificity determining sites might provide the means to validate their prediction accuracy. For example, we found that for smaller distances it holds true that the more reliable the prediction method is, the closer predicted specificity determining sites are to each other and to the ligand. We observed certain similarities of structural features between predicted and actual subsites which might point to their functional relevance. We speculate that majority of the identified potential specificity determining sites might be indirectly involved in specific interactions and could be ideal target for mutagenesis experiments.


Eye Development in Sepia officinalis Embryo: What the Uncommon Gene Expression Profiles Tell Us about Eye Evolution.
In metazoans, there is a remarkable diversity of photosensitive structures; their shapes, physiology, optical properties, and development are different. To approach the evolution of photosensitive structures and visual function, cephalopods are particularly interesting organisms due to their most highly centralized nervous system and their camerular eyes which constitute a convergence with those of vertebrates. The eye morphogenesis in numerous metazoans is controlled mainly by a conserved Retinal Determination Gene Network (RDGN) including pax, six, eya, and dac playing also key developmental roles in non-retinal structures and tissues of vertebrates and Drosophila. Here we have identified and explored the role of Sof-dac, Sof-six1/2, Sof-eya in eye morphogenesis, and nervous structures controlling the visual function in Sepia officinalis. We compare that with the already shown expressions in eye development of Sof-otx and Sof-pax genes. Rhodopsin is the pigment responsible for light sensitivity in metazoan, which correlate to correlate visual function and eye development. We studied Sof-rhodopsin expression during retina differentiation. By in situ hybridization, we show that (1) all of the RDGN genes, including Sof-pax6, are expressed in the eye area during the early developmental stages but they are not expressed in the retina, unlike Sof-otx, which could have a role in retina differentiation; (2) Sof-rhodopsin is expressed in the retina just before vision gets functional, from stage 23 to hatching. Our results evidence a role of Sof-six1/2, Sof-eya, and Sof-dac in eye development. However, the gene network involved in the retinal photoreceptor differentiation remains to be determined. Moreover, for the first time, Sof-rhodopsin expression is shown in the embryonic retina of cuttlefish suggesting the evolutionary conservation of the role of rhodopsin in visual phototransduction within metazoans. These findings are correlated with the physiological and behavioral observations suggesting that S. officinalis is able to react to light stimuli from stage 25 of organogenesis on, as soon as the first retinal pigments appear.


Clustering of Enterococcus faecalis infections in a cardiology hospital neonatal intensive care unit.
Early identification of an outbreak is one of the main advantages of routine epidemiological surveillance. Enterococcus spp. used to be regarded as microorganisms of low pathogenicity, because they are part of the normal microbial flora of the gastrointestinal and genitourinary tract. Recently, they have emerged as important pathogenic agents, sometimes causing infections with high mortality rates. We studied a clustering of primary bloodstream infections caused by Enterococcus faecalis in a cardiology hospital neonatal intensive care unit (NICU). Four cases of primary bloodstream infection by E. faecalis were detected from April 15 to May 13, 2004, during active infection surveillance. The isolates were sensitive to glycopeptides. Some aspects of the management of these patients, including the date of insertion and placement of a central venous catheter, prescription of a specific medication, contiguity of beds, personnel attending the patients, and occurrence of diarrhea were analyzed to look for factors that might affect the spread of the microorganisms. Measures taken to hamper the spread included contact precautions throughout the unit, cleansing and disinfection of equipment and surfaces, bathing children with 2% chlorhexidine-gluconate-containing soap, professional reeducation, and reinforcement of all measures to prevent infections. We suggest that there is a need to re-evaluate preventive infection measures and to review the strategies aimed at decreasing the nosocomial infection rate in the NICU.


Costs of cooperative behaviour in suricates (Suricata suricatta).
Functional interpretations of helping behaviour suggest that it has evolved because helpers increase their direct or indirect fitness by helping. However, recent critiques have suggested that helping may be an unselected extension of normal parental behaviour, pointing to evidence that all mature individuals commonly respond to begging young (whether they are parents, relatives or non-relatives) as well as to the lack of evidence that cooperative activities have appreciable costs to helpers. Here we provide an example of one form of cooperative behaviour that is seldom performed by parents and has substantial energetic costs to helpers. In the cooperative mongoose, Suricata suricatta, non-breeding adults commonly babysit young pups at the natal burrow for a day at a time, foregoing feeding for 24 hours. Parents rarely contribute to babysitting, and babysitting has substantial energetic costs to helpers. Members of small groups compensate for the reduced number of participants by babysitting more frequently, and neither the proportion of time that babysitters are present nor the survival of litters vary with group size.


Regional and sub-regional differences in hippocampal GABAergic neuronal vulnerability in the TgCRND8 mouse model of Alzheimer's disease.
Hippocampal network activity is predominantly coordinated by γ-amino-butyric acid (GABA)ergic neurons. We have previously hypothesized that the altered excitability of hippocampal neurons in Alzheimer's disease (AD), which manifests as increased in vivo susceptibility to seizures in the TgCRND8 mouse model of AD, may be related to disruption of hippocampal GABAergic neurons. In agreement, our previous study in TgCRND8 mice has shown that hippocampal GABAergic neurons are more vulnerable to AD-related neuropathology than other types of neurons. To further explore the mechanisms behind the observed decrease of GABAergic neurons in 6 month-old TgCRND8 mice, we assessed the relative proportion of somatostatin (SOM), neuropeptide Y (NPY) and paravalbumin (PV) sub-types of GABAergic neurons at the regional and sub-regional level of the hippocampus. We found that NPY expressing GABAergic neurons were the most affected, as they were decreased in CA1-CA2 (pyramidal-, stratum oriens, stratum radiatum and molecular layers), CA3 (specifically in the stratum oriens) and dentate gyrus (specifically in the polymorphic layer) in TgCRND8 mice as compared to non-transgenic controls. SOM expressing GABAergic neurons were decreased in CA1-CA2 (specifically in the stratum oriens) and in the stratum radiatum of CA3, whereas PV neurons were significantly altered in stratum oriens sub-region of CA3. Taken together, these data provide new evidence for the relevance of hippocampal GABAergic neuronal network disruption as a mechanism underlying AD sequelae such as aberrant neuronal excitability, and further point to complex hippocampal regional and sub-regional variation in susceptibility to AD-related neuronal loss.


