Methylation analysis and HPV genotyping of self-collected cervical samples from women not responding to screening invitation and review of the literature.
To assess the feasibility of partial HPV genotyping and methylation analysis of CADM1, MAL, and miR124-2 genes as triage tests in assaying self-collected cervical samples positive for high-risk HPV on primary screening, and to review the literature regarding host cellular gene methylation analysis of self-collected cervical samples. Women residing in North-East Italy who had failed to respond to the invitation to participate in an organized population-based program were invited to provide a self-sample. Their stored baseline (self-collected) and follow-up (clinician-collected) cervical samples were included in the study. DNA was extracted from HPV-positive (Qiagen's Hybrid Capture 2, HC2) samples. Partial genotyping with separate detection of HPV types 16 and 18 was performed with a hybrid capture-based method and a quantitative PCR assay. Methylation was assayed with a quantitative methylation-specific PCR. High-risk HPV infection was detected in 48% of baseline and 71% of follow-up HC2-positive samples. Methylation was demonstrated respectively in 15% and 23.5% of baseline and follow-up samples and chiefly involved a single gene (miR124-2). Invalid quantitative PCR results were recorded in 5% of self-collected samples. The specificity of miR124-1, MAL, and CADM1 methylation was 84%, 94%, and 98%, respectively, and the specificity of the three markers combined was 84%. Sensitivity was not estimated due to the lack of CIN2+ samples. The systematic review showed that different methylation assays yield different accuracy values. Self-collected samples are suitable for methylation assays included in reflex triage testing. The reproducibility and accuracy of the methylation tests described in the literature should be improved.


Fulminant disseminated pulmonary adiaspiromycosis in humans.
A case of fulminant disseminated pulmonary adiaspiromycosis is reported. The patient, a 35-year-old black male farm worker, presented with a four-week history of generalized weakness, unproductive cough, evening fever, and a weight loss of 8 kg. He died 12 days after hospitalization of respiratory failure due to granulomatous lung disease. The clinical and radiographic findings were indistinguishable from those of miliary tuberculosis. Microscopic examination of material obtained at autopsy revealed the large fungus characteristic of adiaspiromycosis in the center of suppurative granulomas throughout the lungs. This is believed to be the first fatal case of pulmonary adiaspiromycosis reported in humans, and it may have been occupationally acquired.


Motility of active nematic films driven by "active anchoring".
We provide a minimal model for an active nematic film in contact with both a solid substrate and a passive isotropic fluid, and explore its dynamics in one and two dimensions using a combination of hybrid Lattice Boltzmann simulations and analytical calculations. By imposing nematic anchoring at the substrate while active flows induce a preferred alignment at the interface ("active anchoring"), we demonstrate that directed fluid flow spontaneously emerges in cases where the two anchoring types are opposing. In one dimension, our model reduces to an analogue of a loaded elastic column. Here, the transition from a stationary to a motile state is akin to the buckling bifurcation, but offers the possibility to reverse the flow direction for a given set of parameters and boundary conditions solely by changing initial conditions. The two-dimensional variant of our model allows for additional tangential instabilities, and it is found that undulations form in the interface above a threshold activity. Our results might be relevant for the design of active microfluidic geometries or curvature-guided self-assembly.


Cyberknife targeting the pterygopalatine ganglion for the treatment of chronic cluster headaches.
Cluster headache (CH) is a severe unilateral and periorbital facial pain syndrome that is often associated with autonomic symptoms, including ipsilateral lacrimation, nasal congestion, conjunctival injection, miosis, ptosis, and eyelid edema. We evaluated the treatment of medically refractory CH with CyberKnife (Accuray, Inc., Sunnyvale, CA) stereotactic radiosurgery targeting the pterygopalatine ganglion. A 56-year-old man presented with a 20-year history of medically refractory CH. His symptoms were described as left-sided, severe, stabbing, burning, and often being associated with tearing and rhinorrhea. These headaches occurred virtually every morning and interfered with sleep, lifestyle, and work performance. The patient underwent two pterygopalatine nerve block trials, both of which resulted in the complete relief of headaches for a 24-hour period. Contrast-enhanced computed axial tomography and magnetic resonance imaging scans were fused for target identification and treatment planning. The target volume measured 0.296 cm3 and a single fraction of 45.50 Gy was delivered to the 78% isodose line with a maximum dose of 65 Gy. The patient kept a detailed diary of his headaches and was followed for 12 months after treatment. Results of CyberKnife targeting of the pterygopalatine ganglion in a patient with medically intractable CHs have revealed a significant decrease in the severity and frequency of headaches after a 12-month follow-up period. In addition, the patient has been able to reduce his medication intake, allowing for a significant decrease in medication-related side effects. Longer follow-up periods and additional studies are required to determine the long-term efficacy and late side effects of this treatment strategy.


ReSTART: A Novel Framework for Resource-Based Triage in Mass-Casualty Events.
Current guidelines for mass-casualty triage do not explicitly use information about resource availability. Even though this limitation has been widely recognized, how it should be addressed remains largely unexplored. The authors present a novel framework developed using operations research methods to account for resource limitations when determining priorities for transportation of critically injured patients. To illustrate how this framework can be used, they also develop two specific example methods, named ReSTART and Simple-ReSTART, both of which extend the widely adopted triage protocol Simple Triage and Rapid Treatment (START) by using a simple calculation to determine priorities based on the relative scarcity of transportation resources. The framework is supported by three techniques from operations research: mathematical analysis, optimization, and discrete-event simulation. The authors? algorithms were developed using mathematical analysis and optimization and then extensively tested using 9,000 discrete-event simulations on three distributions of patient severity (representing low, random, and high acuity). For each incident, the expected number of survivors was calculated under START, ReSTART, and Simple-ReSTART. A web-based decision support tool was constructed to help providers make prioritization decisions in the aftermath of mass-casualty incidents based on ReSTART. In simulations, ReSTART resulted in significantly lower mortality than START regardless of which severity distribution was used (paired t test, p<.01). Mean decrease in critical mortality, the percentage of immediate and delayed patients who die, was 8.5% for low-acuity distribution (range ?2.2% to 21.1%), 9.3% for random distribution (range ?0.2% to 21.2%), and 9.1% for high-acuity distribution (range ?0.7% to 21.1%). Although the critical mortality improvement due to ReSTART was different for each of the three severity distributions, the variation was less than 1 percentage point, indicating that the ReSTART policy is relatively robust to different severity distributions. Taking resource limitations into account in mass-casualty situations, triage has the potential to increase the expected number of survivors. Further validation is required before field implementation; however, the framework proposed in here can serve as the foundation for future work in this area.


Role of anesthesia in endovascular stroke therapy.
Recent randomized clinical trials have demonstrated strong efficacy of endovascular therapy (EVT) for acute ischemic stroke (AIS) from large vessel occlusions; in the USA alone, tens of thousands of patients annually may benefit. The impact of the type of anesthesia used during mechanical thrombectomy on patient outcomes remains controversial. This review discusses the current literature on the effects of anesthesia type on patient outcome following endovascular stroke therapy. EVT is the standard of treatment for intracranial large vessel occlusions. Recent studies show that general anesthesia is associated with negative clinical outcome in AIS patients undergoing EVT. Two of the possible mechanisms of this finding are systolic hypotension and hypocapnia. However, the only published randomized controlled studies to date, sedation vs. intubation for endovascular stroke treatment and anesthesia during stroke showed no difference in short-term clinical outcome between EVT patients treated with general anesthesia and conscious sedation and improved longer-term outcome in the general anesthesia group. Retrospective reports, and the 2015 American Heart Association/American Stroke Association Guideline (focused update of the 2013 guidelines for the early management of patients with AIS regarding endovascular treatment) based on these reports, are in favor of sedation (conscious sedation) over general anesthesia for endovascular stroke thrombectomy. However, the two randomized controlled prospective studies published provide inconclusive evidence as to the best anesthetic practice for endovascular stroke therapy. More randomized clinical trials are needed to optimize anesthetic patient care in AIS.


Developing process guidelines for trauma care in the Netherlands for severely injured patients: results from a Delphi study.
In organised trauma systems the process of care is the key to quality. Nevertheless, the optimal process of trauma care remains unclear due to lack of or inconclusive evidence. Because monitoring and improving the performance of a trauma system is complex, this study aimed to develop consensus-based process guidelines for trauma care in the Netherlands for severely injured patients. A five-round Delphi study was conducted with 141 participants that represent all professions involved in trauma care. Sensitivity analyses were carried out to evaluate whether consensus extended across all professions and to detect possible bias. Consensus was reached on 21 guidelines within 4 categories: timeliness, actions, competent teams and interdisciplinary process. Timeliness guidelines set specific critical limits and definitions for 10 time intervals in the time period from an emergency call until the patient leaves the trauma room. Action guidelines reflect aspects of appropriate care and strongly rely on the international Advanced Trauma Life Support principles. Competence guidelines include flow charts to assess the competence of prehospital and emergency department teams. Essential to competent teams are education and experience of all team members. The interdisciplinary process guideline focuses on cooperation, communication and feedback within and between all professions involved. Consensus was extended across all professions and no bias was detected. In this Delphi study, a large expert panel agreed on a set of guidelines describing the optimal process of care for severely injured trauma patients in the Netherlands. In addition to time intervals and appropriate actions, these guidelines emphasise the importance of team competence and interdisciplinary processes in trauma care. The guidelines can be seen as a description of a best practice and a new field standard in the Netherlands. The next step is to implement the guidelines and monitor the performance of the Dutch trauma system based on the guidelines.


Influence of ethanol on thermoregulation: mapping quantitative trait loci.
The genetic basis for the effects of ethanol on thermoregulation was investigated by utilizing recombinant inbred mouse strains from C57BL/6J and DBA/2J progenitor strains. Changes in core body temperature (T(c)) and the degree of fluctuation of T(c) were monitored in male mice following the administration of ethanol in an environment with cyclic changes in ambient temperature (T(a)). Changes in T(c) were utilized to assess ethanol-induced effects on regulated T(c), whereas fluctuations in T(c) were utilized to assess thermoregulatory disruption. Ethanol was administered intraperitoneally at 1.5, 2.5, and 3.5 g/kg for all strains. Change in T(c) and increase in tail temperature were also evaluated at 2.5 g/kg ethanol in a constant T(a) of 26 degrees C. Associations between the measured physiological responses and previously mapped genetic markers were used to identify quantitative trait loci (QTLs). This established probable chromosome locations for a number of genes for the responses. To our knowledge, this is the first report of QTLs that underlie changes in regulation as well as the disruption of a physiological regulatory system.


