Personal medication preparedness among veteran and nonveteran men and women in the California population.
The health of people with chronic medical conditions is particularly vulnerable to the disruptions caused by public health disasters, especially when there is massive damage to the medical infrastructure. Government agencies and national organizations recommend that people with chronic illness prepare for disasters by stockpiling extra supplies of medications. A wide range of chronic illnesses has long been documented among veterans of the US armed forces. Veterans with chronic illness could be at great risk of complications due to disaster-related medication disruptions; however, the prevalence of personal medication preparedness among chronically ill veterans is not currently known. Data was used from the 2009 California Health Interview Survey on 28,167 respondents who reported taking daily medications. After adjusting for differences in age, health status, and other characteristics, calculations were made of the percentage of respondents who had a two-week supply of emergency medications and, among respondents without a supply, the percentage who said they could obtain one. Veteran men, veteran women, nonveteran men, and nonveteran women were compared. Medication supplies among veteran men (81.9%) were higher than among nonveteran women (74.8%; P < .0001) and veteran women (81.1%; P = 0.014). Among respondents without medication supplies, 67.2% of nonveteran men said that they could obtain a two-week supply, compared with 60.1% of nonveteran women (P = .012). Discussion Among adults in California with chronic illness, veteran men are more likely to have personal emergency medication supplies than are veteran and nonveteran women. Veteran men may be more likely to be prepared because of their training to work in combat zones and other emergency situations, which perhaps engenders in them a culture of preparedness or self-reliance. It is also possible that people who choose to enlist in the military are different from the general population in ways that make them more likely to be better prepared for emergencies. Veterans in California have a relatively high level of emergency medication preparedness. Given the health complications that can result from disaster-related medication disruptions, this is a promising finding. Disasters are a national concern, however, and the personal preparedness of veterans in all parts of the nation should be assessed; these findings could serve as a useful reference point for such work in the future.


Depression and unemployment incidence rate evolution in Portugal, 1995-2013: General Practitioner Sentinel Network data.
Quantify, for both genders, the correlation between the depression incidence rate and the unemployment rate in Portugal between 1995 and 2013. An ecological study was developed to correlate the evolution of the depression incidence rates estimated by the General Practitioner Sentinel Network and the annual unemployment rates provided by the National Statistical Institute in official publications. There was a positive correlation between the depression incidence rate and the unemployment rate in Portugal, which was significant only for males (R2 = 0.83, p = 0.04). For this gender, an increase of 37 new cases of depression per 100,000 inhabitants was estimated for each 1% increase in the unemployment rate between 1995 and 2013. Although the study design does not allow the establishment of a causal association between unemployment and depression, the results suggest that the evolution of unemployment in Portugal may have had a significant impact on the level of mental health of the Portuguese, especially among men.


PRDM16 Upregulation Induced by MicroRNA-448 Inhibition Alleviates Atherosclerosis via the TGF-β Signaling Pathway Inactivation.
The dysregulated expression of microRNAs (miRs) has been associated with pathological and physiological processes of atherosclerosis (AS). In addition, PR domain-containing 16 (PRDM16), a transcriptional mediator of brown fat cell identity and smooth muscle cell activities, may be involved in the hypercholesterolemia during development of AS. The bioinformatic analysis identified a regulatory miR-448 of PRDM16. Hence, the current study aimed to explore whether miR-448 influenced the activities of aortic smooth muscle cell (ASMCs) in AS. We validated that miR-448 was highly expressed in peripheral blood of patients with AS and aortic smooth muscle of AS model mice. Whereas, PRDM16 was downregulated in the aortic smooth muscle of AS model mice. PRDM16 overexpression was observed to inhibit oxidative stress injury and cell proliferation, and promote apoptosis of ASMCs. Mechanistic studies revealed that miR-448 targeted PRDM16 and negatively regulated the PRDM16 expression, while PRDM16 blocked the TGF-β signaling pathway. Furthermore, Downregulated miR-448 alleviated oxidative stress injury, and attenuated ASMC cell proliferation, migration and enhanced cell apoptosis through upregulation of PRDM16. Taken together, silencing of miR-448 upregulates PRDM16 and inactivates the TGF-β signaling pathway, thereby impeding development of AS by repressing the proliferation, migration and invasion of ASMCs.


Human herpes virus-8 is not associated with primary central nervous system lymphoma in HIV-negative patients.
Primary central nervous system lymphomas (PCNSL) are derived from germinal center B cells. Recent molecular studies indicate that the tumor cells or their precursors have experienced antigenic stimulation. Attractive candidates for such antigens are pathogens with the capacity to reside in the brain. The aim of the present study was to evaluate whether human herpes virus (HHV)-8 is involved in the pathogenesis of PCNSL. A series of 46 PCNSL, 31 from HIV-negative and 15 from HIV-positive patients, were analyzed using various molecular biological and immunological approaches. Nested PCR with two different protocols unequivocally demonstrated that PCNSL from HIV-negative patients did not harbor HHV-8 DNA. Among AIDS-associated PCNSL, HHV-8 DNA was found in only 1 tumor. In situ hybridization studies revealed that the lymphoma cells were HHV-8 negative in all cases. Single small mononuclear cells, most likely corresponding to bystander lymphocytes, were identified as the cellular source of HHV-8 in the HIV-positive patient with an HHV-8 PCR signal. These studies largely rule out a role for HHV-8 in the pathogenesis of PCNSL in both HIV-negative as well as HIV-positive patients.


Model-free characterization of brain functional networks for motor sequence learning using fMRI.
Neuroimaging experiments have identified several brain regions that appear to play roles in motor learning. Here we apply a novel multivariate analytical approach to explore the dynamic interactions of brain activation regions as spatio-temporally coherent functional networks. We acquired BOLD fMRI signal during explicit motor sequence learning task to characterize the adaptive functional changes in the early phase of motor learning. Subjects practiced a 10-digit, visually cued, fixed motor sequence during 15 consecutive 30 s practice blocks interleaved with similarly cued random sequence blocks. Tensor Independent Component Analysis (TICA) decomposed the data into statistically independent spatio-temporal processes. Two components were identified that represented task-related activations. The first component showed decreasing activity of a fronto-parieto-cerebellar network during task conditions. The other exclusively related to sequence learning blocks showed activation in a network including the posterior parietal and premotor cortices. Variation in expression of this component across individual subjects correlated with differences in behavior. Relative deactivations also were found in patterns similar to those described previously as "resting state" networks. Some of these deactivation components also showed task- and time-related modulations and were related to the behavioral improvement. The spatio-temporal coherence within these networks suggests that their elements are functionally integrated. Their anatomical plausibility and correlation with behavioral measures also suggest that this approach allows characterization of the interactions of functional networks relevant to the task. Particular value for multi-variant, model-free methods such as TICA lies in the potential for generating hypotheses regarding functional anatomical networks underlying specific behaviors.


Waveguide-enhanced mid-infrared chem/bio sensors.
Despite providing the opportunity for directly sensing molecular constituents with inherent fingerprint specificity in the 2.5-20 μm spectral regime, mid-infrared optical sensing technologies have not yet achieved the same penetration in waveguide-based chem/bio sensing compared to related sensing schemes operating at visible and near-infrared frequencies. In this review, current advances in mid-infrared chem/bio sensor technology will be highlighted and contrasted with the prevalent bottlenecks that have to date limited a more widespread adoption of mid-infrared sensing devices. However, with the increasing availability of advanced light sources such as quantum cascade lasers and the advent of on-chip semiconductor waveguide technologies, a prosperous future of this sensing concept for label-free detection in environmental analysis, process monitoring, and bioanalytics is perceived.


GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes.
The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5' and 3' ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5' end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3' ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5' and 3' ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.


Stomach lysozymes of the three-toed sloth (Bradypus variegatus), an arboreal folivore from the Neotropics.
Lysozymes are antimicrobial defences that act as digestive enzymes when expressed in the stomach of herbivores with pre-gastric fermentation. We studied this enzyme in the complex stomach of the three-toed sloth (Bradypus variegatus), a folivore with pre-gastric fermentation. Lysozymes were identified by SDS-PAGE and immunoblotting in all portions: diverticulum, pouch, glandular and muscular prepyloric area with 14.3 kDa of molecular mass. Purified lysozymes from all areas but the diverticulum were characterized by MALDI-TOF, optimal pH, optimal ionic strength, and specific activity. The differences observed suggested at least three isoforms. The optimal pHs were similar to the pH of the stomach portion where the enzymes were isolated. The lysozyme from the pouch (fermentation chamber) exhibited higher specific activity and concentration than the others. The specific activity of the enzyme from the acid muscular prepyloric portion was comparable to that reported in the cow abomasums; however, its concentration was lower than that observed in cow. This distinctive pattern of secretion/specific activity and overall low concentration suggests different roles for the lysozymes in this herbivore compared to Artiodactyla. We postulate that sloth stomach lysozymes may still be antimicrobial defences by protecting the microbial flora of the fermentation chamber against foreign bacteria.


Tagged mutagenesis by efficient Minos-based germ line transposition.
Germ line gene transposition technology has been used to generate "libraries" of flies and worms carrying genomewide mutations. Phenotypic screening and DNA sequencing of such libraries provide functional information resulting from insertional events in target genes. There is also a great need to have a fast and efficient way to generate mouse mutants in vivo to model developmental defects and human diseases. Here we describe an optimized mammalian germ line transposition system active during early mouse spermatogenesis using the Minos transposon. Transposon-positive progeny carry on average more than 2 new transpositions, and 45 to 100% of the progeny carry an insertion in a gene. The optimized Minos-based system was tested in a small rapid dominant functional screen to identify mutated genes likely to cause measurable cardiovascular "disease" phenotypes in progeny/embryos. Importantly this system allows rapid screening for modifier genes.