Optic neuropathy and congenital glaucoma associated with probable Zika virus infection in Venezuelan patients.
Although the current Zika virus (ZIKV) epidemic is a major public health concern, most reports have focused on congenital ZIKV syndrome, its most devastating manifestation. Severe ocular complications associated with ZIKV infections and possible pathogenetic factors are rarely described. Here, we describe three Venezuelan patients who developed severe ocular manifestations following ZIKV infections. We also analyse their serological response to ZIKV and dengue virus (DENV). One adult with bilateral optic neuritis, a child of 4 years of age with retrobulbar neuritis [corrected]. and a newborn with bilateral congenital glaucoma had a recent history of an acute exanthematous infection consistent with ZIKV infection. The results of ELISA tests indicated that all patients were seropositive for ZIKV and four DENV serotypes. Patients with ZIKV infection can develop severe ocular complications. Anti-DENV antibodies from previous infections could play a role in the pathogenesis of these complications. Well-designed epidemiological studies are urgently needed to measure the risk of ZIKV ocular complications and confirm whether they are associated with the presence of anti-flaviviral antibodies.


Characterization of single actin-myosin interactions.
The feedback-enhanced laser trap assay (Finer et al., 1994) allows the measurement of force and displacement produced by single myosin molecules interacting with an actin filament suspended in solution by two laser traps. The average displacement of 11 nm at low load and the average force of 4 pN near isometric conditions are consistent with the conventional swinging cross-bridge model of muscle contraction (Huxley, 1969). The durations of single actin-myosin interactions at low load, 3-7 ms, suggest a relatively small duty ratio. Event durations can be increased either by reducing the ATP concentration until ATP binding is rate-limiting or by lowering the temperature. For sufficiently long interactions near isometric conditions, low frequency force fluctuations were observed within the time frame of a single event. Single myosin events can be measured at ionic strengths that disrupt weak binding actomyosin interactions, supporting the postulate of distinct weak and strong binding states. Myosin-generated force and displacement were measured simultaneously against several different loads to generate a force-displacement curve. The linear appearance of this curve suggests that the myosin powerstroke is driven by the release of a strained linear elastic element with a stiffness of approximately 0.4 pN nm-1.


Acute and chronic effects of exercise on leptin levels in humans.
The acute (single bout of exercise) and chronic (exercise training) effects of exercise on plasma leptin were investigated in 97 sedentary adult men (n = 51) and women (n = 46) participating in the HERITAGE Family Study. Exercise training consisted of a standardized 20-wk endurance training program performed in the laboratory on a computer-controlled cycle ergometer. Maximal oxygen uptake, body composition assessed by hydrostatic weighing, and fasting insulin level were also measured before and after training. Pre- and posttraining blood samples were obtained before and after completion of a maximal exercise test on the cycle ergometer. Exercise training resulted in significant changes in maximal oxygen uptake (increase in both genders) and body composition (reduction of fat mass in men and increase in fat-free mass in women). There were considerable interindividual differences in the leptin response to acute and chronic effects of exercise, some individuals showing either increase or reduction in leptin, others showing almost no change. On average, leptin levels were not acutely affected by exercise. After endurance training was completed, leptin levels decreased significantly in men (from 4.6 to 3.9 ng/ml; P = 0.004) but not in women. However, after the training-induced changes in body fat mass were accounted for, the effects of exercise training were no longer significant. Most of the variation observed in leptin levels after acute exercise or endurance training appears to be within the confidence intervals of the leptin assay. We conclude that there are no meaningful acute or chronic effects of exercise, independent of the amount of body fat, on leptin levels in humans.


Bacteria-mediated effects of antibiotics on Daphnia nutrition.
In polluted environments, contaminant effects may be manifested via both direct toxicity to the host and changes in its microbiota, affecting bacteria-host interactions. In this context, particularly relevant is exposure to antibiotics released into environment. We examined effects of the antibiotic trimethoprim on microbiota of Daphnia magna and concomitant changes in the host feeding. In daphnids exposed to 0.25 mg L(-1) trimethoprim for 24 h, the microbiota was strongly affected, with (1) up to 21-fold decrease in 16S rRNA gene abundance and (2) a shift from balanced communities dominated by Curvibacter, Aquabacterium, and Limnohabitans in controls to significantly lower diversity under dominance of Pelomonas in the exposed animals. Moreover, decreased feeding and digestion was observed in the animals exposed to 0.25-2 mg L(-1) trimethoprim for 48 h and then fed 14C-labeled algae. Whereas the proportion of intact algal cells in the guts increased with increased trimethoprim concentration, ingestion and incorporation rates as well as digestion and incorporation efficiencies decreased significantly. Thus, antibiotics may impact nontarget species via changes in their microbiota leading to compromised nutrition and, ultimately, growth. These bacteria-mediated effects in nontarget organisms may not be unique for antibiotics, but also relevant for environmental pollutants of various nature.


Isomorphic decisional biases across perceptual tasks.
Humans adjust their behavioral strategies to maximize rewards. However, in the laboratory, human decisional biases exist and persist in two alternative tasks, even when this behavior leads to a loss in utilities. Such biases constitute the tendency to choose one action over others and emerge from a combination of external and internal factors that are specific for each individual. Here, we explored the idea that internally-mediated decisional biases should stably occur and, hence, be reflected across multiple behavioral tasks. Our experimental results confirm this notion and illustrate how participants exhibited similar choice biases across days and tasks. Moreover, we show how side-choice behavior in a two alternative choice task served to identify participants, suggesting that individual traits could underlie these choice biases. The tasks and analytic tools developed for this study should become instrumental in exploring the interaction between internal and external factors that contribute to decisional biases. They could also serve to detect psychopathologies that involve aberrant levels of choice variability.


Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates.
During germ cell and preimplantation development, mammalian cells undergo nearly complete reprogramming of DNA methylation patterns. We profiled the methylomes of human and chimp sperm as a basis for comparison to methylation patterns of ESCs. Although the majority of promoters escape methylation in both ESCs and sperm, the corresponding hypomethylated regions show substantial structural differences. Repeat elements are heavily methylated in both germ and somatic cells; however, retrotransposons from several subfamilies evade methylation more effectively during male germ cell development, whereas other subfamilies show the opposite trend. Comparing methylomes of human and chimp sperm revealed a subset of differentially methylated promoters and strikingly divergent methylation in retrotransposon subfamilies, with an evolutionary impact that is apparent in the underlying genomic sequence. Thus, the features that determine DNA methylation patterns differ between male germ cells and somatic cells, and elements of these features have diverged between humans and chimpanzees.


In vivo tomographic imaging of red-shifted fluorescent proteins.
We have developed a spectral inversion method for three-dimensional tomography of far-red and near-infrared fluorescent proteins in animals. The method was developed in particular to address the steep light absorption transition of hemoglobin from the visible to the far-red occurring around 600 nm. Using an orthotopic mouse model of brain tumors expressing the red-shifted fluorescent protein mCherry, we demonstrate significant improvements in imaging accuracy over single-wavelength whole body reconstructions. Furthermore, we show an improvement in sensitivity of at least an order of magnitude over green fluorescent protein (GFP) for whole body imaging. We discuss how additional sensitivity gains are expected with the use of further red-shifted fluorescent proteins and we explain the differences and potential advantages of this approach over two-dimensional planar imaging methods.