ALS patients' regulatory T lymphocytes are dysfunctional, and correlate with disease progression rate and severity.
Neuroinflammation is a pathological hallmark of ALS in both transgenic rodent models and patients, and is characterized by proinflammatory T lymphocytes and activated macrophages/microglia. In ALS mouse models, decreased regulatory T lymphocytes (Tregs) exacerbate the neuroinflammatory process, leading to accelerated motoneuron death and shortened survival; passive transfer of Tregs suppresses the neuroinflammation and prolongs survival. Treg numbers and FOXP3 expression are also decreased in rapidly progressing ALS patients. A key question is whether the marked neuroinflammation in ALS can be attributed to the impaired suppressive function of ALS Tregs in addition to their decreased numbers. To address this question, T lymphocyte proliferation assays were performed. Compared with control Tregs, ALS Tregs were less effective in suppressing responder T lymphocyte proliferation. Although both slowly and rapidly progressing ALS patients had dysfunctional Tregs, the greater the clinically assessed disease burden or the more rapidly progressing the patient, the greater the Treg dysfunction. Epigenetically, the percentage methylation of the Treg-specific demethylated region was greater in ALS Tregs. After in vitro expansion, ALS Tregs regained suppressive abilities to the levels of control Tregs, suggesting that autologous passive transfer of expanded Tregs might offer a novel cellular therapy to slow disease progression.


Two roles for the Drosophila IKK complex in the activation of Relish and the induction of antimicrobial peptide genes.
The Drosophila NF-kappaB transcription factor Relish is an essential regulator of antimicrobial peptide gene induction after gram-negative bacterial infection. Relish is a bipartite NF-kappaB precursor protein, with an N-terminal Rel homology domain and a C-terminal IkappaB-like domain, similar to mammalian p100 and p105. Unlike these mammalian homologs, Relish is endoproteolytically cleaved after infection, allowing the N-terminal NF-kappaB module to translocate to the nucleus. Signal-dependent activation of Relish, including cleavage, requires both the Drosophila IkappaB kinase (IKK) and death-related ced-3/Nedd2-like protein (DREDD), the Drosophila caspase-8 like protease. In this report, we show that the IKK complex controls Relish by direct phosphorylation on serines 528 and 529. Surprisingly, these phosphorylation sites are not required for Relish cleavage, nuclear translocation, or DNA binding. Instead they are critical for recruitment of RNA polymerase II and antimicrobial peptide gene induction, whereas IKK functions noncatalytically to support Dredd-mediated cleavage of Relish.


Nonlinear effects of hyperpolarizing shifts in activation of mutant Nav1.7 channels on resting membrane potential.
The Nav1.7 sodium channel is preferentially expressed within dorsal root ganglion (DRG) and sympathetic ganglion neurons. Gain-of-function mutations that cause the painful disorder inherited erythromelalgia (IEM) shift channel activation in a hyperpolarizing direction. When expressed within DRG neurons, these mutations produce a depolarization of resting membrane potential (RMP). The biophysical basis for the depolarized RMP has to date not been established. To explore the effect on RMP of the shift in activation associated with a prototypical IEM mutation (L858H), we used dynamic-clamp models that represent graded shifts that fractionate the effect of the mutation on activation voltage dependence. Dynamic-clamp recording from DRG neurons using a before-and-after protocol for each cell made it possible, even in the presence of cell-to-cell variation in starting RMP, to assess the effects of these graded mutant models. Our results demonstrate a nonlinear, progressively larger effect on RMP as the shift in activation voltage dependence becomes more hyperpolarized. The observed differences in RMP were predicted by the "late" current of each mutant model. Since the depolarization of RMP imposed by IEM mutant channels is known, in itself, to produce hyperexcitability of DRG neurons, the development of pharmacological agents that normalize or partially normalize activation voltage dependence of IEM mutant channels merits further study.NEW & NOTEWORTHY Inherited erythromelalgia (IEM), the first human pain disorder linked to a sodium channel, is widely regarded as a genetic model of neuropathic pain. IEM is produced by Nav1.7 mutations that hyperpolarize activation. These mutations produce a depolarization of resting membrane potential (RMP) in dorsal root ganglion neurons. Using dynamic clamp to explore the effect on RMP of the shift in activation, we demonstrate a nonlinear effect on RMP as the shift in activation voltage dependence becomes more hyperpolarized.


The human-snail transmission environment shapes long term schistosomiasis control outcomes: Implications for improving the accuracy of predictive modeling.
Schistosomiasis is a chronic parasitic trematode disease that affects over 240 million people worldwide. The Schistosoma lifecycle is complex, involving transmission via specific intermediate-host freshwater snails. Predictive mathematical models of Schistosoma transmission have often chosen to simplify or ignore the details of environmental human-snail interaction in their analyses. Schistosome transmission models now aim to provide better precision for policy planning of elimination of transmission. This heightens the importance of including the environmental complexity of vector-pathogen interaction in order to make more accurate projections. We propose a nonlinear snail force of infection (FOI) that takes into account an intermediate larval stage (miracidium) and snail biology. We focused, in particular, on the effects of snail force of infection (FOI) on the impact of mass drug administration (MDA) in human communities. The proposed (modified) model was compared to a conventional model in terms of their predictions. A longitudinal dataset generated in Kenya field studies was used for model calibration and validation. For each sample community, we calibrated modified and conventional model systems, then used them to model outcomes for a range of MDA regimens. In most cases, the modified model predicted more vigorous post-MDA rebound, with faster relapse to baseline levels of infection. The effect was pronounced in higher risk communities. When compared to observed data, only the modified system was able to successfully predict persistent rebound of Schistosoma infection. The observed impact of varying location-specific snail inputs sheds light on the diverse MDA response patterns noted in operational research on schistosomiasis control, such as the recent SCORE project. Efficiency of human-to-snail transmission is likely to be much higher than predicted by standard models, which, in practice, will make local elimination by implementation of MDA alone highly unlikely, even over a multi-decade period.


Genome-wide copy number variation (CNV) in patients with autoimmune Addison's disease.
Addison's disease (AD) is caused by an autoimmune destruction of the adrenal cortex. The pathogenesis is multi-factorial, involving genetic components and hitherto unknown environmental factors. The aim of the present study was to investigate if gene dosage in the form of copy number variation (CNV) could add to the repertoire of genetic susceptibility to autoimmune AD. A genome-wide study using the Affymetrix GeneChip® Genome-Wide Human SNP Array 6.0 was conducted in 26 patients with AD. CNVs in selected genes were further investigated in a larger material of patients with autoimmune AD (n = 352) and healthy controls (n = 353) by duplex Taqman real-time polymerase chain reaction assays. We found that low copy number of UGT2B28 was significantly more frequent in AD patients compared to controls; conversely high copy number of ADAM3A was associated with AD. We have identified two novel CNV associations to ADAM3A and UGT2B28 in AD. The mechanism by which this susceptibility is conferred is at present unclear, but may involve steroid inactivation (UGT2B28) and T cell maturation (ADAM3A). Characterization of these proteins may unravel novel information on the pathogenesis of autoimmunity.


Do constraints associated with the locomotor habitat drive the evolution of forelimb shape? A case study in musteloid carnivorans.
Convergence in morphology can result from evolutionary adaptations in species living in environments with similar selective pressures. Here, we investigate whether the shape of the forelimb long bones has converged in environments imposing similar functional constraints, using musteloid carnivores as a model. The limbs of quadrupeds are subjected to many factors that may influence their shape. They need to support body mass without collapsing or breaking, yet at the same time resist the stresses and strains induced by locomotion. This likely imposes strong constraints on their morphology. Our geometric morphometric analyses show that locomotion, body mass and phylogeny all influence the shape of the forelimb. Furthermore, we find a remarkable convergence between: (i) aquatic and semi-fossorial species, both displaying a robust forelimb, with a shape that improves stability and load transfer in response to the physical resistance imposed by the locomotor environment; and (ii) aquatic and arboreal/semi-arboreal species, with both groups displaying a broad capitulum. This augments the degree of pronation/supination, an important feature for climbing as well as grasping and manipulation ability, behaviors common to aquatic and arboreal species. In summary, our results highlight how musteloids with different locomotor ecologies show differences in the anatomy of their forelimb bones. Yet, functional demands for limb movement through dense media also result in convergence in forelimb long-bone shape between diverse groups, for example, otters and badgers.


Induction of mutations in Drosophila melanogaster gypsy retroelements by modulation of intracellular deoxynucleoside triphosphate pools in vivo.
The retroviral mutation rate is susceptible to a number of variables, including the balance between intracellular deoxynucleoside triphosphate (dNTP) pools. While this follows from tissue culture studies, the issue has never been addressed directly in vivo. To explore this question in a tractable experimental system, we analyzed the impact of thymidine treatment on the synthesis of gypsy retroelement cDNA from Drosophila melanogaster during development through to hatching. The mutation frequency was enhanced approximately 16-fold over the levels seen in the experimental background. Due to the lack of proofreading, these gypsy elements represent hypervariable loci within the Drosophila genome, suggesting that dNTP pool imbalances in vivo are mutagenic.