G6PC2: a negative regulator of basal glucose-stimulated insulin secretion.
Elevated fasting blood glucose (FBG) is associated with increased risk for the development of type 2 diabetes and cardiovascular-associated mortality. Genome-wide association studies (GWAS) have linked polymorphisms in G6PC2 with variations in FBG and body fat, although not insulin sensitivity or glucose tolerance. G6PC2 encodes an islet-specific, endoplasmic reticulum-resident glucose-6-phosphatase catalytic subunit. A combination of in situ perfused pancreas, in vitro isolated islet, and in vivo analyses were used to explore the function of G6pc2 in mice. G6pc2 deletion had little effect on insulin sensitivity and glucose tolerance, whereas body fat was reduced in female G6pc2 knockout (KO) mice on both a chow and high-fat diet, observations that are all consistent with human GWAS data. G6pc2 deletion resulted in a leftward shift in the dose-response curve for glucose-stimulated insulin secretion (GSIS). As a consequence, under fasting conditions in which plasma insulin levels were identical, blood glucose levels were reduced in G6pc2 KO mice, again consistent with human GWAS data. Glucose-6-phosphatase activity was reduced, whereas basal cytoplasmic calcium levels were elevated in islets isolated from G6pc2 KO mice. These data suggest that G6pc2 represents a novel, negative regulator of basal GSIS that acts by hydrolyzing glucose-6-phosphate, thereby reducing glycolytic flux.


Porous Hydroxyapatite and Aluminium-Oxide Ceramic Orbital Implant Evaluation Using CBCT Scanning: A Method for In Vivo Porous Structure Evaluation and Monitoring.
Objective. This study aimed to define CBCT as a technique for postimplantation in vivo examination of porous hydroxyapatite and aluminium-oxide orbital implant shape, volume and density changes. Methods and Materials. CBCT was used to evaluate 30 enucleated patients treated with spherical polyglactin 910 wrapped hydroxyapatite and aluminum-oxide orbital implants. The mean duration of patient followup was 3.2 years or 1338 days with a range of 0.2 to 7.2 years or 79 to 2636 days in a population with an average age of 40.8 years. Results. The resolution of currently clinically used CBCT equipment allowed detailed structural observation of the orbital hydroxyapatite implants with some modifications. Volume and shape estimations were possible while density evaluation was more complicated compared to medical source computed tomography. The mean densities of the orbital implants were followed and a consistent gradual decrease identified from the beginning of implantation which was better defined after the applied correction procedure. Conclusion. CBCT with lower dosages of radiation exposure can be used to follow changes in implanted high-density porous structures. The density evaluation is possible with calibration modifications. Changes in orbital implant densities identified in this study may correspond to healing and maturation of soft tissues surrounding and penetrating the implants.


Clinical trial of common treatments for low back pain in family practice.
The results of a multicentered randomised clinical trial are reported of bed rest and of a physiotherapy and education programme for patients who presented in family practice with an acute episode of low back pain. No beneficial effect of either treatment was observed on several clinical outcome measures, including straight leg raising, lumbar flexion, activities of daily living, and pain. In fact the results favoured early mobilisation over bed rest and suggested that the physiotherapy and education programme was doing more harm than good. Moreover, additional analyses, which focused on clinically interesting patient subgroups, discovered no subset of patients who benefited from either of the treatments under study. Having failed to identify any clinically important benefits, or other explanations for these negative results, we can only conclude that family doctors have little reason to prescribe either bed rest or isometric exercises to patients who suffer from low back pain.


A gene's-eye view of sexual antagonism.
Females and males may face different selection pressures. Accordingly, alleles that confer a benefit for one sex often incur a cost for the other. Classic evolutionary theory holds that the X chromosome, whose sex-biased transmission sees it spending more time in females, should value females more than males, whereas autosomes, whose transmission is unbiased, should value both sexes equally. However, recent mathematical and empirical studies indicate that male-beneficial alleles may be more favoured by the X chromosome than by autosomes. Here we develop a gene's-eye-view approach that reconciles the classic view with these recent discordant results, by separating a gene's valuation of female versus male fitness from its ability to induce fitness effects in either sex. We use this framework to generate new comparative predictions for sexually antagonistic evolution in relation to dosage compensation, sex-specific mortality and assortative mating, revealing how molecular mechanisms, ecology and demography drive variation in masculinization versus feminization across the genome.


Nutritional supplementation in stable chronic obstructive pulmonary disease.
Low body weight in patients with chronic obstructive pulmonary disease (COPD) is associated with an impaired pulmonary status, reduced diaphragmatic mass, lower exercise capacity and higher mortality rate when compared to adequately nourished individuals with this disease. Nutritional support may therefore be a useful part of their comprehensive care. To conduct a systematic review of randomized controlled trials (RCTs) to clarify whether nutritional supplementation (caloric supplementation for at least 2 weeks) improved anthropometric measures, pulmonary function, respiratory muscle strength and functional exercise capacity in patients with stable COPD. Randomized controlled trials (RCTs) were identified from the Cochrane Airways Group register of RCTs, a hand-search of abstracts presented at international meetings and consultation with experts. Two reviewers independently selected trials for inclusion, assessed quality and extracted the data. Within each trial and for each outcome, we calculated an effect size. The effect sizes were then pooled by a random-effects model. Homogeneity among the effect sizes was also tested. From 272 references, nine RCTs were ultimately included. Six papers were considered as high quality and only two studies were double-blinded. For each of the outcomes studied, the effect of nutritional support was small: the 95% confidence intervals around the pooled effect sizes all included zero. The effect of nutritional support was homogeneous across studies. Nutritional support had no significant effect on anthropometric measures, lung function or exercise capacity in patients with stable COPD.


Improving care for people after stroke: how change was actively facilitated.
This paper aims to report on the approach to change used in the development of a tool to assess patient status six months after stroke (the Greater Manchester Stroke Assessment Tool: GM-SAT). The overall approach to change is based on the Promoting Action on Research Implementation in Health Services (PARiHS) Framework, which involves extensive stakeholder engagement before implementation. A key feature was the use of a facilitator without previous clinical experience. The active process of change involved a range of stakeholders--commissioners, patients and professionals--as well as review of published research evidence. The result of this process was the creation of the GM-SAT. The details of the decision processes within the tool included a range of perspectives; the process of localisation led commissioners to identify gaps in care provision as well as learning from others in terms of how services might be provided and organised. The facilitator role was key at all stages in bringing together the wide range of perspectives; the relatively neutral perceived status of the facilitator enabled resistance to change to be minimised. The output of this project, the GM-SAT, has the potential to significantly improve patients' physical, psychological and social outcomes and optimise their quality of life. This will be explored further in future phases of work. A structured process of change which included multiple stakeholder involvement throughout, localisation of approaches and a dedicated independent facilitator role was effective in achieving the development of a useful tool (GM-SAT).


Increase in salicylic Acid at the onset of systemic acquired resistance in cucumber.
In an effort to identify the signal compound that mediates systemic acquired resistance (SAR), changes in the content of phloem sap were monitored in cucumber plants inoculated with either tobacco necrosis virus or the fungal pathogen Colletotrichum lagenarium. The concentration of a fluorescent metabolite was observed to increase transiently after inoculation, with a peak reached before SAR was detected. The compound was purified and identified by gas chromatography-mass spectrometry as salicylic acid, a known exogenous inducer of resistance. The data suggest that salicylic acid could function as the endogenous signal in the transmission of SAR in cucumber.


Molecular DFT+U: A Transferable, Low-Cost Approach to Eliminate Delocalization Error.
While density functional theory (DFT) is widely applied for its combination of cost and accuracy, corrections (e.g., DFT+U) that improve it are often needed to tackle correlated transition-metal chemistry. In principle, the functional form of DFT+U, consisting of a set of localized atomic orbitals (AOs) and a quadratic energy penalty for deviation from integer occupations of those AOs, enables the recovery of the exact conditions of piecewise linearity and the derivative discontinuity. Nevertheless, for practical transition-metal complexes, where both atomic states and ligand orbitals participate in bonding, standard DFT+U can fail to eliminate delocalization error (DE). Here, we show that by introducing an alternative valence-state (i.e., molecular orbital or MO) basis to the DFT+U approach, we recover exact conditions in cases for which standard DFT+U corrections have no error-reducing effect. This MO-based DFT+U also eliminates DE where standard AO-based DFT+U is already successful. We demonstrate the transferability of our approach on representative transition-metal complexes with a range of ligand field strengths, electron configurations (i.e., from Sc to Zn), and spin states.


Penicillium Species Associated with Preharvest Wet Core Rot in South Africa and Their Pathogenicity on Apple.
Symptoms associated with the core region of apple fruits (Malus domestica) can be classified as moldy core (MC), wet core rot (WCR), and dry core rot (DCR). Infections leading to WCR are thought to occur primarily postharvest, although in South Africa preharvest symptoms also have been reported. The first aim of this study was to investigate the causative agent(s) of preharvest WCR by isolating fungi from eight internal positions in asymptomatic, MC, WCR, and DCR fruits. Secondly, the pathogenicity and virulence of all Penicillium isolates were investigated using three apple fruit inoculation methods: surface wounding, deep wounding, and nonwounding. Isolation of fungi from WCR fruits showed that Penicillium was the predominant fungal genus from most isolation positions including the lesion area. Penicillium ramulosum was the predominant species isolated from all fruits. However, in WCR fruits, the incidence (58%) of P. ramulosum was much higher than in MC (6%), DCR (7%), or asymptomatic (7%) fruits. Less frequently isolated Penicillium species included P. expansum and a few other species. Pathogenicity testing using the nonwounding method was best at discriminating highly virulent isolates. P. expansum was the most virulent species, followed by a putative new Penicillium species with closest sequence similarity to P. dendriticum. P. ramulosum isolates, although showing varying degrees of virulence, all had low virulence, causing only small lesions in wounded apple fruits.