Prevention of falls in older patients.
Falls are one of the most common geriatric syndromes threatening the independence of older persons. Between 30 and 40 percent of community-dwelling adults older than 65 years fall each year, and the rates are higher for nursing home residents. Falls are associated with increased morbidity, mortality, and nursing home placement. Most falls have multiple causes. Risk factors for falls include muscle weakness, a history of falls, use of four or more prescription medications, use of an assistive device, arthritis, depression, age older than 80 years, and impairments in gait, balance, cognition, vision, and activities of daily living. Physicians caring for older patients should ask about any falls that have occurred in the past year. Assessment should include evaluating the circumstances of the fall and a complete history and physical examination, looking for potential risk factors. The most effective fall prevention strategies are multifactorial interventions targeting identified risk factors, exercises for muscle strengthening combined with balance training, and withdrawal of psychotropic medication. Home hazard assessment and modification by a health professional also is helpful.


Catcher in the rel: Nanoparticles-antibody conjugate as NF-κB nuclear translocation blocker.
Transcription factor complex NF-κB (p65/p50) is localized to the cytoplasm by its inhibitor IκBα. Upon activation, the Rel proteins p65/p50 are released from IκBα and transported through nuclear pore to affect many gene expressions. While inhibitions of up or down stream signal pathways are often ineffective due to crosstalks and compensations, direct blocking of the Rel proteins p65/p50 has long been proposed as a potential target for cancer therapy. In this work, a nanoparticle/antibody complex targeting NF-κB is employed to catch the Rel protein p65 in perinuclear region and thus blocking the translocation near the nuclear pore gate. TAT peptide conjugated on mesoporous silica nanoparticles (MSN) help non-endocytosis cell-membrane transducing and converge toward perinuclear region, where the p65 specific antibody performed the targeting and catching against active NF-κB p65 effectively. The size of the p65 bound nanoparticle becomes too big to enter nucleus. Simultaneous treatment of mice with the hybrid MSN and doxorubicin conferred a significant therapeutic effect against 4T1 tumor-bearing mice. The new approach of anti-body therapy targeting on transcription factor with "nucleus focusing" and "size exclusion blocking" effects of the antibody-conjugated nanoparticle is general and may be applicable to modulating other transcription factors.


The Cohesive Metastasis Phenotype in Human Prostate Cancer.
A critical barrier for the successful prevention and treatment of recurrent prostate cancer is detection and eradication of metastatic and therapy-resistant disease. Despite the fall in diagnoses and mortality, the reported incidence of metastatic disease has increased 72% since 2004. Prostate cancer arises in cohesive groups as intraepithelial neoplasia, migrates through muscle and leaves the gland via perineural invasion for hematogenous dissemination. Current technological advances have shown cohesive-clusters of tumor (also known as microemboli) within the circulation. Circulating tumor cell (CTC) profiles are indicative of disseminated prostate cancer, and disseminated tumor cells (DTC) are found in cohesive-clusters, a phenotypic characteristic of both radiation- and drug-resistant tumors. Recent reports in cell biology and informatics, coupled with mass spectrometry, indicate that the integrin adhesome network provides an explanation for the biophysical ability of cohesive-clusters of tumor cells to invade thorough muscle and nerve microenvironments while maintaining adhesion-dependent therapeutic resistance. Targeting cohesive-clusters takes advantage of the known ability of extracellular matrix (ECM) adhesion to promote tumor cell survival and represents an approach that has the potential to avoid the progression to drug- and radiotherapy-resistance. In the following review we will examine the evidence for development and dissemination of cohesive-clusters in metastatic prostate cancer.


Dual Targeting of Mesenchymal and Amoeboid Motility Hinders Metastatic Behavior.
Commonly upregulated in human cancers, the scaffolding protein NEDD9/HEF1 is a known regulator of mesenchymal migration and cancer cell plasticity. However, the functional role of NEDD9 as a regulator of different migration/invasion modes in the context of breast cancer metastasis is currently unknown. Here, it is reported that NEDD9 is necessary for both mesenchymal and amoeboid individual cell migration/invasion in triple-negative breast cancer (TNBC). NEDD9 deficiency results in acquisition of the amoeboid morphology, but severely limits all types of cell motility. Mechanistically, NEDD9 promotes mesenchymal migration via VAV2-dependent Rac1 activation, and depletion of VAV2 impairs the ability of NEDD9 to activate Rac1. In addition, NEDD9 supports a mesenchymal phenotype through stimulating polymerization of actin via promoting CTTN phosphorylation in an AURKA-dependent manner. Interestingly, an increase in RhoA activity in NEDD9-depleted cells does not facilitate a switch to functional amoeboid motility, indicating a role of NEDD9 in the regulation of downstream RhoA signaling effectors. Simultaneous depletion of NEDD9 or inhibition of AURKA in combination with inhibition of the amoeboid driver ROCK results in an additional decrease in cancer cell migration/invasion. Finally, we confirmed that a dual targeting strategy is a viable and efficient therapeutic approach to hinder the metastasis of breast cancer in xenograft models, showcasing the important need for further clinical evaluation of this regimen to impede the spread of disease and improve patient survival.Implications: This study provides new insight into the therapeutic benefit of combining NEDD9 depletion with ROCK inhibition to reduce tumor cell dissemination and discovers a new regulatory role of NEDD9 in the modulation of VAV2-dependent activation of Rac1 and actin polymerization. Mol Cancer Res; 15(6); 670-82. ©2017 AACR.


Social cognitive correlates of sexual experience and condom use among 13- through 15-year-old adolescents.
To examine the role of self-efficacy, outcome expectancies, and perception of peer attitudes in the delay of onset of sexual activity among 13- through 15-year-old adolescents. We also explored the role of self-efficacy, outcome expectancies, and perception of friends' condom use behavior in explaining the use of condoms among sexually active adolescents. This study was part of a larger cross-sectional study to evaluate personal characteristics and maternal factors associated with early initiation of sexual intercourse. Mothers and adolescents were recruited from a community-based organization that offered afterschool and summer programs for youth. Enrollment was limited to adolescents aged 13-15 years and their mothers. Mothers and adolescents completed separate interviews. For adolescents, the interviews included the assessment of the variables in the present study. Each interview lasted about 60 min and was conducted by a trained interviewer. Data were analyzed using descriptive statistics and regression analysis. The average age of the 405 adolescent participants was 13.86 years, and approximately 30% of them had engaged in sexual intercourse. Slightly more than half (56%) of participants were male, and 82% were African-American. Participants who were less likely to believe that their friends favored intercourse for adolescents and who held more favorable attitudes about the personal benefits of abstaining from sex were less likely to have initiated sexual intercourse. Among sexually active adolescents, those who expressed confidence in putting on a condom, and in being able to refuse sex with a sexual partner, and who expressed more favorable outcome expectancies associated with using a condom were more likely to use condoms consistently. Human immunodeficiency virus and pregnancy prevention programs should emphasize peer influences in both the initiation of sexual intercourse and the use of safer sex practices among sexually active adolescents, as well as personal attitudes about consequences to self and confidence in negotiating safer sex practices with one's partner.