Assessment of epicutaneous testing of a monovalent Influenza A (H1N1) 2009 vaccine in egg allergic patients.
H1N1 is responsible for the first influenza pandemic in 41 years. In the fall of 2009, an H1N1 vaccine became available in Canada with the hopes of reducing the overall effect of the pandemic. The purpose of this study was to assess the safety of administering 2 different doses of a monovalent split virus 2009 H1N1 vaccine in egg allergic patients. Patients were skin tested to the H1N1 vaccine in the outpatient paediatric and adult allergy and immunology clinics of the Health Sciences Centre and Children's Hospital of Winnipeg, Manitoba Canada. Individuals <9 years of age were administered 1.88 μg's of hem-agglutinin antigen per 0.25 ml dose and individuals ≥9 years were administered 3.75 μg's of hemagglutinin antigen per 0.5 ml dose. Upon determination of a negative skin test, the vaccine was administered with a 30 minute observation period. A total of 61 patients with egg allergy (history of an allergic reaction to egg with either positive skin test &/or specific IgE to egg >0.35 Ku/L) were referred to our allergy clinics for skin testing to the H1N1 vaccine. 2 patients were excluded, one did not have a skin prick test to the H1N1 vaccine (only vaccine administration) and the other passed an egg challenge during the study period. Ages ranged from 1 to 27 years (mean 5.6 years). There were 41(69.5%) males and 18(30.5%) females. All but one patient with a history of egg allergy, positive skin test to egg and/or elevated specific IgE level to egg had negative skin tests to the H1N1 vaccine. The 58 patients with negative skin testing to the H1N1 vaccine were administered the vaccine and observed for 30 minutes post vaccination with no adverse results. The patient with the positive skin test to the H1N1 vaccine was also administered the vaccine intramuscularly with no adverse results. Despite concern regarding possible anaphylaxis to the H1N1 vaccine in egg allergic patients, in our case series 1/59(1.7%) patients with sensitization to egg were also sensitized to the H1N1 vaccine. Administration of the H1N1 vaccine in egg allergic patients with negative H1N1 skin tests and observation is safe. Administering the vaccine in a 1 or 2 dose protocol without skin testing is a reasonable alternative as per the CSACI guidelines.


Effect of unisexual Schistosoma mansoni infections on hepatic drug metabolism of mice.
The effect of unisexual schistosome infection on the activities of several hepatic enzymes was studied in mice. The activities of hepatic drug-metabolizing enzymes in mice infected with either female or male schistosomes were not significantly different from those of noninfected control animals. However, the total amount of heme pigment in the liver of infected mice was 2.7 (female infection) and 8.9 (male infection) times greater than that of control animals. The durations of hexobarbital sleeping times and of zoxazolamine paralysis in unisexual schistosome infections did not differ from those of uninfected controls. Therefore, an accumulation of schistosome pigment without egg deposition, as in this unisexual infection study, does not result in a severe reduction of hepatic drug-metabolizing capacity.


IR-induced conformational isomerization of a helical peptide in a cold ion trap.
In this work, we use laser-induced population transfer techniques to study the conformational isomerization of a helical peptide, Ac-Phe-(Ala)5-LysH(+), in a cold ion trap. In one scheme, called IR-UV hole-filling spectroscopy, a single conformation is selectively excited with an IR pump laser via a distinct NH stretch vibration. After giving the vibrationally excited ions sufficient time to isomerize and re-cool in the trap, the new conformational redistribution is detected by UV photofragment spectroscopy. While we clearly observe a redistribution of the conformer populations due to isomerization, only those conformations that initially have population participate in this redistribution-we do not form conformers that were not initially present in the trap. In a second scheme, called IR-induced population transfer spectroscopy, we determine the fractional populations of the four stable conformations of Ac-Phe-(Ala)5-LysH(+) by scanning the IR laser while selectively detecting a specific conformation using UV photofragment spectroscopy.


Brief report: feasibility of social cognition and interaction training for adults with high functioning autism.
The goal of this study was to evaluate the feasibility and utility of a group-based cognitive behavioral intervention to improve social-cognitive functioning in adults with high-functioning autism (HFA). We modified the treatment manual of a previously validated intervention, Social Cognition and Interaction Training (SCIT), for optimal use with HFA adults (SCIT-A). We then conducted a pilot study to compare SCIT-A (n = 6) to treatment as usual (TAU) (n = 5) for adults with HFA. Feasibility was supported; attendance was high (92%) and satisfaction reports were primarily positive. Participants in SCIT-A showed significant improvement in theory-of-mind skills and trend level improvements in social communication skills; TAU participants did not show these improvements. Findings indicate SCIT-A shows promise as an intervention for adults with HFA.


The Intestinal Microbiota in Metabolic Disease.
Gut bacteria exert beneficial and harmful effects in metabolic diseases as deduced from the comparison of germfree and conventional mice and from fecal transplantation studies. Compositional microbial changes in diseased subjects have been linked to adiposity, type 2 diabetes and dyslipidemia. Promotion of an increased expression of intestinal nutrient transporters or a modified lipid and bile acid metabolism by the intestinal microbiota could result in an increased nutrient absorption by the host. The degradation of dietary fiber and the subsequent fermentation of monosaccharides to short-chain fatty acids (SCFA) is one of the most controversially discussed mechanisms of how gut bacteria impact host physiology. Fibers reduce the energy density of the diet, and the resulting SCFA promote intestinal gluconeogenesis, incretin formation and subsequently satiety. However, SCFA also deliver energy to the host and support liponeogenesis. Thus far, there is little knowledge on bacterial species that promote or prevent metabolic disease. Clostridium ramosum and Enterococcus cloacae were demonstrated to promote obesity in gnotobiotic mouse models, whereas bifidobacteria and Akkermansia muciniphila were associated with favorable phenotypes in conventional mice, especially when oligofructose was fed. How diet modulates the gut microbiota towards a beneficial or harmful composition needs further research. Gnotobiotic animals are a valuable tool to elucidate mechanisms underlying diet-host-microbe interactions.


Mutationmapper: a tool to aid the mapping of protein mutation data.
There has been a rapid increase in the amount of mutational data due to, amongst other things, an increase in single nucleotide polymorphism (SNP) data and the use of site-directed mutagenesis as a tool to help dissect out functional properties of proteins. Many manually curated databases have been developed to index point mutations but they are not sustainable with the ever-increasing volume of scientific literature. There have been considerable efforts in the automatic extraction of mutation specific information from raw text involving use of various text-mining approaches. However, one of the key problems is to link these mutations with its associated protein and to present this data in such a way that researchers can immediately contextualize it within a structurally related family of proteins. To aid this process, we have developed an application called MutationMapper. Point mutations are extracted from abstracts and are validated against protein sequences in Uniprot as far as possible. Our methodology differs in a fundamental way from the usual text-mining approach. Rather than start with abstracts, we start with protein sequences, which facilitates greatly the process of validating a potential point mutation identified in an abstract. The results are displayed as mutations mapped on to the protein sequence or a multiple sequence alignment. The latter enables one to readily pick up mutations performed at equivalent positions in related proteins. We demonstrate the use of MutationMapper against several examples including a single sequence and multiple sequence alignments. The application is available as a web-service at http://mutationmapper.bioch.ox.ac.uk.


Plasma nonesterified fatty acids in the Dahl rat. Response to salt loading.
The link between dietary salt intake and the development of hypertension in the salt-sensitive Dahl strain of rats remains elusive. There is evidence that Dahl salt-sensitive rats (DS) produce less vasodilator and natriuretic prostaglandins in response to salt loading than do control salt-resistant rats (DR), although the reason for this blunted response is unknown. We examined the effects of chronic dietary salt loading on the plasma levels of nonesterified fatty acids in DS and DR. Animals were fed the same chow containing either 0.4% or 4% NaCl (wt/wt). At 12 weeks, 75 microliters of tail capillary blood was obtained from restrained, conscious rats, and principal nonesterified fatty acids were measured by high performance liquid chromatography. Total nonesterified fatty acids rose in the 15 DR on high salt diets compared with values in 11 rats eating low salt (0.57 +/- 0.05 vs 0.35 +/- 0.01 mM; p less than 0.001). The greatest changes occurred in levels of arachidonic acid (+287%) and in the arachidonic precursors, linoleic (+89%) and linolenic (+107%) acids. In marked contrast, there was no change in levels of plasma nonesterified fatty acids in DS fed 4% NaCl compared with DS fed 0.4% NaCl. These observations suggest that defective production of natriuretic and vasodilator prostaglandins by DS may be due in part to an inability to produce or release eicosanoid precursors from phospholipid stores in response to dietary salt.


Effects of different transcranial direct current stimulation protocols on visuo-spatial contextual learning formation: evidence of homeostatic regulatory mechanisms.
In the present study we tested the effects of different transcranial direct current stimulation (tDCS) protocols in the formation of visuo-spatial contextual learning (VSCL). The study comprised three experiments designed to evaluate tDCS-induced changes in VSCL measures collected during the execution of a visual search task widely used to examine statistical learning in the visuo-spatial domain. In Experiment 1, we probed for the effects of left-posterior parietal cortex (PPC) anodal-tDCS (AtDCS) at different timings (i.e. offline and online) and intensities (i.e. 3 mA and 1.5 mA). The protocol producing the more robust effect in Experiment 1 was used in Experiment 2 over the right-PPC, while in Experiment 3, cathodal-tDCS (CtDCS) was applied over the left-PPC only at a high intensity (i.e. 3 mA) but varying timing of application (offline and online). Results revealed that high intensity offline AtDCS reduced VSCL regardless of the stimulation side (Experiment 1 and 2), while no significant behavioral changes were produced by both online AtDCS protocols (Experiment 1) and offline/online CtDCS (Experiment 3). The reduced VSCL could result from homeostatic regulatory mechanisms hindering normal task-related neuroplastic phenomena.


The tethered motor domain of a kinesin-microtubule complex catalyzes reversible synthesis of bound ATP.
Although the steps for the forward reaction of ATP hydrolysis by the motor protein kinesin have been studied extensively, the rates for the reverse reactions and thus the energy changes at each step are not as well defined. Oxygen isotopic exchange between water and P(i) was used to evaluate the reverse rates. The fraction of the kinesin x ADP x P(i) complex that reverts to ATP before release of P(i) during net hydrolysis was approximately 0 and approximately 2.6% in the absence and presence of microtubules (MTs), respectively. The rate of synthesis of bound ATP from free P(i) and the MT x kinesin x ADP complex was approximately 1.7 M(-1) x s(-1) (K0.5 ADP = 70 microM) with monomeric kinesin in the absence of net hydrolysis. Synthesis of bound ATP from the ADP of the tethered head of a dimer-MT complex was 20-fold faster than for the monomer-MT complex. This MT-activated ATP synthesis at the tethered head is in marked contrast to the lack of MT stimulation of ADP release from the same site. The more rapid ATP synthesis with dimers suggests that the tethered head binds behind the strongly attached head, because this positions the neck linker of the tethered head toward the plus end of the MT and would thus facilitate its docking on synthesis of ATP. The observed rate of ATP synthesis also puts limits on the overall energetics that suggest that a significant fraction of the free energy of ATP hydrolysis is available to drive the docking of the neck linker on binding of ATP.