Making the grade: assuring trustworthiness in evidence.
Despite evidence-based medicine's (EBM's) significant evolution and maturation from its revolutionary origins to its current form as the preeminent means of practicing medicine, there are still good reasons to be unsatisfied with EBM. This essay explores two important new developments in EBM: recently articulated accounts of the scientific basis of EBM, and the related writings of the GRADE Working Group to create standards for interpretation of the medical literature and evaluation of recommendations. A review of Karanicolas, Kunz, and Guyatt's (2008) three-step articulation of EBM's scientific basis demonstrates that the supposed soundness of each principle is not attributable to its scientific status; instead, the normative language of each principle highlights EBM's grounding in an only partially articulated philosophical framework. The GRADE Working Group's effort similarly relies on credibility, consensus, and trust in its defense and justification of EBM. These recent developments in EBM reveal that if the clinical research literature is to be informative or foundational to the enterprise of health care, much work needs to be done to secure its trustworthiness and integrity. An agenda for examining trust and trustworthiness in the context of health research is proposed.


Epithelial-mesenchymal conversion of dermatome progenitors requires neural tube-derived signals: characterization of the role of Neurotrophin-3.
Development of the somite-derived dermatome involves conversion of the epithelial dermatome progenitors into mesenchymal cells of the dermis. In chick embryos, neural tube-derived signals are required for this conversion, as the interposition of a membrane between neural tube and somites results in a failure of the dermatome to lose its epithelial arrangement. However, dermis formation can be completely rescued by coating the membranes with Neurotrophin-3, but not with the related molecule Nerve growth factor. Neurotrophin-3 was also found to be necessary for dermatome dissociation using in vitro explants or partially dissociated dermomyotomes. The functional relevance of these observations was investigated by neutralizing endogenous Neurotrophin-3 using a specific blocking antibody. Antibody-treated embryos revealed the presence of tightly aggregated cells between myotome and ectoderm instead of the loose dermal mesenchyme observed in embryos treated with control antibodies. As previous studies have demonstrated the presence of Neurotrophin-3 in the neural tube, these results suggest that it may be a necessary neural tube-derived signal required for early stages of dermis formation.


Prospective examination of objectively assessed physical activity and sedentary time after breast cancer treatment: sitting on the crest of the teachable moment.
This study prospectively examined patterns of objectively assessed sedentary time and moderate-to-vigorous physical activity (MVPA) during a 1-year period following completion of primary treatment among breast cancer survivors. The potential moderating effect of weight status on sedentary and MVPA time was also examined. Breast cancer survivors [n = 177; M(SD)age = 54.9 (11.1) years, 85% White/Caucasian; 82% stage I or II cancer; M(SD)time since treatment = 3.5 (2.4) months] who were recruited into a convenience sample had weight, height, and waist circumference measured and wore Actigraph GT3X accelerometers for 1 week every 3 months for 1 year. Data were analyzed using repeated measures ANOVA. Survivors spent nearly 78% of their day sedentary across all time points compared with less than 2% of their day engaged in MVPA. Sedentary time remained fairly stable over 12 months, whereas MVPA levels significantly decreased. Survivors with an overweight body mass index and unhealthy waist-to-height ratio engaged in significantly less MVPA than healthy weight survivors, with significant waist-to-height ratio moderator effects for both sedentary and MVPA. Sedentary time remains high in the first year following treatment for breast cancer, and MVPA decreases. These trends are more pronounced for survivors who are overweight, with stronger effects noted when waist-to-height ratio was examined compared with body mass index. These findings suggest that breast cancer survivors may be doing very little to improve their lifestyle behaviors following a cancer diagnosis and treatments.


Environmental factors promoting the effective use of a computer-assisted clinical case for second-year osteopathic medical students.
Computer-aided clinical cases (CACC) have the potential to complement and/or supplement other types of problem-based learning exercises in modern medical curricula. Deploying a CACC learning experience requires institutional commitment to technology and a belief by administration, faculty, and students that "climbing a steep growth curve" is worth the effort. Several aspects of the institutional environment at the Kirksville College of Osteopathic Medicine (KCOM) led to the development of the CACC exercise described in this article, including the need to design a uniform, supplemental, Internet-based learning experience and assessment exercises for students doing clinical rotations at off-site facilities. The CACC learning experience was enthusiastically accepted by second-year medical students as an integrative and clinically relevant educational experience. The success of this CACC exercise has helped to promote the development of other innovative applications of technology of medical education at KCOM.


Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes.
Influenza A virus is an important human pathogen causing significant morbidity and mortality every year and threatening the human population with epidemics and pandemics. Therefore, it is important to understand the biology of this virus to develop strategies to control its pathogenicity. Here, we demonstrate that influenza A virus inhibits macroautophagy, a cellular process known to be manipulated by diverse pathogens. Influenza A virus infection causes accumulation of autophagosomes by blocking their fusion with lysosomes, and one viral protein, matrix protein 2, is necessary and sufficient for this inhibition of autophagosome degradation. Macroautophagy inhibition by matrix protein 2 compromises survival of influenza virus-infected cells but does not influence viral replication. We propose that influenza A virus, which also encodes proapoptotic proteins, is able to determine the death of its host cell by inducing apoptosis and also by blocking macroautophagy.


Chromosomal Instability in Farmers Exposed to Pesticides: High Prevalence of Clonal and Non-Clonal Chromosomal Alterations.
An important economic activity in Colombia is agricultural production and farmers are frequently exposed to pesticides. Occupational exposure to pesticides is associated with an increased incidence of various diseases, including cancer, Parkinson's disease, Alzheimer's disease, reproductive disorders, and birth defects. However, although high genotoxicity is associated with these chemicals, information about the type and frequency of specific chromosomal alterations (CAs) and the level of chromosomal instability (CIN) induced by exposure to pesticides is scarce or absent. In this study, CAs and CIN were assessed in peripheral blood lymphocytes (PBLs) from five farmers occupationally exposed to pesticides and from five unexposed individuals using GTG-banding and molecular cytogenetic analysis. A significant increase in clonal and non-clonal chromosomal alterations was observed in pesticide-exposed individuals compared with unexposed individuals (510±12,2 vs 73±5,7, respectively; p<0.008). Among all CAs, monosomies and deletions were more frequently observed in the exposed group. Also, a high frequency of fragilities was observed in the exposed group. Together, these findings suggest that exposure to pesticides could be associated with CIN in PBLs and indicate the need for the establishment of educational programs on safety precautions when handling pesticides, such as wearing gloves, masks and boots, changing clothes and maintaining proper hygiene, among others. Further evaluation in other similar studies that include a greater number of individuals exposed to pesticides is necessary.


Mediterranean diet adherence and risk of incident kidney stones.
Diet plays an important role in kidney stone formation. Several individual components have been associated with the risk of kidney stone formation, but there is limited evidence regarding the role of healthful dietary patterns. To prospectively study the association between adherence to the Mediterranean diet and the risk of incident kidney stones. We conducted a longitudinal study using 3 different cohorts: the Health Professionals Follow-up Study (n = 42,902 men), the Nurses' Health Study I (n = 59,994 women), and the Nurses' Health Study II (n = 90,631 women). We assessed diet every 4 y using an FFQ and calculated adherence to a Mediterranean diet using the alternate Mediterranean diet score (aMED). A subgroup of 6077 participants provided ≥1 24-h urine sample, and urinary solute excretion was analyzed. We used Cox proportional hazards regression to examine the independent association between the aMED and incidence of kidney stones, adjusting for potential confounders. We used adjusted linear regression models to study the relation between aMED and urine composition. During 3,316,633 person-years of follow-up, 6576 cases of incident kidney stones were identified. For participants in the highest aMED score category, the risk of developing a kidney stone was between 13% and 41% lower compared with participants in the lowest score (pooled HR: 0.72, 95% CI: 0.59, 0.87; P value for trend <0.001). A higher aMED score was associated with higher urinary citrate, magnesium, oxalate, phosphate, uric acid, volume, and pH, and lower urinary sodium, resulting in lower supersaturation for calcium oxalate, calcium phosphate, and uric acid. Adherence to a Mediterranean diet is associated with a lower risk of developing a kidney stone.


Enhanced photoinduced chi((2)) in gamma-ray-irradiated bulk glass.
Gamma-ray-irradiated light-flint silicate bulk glass (Schott Glass LF5), which contains a large amount of lead oxide, displays enhanced photoinduced quasi-phase-matched second-harmonic generation (PSHG), whereas nonirradiated glass under the same experimental conditions does not generate this nonlinear effect. The dependence of the efficiency of PSHG on the amount of gamma radiation (up to 530 krad) is experimentally studied, as is the role of thermal recovery (bleaching) of the color centers as a result of seeding with the second harmonic. The effect of long-term fading is studied with a sample that was irradiated 8 years ago. Gamma irradiation of boron-crown silicate glass (BK7) does not show this enhancement.


Genome sequence-based species delimitation with confidence intervals and improved distance functions.
For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept. Correlation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions. Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms.