'SOSORT consensus paper on brace action: TLSO biomechanics of correction (investigating the rationale for force vector selection)'.
The effectiveness of orthotic treatment continues to be controversial in international medical literature due to differences in the reported results and conclusions of various studies. Heterogeneity of the samples has been suggested as a reason for conflicting results. Besides the obvious theoretical differences between the brace concepts, the variability in the technical factors can also explain the contradictory results between same brace types. This paper will investigate the degree of variability among responses of scoliosis specialists from the Brace Study Ground of the International Society on Scoliosis Orthopedic and Rehabilitation Treatment SOSORT. Ultimately, this information could be a foundation for establishing a consensus and framework for future prospective controlled studies. A preliminary questionnaire on the topic of 'brace action' relative to the theory of three-dimensional scoliosis correction and brace treatment was developed and circulated to specialists interested in the conservative treatment of adolescent idiopathic scoliosis. A particular case was presented (main thoracic curve with minor lumbar). Several key points emerged and were used to develop a second questionnaire which was discussed and full filed after the SOSORT consensus meeting (Milano, Italy, January 2005). Twenty-one questionnaires were completed. The Chêneau brace was the most frequently recommended. The importance of the three point system mechanism was stressed. Options about proper pad placement on the thoracic convexity were divided 50% for the pad reaching or involving the apical vertebra and 50% for the pad acting caudal to the apical vertebra. There was agreement about the direction of the vector force, 85% selecting a 'dorso lateral to ventro medial' direction but about the shape of the pad to produce such a force. Principles related to three-dimensional correction achieved high consensus (80%-85%), but suggested methods of correction were quite diverse. This study reveals that among participating SOSORT specialists there continues to be a strongly held and conflicting if not a contentious opinion regarding brace design and treatment. If the goal of a 'treatment consensus' is realistic and achievable, significantly more effort will be required to reconcile these differences.


Radiation dose associated with common computed tomography examinations and the associated lifetime attributable risk of cancer.
Use of computed tomography (CT) for diagnostic evaluation has increased dramatically over the past 2 decades. Even though CT is associated with substantially higher radiation exposure than conventional radiography, typical doses are not known. We sought to estimate the radiation dose associated with common CT studies in clinical practice and quantify the potential cancer risk associated with these examinations. We conducted a retrospective cross-sectional study describing radiation dose associated with the 11 most common types of diagnostic CT studies performed on 1119 consecutive adult patients at 4 San Francisco Bay Area institutions in California between January 1 and May 30, 2008. We estimated lifetime attributable risks of cancer by study type from these measured doses. Radiation doses varied significantly between the different types of CT studies. The overall median effective doses ranged from 2 millisieverts (mSv) for a routine head CT scan to 31 mSv for a multiphase abdomen and pelvis CT scan. Within each type of CT study, effective dose varied significantly within and across institutions, with a mean 13-fold variation between the highest and lowest dose for each study type. The estimated number of CT scans that will lead to the development of a cancer varied widely depending on the specific type of CT examination and the patient's age and sex. An estimated 1 in 270 women who underwent CT coronary angiography at age 40 years will develop cancer from that CT scan (1 in 600 men), compared with an estimated 1 in 8100 women who had a routine head CT scan at the same age (1 in 11 080 men). For 20-year-old patients, the risks were approximately doubled, and for 60-year-old patients, they were approximately 50% lower. Radiation doses from commonly performed diagnostic CT examinations are higher and more variable than generally quoted, highlighting the need for greater standardization across institutions.


Novel Common Genetic Susceptibility Loci for Colorectal Cancer.
Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk. We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided. The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0. This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.


Coupling of organotypic brain slice cultures to silicon-based arrays of electrodes.
Fetal or early postnatal brain tissue can be cultured in viable and healthy condition for several weeks with development and preservation of the basic cellular and connective organization as so-called organotypic brain slice cultures. Here we demonstrate and describe how it is possible to establish such hippocampal rat brain slice cultures on biocompatible silicon-based chips with arrays of electrodes with a histological organization comparable to that of conventional brain slice cultures grown by the roller drum technique and on semiporous membranes. Intracellular and extracellular recordings from neurons in the slice cultures show that the electroresponsive properties of the neurons and synaptic circuitry are in accordance with those described for cells in acutely prepared slices of the adult rat hippocampus. Based on the recordings and the possibilities of stimulating the cultured cells through the electrode arrays it is anticipated that the setup eventually will allow long-term studies of defined neuronal networks and provide valuable information on both normal and neurotoxicological and neuropathological conditions.


Vitamin E δ-tocotrienol augments the antitumor activity of gemcitabine and suppresses constitutive NF-κB activation in pancreatic cancer.
The NF-κB transcription factor functions as a crucial regulator of cell survival and chemoresistance in pancreatic cancer. Recent studies suggest that tocotrienols, which are the unsaturated forms of vitamin E, are a promising class of anticancer compounds that inhibit the growth and survival of many cancer cells, including pancreatic cancer. Here, we show that tocotrienols inhibited NF-κB activity and the survival of human pancreatic cancer cells in vitro and in vivo. Importantly, we found the bioactivity of the four natural tocotrienol compounds (α-, β-, δ-, and γ-tocotrienol) to be directly related to their ability to suppress NF-κB activity in vitro and in vivo. The most bioactive tocotrienol for pancreatic cancer, δ-tocotrienol, significantly enhanced the efficacy of gemcitabine to inhibit pancreatic cancer growth and survival in vitro and in vivo. Moreover, we found that δ-tocotrienol augmentation of gemcitabine activity in pancreatic cancer cells and tumors is associated with significant suppression of NF-κB activity and the expression of NF-κB transcriptional targets (Bcl-X(L), X-linked inhibitor of apoptosis, and survivin). Our study represents the first comprehensive preclinical evaluation of the activity of natural vitamin E compounds in pancreatic cancer. Given these results, we are conducting a phase I trial of δ-tocotrienol in patients with pancreatic cancer using pancreatic tumor cell survival and NF-κB signaling components as intermediate biomarkers. Our data also support future clinical investigation of δ-tocotrienol to augment gemcitabine activity in pancreatic cancer.