A three-colour flow cytometry technique for measuring trophoblast intracellular antigens: the relative expression of TAP1 in human cytotrophoblast and decidual cells.
Flow cytometry is conventionally used to measure cell-surface antigen expression. However, many antigens are found within the cytoplasm, and it is necessary to fix and permeabilize cells to enable antibodies to gain access to them. In this study we have established the conditions for studying intracellular antigens in human trophoblast cells by flow cytometry using an antibody to TAP1 (a key molecule in the process of Class I MHC assembly). We have previously shown by immunocytochemistry that TAP1 expression is apparently greater on Class 1 positive extravillous cytotrophoblast than on any other fetal or maternal tissue. However, as immunohistochemistry is not quantitative we have used three-colour flow cytometry to measure the expression of TAP1 in different trophoblast populations. Villous and extravillous cytotrophoblast were identified in first trimester and term placental and decidual digests on the basis of their expression of cytokeratin and Class I MHC antigens. The level of expression of TAP1 for each population was investigated using a commercial kit that determines the number of antibody-binding sites per cell. TAP expression was found to be three- to fivefold higher in extravillous cytotrophoblast, confirming our previous findings. The techniques developed here are directly applicable to the measurement of other intracellular molecules in trophoblast, in particular cytokines.


Influence of Sociodemographic, Premorbid, and Injury-Related Factors on Post-Concussion Symptoms after Traumatic Brain Injury.
Post-concussion symptoms (PCS) are often reported as consequences of mild and moderate traumatic brain injury (TBI), but these symptoms are not well documented in severe TBI. There is a lack of agreement as to which factors and covariates affect the occurrence, frequency, and intensity of PCS among TBI severity groups. The present study therefore aims to examine the association between sociodemographic, premorbid, and injury-related factors and PCS. A total of 1391 individuals (65% male) from the CENTER-TBI study were included in the analyses. The occurrence, frequency (number of PCS), and intensity (severity) of PCS were assessed using the Rivermead Post-concussion Symptoms Questionnaire (RPQ) at six months after TBI. To examine the association between selected factors (age, sex, living situation, employment status, educational background, injury and TBI severity, and premorbid problems) and PCS, a zero-inflated negative binomial model (ZINB) for occurrence and frequency of PCS and a standard negative binomial regression (NB) for intensity were applied. Of the total sample, 72% of individuals after TBI reported suffering from some form of PCS, with fatigue being the most frequent among all TBI severity groups, followed by forgetfulness, and poor concentration. Different factors contributed to the probability of occurrence, frequency, and intensity of PCS. While the occurrence of PCS seemed to be independent of the age and sex of the individuals, both the frequency and intensity of PCS are associated with them. Both injury and TBI severity influence the occurrence and frequency of PCS, but are associated less with its intensity (except "acute" symptoms such as nausea, vomiting, and headaches). Analyses focusing on the mTBI subgroup only yielded results comparable to those of the total sample. In line with previous studies, the results support a multifactorial etiology of PCS and show the importance of differentiating between their occurrence, frequency, and intensity to better provide appropriate treatment for individual subgroups with different symptoms (e.g., multiple PCS or more intense PCS). Although PCS often occur in mild to moderate TBI, individuals after severe TBI also suffer from PCS or post-concussion-like symptoms that require appropriate treatment. The chosen statistical approaches (i.e., ZINB and NB models) permit an ameliorated differentiation between outcomes (occurrence, frequency, and intensity of PCS) and should be used more widely in TBI research.


Differential role of transcription-coupled repair in UVB-induced G2 arrest and apoptosis in mouse epidermis.
Nucleotide excision repair (NER), apoptosis, and cell-cycle regulation are major defense mechanisms against the carcinogenic effects of UVB light. NER eliminates UVB-induced DNA photolesions via two subpathways: global genome repair (GGR) and transcription-coupled repair (TCR). Defects in NER result in the human disorders xeroderma pigmentosum (XP) and Cockayne syndrome (CS), displaying severe UV sensitivity and in the case of XP, cancer proneness. We investigated the impact of deficiencies in NER subpathways on apoptosis, hyperplasia, and cell cycle progression in the epidermis of UVB-exposed CS group B (Csb(-/-)) mice (no TCR), XP group C (Xpc(-/-)) mice (no GGR), and XP group A (Xpa(-/-)) mice (no TCR and no GGR). On UVB treatment (250 J/m(2)), Xpa(-/-) and Csb(-/-) mice revealed an extensive apoptotic response in the skin, a blockage of cell cycle progression of epidermal cells, and strong hyperplasia. Interestingly, the absence of this apoptotic response in the skin of wild-type and Xpc(-/-) mice coincided with the ability of epidermal cells to enter the S phase. However, only epidermal cells of Xpc(-/-) mice subsequently became arrested in the G(2) phase. Our data demonstrate that TCR (and/or restoration of UVB-inhibited transcription) enables damaged cells to progress through S phase and prevents the induction of apoptosis and hyperplasia. G(2) arrest is manifest only under conditions of proficient TCR in combination with deficient GGR, indicating that epidermal cells become arrested in the G(2) phase as a result of persisting damage in their genome.


Dietary and genetic control of glucose transporter 2 glycosylation promotes insulin secretion in suppressing diabetes.
Pancreatic beta cell-surface expression of glucose transporter 2 (Glut-2) is essential for glucose-stimulated insulin secretion, thereby controlling blood glucose homeostasis in response to dietary intake. We show that the murine GlcNAcT-IVa glycosyltransferase is required for Glut-2 residency on the beta cell surface by constructing a cell-type- and glycoprotein-specific N-glycan ligand for pancreatic lectin receptors. Loss of GlcNAcT-IVa, or the addition of glycan-ligand mimetics, attenuates Glut-2 cell-surface half-life, provoking endocytosis with redistribution into endosomes and lysosomes. The ensuing impairment of glucose-stimulated insulin secretion leads to metabolic dysfunction diagnostic of type 2 diabetes. Remarkably, the induction of diabetes by chronic ingestion of a high-fat diet is associated with reduced GlcNAcT-IV expression and attenuated Glut-2 glycosylation coincident with Glut-2 endocytosis. We infer that beta cell glucose-transporter glycosylation mediates a link between diet and insulin production that typically suppresses the pathogenesis of type 2 diabetes.


Empirical confirmation of creative destruction from world trade data.
We show that world trade network datasets contain empirical evidence that the dynamics of innovation in the world economy indeed follows the concept of creative destruction, as proposed by J.A. Schumpeter more than half a century ago. National economies can be viewed as complex, evolving systems, driven by a stream of appearance and disappearance of goods and services. Products appear in bursts of creative cascades. We find that products systematically tend to co-appear, and that product appearances lead to massive disappearance events of existing products in the following years. The opposite-disappearances followed by periods of appearances-is not observed. This is an empirical validation of the dominance of cascading competitive replacement events on the scale of national economies, i.e., creative destruction. We find a tendency that more complex products drive out less complex ones, i.e., progress has a direction. Finally we show that the growth trajectory of a country's product output diversity can be understood by a recently proposed evolutionary model of Schumpeterian economic dynamics.


Seed priming with iron and zinc in bread wheat: effects in germination, mitosis and grain yield.
Currently, the biofortification of crops like wheat with micronutrients such as iron (Fe) and zinc (Zn) is extremely important due to the deficiencies of these micronutrients in the human diet and in soils. Agronomic biofortification with Fe and Zn can be done through different exogenous strategies such as soil application, foliar spraying, and seed priming. However, the excess of these micronutrients can be detrimental to the plants. Therefore, in the last decade, a high number of studies focused on the evaluation of their phytotoxic effects to define the best strategies for biofortification of bread wheat. In this study, we investigated the effects of seed priming with different dosages (1 mg L-1 to 8 mg L-1) of Fe and/or Zn in germination, mitosis and yield of bread wheat cv. 'Jordão' when compared with control. Overall, our results showed that: micronutrient dosages higher than 4 mg L-1 negatively affect the germination; Fe and/or Zn concentrations higher than 2 mg L-1 significantly decrease the mitotic index and increase the percentage of dividing cells with anomalies; treatments performed with 8 mg L-1 of Fe and/or 8 mg L-1 Zn caused negative effects in germination, mitosis and grain yield. Moreover, seed priming with 2 mg L-1 Fe + 2 mg L-1 Zn has been shown to be non-cytotoxic, ensuring a high rate of germination (80%) and normal dividing cells (90%) as well as improving tillering and grain yield. This work revealed that seed priming with Fe and Zn micronutrients constitutes a useful and alternative approach for the agronomic biofortification of bread wheat.


Sex-Dependent Association between Weight Change and Thyroid Dysfunction: Population-Level Analysis Using the Korean National Health and Nutrition Examination Survey.
Although body weight change (BWC) is a common manifestation of thyroid dysfunction, solid evidence for whether to perform or on whom to perform thyroid function test in subjects complaining of BWC is lacking. To evaluate the association between thyroid dysfunction and BWC using a nationwide survey. Data was obtained from the Korea National Health and Nutrition Examination Survey VI 2013-2015 and 5,456 subjects without previous thyroid disease were included. Serum thyroid-stimulating hormone (TSH), free T4, and self-reported BWC during the previous year were used for the evaluation. Weight loss or gain was defined as weight change of at least 3 kg. In total, 1,017 men (37.3%) and 1,175 women (43.0%) reported BWCs during the previous year. The overall weighted prevalence of thyroid dysfunction was not significantly associated with the extent of BWC in men (p = 0.705) or women (p = 0.094). However, when the impact of TSH levels on weight change was separately evaluated for weight gain and loss after adjusting for age and body mass index in each sex, weight loss in women was significantly associated with TSH levels (hazard ratio 0.64, 95% CI 0.47-0.85, p = 0.03). No association of thyroid dysfunction was observed for weight gain in women (p = 0.23) or any changes in men (p = 0.875 in weight gain, p = 0.923 in weight loss). This study highlights the necessity of performing thyroid function testing in women who complain of weight loss, but such testing may be less vital in women with weight gain or men with any changes in weight.