Post-mortem virtual estimation of free abdominal blood volume.
The purpose of this retrospective study was to examine the reliability of virtually estimated abdominal blood volume using segmentation from postmortem computed tomography (PMCT) data. Twenty-one cases with free abdominal blood were investigated by PMCT and autopsy. The volume of the blood was estimated using a manual segmentation technique (Amira, Visage Imaging, Germany) and the results were compared to autopsy data. Six of 21 cases had undergone additional post-mortem computed tomographic angiography (PMCTA). The virtually estimated abdominal blood volumes did not differ significantly from those measured at autopsy. Additional PMCTA did not bias data significantly. Virtual estimation of abdominal blood volume is a reliable technique. The virtual blood volume estimation is a useful tool to deliver additional information in cases where autopsy is not performed or in cases where a postmortem angiography is performed.


Cell adhesion peptide modification of gold-coated polyurethanes for vascular endothelial cell adhesion.
Gold-coated polyurethanes were chemisorbed with three cell-adhesion peptides having an N-terminal cysteine: cys-arg-gly-asp (CRGD), cys-arg-glu-asp-val (CREDV), and the cyclic peptide cys-cys-arg-arg-gly-asp-try-leu-cys (CCRRGDWLC). The peptides were selected based on their presumed preferential interactions with the cell-surface integrins on vascular endothelial cells. The ability of the surfaces to support the preferential adhesion of human vascular endothelial cells was studied by comparing in vitro adhesion results for these cells with those from mouse 3T3 fibroblasts. Surface modification with the peptides was confirmed by water-contact angles and XPS. Surface morphology was determined by AFM and SEM. In vitro cell-culture studies in conjunction with plasma-protein adsorption and immunoblotting were performed on the various modified surfaces. The data suggest that peptide-modified surfaces have significant potential for supporting cell adhesion. Little or no cell adhesion was noted on gold- or cysteine-modified control surfaces. Human vascular endothelial cells showed the greatest adhesion to the CCRRGDWLC-modified surfaces, and the 3T3 fibroblasts adhered best to the CREDV-modified surfaces. Protein adsorption studies suggest that the preferential adsorption of the cell-adhesive proteins fibronectin and vitronectin is not likely mediating the differences noted. It is concluded that the cell-adhesive peptide-modified gold-coated polymers have significant potential for further development both as model substrates for fundamental studies and for use in biomaterials applications.


A Review of the Molecular Mechanisms Underlying the Development and Progression of Cardiac Remodeling.
Pathological molecular mechanisms involved in myocardial remodeling contribute to alter the existing structure of the heart, leading to cardiac dysfunction. Among the complex signaling network that characterizes myocardial remodeling, the distinct processes are myocyte loss, cardiac hypertrophy, alteration of extracellular matrix homeostasis, fibrosis, defective autophagy, metabolic abnormalities, and mitochondrial dysfunction. Several pathophysiological stimuli, such as pressure and volume overload, trigger the remodeling cascade, a process that initially confers protection to the heart as a compensatory mechanism. Yet chronic inflammation after myocardial infarction also leads to cardiac remodeling that, when prolonged, leads to heart failure progression. Here, we review the molecular pathways involved in cardiac remodeling, with particular emphasis on those associated with myocardial infarction. A better understanding of cell signaling involved in cardiac remodeling may support the development of new therapeutic strategies towards the treatment of heart failure and reduction of cardiac complications. We will also discuss data derived from gene therapy approaches for modulating key mediators of cardiac remodeling.


The posterior medial blind spot of the distal tibia: implications for surgical fixation.
The distal tibial blind spot represents an area where improperly measured long screws may pose a risk to surrounding anatomic structures and is not well visualized on AP, mortise, and lateral radiographs. Awareness of this area as well as the use of a 45° external rotation oblique view when placing fixation in this area may prevent iatrogenic injury. Level V, Expert Opinion.


Diffusion-weighted imaging in stroke attributable to internal carotid artery dissection: the significance of vessel patency.
In stroke attributable to spontaneous dissection of the internal carotid artery (sICAD), arterial patency may influence the pattern and extent of cerebral ischemia. In 40 consecutive patients with stroke caused by sICAD, we compared the number, size and pattern of cerebral diffusion-weighted imaging lesions between patients with stenotic sICAD (n=15) and occlusive sICAD (n=25). Patients with stenotic sICAD had more ischemic lesions (median 5, interquartile range 1 to 10) than patients with occlusive sICAD (2, 1 to 3; P=0.014). Lesion diameters were larger in occlusive sICAD (62, 50 to 99 mm) than in stenotic sICAD (25, 10 to 50 mm; P=0.007). Border-zone infarction occurred only in stenotic sICAD (7/15, 47%). Most patients with occlusive sICAD had territorial infarcts (22/25, 88%). In stroke attributable to sICAD, diffusion-weighted imaging characteristics may be influenced by the patency of the carotid artery. Differences in the pathogenesis of cerebral ischemia might exist between patients with stenotic and those with occlusive sICAD.


Medicinal chemistry optimization of antiplasmodial imidazopyridazine hits from high throughput screening of a SoftFocus kinase library: part 1.
A novel class of imidazopyridazines identified from whole cell screening of a SoftFocus kinase library was synthesized and evaluated for antiplasmodial activity against K1 (multidrug resistant strain) and NF54 (sensitive strain). Structure-activity relationship studies led to the identification of highly potent compounds against both strains. Compound 35 was highly active (IC50: K1 = 6.3 nM, NF54 = 7.3 nM) and comparable in potency to artesunate, and 35 exhibited 98% activity in the in vivo P. berghei mouse model (4-day test by Peters) at 4 × 50 mg/kg po. Compound 35 was also assessed against P. falciparum in the in vivo SCID mouse model where the efficacy was found to be more consistent with the in vitro activity. Furthermore, 35 displayed high (78%) rat oral bioavailability with good oral exposure and plasma half-life. Mice exposure at the same dose was 10-fold lower than in rat, suggesting lower oral absorption and/or higher metabolic clearance in mice.


The effect of melatonin in patients with fibromyalgia: a pilot study.
The aim of the study was to determine the possible effect of melatonin treatment on disturbed sleep, fatigue and pain symptoms observed in fibromyalgia (FM) patients. Twenty-one consecutive patients with FM were included in an open 4-week-duration pilot study. Before and after treatment with melatonin 3 mg at bedtime, patients were evaluated using tender point count by palpation of 18 classic anatomical regions, pain score in four predesignated areas, pain severity on a 10 cm visual analogue scale (VAS), sleep disturbances, fatigue, depression, anxiety, and patient and physician global assessments, also by a VAS. Urine 6-sulphatoxymelatonin levels (aMT-6S) were measured in the patients and 20 age- and sex-matched controls. Nineteen patients completed the study. One patient withdrew because of migraine and another was lost to follow-up. At day 30, median values for the tender point count and severity of pain at selected points, patient and physician global assessments and VAS for sleep significantly improved with melatonin treatment. Other variables improved but did not reach statistical significance. Adverse events were mild and transient. Lower levels of aMT-6S were found in FM patients compared with normal median controls (+/-SD, 9.16 +/- 7.9 microg/24 h vs 16.8 +/- 12.8 microg/24 h) (p = 0.06). Although this is an open study, our preliminary results suggest that melatonin can be an alternative and safe treatment for patients with FM. Double-blind placebo controlled studies are needed.


Habitat productivity constrains the distribution of social spiders across continents - case study of the genus Stegodyphus.
Sociality has evolved independently multiple times across the spider phylogeny, and despite wide taxonomic and geographical breadth the social species are characterized by a common geographical constrain to tropical and subtropical areas. Here we investigate the environmental factors that drive macro-ecological patterns in social and solitary species in a genus that shows a Mediterranean-Afro-Oriental distribution (Stegodyphus). Both selected drivers (productivity and seasonality) may affect the abundance of potential prey insects, but seasonality may further directly affect survival due to mortality caused by extreme climatic events. Based on a comprehensive dataset including information about the distribution of three independently derived social species and 13 solitary congeners we tested the hypotheses that the distribution of social Stegodyphus species relative to solitary congeners is: (1) restricted to habitats of high vegetation productivity and (2) constrained to areas with a stable climate (low precipitation seasonality). Using spatial logistic regression modelling and information-theoretic model selection, we show that social species occur at higher vegetation productivity than solitary, while precipitation seasonality received limited support as a predictor of social spider occurrence. An analysis of insect biomass data across the Stegodyphus distribution range confirmed that vegetation productivity is positively correlated to potential insect prey biomass. Habitat productivity constrains the distribution of social spiders across continents compared to their solitary congeners, with group-living in spiders being restricted to areas with relatively high vegetation productivity and insect prey biomass. As known for other taxa, permanent sociality likely evolves in response to high predation pressure and imposes within-group competition for resources. Our results suggest that group living is contingent upon productive environmental conditions where elevated prey abundance meet the increased demand for food of social groups.


Background frequencies for residue variability estimates: BLOSUM revisited.
Shannon entropy applied to columns of multiple sequence alignments as a score of residue conservation has proven one of the most fruitful ideas in bioinformatics. This straightforward and intuitively appealing measure clearly shows the regions of a protein under increased evolutionary pressure, highlighting their functional importance. The inability of the column entropy to differentiate between residue types, however, limits its resolution power. In this work we suggest generalizing Shannon's expression to a function with similar mathematical properties, that, at the same time, includes observed propensities of residue types to mutate to each other. To do that, we revisit the original construction of BLOSUM matrices, and re-interpret them as mutation probability matrices. These probabilities are then used as background frequencies in the revised residue conservation measure. We show that joint entropy with BLOSUM-proportional probabilities as a reference distribution enables detection of protein functional sites comparable in quality to a time-costly maximum-likelihood evolution simulation method (rate4site), and offers greater resolution than the Shannon entropy alone, in particular in the cases when the available sequences are of narrow evolutionary scope.