Obesity and endocrine dysfunction in mice with deletions of both neuropeptide Y and galanin.
Neuropeptide Y (NPY) and galanin have both been implicated in the regulation of body weight, yet mice bearing deletions of either of these molecules have unremarkable metabolic phenotypes. To investigate whether galanin and NPY might compensate for one another, we produced mutants lacking both neuropeptides (GAL(-/-)/NPY(-/-)). We found that male GAL(-/-)/NPY(-/-) mice ate significantly more and were much heavier (30%) than wild-type (WT) controls. GAL(-/-)/NPY(-/-) mice responded to a high-fat diet by gaining more weight than WT mice gain, and they were unable to regulate their weight normally after a change in diet. GAL(-/-)/NPY(-/-) mice had elevated levels of leptin, insulin, and glucose, and they lost more weight than WT mice during chronic leptin treatment. Galanin mRNA was increased in the hypothalamus of NPY(-/-) mice, providing evidence of compensatory regulation in single mutants. The disruption of energy balance observed in GAL(-/-)/NPY(-/-) double knockouts is not found in the phenotype of single knockouts of either molecule. The unexpected obesity phenotype may result from the dysregulation of the leptin and insulin systems that normally keep body weight within the homeostatic range.


Characterization of the bone morphogenetic protein (BMP) system in human pulmonary arterial smooth muscle cells isolated from a sporadic case of primary pulmonary hypertension: roles of BMP type IB receptor (activin receptor-like kinase-6) in the mitotic action.
The functional involvement of bone morphogenetic protein (BMP) system in primary pulmonary hypertension (PPH) remains unclear. Here we demonstrate a crucial role of the BMP type IB receptor, activin receptor-like kinase (ALK)-6 for pulmonary arterial smooth muscle cell (pphPASMC) mitosis isolated from a sporadic PPH patient bearing no mutations in BMPR2 gene. A striking increase in the levels of ALK-6 mRNA was revealed in pphPASMC compared with control PASMCs, in which ALK-6 transcripts were hardly detectable. BMP-2 and -7 stimulated the mitosis of pphPASMCs, which was opposite to their suppressive effects on the mitosis of the control PASMCs. BMP-4 and -6 and activin inhibited pphPASMC mitosis, whereas these did not affect control PASMCs. The presence of BMP signaling machinery in pphPASMCs was elucidated based on the analysis on Id-1 transcription and Smad-reporter genes. Overexpression of a dominant-negative ALK-6 construct revealed that ALK-6 plays a key role in the mitosis as well as intracellular BMP signaling of pphPASMCs. Gene silencing of ALK-6 using small interfering RNA also reduced DNA synthesis as well as Id-1 transcription in pphPASMCs regardless of BMP-2 stimulation. Although Id-1 response was not stimulated by BMP-2 in control PASMCs, the gene delivery of wild-type ALK-6 caused significant increase in the Id-1 transcripts in response to BMP-2. Additionally, inhibitors of ERK and p38 MAPK pathways suppressed pphPASMC mitosis induced by BMP-2, implying that the mitotic action is in part MAPK dependent. Thus, the BMP system is strongly involved in pphPASMC mitosis through ALK-6, which possibly leads to activation of Smad and MAPK, resulting in the progression of vascular remodeling of pulmonary arteries in PPH.


Ginsenoside Rg3 inhibits keloid fibroblast proliferation, angiogenesis and collagen synthesis in vitro via the TGF‑β/Smad and ERK signaling pathways.
A wide range of therapeutic options exists for the treatment of keloids, all of which have their own strengths; however, a high risk of side‑effects and frequent recurrence remains. Therefore, the present study aimed to identify improved therapeutic approaches or drugs for the treatment of keloids. Ginsenoside Rg3 (Rg3) has been reported to exert numerous antitumor effects, thus indicating that Rg3 may be a potential therapeutic agent that targets keloids. The present study determined the effects of Rg3 on human keloid fibroblasts (KFs) in vitro, and further explored the associated molecular and cellular mechanisms. Keloid scar specimens were obtained from patients, aged between 22 and 35 years, without systemic diseases and primary cells were isolated from keloid tissues. In each assay, KFs were divided into three groups and were cultured in medium with or without various concentrations of Rg3 (50 or 100 µg/ml). Cell viability assay, flow cytometry, quantitative polymerase chain reaction, cell migration assay, immunofluorescence staining, western blot analysis, Transwell cell invasion assay and immunohistochemical analysis were used to analyze the KFs and keloid explant cultures. The results of the present study demonstrated that Rg3 was able to exert an inhibitory effect on the transforming growth factor‑β/Smad and extracellular signal‑regulated kinase signaling pathways in KFs. The proliferation, migration, invasion, angiogenesis and collagen synthesis of KFs were markedly suppressed following treatment with Rg3. Furthermore, the results of an ex vivo assay indicated that Rg3 inhibited angiogenesis and reduced collagen accumulation in keloids. Significant statistical differences existed between the control and Rg3‑treated groups (P<0.05). All of these experimental results suggested that Rg3 may serve as a reliable drug for the treatment of patients with keloids.


Optimizing intensive care capacity using individual length-of-stay prediction models.
Effective planning of elective surgical procedures requiring postoperative intensive care is important in preventing cancellations and empty intensive care unit (ICU) beds. To improve planning, we constructed, validated and tested three models designed to predict length of stay (LOS) in the ICU in individual patients. Retrospective data were collected from 518 consecutive patients who underwent oesophagectomy with reconstruction for carcinoma between January 1997 and April 2005. Three multivariable linear regression models for LOS, namely preoperative, postoperative and intra-ICU, were constructed using these data. Internal validation was assessed using bootstrap sampling in order to obtain validated estimates of the explained variance (r2). To determine the potential gain of the best performing model in day-to-day clinical practice, prospective data from a second cohort of 65 consecutive patients undergoing oesophagectomy between May 2005 and April 2006 were used in the model, and the predictive performance of the model was compared with prediction based on mean LOS. The intra-ICU model had an r2 of 45% after internal validation. Important prognostic variables for LOS included greater patient age, comorbidity, type of surgical approach, intraoperative respiratory minute volume and complications occurring within 72 hours in the ICU. The potential gain of the best model in day-to-day clinical practice was determined relative to mean LOS. Use of the model reduced the deficit number (underestimation) of ICU days by 65 and increased the excess number (overestimation) of ICU days by 23 for the cohort of 65 patients. A conservative analysis conducted in the second, prospective cohort of patients revealed that 7% more oesophagectomies could have been accommodated, and 15% of cancelled procedures could have been prevented. Patient characteristics can be used to create models that will help in predicting LOS in the ICU. This will result in more efficient use of ICU beds and fewer cancellations.