Effect of NGF on the survival of rat retinal ganglion cells following optic nerve section.
The ability of NGF (2.5S subunit) to support the survival of adult rat retinal ganglion cells (RGCs) and optic nerve fibers after intracranial section of the optic nerve was investigated. NGF was injected intraocularly at a dose of 3 micrograms/injection every 2.3 d from the day of axotomy to analysis. Control animals received cytochrome c injections. The survival of RGCs was analyzed in whole-mounted retinas after either cresyl violet staining or labeling with HRP applied to the proximal stump of the optic nerve. Survival times were 5 and 7 weeks. Diameter distribution and number of myelinated optic nerve fibers were assessed in ultrathin cross sections of the optic nerve. We found that RGCs surviving axotomy were much more numerous following NGF treatment compared with controls. Large-size cells were, in particular, preserved by NGF treatment. The quantitative ultrastructural studies indicated that the number of myelinated optic nerve fibers at 5 and 7 weeks postaxotomy was significantly greater in the NGF group with respect to the cytochrome c group. In agreement with the results obtained at the level of the RGCs, large-diameter axons were, in particular, preserved. We conclude that NGF injected intraocularly is effective in promoting the survival of RGCs and optic nerve fibers at least for a period as long as 7 weeks after intracranial section of the optic nerve.


The role of flexibility and optimality in the prediction of intracellular fluxes of microbial central carbon metabolism.
Prediction of intracellular metabolic fluxes based on optimal biomass assumption is a well-known computational approach. While there has been a significant emphasis on the optimality, cellular flexibility, the co-occurrence of suboptimal flux distributions in a microbial population, has hardly been considered in the related computational methods. We have implemented a flexibility-incorporated optimization framework to calculate intracellular fluxes based on a few extracellular measurement constraints. Taking into account slightly suboptimal flux distributions together with a dual-optimality framework (maximization of the growth rate followed by the minimization of the total enzyme amount) we were able to show the positive effect of incorporating flexibility and minimal enzyme consumption on the better prediction of intracellular fluxes of central carbon metabolism of two microorganisms: E. coli and S. cerevisiae.


Frequent structural variations involving programmed death ligands in Epstein-Barr virus-associated lymphomas.
Viral infection induces potent cellular immunity and activated intracellular signaling, which may dictate the driver events involved in immune escape and clonal selection of virus-associated cancers, including Epstein-Barr virus (EBV)-positive lymphomas. Here, we thoroughly interrogated PD-L1/PD-L2-involving somatic aberrations in 384 samples from various lymphoma subtypes using high-throughput sequencing, particularly focusing on virus-associated lymphomas. A high frequency of PD-L1/PD-L2-involving genetic aberrations was observed in EBV-positive lymphomas [33 (22%) of 148 cases], including extranodal NK/T-cell lymphoma (ENKTL, 23%), aggressive NK-cell leukemia (57%), systemic EBV-positive T-cell lymphoproliferative disorder (17%) as well as EBV-positive diffuse large B-cell lymphoma (DLBCL, 19%) and peripheral T-cell lymphoma-not otherwise specified (15%). Predominantly causing a truncation of the 3'-untranslated region, these alterations represented the most prevalent somatic lesions in ENKTL. By contrast, the frequency was much lower in EBV-negative lymphomas regardless of histology type [12 (5%) of 236 cases]. Besides PD-L1/PD-L2 alterations, EBV-positive DLBCL exhibited a genetic profile distinct from EBV-negative one, characterized by frequent TET2 and DNMT3A mutations and the paucity of CD79B, MYD88, CDKN2A, and FAS alterations. Our findings illustrate unique genetic features of EBV-associated lymphomas, also suggesting a potential role of detecting PD-L1/PD-L2-involving lesions for these lymphomas to be effectively targeted by immune checkpoint blockade.


Unintended pregnancy in the United States: incidence and disparities, 2006.
The incidence of unintended pregnancy is among the most essential health status indicators in the field of reproductive health. One ongoing goal of the US Department of Health and Human Services is to reduce unintended pregnancy, but the national rate has not been estimated since 2001. We combined data on women's pregnancy intentions from the 2006-2008 and 2002 National Survey of Family Growth with a 2008 national survey of abortion patients and data on births from the National Center for Health Statistics, induced abortions from a national abortion provider census, miscarriages estimated from the National Survey of Family Growth and population data from the US Census Bureau. Nearly half (49%) of pregnancies were unintended in 2006, up slightly from 2001 (48%). The unintended pregnancy rate increased to 52 per 1000 women aged 15-44 years in 2006 from 50 in 2001. Disparities in unintended pregnancy rates among subgroups persisted and in some cases increased, and women who were 18-24 years old, poor or cohabiting had rates two to three times the national rate. The unintended pregnancy rate declined notably for teens 15-17 years old. The proportion of unintended pregnancies ending in abortion decreased from 47% in 2001 to 43% in 2006, and the unintended birth rate increased from 23 to 25 per 1000 women 15-44 years old. Since 2001, the United States has not made progress in reducing unintended pregnancy. Rates increased for nearly all groups and remain high overall. Efforts to help women and couples plan their pregnancies, such as increasing access to effective contraceptives, should focus on groups at greatest risk for unintended pregnancy, particularly poor and cohabiting women.


Active living in the trucking sector: environmental barriers and health promotion strategies.
As one of the most underserved segments of the U.S. labor force, truck drivers have been associated with a series of morbid conditions intimately linked to their occupational milieux, their mostly unhealthful nutritional intake and sedentary lifestyles, and their resulting excess weight-gain. This paper reports data from a baseline assessment of 25 trucking work settings located around interstate highways I-40 and I-85 in North Carolina. It examines how the environmental attributes of these work settings influence the physical and recreational activity behaviors of truckers, compares findings with those from other occupational environments, and brings to the fore a new health promotion paradigm for trucking worksites. Findings support growing empirical and anecdotal evidence that trucking work settings remain not only active-living deserts, but overall unhealthful places. A scan of physical, social, and information environments within trucking worksites as well as physical environments of surrounding communities reveal only meager opportunities for physical and recreational activity for truckers. This paper places the highly underserved population of truckers firmly within the discourse of worksite health promotion, and calls for comprehensive multistakeholder wellness strategies that address a multitude of risk factors linked to the occupational context.


Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway.
Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those from Scandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012-0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018-0.022). The NJ tree does not show evidence of any single clades grouping together all individuals from the same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations.


Biocatalytic Cross-Coupling of Aryl Halides with a Genetically Engineered Photosensitizer Artificial Dehalogenase.
Devising artificial photoenzymes for abiological bond-forming reactions is of high synthetic value but also a tremendous challenge. Disclosed herein is the first photobiocatalytic cross-coupling of aryl halides enabled by a designer artificial dehalogenase, which features a genetically encoded benzophenone chromophore and site-specifically modified synthetic NiII(bpy) cofactor with tunable proximity to streamline the dual catalysis. Transient absorption studies suggest the likelihood of energy transfer activation in the elementary organometallic event. This design strategy is viable to significantly expand the catalytic repertoire of artificial photoenzymes for useful organic transformations.


Image driven subject-specific finite element models of spinal biomechanics.
Finite element (FE) modelling is an established technique for investigating spinal biomechanics. Using image data to produce FE models with subject-specific geometry and displacement boundary conditions may help extend their use to the assessment spinal loading in individuals. Lumbar spine magnetic resonance images from nine participants in the supine, standing and sitting postures were obtained and 2D poroelastic FE models of the lumbar spine were created from the supine data. The rigid body translation and rotation of the vertebral bodies as the participant moved to standing or sitting were applied to the model. The resulting pore pressure in the centre of the L4/L5 disc was determined and the sensitivity to the material properties and vertebral body displacements was assessed. Although the limitations of using a 2D model mean the predicted pore pressures are unlikely to be accurate, the results showed that subject-specific variation in geometry and motion during postural change leads to variation in pore pressure. The model was sensitive to the Young׳s modulus of the annulus matrix, the permeability of the nucleus, and the vertical translation of the vertebrae. This study demonstrates the feasibility of using image data to drive subject-specific lumbar spine FE models and indicates where further development is required to provide a method for assessing spinal biomechanics in a wide range of individuals.


Hyperactivation of oxidative mitochondrial metabolism in epithelial cancer cells in situ: visualizing the therapeutic effects of metformin in tumor tissue.
We have recently proposed a new mechanism for explaining energy transfer in cancer metabolism. In this scenario, cancer cells behave as metabolic parasites, by extracting nutrients from normal host cells, such as fibroblasts, via the secretion of hydrogen peroxide as the initial trigger. Oxidative stress in the tumor microenvironment then leads to autophagy-driven catabolism, mitochondrial dys-function, and aerobic glycolysis. This, in turn, produces high-energy nutrients (such as L-lactate, ketones, and glutamine) that drive the anabolic growth of tumor cells, via oxidative mitochondrial metabolism. A logical prediction of this new "parasitic" cancer model is that tumor-associated fibroblasts should show evidence of mitochondrial dys-function (mitophagy and aerobic glycolysis). In contrast, epithelial cancer cells should increase their oxidative mitochondrial capacity. To further test this hypothesis, here we subjected frozen sections from human breast tumors to a staining procedure that only detects functional mitochondria. This method detects the in situ enzymatic activity of cytochrome C oxidase (COX), also known as Complex IV. Remarkably, cancer cells show an over-abundance of COX activity, while adjacent stromal cells remain essentially negative. Adjacent normal ductal epithelial cells also show little or no COX activity, relative to epithelial cancer cells. Thus, oxidative mitochondrial activity is selectively amplified in cancer cells. Although COX activity staining has never been applied to cancer tissues, it could now be used routinely to distinguish cancer cells from normal cells, and to establish negative margins during cancer surgery. Similar results were obtained with NADH activity staining, which measures Complex I activity, and succinate dehydrogenase (SDH) activity staining, which measures Complex II activity. COX and NADH activities were blocked by electron transport inhibitors, such as Metformin. This has mechanistic and clinical implications for using Metformin as an anti-cancer drug, both for cancer therapy and chemo-prevention. We also immuno-stained human breast cancers for a series of well-established protein biomarkers of metabolism. More specifically, we now show that cancer-associated fibroblasts over-express markers of autophagy (cathepsin B), mitophagy (BNIP3L), and aerobic glycolysis (MCT4). Conversely, epithelial cancer cells show the over-expression of a mitochondrial membrane marker (TOMM20), as well as key components of Complex IV (MT-CO1) and Complex II (SDH-B). We also validated our observations using a bioinformatics approach with data from > 2,000 breast cancer patients, which showed the transcriptional upregulation of mitochondrial oxidative phosphorylation (OXPHOS) in human breast tumors (p < 10(-20)), and a specific association with metastasis. Therefore, upregulation of OXPHOS in epithelial tumor cells is a common feature of human breast cancers. In summary, our data provide the first functional in vivo evidence that epithelial cancer cells perform enhanced mitochondrial oxidative phosphorylation, allowing them to produce high amounts of ATP. Thus, we believe that mitochondria are both the "powerhouse" and "Achilles' heel" of cancer cells.