Biomarker of exposure level data set in smokers switching from conventional cigarettes to Tobacco Heating System 2.2, continuing smoking or abstaining from smoking for 5 days.
Levels of biomarkers of exposure to selected harmful and potentially harmful smoke constituents found in cigarette smoke, in addition to nicotine were measured in 160 smokers randomized for 5 days to continuing smoking conventional cigarettes (41 participants), switching to Tobacco Heating System 2.2 (THS 2.2) (80 participants), or abstaining from smoking (39 participants). The data reported here are descriptive statistics of the levels of each biomarker of exposure expressed as concentrations adjusted to creatinine; at baseline, and at the end of the study, and their relative change from baseline. Reductions in the levels of biomarkers of exposure when expressed as quantity excreted, are also reported. Detailed descriptions of bioanalytical assays used are also provided. The data presented here are related to the article entitled "Evaluation of the Tobacco Heating System 2.2. Part 8: 5-Day randomized reduced exposure clinical study in Poland" (Haziza et al., 2016) [1].


Depression can be prevented by astaxanthin through inhibition of hippocampal inflammation in diabetic mice.
The critical factor considered in a depression induced by diabetes is the inflammation eliciting hippocampal, amygdala and thalamic neuronal injury. Therefore, inhibiting inflammatory reactions in the brain and reducing neuronal injury can alleviate depression in rodents suffering from diabetes mellitus. The oral administration of astaxanthin has been employed in emotional disorders and diabetic complications due to its anti-depressant, anti-inflammatory and anti-apoptotic functions. However, it has not been reported whether astaxanthin can improve diabetes-related depression-like behavior, and its potential mechanisms have not been elucidated. The objective of the present study is to elucidate the effect of astaxanthin on depression in diabetic mice and to understand the underlying molecular mechanisms. In this study, experimental diabetic mice were given a single intraperitoneal injection of streptozotocin (STZ, 150mg/kg, dissolved in citrate buffer) after fasting for 12h. The diabetic model was assessed 72h after STZ injection, and mice with a fasting blood glucose level more than or equal to 16.7mmol/L were used in this study, and oral astaxanthin (25mg/kg) was provided uninterrupted for ten weeks. Depression-like behavior was evaluated by the tail suspension test (TST) and forced swimming test (FST). The glial fibrillary acidic protein (GFAP) and cleaved caspase-3-positive cells were measured by immunohistochemistry, and the western blotting was used to test the protein levels of interleukin-6 (IL-6), interleukin-1β (IL-1β) and cyclooxygenase (COX-2). The results showed that astaxanthin had an anti-depressant effect on diabetic mice. Furthermore, we observed that astaxanthin significantly reduced the number of GFAP-positive cells in the hippocampus and hypothalamus, and also the expression of cleaved caspase-3 in the hippocampus, amygdala and hypothalamus was decreased as well. Moreover, astaxanthin could down-regulate the expression of IL-6, IL-1β and COX-2 in the hippocampus. These findings suggest that the mechanism of astaxanthin in preventing depression in diabetic mice involves the inhibition of inflammation/inflammation inhibition, thereby protecting neurons in hippocampus, amygdala and hypothalamus against hyperglycemic damage.


Electronic and optical properties of nanocrystalline WO₃ thin films studied by optical spectroscopy and density functional calculations.
The optical and electronic properties of nanocrystalline WO3 thin films prepared by reactive dc magnetron sputtering at different total pressures (Ptot) were studied by optical spectroscopy and density functional theory (DFT) calculations. Monoclinic films prepared at low Ptot show absorption in the near infrared due to polarons, which is attributed to a strained film structure. Analysis of the optical data yields band-gap energies Eg ≈ 3.1 eV, which increase with increasing Ptot by 0.1 eV, and correlate with the structural modifications of the films. The electronic structures of triclinic δ-WO3, and monoclinic γ- and ε-WO3 were calculated using the Green function with screened Coulomb interaction (GW approach), and the local density approximation. The δ-WO3 and γ-WO3 phases are found to have very similar electronic properties, with weak dispersion of the valence and conduction bands, consistent with a direct band-gap. Analysis of the joint density of states shows that the optical absorption around the band edge is composed of contributions from forbidden transitions (>3 eV) and allowed transitions (>3.8 eV). The calculations show that Eg in ε-WO3 is higher than in the δ-WO3 and γ-WO3 phases, which provides an explanation for the Ptot dependence of the optical data.


"Have no regrets:" Parents' experiences and developmental tasks in pregnancy with a lethal fetal diagnosis.
Lethal fetal diagnoses are made in 2% of all pregnancies. The pregnancy experience is certainly changed for the parents who choose to continue the pregnancy with a known fetal diagnosis but little is known about how the psychological and developmental processes are altered. This longitudinal phenomenological study of 16 mothers and 14 fathers/partners sought to learn the experiences and developmental needs of parents who continue their pregnancy despite the lethal diagnosis. The study was guided by Merleau-Ponty's philosophic view of embodiment. Interviews (N = 90) were conducted with mothers and fathers over time, from mid-pregnancy until 2-3 months post birth. Data analysis was iterative, through a minimum of two cycles of coding, theme identification, within- and cross-case analysis, and the writing of results. Despite individual differences, parents were quite consistent in sharing that their overall goal was to "Have no regrets" when all was said and done. Five stages of pregnancy were identified: Pre-diagnosis, Learning Diagnosis, Living with Diagnosis, Birth & Death, and Post Death. Developmental tasks of pregnancy that emerged were 1) Navigating Relationships, 2) Comprehending Implication of the Condition, 3) Revising Goals of Pregnancy, 4) Making the Most of Time with Baby, 5) Preparing for Birth and Inevitable Death, 6) Advocating for Baby with Integrity, and 7) Adjusting to Life in Absence of Baby. Prognostic certainty was found to be highly influential in parents' progression through developmental tasks. The framework of parents' pregnancy experiences with lethal fetal diagnosis that emerged can serve as a useful guide for providers who care for families, especially in perinatal palliative care. Providing patient-centered care that is matched to the stage and developmental tasks of these families may lead to improved care and greater parent satisfaction.


Society for Academic Continuing Medical Education Intervention Guideline Series: Guideline 2, Practice Facilitation.
The Society for Academic Continuing Medical Education commissioned a study to clarify and, if possible, standardize the terminology for a set of important educational interventions. In the form of a guideline, this article describes one such intervention, practice facilitation, which is a common strategy in primary care to help practices develop capacity and infrastructure to support their ability to improve patient care. Based on a review of recent evidence and a facilitated discussion with US and Canadian experts, we describe practice facilitation, its terminology, and other important information about the intervention. We encourage leaders and researchers to consider and build on this guideline as they plan, implement, evaluate, and report practice facilitation efforts. Clear and consistent use of terminology is imperative, along with complete and accurate descriptions of interventions, to improve the use and study of practice facilitation.


Risk factors, treatment and prognosis in men and women with heart failure with and without diabetes.
To test the hypothesis that risk factor pattern, treatment and prognosis differ between men and women with heart failure (HF) with and without diabetes in the Swedish Heart Failure Registry. Patients with (n=8809) and without (n=27 465) type 2 diabetes (T2DM) included in the Swedish Heart Failure Registry (2003-2011) were followed for mortality during a median follow-up of 1.9 years (range 0-8.7 years). All-cause mortality, differences in background and HF characteristics were analysed in women and men with and without T2DM and with a special regard to different age groups. Of 36 274 patients, 24% had T2DM and 39% were women. In patients with T2DM, women were older than men (78 years vs 73 years), more frequently had hypertension, renal dysfunction and preserved ventricular function. Regardless of T2DM status, women with reduced ventricular function, compared with their male counterparts, were less frequently offered, for example, ACE inhibitors/angiotensin receptor II blockers (ARB). Absolute mortality was 48% in women with T2DM, 40% in women without; corresponding male mortality rates were 43% and 35%, respectively. Kaplan-Meier curves revealed shorter longevity in women with T2DM but female sex did not remain a significant mortality predictor following adjustment (OR 95% CI 0.90; 0.79 to 1.03). In those without T2DM, women compared with men lived longer; this pattern remained after adjustment (OR 0.72; 0.66 to 0.78). T2DM was a stronger predictor of mortality in women (OR 1.72; 1.53 to 1.94) than in men (OR 1.47; 1.34 to 1.61). T2DM is a strong mortality predictor in men and women with HF, somewhat stronger in women. The shorter survival time in women with T2DM and HF related to comorbidities rather than sex per se. Evidence-based management was less prevalent in women. Mechanisms behind these findings remain incompletely understood and need further attention.


Wnt/PCP signaling controls intracellular position of MTOCs during gastrulation convergence and extension movements.
During vertebrate gastrulation, convergence and extension cell movements are coordinated with the anteroposterior and mediolateral embryonic axes. Wnt planar cell polarity (Wnt/PCP) signaling polarizes the motile behaviors of cells with respect to the anteroposterior embryonic axis. Understanding how Wnt/PCP signaling mediates convergence and extension (C&E) movements requires analysis of the mechanisms employed to alter cell morphology and behavior with respect to embryonic polarity. Here, we examine the interactions between the microtubule cytoskeleton and Wnt/PCP signaling during zebrafish gastrulation. First, we assessed the location of the centrosome/microtubule organizing center (MTOC) relative to the cell nucleus and the body axes, as a marker of cell polarity. The intracellular position of MTOCs was polarized, perpendicular to the plane of the germ layers, independently of Wnt/PCP signaling. In addition, this position became biased posteriorly and medially within the plane of the germ layers at the transition from mid- to late gastrulation and from slow to fast C&E movements. This depends on intact Wnt/PCP signaling through Knypek (Glypican4/6) and Dishevelled components. Second, we tested whether microtubules are required for planar cell polarization. Once the planar cell polarity is established, microtubules are not required for accumulation of Prickle at the anterior cell edge. However, microtubules are needed for cell-cell contacts and initiation of its anterior localization. Reciprocal interactions occur between Wnt/PCP signaling and microtubule cytoskeleton during C&E gastrulation movements. Wnt/PCP signaling influences the polarity of the microtubule cytoskeleton and, conversely, microtubules are required for the asymmetric distribution of Wnt/PCP pathway components.