Red maca (Lepidium meyenii) reduced prostate size in rats.
Epidemiological studies have found that consumption of cruciferous vegetables is associated with a reduced risk of prostate cancer. This effect seems to be due to aromatic glucosinolate content. Glucosinolates are known for have both antiproliferative and proapoptotic actions. Maca is a cruciferous cultivated in the highlands of Peru. The absolute content of glucosinolates in Maca hypocotyls is relatively higher than that reported in other cruciferous crops. Therefore, Maca may have proapoptotic and anti-proliferative effects in the prostate. Male rats treated with or without aqueous extracts of three ecotypes of Maca (Yellow, Black and Red) were analyzed to determine the effect on ventral prostate weight, epithelial height and duct luminal area. Effects on serum testosterone (T) and estradiol (E2) levels were also assessed. Besides, the effect of Red Maca on prostate was analyzed in rats treated with testosterone enanthate (TE). Red Maca but neither Yellow nor Black Maca reduced significantly ventral prostate size in rats. Serum T or E2 levels were not affected by any of the ecotypes of Maca assessed. Red Maca also prevented the prostate weight increase induced by TE treatment. Red Maca administered for 42 days reduced ventral prostatic epithelial height. TE increased ventral prostatic epithelial height and duct luminal area. These increases by TE were reduced after treatment with Red Maca for 42 days. Histology pictures in rats treated with Red Maca plus TE were similar to controls. Phytochemical screening showed that aqueous extract of Red Maca has alkaloids, steroids, tannins, saponins, and cardiotonic glycosides. The IR spectra of the three ecotypes of Maca in 3800-650 cm (-1) region had 7 peaks representing 7 functional chemical groups. Highest peak values were observed for Red Maca, intermediate values for Yellow Maca and low values for Black Maca. These functional groups correspond among others to benzyl glucosinolate. Red Maca, a cruciferous plant from the highland of Peru, reduced ventral prostate size in normal and TE treated rats.


Predicting Novel Therapies and Targets: Regulation of Notch3 by the Bromodomain Protein BRD4.
Systematic approaches for accurate repurposing of targeted therapies are needed. We developed and aimed to biologically validate our therapy predicting tool (TPT) for the repurposing of targeted therapies for specific tumor types by testing the role of Bromodomain and Extra-Terminal motif inhibitors (BETi) in inhibiting BRD4 function and downregulating Notch3 signaling in ovarian cancer.Utilizing established ovarian cancer preclinical models, we carried out in vitro and in vivo studies with clinically relevant BETis to determine their therapeutic effect and impact on Notch3 signaling.Treatment with BETis or siRNA-mediated BRD4 knockdown resulted in decreased cell viability, reduced cell proliferation, and increased cell apoptosis in vitro. In vivo studies with orthotopic mouse models demonstrated that treatment with BETi decreased tumor growth. In addition, knockdown of BRD4 with doxycycline-inducible shRNA increased survival up to 50% (P < 0.001). Treatment with either BETis or BRD4 siRNA decreased Notch3 expression both in vitro and in vivo BRD4 inhibition also decreased the expression of NOTCH3 targets, including HES1 Chromatin immunoprecipitation revealed that BRD4 was present at the NOTCH3 promoter.Our findings provide biological validation for the TPT by demonstrating that BETis can be an effective therapeutic agent for ovarian cancer by downregulating Notch3 expression.The TPT could rapidly identify candidate drugs for ovarian or other cancers along with novel companion biomarkers.


Spatiotemporal coding in the cortex: information flow-based learning in spiking neural networks.
We introduce a learning paradigm for networks of integrate-and-fire spiking neurons that is based on an information-theoretic criterion. This criterion can be viewed as a first principle that demonstrates the experimentally observed fact that cortical neurons display synchronous firing for some stimuli and not for others. The principle can be regarded as the postulation of a nonparametric reconstruction method as optimization criteria for learning the required functional connectivity that justifies and explains synchronous firing for binding of features as a mechanism for spatiotemporal coding. This can be expressed in an information-theoretic way by maximizing the discrimination ability between different sensory inputs in minimal time.


Modulation of adverse cardiac remodeling by STARS, a mediator of MEF2 signaling and SRF activity.
Cytoskeletal proteins have been implicated in the pathogenesis of cardiomyopathy, but how the cytoskeleton influences the transcriptional alterations associated with adverse cardiac remodeling remains unclear. Striated muscle activator of Rho signaling (STARS) is a muscle-specific actin-binding protein localized to the Z disc that activates serum response factor-dependent (SRF-dependent) transcription by inducing nuclear translocation of the myocardin-related SRF coactivators MRTF-A and -B. We show that STARS expression is upregulated in mouse models of cardiac hypertrophy and in failing human hearts. A conserved region of the STARS promoter containing an essential binding site for myocyte enhancer factor-2 (MEF2), a stress-responsive transcriptional activator, mediates cardiac expression of STARS, which in turn activates SRF target genes. Forced overexpression of STARS in the heart sensitizes the heart to pressure overload and calcineurin signaling, resulting in exaggerated deterioration in cardiac function in response to these hypertrophic stimuli. These findings suggest that STARS modulates the responsiveness of the heart to stress signaling by functioning as a cytoskeletal intermediary between MEF2 and SRF.


Supervised learning of quantizer codebooks by information loss minimization.
This paper proposes a technique for jointly quantizing continuous features and the posterior distributions of their class labels based on minimizing empirical information loss such that the quantizer index of a given feature vector approximates a sufficient statistic for its class label. Informally, the quantized representation retains as much information as possible for classifying the feature vector correctly. We derive an alternating minimization procedure for simultaneously learning codebooks in the euclidean feature space and in the simplex of posterior class distributions. The resulting quantizer can be used to encode unlabeled points outside the training set and to predict their posterior class distributions, and has an elegant interpretation in terms of lossless source coding. The proposed method is validated on synthetic and real data sets and is applied to two diverse problems: learning discriminative visual vocabularies for bag-of-features image classification and image segmentation.