Endocannabinoid system and pregnancy.
The endocannabinoid system (eCS), is a complex system, comprising the main endogenous ligands anandamide and 2-arachidonoyl glycerol, the cannabinoid receptors CB1 and CB2 and the biosynthetic and degrading enzymes. Cumulative evidence shows that the eCS plays an important role in reproduction, from egg fertilization to parturition. Therefore, alterations in this system, either by recreation/therapeutic use of cannabis or deregulation of the endogenous cannabinoids, might lead to adverse pregnancy outcomes, including retardation in embryo development, poor blastocyst implantation, inhibition of decidualization, miscarriage and compromised placentation. Nevertheless, the molecular mechanisms by which the eCS participates in different stages of pregnancy remain poorly understood. In this review, we will examine the evidence from animal and human studies to support the role of the eCS in implantation, early-to-late pregnancy and placentation as well as the difficulties of targeting this system for treatment of female infertility.


Hypnosis for pain management during labour and childbirth.
This review is one in a series of Cochrane reviews investigating pain management for childbirth. These reviews all contribute to an overview of systematic reviews of pain management for women in labour, and share a generic protocol. This review updates an earlier version of the review of the same title. To examine the effectiveness and safety of hypnosis for pain management during labour and childbirth. We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (30 September 2015) and the reference lists of primary studies and review articles. Randomised controlled trials (RCTs) and quasi-RCTS comparing preparation for labour using hypnosis and/or use of hypnosis during labour, with or without concurrent use of pharmacological or non-pharmacological pain relief methods versus placebo, no treatment or any analgesic drug or technique. Two review authors independently extracted data and assessed trial quality. Where possible we contacted study authors seeking additional information about data and methodology. We included nine trials randomising a total of 2954 women. The risk of bias in trials was variable, there were several well-designed large trials and some trials where little was reported about trial design. Although eight of the nine trials assessed antenatal hypnotherapy, there were considerable differences between these trials in timing and technique. One trial provided hypnotherapy during labour. In this updated review we compared hypnosis interventions with all control groups (main comparison) and also with specific control conditions: standard care (nine RCTs), supportive counselling (two RCTs) and relaxation training (two RCTs).In the main comparison, women in the hypnosis group were less likely to use pharmacological pain relief or analgesia than those in the control groups, (average risk ratio (RR) 0.73, 95% CI 0.57 to 0.94, eight studies, 2916 women; very low-quality evidence; random-effects model). There were no clear differences between women in the hypnosis group and those in the control groups for most of the other primary outcomes. There were no clear differences for sense of coping with labour (MD 0.22, 95% CI -0.14 to 0.58, one study, 420 women; low-quality evidence) or spontaneous vaginal birth (average RR 1.12, 95% CI 0.96 to 1.32, six studies, 2361 women; low-quality evidence; random-effects model). There were no clear differences for satisfaction with pain relief (measured on a seven-point scale two weeks postnatally) for women in the hypnosis group who also received pethidine (MD 0.41, 95% CI -0.45 to 1.27; one study, 72 women), Entonox (MD 0.19, 95% CI -0.19 to 0.57; one study, 357 women), self-hypnosis (MD 0.28, 95% CI -0.32 to 0.88; one study, 160 women), or epidural (MD -0.03, 95% CI -0.40 to 0.34; one study, 127 women), but a slight benefit in favour of hypnosis was seen for women who received water immersion (MD 0.52, 95% CI 0.04 to 1.00; one study, 174 women (all low-quality evidence). There were no clear differences for satisfaction with pain relief when it was measured as the number of women who reported they had adequate pain relief (risk ratio (RR) 1.06, 95% confidence interval (CI) 0.94 to 1.20, one study, 264 women; low-quality evidence). It should be noted that for pharmacological pain relief and spontaneous vaginal birth, there was evidence of considerable statistical heterogeneity, which could not be fully explained by subgroup analysis.For this review's secondary outcomes, no clear differences were found between women in the hypnosis group and women in the control groups for most outcomes where data were available. There was mixed evidence regarding benefits for women in the hypnosis group compared with all control groups for pain intensity, satisfaction with childbirth experience and postnatal depression. For each of these outcomes, data from more than one trial were available for analysis but could not be combined due to differences in measurement methods. There was evidence that fewer women in the hypnosis group stayed in hospital for more than two days after the birth but this finding was based on one small study (RR 0.11, 95% CI 0.02 to 0.83). No clear differences between women in the hypnosis group and the control groups were found for the other secondary outcomes where data were available.In the comparisons of hypnosis with specific types of control conditions: standard care, supportive counselling and relaxation training, there were no clear differences found between women in the hypnosis group and those in the standard care control groups or the relaxation control groups for the primary outcomes. Compared with the women in the supportive counselling control group, women in the hypnosis group were less likely to use pharmacological analgesia (average RR 0.48, 95% CI 0.32 to 0.73, two studies, 562 women). They were also more likely to have a spontaneous vaginal birth (RR 2.42, 95% CI 1.43 to 4.07), although this finding was based on the results of one small study. Overall these new comparisons displayed much less statistical heterogeneity than the comparison including all control groups. There are still only a relatively small number of studies assessing the use of hypnosis for labour and childbirth. Hypnosis may reduce the overall use of analgesia during labour, but not epidural use. No clear differences were found between women in the hypnosis group and those in the control groups for satisfaction with pain relief, sense of coping with labour or spontaneous vaginal birth. Not enough evidence currently exists regarding satisfaction with pain relief or sense of coping with labour and we would encourage any future research to prioritise the measurement of these outcomes. The evidence for the main comparison was assessed using GRADE as being of low quality for all the primary outcomes with downgrading decisions due to concerns regarding inconsistency of the evidence, limitations in design and imprecision. Further research is needed in the form of large, well-designed randomised controlled trials to assess whether hypnosis is of value for pain management during labour and childbirth.


Maternal position during the first stage of labor: a systematic review.
Policy makers and health professionals are progressively using evidence-based rationale to guide their decisions. There has long been controversy regarding which maternal position is more appropriate during the first stage of labor. This problem has been examined often and repeatedly and the optimal recommendation remains unclear. This is a systematic review of the effect of maternal position during the first stage of labor. The main question addressed here is: Does encouraging women to adopt an upright position or to ambulate during the first stage of labor reduce the duration of this stage? All randomized controlled trials carried out to assess this effect were taken into consideration in this review. The following electronic databases were accessed to identify studies: MEDLINE, Popline, the Scientific Electronic Library On-line and the Latin American and Caribbean Health Science Information. Citation eligibility was independently assessed by two reviewers. The methodological quality of each trial was also evaluated independently by two reviewers and a trial under consideration was included only when consensus had been attained. Allocation concealment and screening for the occurrence of attrition, performance and detection biases were considered when studies were appraised. The decision whether to perform data pooling was based on the clinical similarity of studies. The search strategy resulted in 260 citations, of which 18 were assessed in full-text. Nine eligible randomized controlled trials were included in the systematic review. Randomization methods were not fully described in eight studies. The allocation concealment was considered adequate in four studies and unclear in five. The investigators pooled the data from seven studies in which the length of the first stage of labor and results were in favor of the intervention, but the high level of heterogeneity (I2 = 88.4%) impaired the meaning of this finding. The intervention did not affect other outcomes studied (mode of delivery, use of analgesia, labor augmentation and condition of the child at birth). Adoption of the upright position or ambulation during first stage of labor may be safe, but considering the available evidence and its consistency, it cannot be recommended as an effective intervention to reduce duration of the first stage of labor.


Atmospheric trace gases support primary production in Antarctic desert surface soil.
Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities. Given that phototroph abundance varies across these Antarctic soils, an enduring question is what supports life in those communities with low photosynthetic capacity. Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation. Soil microcosms aerobically scavenged atmospheric H2 and CO at rates sufficient to sustain their theoretical maintenance energy and mediated substantial levels of chemosynthetic but not photosynthetic CO2 fixation. We propose that atmospheric H2, CO2 and CO provide dependable sources of energy and carbon to support these communities, which suggests that atmospheric energy sources can provide an alternative basis for ecosystem function to solar or geological energy sources. Although more extensive sampling is required to verify whether this process is widespread in terrestrial Antarctica and other oligotrophic habitats, our results provide new understanding of the minimal nutritional requirements for life and open the possibility that atmospheric gases support life on other planets.