A model-based approach to capture genetic variation for future association studies.
Genome-wide association studies are still constrained by the cost of genotyping. For this reason, the selection of a reduced set of markers or tags able to capture a significant proportion of the genetic variation is an important aspect of these studies. Most tagging SNP selection methods have been successful in capturing the genetic variation of the data from which the tags have been chosen. However, when these tags are used in an independent data set, a significant proportion of the remaining SNPs (non-tags) are not captured and, in most cases, there is no information on which SNPs are captured. We propose to use a probabilistic model to predict the non-tags based on a set of tags, as a way to capture genetic variation. An important advantage of this method is that it directly predicts the genotype of the non-tags with which we can test for association with the phenotype and which could help to elucidate the location of genes responsible for increasing disease susceptibility. Additionally, this method provides an estimate of the probabilities with which the predictions are made, which reflects the confidence of the probabilistic model. We also propose new methods to select the tagging SNPs. We empirically show by using HapMap data that our approach is able to capture significantly more genetic variation than methods based solely on a pairwise LD measure.


An ethnographic study of physiotherapists' perceptions of their interactions with patients on a chronic pain unit.
Changes in health care brought about by the increased incidence of chronic conditions have resulted in an increased focus on patient self-directed care. This ethnographic study explores from the therapists' perspectives how therapist/patient interactions influence success or contribute to meeting the patients' goals on a pain management program. A team of physiotherapists were observed individually with their patients over a period of 6 months. Their interactions were audiotaped, transcribed, analysed, and cross-referenced to the field notes and the follow-up interviews with the therapists after each observation. The analysis was iterative, guided by questions and contextualised. Codes, categories, and evolving patterns of behaviour were documented, and three major themes were identified. The therapist/patient interactions demonstrated certain consistent standpoints toward the purpose of the program. The team judged those who achieved positive outcomes, as having entered into interactions typified by assertiveness, negotiation, and critical reflection. However, even the most able team of therapists will not be able to create a collaborative framework unless their patients are willing to grasp the opportunity offered to them, and they judged their least successful patients as having adopted unwilling and unrealistic interactions. Interactions of resistance or an inability to carry over problem solving skills into their lives resulted in a negative outcome for the patients and a stunting of the team's potential.


Phase transition from a gel to a fluid phase of cubic symmetry in dimyristoylphosphatidylcholine/myristic acid (1:2, mol/mol) bilayers.
Aqueous dispersions (pH 4.0) of a 2:1 (mol/mol) mixture of myristic acid with dimyristoylphosphatidylcholine undergo a sharp transition at 45-47 degrees C from a lamellar gel phase to a fluid phase which is optically isotropic. This fluid phase gives rise to 31P-NMR spectra, and 2H-NMR spectra of the chain-deuterated components, which are also isotropic. X-ray diffraction studies of the fluid phase at 49 degrees C, reveal reflections with spacings in the ratio square root of 2: (square root of 3): square root of 4: square root of 6: square root of 8, accompanied by a strong diffuse scatter. These reflections index on a cubic lattice of primitive space group Pn3 or Pn3m, or possibly the body-centered group Im3m, with a lattice constant of 21.2 nm. The dimensions of the phase are consistent with a structure composed of two systems of tetrahedrally (octahedrally) oriented inverted lipid cylinders, found for other cubic lipid phases with Pn3m (Im3m) symmetry. At higher temperatures the cubic phase gradually converts, with increasing temperature, to a coexisting inverted hexagonal phase.


In situ hybridization of human immunodeficiency virus (HTLV-III) in cryostat sections of lymph nodes of lymphadenopathy syndrome patients.
The presence of human immunodeficiency virus (HIV, or HTLV-III) genome sequence was investigated by means of in situ hybridization in cryostat sections of lymph nodes from lymphadenopathy syndrome (LAS) patients. The technique employed involved the modification of the DNA probe by chemical insertion of an antigenic sulfone group in cytosine moieties and the visualization of DNA by a double-antibody immunohistochemical reaction. The hybrid formation was revealed in five out of ten cases: in all positive samples, HIV was mainly observed in the cytoplasm of lymph node cells. The method of in situ hybridization described in the present paper is specific and has some advantages if compared with other techniques based on the use of DNA probes labelled with radioisotopes or biotin by nick translation.


Inverted human umbilical arteries with tunable wall thicknesses for nerve regeneration.
Tubular nerve guides have shown a potential to bridge nerve defects, by directing neuronal elongation, localizing growth factors, and inhibiting fibrotic cellular ingrowth. These investigations describe a novel acellular scaffold derived from the human umbilical cord artery that aims to enhance nerve regeneration by presenting a unique mechanical and chemical environment to the damaged nerve ends. A rapid, semiautomated dissection technique is described that isolates the human umbilical artery (HUA) from the umbilical cord, after which the vessel is decellularized using sodium dodecyl sulfate (SDS). The artery is turned inside out to produce a 3D scaffold, that unlike previous vessels for nerve repair, is more resistant to collapse. The scaffold has the potential as either an acellular bridge-implant, or for in vitro nerve regeneration. Stress-strain relationships and suture retention were assessed to determine whether the material had similar mechanical properties to native nerves. A dual process-flow perfusion bioreactor was developed to assess glucose mass transfer, and to investigate the culture of neuronal-like PC12 cells within the scaffold. These investigations have shown the automated dissecting method yields a smooth tubular scaffold, where wall thickness can be tuned to alter the mechanical behavior of the scaffold. Inverting the scaffold prevents collapse, with the decellularized iHUA having comparable mechanical properties to native nerves. Bioreactor cultures with PC12 cells seeded within iHUA lumenal void were shown to adhere and migrate into the preexisting ECM after 11 days of culture. These investigations show the potential of the iHUA as a unique 3D scaffold that may enhance nerve regeneration.


Flap endonuclease overexpression drives genome instability and DNA damage hypersensitivity in a PCNA-dependent manner.
Overexpression of the flap endonuclease FEN1 has been observed in a variety of cancer types and is a marker for poor prognosis. To better understand the cellular consequences of FEN1 overexpression we utilized a model of its Saccharomyces cerevisiae homolog, RAD27. In this system, we discovered that flap endonuclease overexpression impedes replication fork progression and leads to an accumulation of cells in mid-S phase. This was accompanied by increased phosphorylation of the checkpoint kinase Rad53 and histone H2A-S129. RAD27 overexpressing cells were hypersensitive to treatment with DNA damaging agents, and defective in ubiquitinating the replication clamp proliferating cell nuclear antigen (PCNA) at lysine 164. These effects were reversed when the interaction between overexpressed Rad27 and PCNA was ablated, suggesting that the observed phenotypes were linked to problems in DNA replication. RAD27 overexpressing cells also exhibited an unexpected dependence on the SUMO ligases SIZ1 and MMS21 for viability. Importantly, we found that overexpression of FEN1 in human cells also led to phosphorylation of CHK1, CHK2, RPA32 and histone H2AX, all markers of genome instability. Our data indicate that flap endonuclease overexpression is a driver of genome instability in yeast and human cells that impairs DNA replication in a manner dependent on its interaction with PCNA.


Studies using English administrative data (Hospital Episode Statistics) to assess health-care outcomes--systematic review and recommendations for reporting.
Studies using English administrative data from the Hospital Episode Statistics (HES) are increasingly used for the assessment of health-care quality. This study aims to catalogue the published body of studies using HES data to assess health-care outcomes, to assess their methodological qualities and to determine if reporting recommendations can be formulated. Systematic searches of the EMBASE, Medline and Cochrane databases were performed using defined search terms. Included studies were those that described the use of HES data extracts to assess health-care outcomes. A total of 148 studies were included. The majority of published studies were on surgical specialties (60.8%), and the most common analytic theme was of inequalities and variations in treatment or outcome (27%). The volume of published studies has increased with time (r = 0.82, P < 0.0001), as has the length of study period (r = 0.76, P < 0.001) and the number of outcomes assessed per study (r = 0.72, P = 0.0023). Age (80%) and gender (57.4%) were the most commonly used factors in risk adjustment, and regression modelling was used most commonly (65.2%) to adjust for confounders. Generic methodologic data were better reported than those specific to HES data extraction. For the majority of parameters, there were no improvements with time. Studies published using HES data to report health-care outcomes have increased in volume, scope and complexity with time. However, persisting deficiencies related to both generic and context-specific reporting have been identified. Recommendations have been made to improve these aspects as it is likely that the role of these studies in assessing health care, benchmarking practice and planning service delivery will continue to increase.