Deep bottleneck features for spoken language identification.
A key problem in spoken language identification (LID) is to design effective representations which are specific to language information. For example, in recent years, representations based on both phonotactic and acoustic features have proven their effectiveness for LID. Although advances in machine learning have led to significant improvements, LID performance is still lacking, especially for short duration speech utterances. With the hypothesis that language information is weak and represented only latently in speech, and is largely dependent on the statistical properties of the speech content, existing representations may be insufficient. Furthermore they may be susceptible to the variations caused by different speakers, specific content of the speech segments, and background noise. To address this, we propose using Deep Bottleneck Features (DBF) for spoken LID, motivated by the success of Deep Neural Networks (DNN) in speech recognition. We show that DBFs can form a low-dimensional compact representation of the original inputs with a powerful descriptive and discriminative capability. To evaluate the effectiveness of this, we design two acoustic models, termed DBF-TV and parallel DBF-TV (PDBF-TV), using a DBF based i-vector representation for each speech utterance. Results on NIST language recognition evaluation 2009 (LRE09) show significant improvements over state-of-the-art systems. By fusing the output of phonotactic and acoustic approaches, we achieve an EER of 1.08%, 1.89% and 7.01% for 30 s, 10 s and 3 s test utterances respectively. Furthermore, various DBF configurations have been extensively evaluated, and an optimal system proposed.


[Contribution of epigenetics to understand human development].
Epigenetics refers to the study of how genes produce their effect on the phenotype of the organism. This article is a review on the scope and importance of recently discovered epigenetic mechanisms on human development and their relationship to perinatal epidemiological issues. It shows a general view and present concepts about epigenetics and its contribution to the comprehension of several physiologic and pathological conditions of human beings. Secondly, it analyzes the evidence coming from epidemiological and animal studies, about the influence of events that occur in the perinatal and early postnatal periods on adult life and the possible epigenetic mechanisms involved. Lastly, it underscores the implications of these results of future research and the design of public policies that take into account the importance of events in early life in the future development of individuals.


Variations in Dissolved Nitrate, Chloride, and Sulfate in Precipitation, Reservoir, and Tap Waters, Columbus, Ohio.
Urban potable waters can be very susceptible to human activities that can impact water quality and, hence, public health. Columbus, Ohio, is currently the 14th largest city in the United States with an estimated population of ~860,000. Much of the urban population receives its water supply from a series of reservoirs located north of the city proper. These reservoirs are fed by river systems that drain either large agricultural lands, or rapidly growing suburban areas, or both. The agricultural activities introduce dissolved nitrate, and increased usage of de-icing salts on roads and highways within the drainage area introduce chloride into the river/reservoir systems. High nitrate in drinking water poses a potential health risk, particularly to infants, while high chloride, applied as halite, in drinking water can aid in the development of cardiovascular disease. In this work, we present a 19-month time series measuring nitrate, chloride, and sulfate in local precipitation, reservoir and household tap waters in order to better understand the relationship of the hydrologic residence time on the tap water chemistry, as well as to evaluate the anion concentrations. The highest chloride tap water concentration, 6.9 mM, occurred in early February 2011, while increases in nitrate occurred in both early summer and the middle of winter. In general, the anion concentrations in the precipitation are all equal to or lower than the reservoir waters. Similarly, the tap water had concentrations of chloride and sulfate higher than reservoir water, while nitrate was similar to reservoir water. Tap water had higher fluoride and sulfate concentrations, suggesting that they are added during the treatment of the reservoir water prior to residential distribution. These data clearly demonstrate the importance of watershed lands on the quality of water in the human distribution system.


Genetic influences on muscle strength, lean body mass, and bone mineral density: a twin study.
Lean body mass and muscle strength are both associated with bone mineral density (BMD), which is known to be under strong genetic control. In this classical twin study, we examine the size of the genetic component of both muscle strength and lean body mass and to what degree they account for the genetic component of BMD. In all, 706 postmenopausal women were examined; 227 pairs of monozygous (MZ) twins and 126 pairs of dizygous (DZ) twins. Grip strength was measured using a hand-help grip bulb and leg strength using a dynamic leg extensor power rig. Lean body mass and BMD at multiple sites were measured by dual-energy X-ray absorptiometry. BMD correlated with both leg extensor strength (r = 0.16-0.26) and grip strength (r = 0.12-0.21). Lean mass was significantly correlated with BMD at all sites (r = 0.20-0.39). All three muscle variables have a moderate genetic component with heritability estimates of 0.52 for lean body mass, 0.46 for leg extensor strength, and 0.30 for grip strength (all p < 0.05). The genetic component of BMD was not significantly reduced after adjusting for lean mass and muscle strength, with less than 20% of the genetic variance of BMD explained by the muscle variables. In conclusion, these data suggest that the three muscle variables have a modest genetic component, suggesting the potential for clinical intervention and lifestyle modifications. The genetic component to muscle bulk and strength accounts for little of the genetic component to BMD, confirming the rationale for research into bone-specific genes.


Perinatal detection of familial adenomatous polyposis.
Hepatoblastoma is an uncommon fetal neoplasm that may represent an isolated malignancy or a component of a familial cancer or syndromic diagnosis. A large fetal liver mass was detected on routine ultrasound examination of a 23-year-old woman with thyroid nodules and hypertension. Inferior vena cava compression prompted delivery; postnatal biopsy revealed hepatoblastoma. Maternal thyroid biopsy revealed papillary carcinoma. Neonatal and maternal cytomolecular analysis revealed APC gene disruption at 5q22.2. Pedigree analysis exposed multigenerational colon cancer and thyroid cancer, which in conjunction with genetic testing is consistent with familial adenomatous polyposis. This is a novel means of familial adenomatous polyposis diagnosis. Obstetricians and perinatologists should be alert for familial cancer or syndromic diagnoses presenting as fetal neoplasms.


Single-molecule atomic force microscopy force spectroscopy study of Aβ-40 interactions.
Misfolding and aggregation of amyloid β-40 (Aβ-40) peptide play key roles in the development of Alzheimer's disease (AD). However, very little is known about the molecular mechanisms underlying these molecular processes. We developed a novel experimental approach that can directly probe aggregation-prone states of proteins and their interactions. In this approach, the proteins are anchored to the surface of the atomic force microscopy substrate (mica) and the probe, and the interaction between anchored molecules is measured in the approach-retraction cycles. We used dynamic force spectroscopy (DFS) to measure the stability of transiently formed dimers. One of the major findings from DFS analysis of α-synuclein (α-Syn) is that dimeric complexes formed by misfolded α-Syn protein are very stable and dissociate over a range of seconds. This differs markedly from the dynamics of monomers, which occurs on a microsecond to nanosecond time scale. Here we applied the same approach to quantitatively characterize interactions of Aβ-40 peptides over a broad range of pH values. These studies showed that misfolded dimers are characterized by lifetimes in the range of seconds. This value depends on pH and varies between 2.7 s for pH 2.7 and 0.1 s for pH 7, indicating that the aggregation properties of Aβ-40 are modulated by the environmental conditions. The analysis of the contour lengths revealed the existence of various pathways for dimer dissociation, suggesting that dimers with different conformations are formed. These structural variations result in different aggregation pathways, leading to different types of oligomers and higher-order aggregates, including fibrils.


