Transmission of community- and hospital-acquired SARS-CoV-2 in hospital settings in the UK: A cohort study.
Nosocomial spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been widely reported, but the transmission pathways among patients and healthcare workers (HCWs) are unclear. Identifying the risk factors and drivers for these nosocomial transmissions is critical for infection prevention and control interventions. The main aim of our study was to quantify the relative importance of different transmission pathways of SARS-CoV-2 in the hospital setting. This is an observational cohort study using data from 4 teaching hospitals in Oxfordshire, United Kingdom, from January to October 2020. Associations between infectious SARS-CoV-2 individuals and infection risk were quantified using logistic, generalised additive and linear mixed models. Cases were classified as community- or hospital-acquired using likely incubation periods of 3 to 7 days. Of 66,184 patients who were hospitalised during the study period, 920 had a positive SARS-CoV-2 PCR test within the same period (1.4%). The mean age was 67.9 (±20.7) years, 49.2% were females, and 68.5% were from the white ethnic group. Out of these, 571 patients had their first positive PCR tests while hospitalised (62.1%), and 97 of these occurred at least 7 days after admission (10.5%). Among the 5,596 HCWs, 615 (11.0%) tested positive during the study period using PCR or serological tests. The mean age was 39.5 (±11.1) years, 78.9% were females, and 49.8% were nurses. For susceptible patients, 1 day in the same ward with another patient with hospital-acquired SARS-CoV-2 was associated with an additional 7.5 infections per 1,000 susceptible patients (95% credible interval (CrI) 5.5 to 9.5/1,000 susceptible patients/day) per day. Exposure to an infectious patient with community-acquired Coronavirus Disease 2019 (COVID-19) or to an infectious HCW was associated with substantially lower infection risks (2.0/1,000 susceptible patients/day, 95% CrI 1.6 to 2.2). As for HCW infections, exposure to an infectious patient with hospital-acquired SARS-CoV-2 or to an infectious HCW were both associated with an additional 0.8 infection per 1,000 susceptible HCWs per day (95% CrI 0.3 to 1.6 and 0.6 to 1.0, respectively). Exposure to an infectious patient with community-acquired SARS-CoV-2 was associated with less than half this risk (0.2/1,000 susceptible HCWs/day, 95% CrI 0.2 to 0.2). These assumptions were tested in sensitivity analysis, which showed broadly similar results. The main limitations were that the symptom onset dates and HCW absence days were not available. In this study, we observed that exposure to patients with hospital-acquired SARS-CoV-2 is associated with a substantial infection risk to both HCWs and other hospitalised patients. Infection control measures to limit nosocomial transmission must be optimised to protect both staff and patients from SARS-CoV-2 infection.


Effectiveness of recruitment in clinical trials: an analysis of methods used in a trial for irritable bowel syndrome patients.
A successful clinical trial is dependent on recruitment. Between December 2003 and February 2006, our team successfully enrolled 289 participants in a large, single-center, randomized placebo-controlled trial (RCT) studying the impact of the patient-doctor relationship and acupuncture on irritable bowel syndrome (IBS) patients. This paper reports on the effectiveness of standard recruitment methods such as physician referral, newspaper advertisements, fliers, audio and video media (radio and television commercials) as well as relatively new methods not previously extensively reported on such as internet ads, ads in mass-transit vehicles and movie theater previews. We also report the fraction of cost each method consumed and fraction of recruitment each method generated. Our cost per call from potential participants varied from $3-$103 and cost per enrollment participant varied from $12-$584. Using a novel metric, the efficacy index, we found that physician referrals and flyers were the most effective recruitment method in our trial. Despite some methods being more efficient than others, all methods contributed to the successful recruitment. The iterative use of the efficacy index during a recruitment campaign may be helpful to calibrate and focus on the most effective recruitment methods.


Reassuring results with regard to the effect of donor nephrectomy on cardiovascular outcomes.
This article discusses the conclusions of a retrospective cohort study reported by Garg et al. on behalf of the Donor Nephrectomy Outcomes Research (DONOR) Network. This study compared the incidence of cardiovascular events in a cohort of kidney donors with that in a matched control population, to establish whether living kidney donation is associated with increased cardiovascular risk. Garg et al. found that living kidney donors had a very low risk of death or cardiovascular events that was not significantly different to that of the control population (2.0 vs 2.7 events per 1,000 person-years; hazard ratio 0.7, 95% CI 0.4-1.2). During follow-up, hypertension was diagnosed more frequently among donors than controls, but this finding might reflect the close monitoring of donors. Although the study provides reassuring information for counseling potential kidney donors, the sample of patients was not sufficiently large to resolve uncertainties over the influence of reduced kidney function on the risk of cardiovascular disease.