Associations Between Global Mental Health and Response to an App-Based Meditation Intervention in Myeloproliferative Neoplasm Patients.
Background: Depression, anxiety, and sleep disturbance are common problems that greatly affect quality of life for many myeloproliferative neoplasm (MPN) patients. App-based mindfulness meditation is a feasible nonpharmacologic approach for managing symptoms. However, previous research has not considered how patients' overall mental health may influence their responsiveness to these interventions. Objective: The purpose of this study was to conduct an exploratory, secondary analysis of the effects of a smartphone meditation app, Calm, on depression, anxiety, and sleep disturbance in MPN patients based on patients' baseline levels of Global Mental Health (GMH). Methods: Participants (N = 80) were a subset of MPN patients from a larger feasibility study. Patients were enrolled into an intervention (use Calm for 10 minutes daily for 4 weeks) or educational control group. Results: In multilevel models, there were significant 3-way interactions between time, group, and baseline GMH for depression and anxiety symptoms, with participants in the meditation intervention who reported the poorest baseline GMH experiencing the greatest reduction in symptoms over time. For both intervention and control participants, poorer initial GMH was associated with increases in sleep disturbance symptoms over time. Conclusions: Mindfulness meditation apps, such as Calm, may be effective in reducing depression and anxiety symptoms in MPN patients, particularly for those experiencing mental health difficulties. Given the need for accessible tools to self-manage chronic cancer-related symptoms, especially strong negative emotions, these findings warrant larger efficacy studies to determine the effects of app-based meditation for alleviating depression and anxiety in cancer populations.


Mammalian CSAD and GADL1 have distinct biochemical properties and patterns of brain expression.
Variants in the gene encoding the enzyme glutamic acid decarboxylase like 1 (GADL1) have been associated with response to lithium therapy. Both GADL1 and the related enzyme cysteine sulfinic acid decarboxylase (CSAD) have been proposed to be involved in the pyridoxal-5'-phosphate (PLP)-dependent biosynthesis of taurine. In the present study, we compared the catalytic properties, inhibitor sensitivity and expression profiles of GADL1 and CSAD in brain tissue. In mouse and human brain we observed distinct patterns of expression of the PLP-dependent decarboxylases CSAD, GADL1 and glutamic acid decarboxylase 67 (GAD67). CSAD levels were highest during prenatal and early postnatal development; GADL1 peaked early in prenatal development, while GAD67 increased rapidly after birth. Both CSAD and GADL1 are being expressed in neurons, whereas only CSAD mRNA was detected in astrocytes. Cysteine sulfinic acid was the preferred substrate for both mouse CSAD and GADL1, although both enzymes also decarboxylated cysteic acid and aspartate. In silico screening and molecular docking using the crystal structure of CSAD and in vitro assays led to the discovery of eight new enzyme inhibitors with partial selectivity for either CSAD or GADL1. Lithium had minimal effect on their enzyme activities. In conclusion, taurine biosynthesis in vertebrates involves two structurally related PLP-dependent decarboxylases (CSAD and GADL1) that have partially overlapping catalytic properties but different tissue distribution, indicating divergent physiological roles. Development of selective enzyme inhibitors targeting these enzymes is important to further dissect their (patho)physiological roles.


Memory and mental time travel in humans and social robots.
From neuroscience, brain imaging and the psychology of memory, we are beginning to assemble an integrated theory of the brain subsystems and pathways that allow the compression, storage and reconstruction of memories for past events and their use in contextualizing the present and reasoning about the future-mental time travel (MTT). Using computational models, embedded in humanoid robots, we are seeking to test the sufficiency of this theoretical account and to evaluate the usefulness of brain-inspired memory systems for social robots. In this contribution, we describe the use of machine learning techniques-Gaussian process latent variable models-to build a multimodal memory system for the iCub humanoid robot and summarize results of the deployment of this system for human-robot interaction. We also outline the further steps required to create a more complete robotic implementation of human-like autobiographical memory and MTT. We propose that generative memory models, such as those that form the core of our robot memory system, can provide a solution to the symbol grounding problem in embodied artificial intelligence. This article is part of the theme issue 'From social brains to social robots: applying neurocognitive insights to human-robot interaction'.


Notch signaling induces cell cycle arrest in small cell lung cancer cells.
Among the various forms of human lung cancer, small cell lung cancer (SCLC) exhibits a characteristic neuroendocrine (NE) phenotype. Neural and NE differentiation in SCLC depend, in part, on the action of the basic-helix-loop-helix (bHLH) transcription factor human achaete-scute homologue-1 (hASH1). In nervous system development, the Notch signaling pathway is a critical negative regulator of bHLH factors, including hASH1, controlling cell fate commitment and differentiation. To characterize Notch pathway function in SCLC, we explored the consequences of constitutively active Notch signaling in cultured SCLC cells. Recombinant adenoviruses were used to overexpress active forms of Notch1, Notch2, or the Notch effector protein human hairy enhancer of split-1 (HES1) in DMS53 and NCI-H209 SCLC cells. Notch proteins, but not HES1 or control adenoviruses, caused a profound growth arrest, associated with a G1 cell cycle block. We found up-regulation of p21(waf1/cip1) and p27kip1 in concert with the cell cycle changes. Active Notch proteins also led to dramatic reduction in hASH1 expression, as well as marked activation of phosphorylated extracellular signal-regulated kinase (ERK)1 and ERK2, findings that have been shown to be associated with cell cycle arrest in SCLC cells. These data suggest that the previously described function of Notch proteins as proto-oncogenes is highly context-dependent. Notch activation, in the setting of a highly proliferative hASH1-dependent NE neoplasm, can be associated with growth arrest and apparent reduction in neoplastic potential.


Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer's Disease.
Core spliceosome and related RNA-binding proteins aggregate in Alzheimer's disease (AD) brain even in early asymptomatic stages (AsymAD) of disease. To assess the specificity of RNA-binding protein aggregation in AD, we developed a targeted mass spectrometry approach to quantify broad classes of RNA-binding proteins with other pathological proteins including tau and amyloid beta (Aβ) in detergent insoluble fractions from control, AsymAD, AD and Parkinson's disease (PD) brain. Relative levels of specific insoluble RNA-binding proteins across different disease groups correlated with accumulation of Aβ and tau aggregates. RNA-binding proteins, including splicing factors with homology to the basic-acidic dipeptide repeats of U1-70K, preferentially aggregated in AsymAD and AD. In contrast, PD brain aggregates were relatively depleted of many RNA-binding proteins compared to AsymAD and AD groups. Correlation network analyses resolved 29 distinct modules of co-aggregating proteins including modules linked to spliceosome assembly, nuclear speckles and RNA splicing. Modules related to spliceosome assembly and nuclear speckles showed stage-specific enrichment of insoluble RBPs from AsymAD and AD brains, whereas the RNA splicing module was reduced specifically in PD. Collectively, this work identifies classes of RNA-binding proteins that distinctly co-aggregate in detergent-insoluble fractions across the specific neurodegenerative diseases we examined.


Surgical planning and prosthesis construction using computer technology and medical imaging for immediate loading of implants in the pterygomaxillary region.
This report describes a protocol that uses computerized tomography (CT), computer-aided design/computer-assisted manufacture (CAD/CAM) technology, and the Internet to plan placement of anterior and posterior dental implants and construct a precise surgical template and definitive prosthesis, which is connected at the time of implant placement. This procedure drastically reduces surgical treatment time and the recovery period. Patients with an edentulous arch had a denture with radiopaque markers constructed for CT scans of the appropriate jaw. The CT images, with acquisition slices of 0.5 mm, were transferred into a three-dimensional image-based program for planning and strategic placement of dental implants. After implants were virtually placed on the computer, the surgical treatment plan was sent to a manufacturing facility for construction of a surgical template and the prosthesis, Special surgical guide components were also manufactured for placement of implants in the pterygomaxillary region. The manufactured surgical components, surgical template, and definitive prosthesis were then delivered to the clinical site. Implant placement surgery was performed using the surgical template, without a flap, and the prosthesis was delivered, achieving immediate functional loading. Minor occlusal adjustments were made. The total surgical treatment time required was less than 60 minutes. Postoperative symptoms, such as pain, swelling, and inflammation, were minimal. Identification of the bone in relationship to the tooth position via three-dimensional CT prior to surgery allows precise placement of implants. CAD/CAM technology using the three-dimensional images allows for fabrication of the surgical guide and final prosthesis. This is a significant advancement in implant dentistry and prosthodontics.


Target organ profiles in toxicity studies supporting human dosing: Does severity progress with longer duration of exposure?
We have previously reported the profile of target organs (defined as organs showing histopathological changes) in rodent and non-rodent toxicity studies conducted prior to first-time-in-man (FTiM) for 77 AstraZeneca candidate drugs (CDs). Here, we test the assumption that toxicity is exacerbated by dosing duration by comparing the incidence and severity of target organ toxicities in these ≤ 6 week FTiM studies with those observed in subsequent subchronic/chronic (≥ 3 month) studies. Looking at the effect of dosing duration on severity (pathological score) and incidence (percentage of animals within the group) for the 39 CDs that met the criteria for inclusion (comparable doses between FTiM and subchronic/chronic studies), new toxicities appeared for 31 target organs but existing ones resolved for 29 target organs. Increased severity was more frequent for rodent (16 target organs) than for non-rodent (4 target organs). Most notable changes were a large increase in severity/incidence in liver and in non-rodent lung in contrast to a large decrease in severity and incidence for kidneys/ureter and for the non-rodent thymus. Overall this analysis shows that, even with continued exposure, target organ toxicities of CDs are as likely to show partial or complete recovery as they are to progress in severity.


Genetic influences on social attention in free-ranging rhesus macaques.
An ethological approach to attention predicts that organisms orient preferentially to valuable sources of information in the environment. For many gregarious species, orienting to other individuals provides valuable social information but competes with food acquisition, water consumption and predator avoidance. Individual variation in vigilance behaviour in humans spans a continuum from inattentive to pathological levels of interest in others. To assess the comparative biology of this behavioural variation, we probed vigilance rates in free-ranging macaques during water drinking, a behaviour incompatible with the gaze and postural demands of vigilance. Males were significantly more vigilant than females. Moreover, vigilance showed a clear genetic component, with an estimated heritability of 12%. Monkeys carrying a relatively infrequent 'long' allele of TPH2, a regulatory gene that influences serotonin production in the brain, were significantly less vigilant compared to monkeys that did not carry the allele. These findings resonate with the hypothesis that the serotonin pathway regulates vigilance in primates and by extension provoke the idea that individual variation in vigilance and its underlying biology may be adaptive rather than pathological.