Comparison of unenhanced and enhanced imaging protocols for angle measurements with anterior segment optical coherence tomography.
To compare the intraobserver and interobserver agreement of anterior chamber angle measurements using unenhanced and enhanced imaging protocols for anterior segment optical coherence tomography (AS-OCT). Anterior segments of 30 eyes of 15 healthy subjects (mean age: 33.8 ± 13.0 years, 8 women) were imaged by a single examiner with AS-OCT using unenhanced and enhanced imaging protocol. Two masked observers analyzed each image independently on two separate occasions. The reproducibility of angle parameters was estimated by calculating coefficients of variation separately for each observer. Bland-Altman plots were constructed to assess the intraobserver and interobserver agreement. The intraobserver and interobserver reproducibility was similar between imaging protocols. Intra-observer and interobserver agreements were also similar for all parameters evaluated. The best estimate of scleral spur location was determined in all images by both observers. Measurement variability was similar with the unenhanced and enhanced imaging protocol in this series of eyes with open angles.


Mitochondrial proteomics investigation of a cellular model of impaired dopamine homeostasis, an early step in Parkinson's disease pathogenesis.
Impaired dopamine homeostasis is an early event in the pathogenesis of Parkinson's disease. Generation of intracellular reactive oxygen species consequent to dopamine oxidation leads to mitochondrial dysfunction and eventually cell death. Alterations in the mitochondrial proteome due to dopamine exposure were investigated in the SH-SY5Y human neuroblastoma cell line. The combination of two orthogonal proteomic approaches, two-dimensional electrophoresis and shotgun proteomics (proteomeXchange dataset PXD000838), was used to highlight the specific pathways perturbed by the increase of intracellular dopamine, in comparison with those perturbed by a specific mitochondrial toxin (4-methylphenylpyridinium, MPP(+)), a neurotoxin causing Parkinsonism-like symptoms in animal models. Proteins altered by MPP(+) did not completely overlap with those affected by dopamine treatment. In particular, the MPP(+) target complex I component NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 was not affected by dopamine together with 26 other proteins. The comparison of proteomics approaches highlighted the fragmentation of some mitochondrial proteins, suggesting an alteration of the mitochondrial protease activity. Pathway and disease association analysis of the proteins affected by dopamine revealed the overrepresentation of the Parkinson's disease and the parkin-ubiquitin proteasomal system pathways and of gene ontologies associated with generation of precursor metabolites and energy, response to topologically incorrect proteins and programmed cell death. These alterations may be globally interpreted in part as the result of a direct effect of dopamine on mitochondria (e.g. alteration of the mitochondrial protease activity) and in part as the effect on mitochondria of a general activation of cellular processes (e.g. regulation of programmed cell death).


Disturbances in early parenting of depressed mothers and cortisol secretion in offspring: a preliminary study.
Disturbances in cortisol secretion are associated with risk for psychiatric disorder, including depression. Animal research indicates that early care experiences influence hypothalamic-pituitary-adrenal (HPA) axis functioning in offspring. Similar effects are suggested in human development, but evidence of longitudinal associations between observed early parenting and offspring cortisol secretion is extremely limited. We studied associations between parenting disturbances occurring in the context of maternal postnatal depression (PND), and elevations in morning cortisol secretion in the adolescent offspring of PND mothers. We observed maternal parenting behaviour on four occasions through the first year and at five-year follow-up in postnatally depressed (n=29) and well (n=20) mothers. Observations were coded for maternal sensitivity and withdrawn behaviour. Basal offspring salivary cortisol secretion was measured at 13-years, using collections over 10-days. Postnatal, but not five-year, maternal withdrawal predicted elevated mean and maximum morning cortisol secretion in 13-year-old offspring. There were no significant associations between maternal sensitivity and offspring cortisol secretion. The sample size was relatively small, and effects tended to be reduced to trend level when covariates were considered. The correlational nature of the study (albeit longitudinal) limits conclusions regarding causality. Individual differences in early maternal parenting behaviour may influence offspring cortisol secretion, and thereby risk for depression. Parenting interventions that facilitate active maternal engagement with the infant may be indicated for high-risk populations.


Patients with Tuberculosis Have a Dysfunctional Circulating B-Cell Compartment, Which Normalizes following Successful Treatment.
B-cells not only produce immunoglobulins and present antigens to T-cells, but also additional key roles in the immune system. Current knowledge on the role of B-cells in infections caused by intracellular bacteria is fragmentary and contradictory. We therefore analysed the phenotypical and functional properties of B-cells during infection and disease caused by Mycobacterium tuberculosis (Mtb), the bacillus causing tuberculosis (TB), and included individuals with latent TB infection (LTBI), active TB, individuals treated successfully for TB, and healthy controls. Patients with active or treated TB disease had an increased proportion of antibodies reactive with mycobacteria. Patients with active TB had reduced circulating B-cell frequencies, whereas only minor increases in B-cells were detected in the lungs of individuals deceased from TB. Both active TB patients and individuals with LTBI had increased relative fractions of B-cells with an atypical phenotype. Importantly, these B-cells displayed impaired proliferation, immunoglobulin- and cytokine- production. These defects disappeared upon successful treatment. Moreover, T-cell activity was strongest in individuals successfully treated for TB, compared to active TB patients and LTBI subjects, and was dependent on the presence of functionally competent B-cells as shown by cellular depletion experiments. Thus, our results reveal that general B-cell function is impaired during active TB and LTBI, and that this B-cell dysfunction compromises cellular host immunity during Mtb infection. These new insights may provide novel strategies for correcting Mtb infection-induced immune dysfunction towards restored protective immunity.


The ecological importance of severe wildfires: some like it hot.
Many scientists and forest land managers concur that past fire suppression, grazing, and timber harvesting practices have created unnatural and unhealthy conditions in the dry, ponderosa pine forests of the western United States. Specifically, such forests are said to carry higher fuel loads and experience fires that are more severe than those that occurred historically. It remains unclear, however, how far these generalizations can be extrapolated in time and space, and how well they apply to the more mesic ponderosa pine systems and to other forest systems within the western United States. I use data on the pattern of distribution of one bird species (Black-backed Woodpecker, Picoides arcticus) as derived from 16465 sample locations to show that, in western Montana, this bird species is extremely specialized on severely burned forests. Such specialization has profound implications because it suggests that the severe fires we see burning in many forests in the Intermountain West are not entirely "unnatural" or "unhealthy." Instead, severely burned forest conditions have probably occurred naturally across a broad range of forest types for millennia. These findings highlight the fact that severe fire provides an important ecological backdrop for fire specialists like the Black-backed Woodpecker, and that the presence and importance of severe fire may be much broader than commonly appreciated.


Multiple whole-genome alignments without a reference organism.
Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and six Drosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families-perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.