Relative importance of prenatal and postnatal determinants of stunting: data mining approaches to the MINIMat cohort, Bangladesh.
WHO has set a goal to reduce the prevalence of stunted child growth by 40% by the year 2025. To reach this goal, it is imperative to establish the relative importance of risk factors for stunting to deliver appropriate interventions. Currently, most interventions take place in late infancy and early childhood. This study aimed to identify the most critical prenatal and postnatal determinants of linear growth 0-24 months and the risk factors for stunting at 2 years, and to identify subgroups with different growth trajectories and levels of stunting at 2 years. Conditional inference tree-based methods were applied to the extensive Maternal and Infant Nutrition Interventions in Matlab trial database with 309 variables of 2723 children, their parents and living conditions, including socioeconomic, nutritional and other biological characteristics of the parents; maternal exposure to violence; household food security; breast and complementary feeding; and measurements of morbidity of the mothers during pregnancy and repeatedly of their children up to 24 months of age. Child anthropometry was measured monthly from birth to 12 months, thereafter quarterly to 24 months. Birth length and weight were the most critical factors for linear growth 0-24 months and stunting at 2 years, followed by maternal anthropometry and parental education. Conditions after birth, such as feeding practices and morbidity, were less strongly associated with linear growth trajectories and stunting at 2 years. The results of this study emphasise the benefit of interventions before conception and during pregnancy to reach a substantial reduction in stunting.


Structural brain anomalies and chronic pain: a quantitative meta-analysis of gray matter volume.
The diversity of chronic pain syndromes and the methods employed to study them make integrating experimental findings challenging. This study performed coordinate-based meta-analyses using voxel-based morphometry imaging results to examine gray matter volume (GMV) differences between chronic pain patients and healthy controls. There were 12 clusters where GMV was decreased in patients compared with controls, including many regions thought to be part of the "pain matrix" of regions involved in pain perception, but also including many other regions that are not commonly regarded as pain-processing areas. The right hippocampus and parahippocampal gyrus were the only regions noted to have increased GMV in patients. Functional characterizations were implemented using the BrainMap database to determine which behavioral domains were significantly represented in these regions. The most common behavioral domains associated with these regions were cognitive, affective, and perceptual domains. Because many of these regions are not classically connected with pain and because there was such significance in functionality outside of perception, it is proposed that many of these regions are related to the constellation of comorbidities of chronic pain, such as fatigue and cognitive and emotional impairments. Further research into the mechanisms of GMV changes could provide a perspective on these findings. Quantitative meta-analyses revealed structural differences between brains of individuals with chronic pain and healthy controls. These differences may be related to comorbidities of chronic pain.


Giant enhancement of second harmonic generation in nonlinear photonic crystals with distributed Bragg reflector mirrors.
We theoretically investigate second harmonic generation (SHG) in one-dimensional multilayer nonlinear photonic crystal (NPC) structures with distributed Bragg reflector (DBR) as mirrors. The NPC structures have periodic modulation on both the linear and second-order susceptibility. Three major physical mechanisms, quasi-phase matching (QPM) effect, slow light effect at photonic band gap edges, and cavity effect induced by DBR mirrors can be harnessed to enhance SHG. Selection of appropriate structural parameters can facilitate coexistence of these mechanisms to act collectively and constructively to create very high SHG conversion efficiency with an enhancement by up to seven orders of magnitude compared with the ordinary NPC where only QPM works.


Hypoxia primed placental mesenchymal stem cells for wound healing.
To investigate how Placental Mesenchymal Stem Cells (P-MSCs) would adapt themselves and survive under hypoxic conditions which are prevalent in most injury sites. P-MSCs were isolated from term placenta and characterised under normoxia and hypoxia (2-2.5% O2). Cells were examined for morphology and surface marker variations by flow cytometry analysis. Glucose stimulated insulin secretion was assayed by Insulin ELISA Kit. Gene expression levels were estimated using Real Time PCR for hypoxia inducible factor1 alpha, Insulin (INS), Glucose transporters (GLUT-1, GLUT-2 and GLUT-3), Adhesion Proteins- Integrins, Fibronectin1 (FN1), E-Cadherin (CDH1), and N-Cadherin (CDH2) and angiogenesis marker VEGFA. Immunofluorescence assay was done to confirm the presence of C-Peptide, GLUT 2, E-Cadherin and ITGB3. Adhesion was confirmed assessed on fibronectin binding. We show that insulin secretion is not hampered under hypoxia. We found an upregulation of glucose transporters under hypoxia indicating enhanced glucose uptake needed to cater to metabolic demands of proliferating cells. Up regulation of adhesion molecules was seen under hypoxia indicative of a favoured environment for retention of cells at the injury site. We also found increased level of angiogenesis of P-MSCs under hypoxia. Our present study thus demonstrates for the first time that P-MSCs modulate themselves under hypoxic conditions by secreting insulin, up regulating glucose transporters and adhesion molecules and eventually exhibiting an increased angiogenic potential. We thus infer that priming P-MSCs under hypoxia, could make them more suitable for wound healing applications.


Influence of phytase on water-soluble phosphorus in poultry and swine manure.
The effect of dietary non-phytin phosphorus (NPP) and phytase (PHY) concentration on total phosphorus (TP) and water-soluble phosphorus (WSP) excretion was determined. Diets tested in broiler experiments were: National Research Council nutrient requirements for non-phytin phosphorus (NRC), NRC + PHY, reduced non-phytin phosphorus (RED), and RED + PHY. Turkey and swine experiment diets included NRC, RED, and RED + PHY. For all experiments, except broiler Experiment 1, excreta were: (i) boiled, antibiotic added, then frozen; (ii) boiled, antibiotic added, incubated (37 degrees C for 72 h), then frozen; and (iii) incubated, boiled, antibiotic added, then frozen. In Experiment 1, excreta were collected and frozen or incubated for 24 or 48 h. In broiler Experiment 1, WSP was not affected by phytase but increased with post-excretion incubation. In a broiler Experiment 2, reducing NPP resulted in reduced excreta TP and WSP (11.3 to 8.3 and 5.3 to 2.7 g kg(-1)). Feeding RED + PHY diets resulted in less TP and WSP (7.6 and 0.6 g kg(-1)) as compared with NRC + PHY (11.2 and 3.9 g kg(-1), Experiment 3). Incubation resulted in increased WSP, irrespective of phytase addition such that WSP as a percent of TP was similar among treatments. Addition of antibiotics before incubation prevented the increase in WSP. Similar results were observed with turkey and swine. Therefore, when phytase is used properly (i.e., with a simultaneous reduction of NPP), WSP or WSP as a percent of TP are not affected. The increase in WSP as a percent of TP post-excretion is a function of excreta microbial activity and not dietary phytase addition.


CressExpress: a tool for large-scale mining of expression data from Arabidopsis.
CressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data that computes patterns of correlated expression between user-entered query genes and the rest of the genes in the genome. Unlike other coexpression tools, CressExpress allows characterization of tissue-specific coexpression networks through user-driven filtering of input data based on sample tissue type. CressExpress also performs pathway-level coexpression analysis on each set of query genes, identifying and ranking genes based on their common connections with two or more query genes. This allows identification of novel candidates for involvement in common processes and functions represented by the query group. Users launch experiments using an easy-to-use Web-based interface and then receive the full complement of results, along with a record of tool settings and parameters, via an e-mail link to the CressExpress Web site. Data sets featured in CressExpress are strictly versioned and include expression data from MAS5, GCRMA, and RMA array processing algorithms. To demonstrate applications for CressExpress, we present coexpression analyses of cellulose synthase genes, indolic glucosinolate biosynthesis, and flowering. We show that subselecting sample types produces a richer network for genes involved in flowering in Arabidopsis. CressExpress provides direct access to expression values via an easy-to-use URL-based Web service, allowing users to determine quickly if their query genes are coexpressed with each other and likely to yield informative pathway-level coexpression results. The tool is available at http://www.cressexpress.org.


Action potential and contractility changes in [Na(+)](i) overloaded cardiac myocytes: a simulation study.
Sodium overload of cardiac cells can accompany various pathologies and induce fatal cardiac arrhythmias. We investigate effects of elevated intracellular sodium on the cardiac action potential (AP) and on intracellular calcium using the Luo-Rudy model of a mammalian ventricular myocyte. The results are: 1) During rapid pacing, AP duration (APD) shortens in two phases, a rapid phase without Na(+) accumulation and a slower phase that depends on [Na(+)](i). 2) The rapid APD shortening is due to incomplete deactivation (accumulation) of I(Ks). 3) The slow phase is due to increased repolarizing currents I(NaK) and reverse-mode I(NaCa), secondary to elevated [Na(+)](i). 4) Na(+)-overload slows the rate of AP depolarization, allowing time for greater I(Ca(L)) activation; it also enhances reverse-mode I(NaCa). The resulting increased Ca(2+) influx triggers a greater [Ca(2+)](i) transient. 5) Reverse-mode I(NaCa) alone can trigger Ca(2+) release in a voltage and [Na(+)](i)-dependent manner. 6) During I(NaK) block, Na(+) and Ca(2+) accumulate and APD shortens due to enhanced reverse-mode I(NaCa); contribution of I(K(Na)) to APD shortening is negligible. By slowing AP depolarization (hence velocity) and shortening APD, Na(+)-overload acts to enhance inducibility of reentrant arrhythmias. Shortened APD with elevated [Ca(2+)](i) (secondary to Na(+)-overload) also predisposes the myocardium to arrhythmogenic delayed afterdepolarizations.


The relative dose response test based on retinol-binding protein 4 is not suitable to assess vitamin A status in very low birth weight infants.
The relative dose response (RDR) test, which quantifies the increase in serum retinol after vitamin A administration, is a qualitative measure of liver vitamin A stores. Particularly in preterm infants, the feasibility of the RDR test involving blood is critically dependent on small sample volumes. This study aimed to assess whether the RDR calculated with retinol-binding protein 4 (RBP4) might be a substitute for the classical retinol-based RDR test for assessing vitamin A status in very preterm infants. This study included preterm infants with a birth weight below 1,500 g (n = 63, median birth weight 985 g, median gestational age 27.4 weeks) who were treated with 5,000 IU retinyl palmitate intramuscularly 3 times a week for 4 weeks. On day 3 (first vitamin A injection) and day 28 of life (last vitamin A injection), the RDR was calculated and compared using serum retinol and RBP4 concentrations. The concentrations of retinol (p < 0.001) and RBP4 (p < 0.01) increased significantly from day 3 to day 28. On day 3, the median (IQR) retinol-RDR was 27% (8.4-42.5) and the median RBP4-RDR was 8.4% (-3.4 to 27.9), compared to 7.5% (-10.6 to 20.8) and -0.61% (-19.7 to 15.3) on day 28. The results for retinol-RDR and RBP4-RDR revealed no significant correlation. The agreement between retinol-RDR and RBP4-RDR was poor (day 3: Cohen's κ = 0.12; day 28: Cohen's κ = 0.18). The RDR test based on circulating RBP4 is unlikely to reflect the hepatic vitamin A status in preterm infants.