Air bubble contact with endothelial cells causes a calcium-independent loss in mitochondrial membrane potential.
Gas microembolism remains a serious risk associated with surgical procedures and decompression. Despite this, the signaling consequences of air bubbles in the vasculature are poorly understood and there is a lack of pharmacological therapies available. Here, we investigate the mitochondrial consequences of air bubble contact with endothelial cells. Human umbilical vein endothelial cells were loaded with an intracellular calcium indicator (Fluo-4) and either a mitochondrial calcium indicator (X-Rhod-1) or mitochondrial membrane potential indicator (TMRM). Contact with 50-150 µm air bubbles induced concurrent rises in intracellular and mitochondrial calcium, followed by a loss of mitochondrial membrane potential. Pre-treating cells with 1 µmol/L ruthenium red, a TRPV family calcium channel blocker, did not protect cells from the mitochondrial depolarization, despite blocking the intracellular calcium response. Mitigating the interactions between the air-liquid interface and the endothelial surface layer with 5% BSA or 0.1% Pluronic F-127 prevented the loss of mitochondrial membrane potential. Finally, inhibiting protein kinase C-α (PKCα), with 5 µmol/L Gö6976, protected cells from mitochondrial depolarization, but did not affect the intracellular calcium response. Our results indicate that air bubble contact with endothelial cells activates a novel, calcium-independent, PKCα-dependent signaling pathway, which results in mitochondrial depolarization. As a result, mitochondrial dysfunction is likely to be a key contributor to the pathophysiology of gas embolism injury. Further, this connection between the endothelial surface layer and endothelial mitochondria may also play an important role in vascular homeostasis and disease.


MR-guided endoscopic sinus surgery.
We describe an interactive, intraoperative imaging-guided method for performing endoscopic sinus surgery (ESS) within a vertically open MR system. The procedure was performed with intraoperative imaging using a 0.5-T magnet with a 56-cm vertical gap. Interactive control of imaging planes was accomplished by optical tracking with two infrared light-emitting diodes mounted on an aspirator probe. The probe's position defined the location of the orthogonal imaging planes. Twelve patients with varying degrees of sinus disease underwent ESS with MR imaging guidance. Patients had acute and chronic sinusitis, nasal polyposis causing airway obstruction, or tumor requiring tissue biopsy. All procedures were performed with the patients under general anesthesia. The integration of endoscopy with optical tracking and intraoperative interactive imaging allowed localization of anatomic landmarks during ESS. No complications were encountered.


A complex of mammalian ufd1 and npl4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport pathways.
The AAA-ATPase, p97/Cdc48p, has been implicated in many different pathways ranging from membrane fusion to ubiquitin-dependent protein degradation. Binding of the p47 complex directs p97 to act in the post-mitotic fusion of Golgi membranes. We now describe another binding complex comprising mammalian Ufd1 and Npl4. Yeast Ufd1p is required for ubiquitin-dependent protein degradation whereas yeast Npl4p has been implicated in nuclear transport. In rat liver cytosol, Ufd1 and Npl4 form a binary complex, which exists either alone or bound to p97. Ufd1/Npl4 competes with p47 for binding to p97 and so inhibits Golgi membrane fusion. This suggests that it is involved in another cellular function catalysed by p97, the most likely being ubiquitin-dependent events during mitosis. The fact that the binding of p47 and Ufd1/Npl4 is mutually exclusive suggests that these protein complexes act as adapters, directing a basic p97 activity into different cellular pathways.


ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.
Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. We describe a new extension and assessment of Relief-F for feature selection in RNA-seq data. The ReliefSeq implementation adapts the number of nearest neighbors (k) for each gene to optimize the Relief-F test statistics (importance scores) for finding both main effects and interactions. We compare this gene-wise adaptive-k (gwak) Relief-F method with standard RNA-seq feature selection tools, such as DESeq and edgeR, and with the popular machine learning method Random Forests. We demonstrate performance on a panel of simulated data that have a range of distributional properties reflected in real mRNA-seq data including multiple transcripts with varying sizes of main effects and interaction effects. For simulated main effects, gwak-Relief-F feature selection performs comparably to standard tools DESeq and edgeR for ranking relevant transcripts. For gene-gene interactions, gwak-Relief-F outperforms all comparison methods at ranking relevant genes in all but the highest fold change/highest signal situations where it performs similarly. The gwak-Relief-F algorithm outperforms Random Forests for detecting relevant genes in all simulation experiments. In addition, Relief-F is comparable to the other methods based on computational time. We also apply ReliefSeq to an RNA-Seq study of smallpox vaccine to identify gene expression changes between vaccinia virus-stimulated and unstimulated samples. ReliefSeq is an attractive tool for inclusion in the suite of tools used for analysis of mRNA-Seq data; it has power to detect both main effects and interaction effects. Software Availability: http://insilico.utulsa.edu/ReliefSeq.php.


Relationship of periapical lesion radiologic size, apical resection, and retrograde filling with the prognosis of periapical surgery.
Periapical surgery eliminates the periradicular inflammatory tissue and seals the apical foramen. The present study relates the radiologic size of the periapical lesion, apical resection, and retrograde filling to the middle- and long-term success of periapical surgery. In a prospective study, 235 patients and 333 teeth were subjected to ultrasound instrumentation and retrograde filling with silver amalgam. Radiographic measurements were made of the maximum and minimum diameters of 320 periapical lesions before surgery. In the 384 apicoectomized roots, calculations were made of the eliminated apical portion, and in 526 root canals the magnitude of retrograde filling was determined. The patients were subjected to a minimum follow-up period of 12 months, with a mean of 27.8 months (range 12 months to 10 years). Global evaluation showed a success rate of 73.9% after 12 months. The mean periapical area before surgery was 37 mm(2) (maximum diameter, 7.4 mm; minimum diameter, 5 mm). The mean apical resection was 6.48 mm(2) (height, 2.7 mm; base, 2.4 mm). The mean area of the retrograde cavities was 3.05 mm(2) (long side, 2.25 mm; short side, 1.1 mm). A positive correlation was observed between the dimensions of the lesion and apical resection with the treatment failure. None of the dimensions of the filling cavity was related to treatment failure. The prognosis of periapical surgery improves with decreasing periapical lesion size and lesser apical resection, and is not dependent on the magnitude of retrograde filling.


Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC.T mismatch by simulation.
A 1.5 ns long molecular dynamics simulation was conducted to compare the structure and stability of a model DNA triplex in saline solution with that found from experiments. The model DNA was an antiparallel py.pu.pu (CG.G) 7-mer structure which contained a GC.T mismatch triplet at the middle of the sequence. The local conformation of the mismatch triplet and the effects of this triplet on the global helical structure suggest that the GC.T triplet forms stable hydrogen bonds and shows distortions from an in-plane alignment. The overall rms deviation of the triplex is similar to one without a mismatch, although the thymine base in the mismatch triplet shows significantly higher mobility. A high coordination probability for water between the G and T bases in the mismatch triplet was observed to have an effect on the stability of non-hydrogen-bonded base pairs. Average helical parameters, sugar pucker, and backbone dihedral angles indicate that the CG.G triplets on the 3' side of the mismatch triplet possess different structural and dynamical properties than that of the 5' side. These observations are consistent with recently available experimental results and provide an interpretation of the observed experimental structure. They also suggest that inclusion of explicit water molecules is necessary in order to understand and predict the interaction between the third strand and duplex DNA.


The antiviral activity of HIV-specific CD8+ CTL clones is limited by elimination due to encounter with HIV-infected targets.
Adoptive immunotherapy of virus infection with viral-specific CTL has shown promise in animal models and human virus infections and is being evaluated as a therapy for established HIV-1 infection. Defining the individual obstacles for success is difficult in human trials. We have therefore examined the localization, persistence, and antiviral activity of HIV-1 gag-specific CTL clones in both HIV-1-infected and uninfected haplotype-matched human (hu)-PBL-SCID mice. Injection of gag-specific clones but not control CTL into HIV-1-infected hosts reduced plasma viremia by >10-fold but failed to eliminate the virus infection from most treated animals. The failure to eradicate virus did not reflect selection of escape variants because the gag epitope remained unmutated in virus isolates obtained after CTL therapy. Injection of carboxyfluorescein diacetate succinimide ester-labeled CTL demonstrated markedly different fates for gag-specific CTL in the presence or absence of HIV-1 infection. HIV-1-specific CTL rapidly disappeared in infected recipients, whereas they were maintained at high numbers in uninfected mice. By contrast, control CTL were long lived in both infected and uninfected recipients. Thus, interaction of CTL with virus-infected target cells in vivo leads not only to target destruction but also to the rapid disappearance of the infused CTL, and it limits the capacity of CTL therapy to eliminate HIV-1 infection.


A decade of molecular pathogenomic analysis of group A Streptococcus.
Molecular pathogenomic analysis of the human bacterial pathogen group A Streptococcus has been conducted for a decade. Much has been learned as a consequence of the confluence of low-cost DNA sequencing, microarray technology, high-throughput proteomics, and enhanced bioinformatics. These technical advances, coupled with the availability of unique bacterial strain collections, have facilitated a systems biology investigative strategy designed to enhance and accelerate our understanding of disease processes. Here, we provide examples of the progress made by exploiting an integrated genome-wide research platform to gain new insight into molecular pathogenesis. The studies have provided many new avenues for basic and translational research.