Neuromuscular function of the plantar flexors and predictors of peak power in middle-aged and older males.
Little evidence exists regarding the contribution of torque and velocity to the age-related decrease in peak power (PP) for the plantar flexors (PFs). A comprehensive assessment of PF neuromuscular function is necessary to elucidate age-related changes, especially between middle-aged and older adults, in order to identify early, age-related decrements. Thus, the purpose of this study was to examine neuromuscular function of the PFs in middle-aged and older males, and identify predictors of PP. Twenty-eight healthy, middle-aged (n = 13; 45.1 ± 2.7 yrs) and older (n = 15; 65.3 ± 3.2 yrs) males performed concentric isotonic PF contractions ranging in intensity from 20% to 70% isometric strength using a dynamometer. PP in addition to velocity and torque at the moment in time PP occurred, as well as the rate of velocity, torque (RTD), and power (RPD) development were recorded. The rate of electromyography rise (RER) was derived from the linear slope of the normalized electromyography signal. Isometric and concentric dynamic strength were assessed, as well as cross-sectional area and muscle quality (i.e., echo intensity) of the PFs via panoramic ultrasonography. The relationship between serum c-terminal agrin levels and select variables was examined to explore the potential role of neuromuscular junction deterioration. Appendicular lean mass and physical activity level were similar between groups (p > 0.05), and only PP (p = 0.046; d = 0.79), RPD (p = 0.026; d = 0.90), RTD (p = 0.022; d = 0.91), and RER (p = 0.010; d = 1.04) were lower in older males. When groups were collapsed, RTD was the only significant predictor of PP, while c-terminal agrin levels were not associated with any variables. Our findings indicate that PP and time-dependent parameters of muscle activation and contractile function of the PFs are dramatically diminished in older adults compared to middle-aged adults. PP is produced at the same velocity and relative intensity in middle-aged and older males, and RTD is most influential for PP. The inability of the PFs to be rapidly activated appeared to be influential for the age-related impairment in PP and time-dependent contractile parameters.


Evaluation of a rapid test for the detection of antibodies to human immunodeficiency virus type 1 and 2 in the setting of multiple transmitted viral subtypes.
Rapid HIV testing is an appealing strategy in the approach to HIV diagnosis in developing countries. Concern has been raised about the use of these tests in the setting of multiple transmitted HIV subtypes. We sought to compare the OraQuick(TM) HIV-1/2 Test, a qualitative immunochromatographic test for the detection of antibodies to HIV-1 and HIV-2 using stored sera, with a conventional enzyme immunoassay (EIA)/Western blot (WB) algorithm. The study design used was a blinded retrospective study. Samples were collected on patients attending sexually transmitted disease clinics and tuberculosis clinics in Kinshasa, the Democratic Republic of Congo and included 72 known HIV seropositive and 131 known HIV seronegative subjects. All 72 known HIV seropositive samples were positive by OraQuick and all 131 known HIV seronegative samples were negative by OraQuick resulting in 100% sensitivity and specificity. We conclude that the OraQuick rapid HIV-1/2 test performs well in the setting of diverse HIV viral subtypes.


Flow-induced demixing of polymer-colloid mixtures in microfluidic channels.
We employ extensive computer simulations to study the flow behavior of spherical, nanoscale colloids in a viscoelastic solvent under Poiseuille flow. The systems are confined in a slit-like microfluidic channel, and viscoelasticity is introduced explicitly through the inclusion of polymer chains on the same length scale as the dispersed solute particles. We systematically study the effects of flow strength and polymer concentration, and identify a regime in which the colloids migrate to the centerline of the microchannel, expelling the polymer chains to the sides. This behavior was recently identified in experiments, but a detailed understanding of the underlying physics was lacking. To this end, we provide a detailed analysis of this phenomenon and discuss ways to maximize its effectiveness. The focusing mechanism can be exploited to separate and capture particles at the sub-micrometer scale using simple microfluidic devices, which is a crucial task for many biomedical applications, such as cell counting and genomic mapping.


Diagnostics in Ebola Virus Disease in Resource-Rich and Resource-Limited Settings.
The Ebola virus disease (EVD) outbreak in West Africa was unprecedented in scale and location. Limited access to both diagnostic and supportive pathology assays in both resource-rich and resource-limited settings had a detrimental effect on the identification and isolation of cases as well as individual patient management. Limited access to such assays in resource-rich settings resulted in delays in differentiating EVD from other illnesses in returning travellers, in turn utilising valuable resources until a diagnosis could be made. This had a much greater impact in West Africa, where it contributed to the initial failure to contain the outbreak. This review explores diagnostic assays of use in EVD in both resource-rich and resource-limited settings, including their respective limitations, and some novel assays and approaches that may be of use in future outbreaks.


Effect of spatial coherence on scattering from optically inhomogeneous media.
The properties of light scattered from material systems depend on the characteristics of input optical fields. We study numerically the effect of the state of spatial coherence on the properties of scattered fields. Using a customized coupled dipole technique, we demonstrate that this influence manifests in changes of the statistics of intensities scattered at different angles.


Enumeration of Salmonella and Escherichia coli O157:H7 in ground beef, cattle carcass, hide and faecal samples using direct plating methods.
To develop and validate high throughput methods for the direct enumeration of viable and culturable Salmonella and Escherichia coli O157:H7 in ground beef, carcass, hide and faecal (GCHF) samples from cattle. The hydrophobic grid membrane filtration (HGMF) method and the spiral plate count method (SPCM) were evaluated as rapid tools for the estimation of pathogen load using GCHF samples spiked with known levels of Salmonella serotype Typhimurium. Validation studies showed that for a single determination of each sample type the low end of the detection limits were approx. 2.0 x 10(0) CFU g(-1) for ground beef, 5.0 x 10(-1) CFU (100 cm(2))(-1) for Salmonella and 8.0 x 10(-1) CFU (100 cm(2))(-1) for E. coli O157:H7 on carcasses, 4.0 x 10(1) CFU (100 cm(2))(-1) for hide and 2.0 x 10(2) CFU g(-1) for faecal samples. In addition, ground beef (n = 609), carcass (n = 1520) and hide (n = 3038) samples were collected from beef-processing plants and faecal samples (n = 3190) were collected from feed-lot cattle, and these samples were tested for the presence of Salmonella and E. coli O157:H7 by enrichment and enumeration methods. The direct enumeration methods described here are amenable to high throughput sample processing and were found to be cost-effective alternatives to other enumeration methods for the estimation of Salmonella and E. coli O157:H7, in samples collected during cattle production and beef processing. Use of the methods described here would allow for more routine testing and quantification data collection, providing useful information about the effectiveness of beef processing intervention strategies.


Structural analysis of a new series of oligosaccharide-alditols released by reductive beta-elimination from oviducal mucins of Rana utricularia.
Egg jelly coats from Rana utricularia are formed by components secreted along the oviduct. These secretion products overlay the oocytes as they pass along the different oviducal portions. In this study, carbohydrate chains of the jelly coat surrounding the eggs of R. utricularia were released by alkali/borohydride treatment. Fractionation of O-linked oligosaccharide-alditols was achieved by a combination of chromatographic techniques comprising anion-exchange chromatography, gel-permeation chromatography and HPLC on a silica column bonded with aminopropyl groups. Structural characterization was performed by one- and two-dimensional 1H-NMR spectroscopy in combination with matrix-assisted laser-desorption ionization-time of flight MS and methylation analysis. Ten oligosaccharide structures possessing a core consisting of Galbeta(1-->3)GalNAc-ol with or without branching through a GlcNAc residue linked beta(1-->6) to the GalNAc residue (core type 2 or core type 1 respectively) are described. The most representative carbohydrate sequences are: GlcNAc(beta1-3)[Fuc(alpha1-4)]GlcNAc, GalNAc(alpha1-3)[Fuc(alpha1-2)]Gal(beta1-4)GlcNAc(beta1-3)GlcNAc and Gal(beta1-3)GlcNAc(alpha1-3)[Fuc(alpha1-2)]Gal(beta1-4)GlcNAc. The carbohydrate chains isolated from R. utricularia are quite different from those found in other amphibian species, in which the presence of species-specific material has been characterized. Since the jellies surrounding amphibian eggs are involved in egg-sperm interactions, these structural investigations can provide biochemical support for investigation of the fertilization process.


Prevalence of sleepiness while driving four-wheel motor vehicles in Fiji: a population-based survey (TRIP 9).
Sleepiness has been shown to be a risk factor for road crashes in high-income countries, but has received little attention in low- and middle-income countries. We examined the prevalence of sleepiness and sleep-related disorders among drivers of four-wheel motor vehicles in Fiji. Using a two-stage cluster sampling roadside survey conducted over 12 months, we recruited a representative sample of people driving four-wheel motor vehicles on the island of Viti Levu, Fiji. A structured interviewer-administered questionnaire sought self-report information on driver characteristics including sleep-related measures. The 752 motor vehicle drivers recruited (84% response rate) were aged 17-75 years, with most driving in Viti Levu undertaken by male subjects (93%), and those identifying with Indian (70%) and Fijian (22%) ethnic groups. Drivers who reported that they were not fully alert accounted for 17% of driving, while a further 1% of driving was undertaken by those who reported having difficulty staying awake or feeling sleepy. A quarter of the driving time among 15-24-year-olds included driving while sleepy or not fully alert, with a similar proportion driving while chronically sleep deprived (ie, with less than five nights of adequate sleep in the previous week=27%). Driving while acutely or chronically sleep deprived was generally more common among Fijians compared with Indians. Driving while not fully alert is relatively common in Fiji. Sleepiness while driving may be an important contributor to road traffic injuries in this and other low- and middle-income countries.