Acanthosis nigricans in a patient with metastatic insulinoma post peptide receptor radionuclide therapy.
Acanthosis nigricans (AN) is a common dermatosis associated with hyperinsulinemia and insulin resistance. However, AN has been rarely reported in patients with insulinoma, a state of persistent hyperinsulinemia. We present a case of metastatic insulinoma, in whom AN manifested after the first cycle of peptide receptor radionuclide therapy (PRRT). A 40-year-old man was diagnosed with metastatic insulinoma after 5 months of symptomatic hypoglycemia. Within 1 month post PRRT, the patient became euglycemic but developed a pigmented, pruritic rash which was confirmed on biopsy as AN. We discuss the rare manifestation of AN in subjects with insulinoma, the role of insulin in the pathogenesis of AN, malignant AN in non-insulin-secreting malignancies and association with other insulin-resistant endocrinopathies such as acromegaly. Acanthosis nigricans (AN) is a common dermatosis which is typically asymptomatic and associated with the hyperinsulinemic state. Malignant AN can rapidly spread, cause pruritus and affect mucosa and the oral cavity. AN is extremely rare in patients with insulinoma despite marked hyperinsulinemia. Peptide receptor radionuclide therapy might have triggered TGF-α secretion in this subject which led to malignant AN. Rapid spread or unusual distribution of pruritic AN warrants further investigation to exclude underlying malignancy.


A mathematical model of the metabolic and perfusion effects on cortical spreading depression.
Cortical spreading depression (CSD) is a slow-moving ionic and metabolic disturbance that propagates in cortical brain tissue. In addition to massive cellular depolarizations, CSD also involves significant changes in perfusion and metabolism-aspects of CSD that had not been modeled and are important to traumatic brain injury, subarachnoid hemorrhage, stroke, and migraine. In this study, we develop a mathematical model for CSD where we focus on modeling the features essential to understanding the implications of neurovascular coupling during CSD. In our model, the sodium-potassium-ATPase, mainly responsible for ionic homeostasis and active during CSD, operates at a rate that is dependent on the supply of oxygen. The supply of oxygen is determined by modeling blood flow through a lumped vascular tree with an effective local vessel radius that is controlled by the extracellular potassium concentration. We show that during CSD, the metabolic demands of the cortex exceed the physiological limits placed on oxygen delivery, regardless of vascular constriction or dilation. However, vasoconstriction and vasodilation play important roles in the propagation of CSD and its recovery. Our model replicates the qualitative and quantitative behavior of CSD--vasoconstriction, oxygen depletion, extracellular potassium elevation, prolonged depolarization--found in experimental studies. We predict faster, longer duration CSD in vivo than in vitro due to the contribution of the vasculature. Our results also help explain some of the variability of CSD between species and even within the same animal. These results have clinical and translational implications, as they allow for more precise in vitro, in vivo, and in silico exploration of a phenomenon broadly relevant to neurological disease.


Anterior brain electrical asymmetries in response to reward and punishment.
A variety of recent research indicates that when subjects are induced to experience certain negative emotions, there is greater suppression of alpha power in the right than left frontal region, while during the experience of positive emotion, alpha power asymmetry in this region shows the opposite pattern. We have conceptualized this asymmetry as reflecting specialization for approach and withdrawal processes in the left and right frontal regions, respectively. In this experiment, reward and punishment contingencies were directly manipulated to produce approach and withdrawal emotional states. In addition, subjects responded to imperative stimuli using either an approach response (finger press) or a withdrawal response (finger lift). EEG was recorded from multiple scalp locations. During the foreperiod prior to the response to the imperative stimuli, the EEG was extracted, Fourier-transformed and power computed in the theta, alpha and beta frequency bands. In addition, the contingent negative variation (CNV) was derived from the identical epoch. Reward trials were associated with greater left frontal alpha power suppression than punishment trials, while during the latter trials, there was greater right-sided frontal alpha power suppression than during reward trials. There was also some evidence to indicate that withdrawal responses were associated with greater right-sided alpha power suppression in the temporo-parietal region compared with approach responses. Power in the theta and beta bands did not systematically vary with condition. The CNV was larger during trials on which subjects responded quickly compared with slow trials, but did not differentiate between reward and punishment contingencies. The findings support the hypothesis that approach-related processes can be differentiated from withdrawal-related processes on the basis of asymmetrical shifts in alpha power in the frontal region. They also indicate that the CNV and spectral power estimates from the identical epochs reflect different neural processes.


Chemotactic cell trapping in controlled alternating gradient fields.
Directed cell migration toward spatio-temporally varying chemotactic stimuli requires rapid cytoskeletal reorganization. Numerous studies provide evidence that actin reorganization is controlled by intracellular redistribution of signaling molecules, such as the PI4,5P2/PI3,4,5P3 gradient. However, exploring underlying mechanisms is difficult and requires careful spatio-temporal control of external chemotactic stimuli. We designed a microfluidic setup to generate alternating chemotactic gradient fields for simultaneous multicell exposure, greatly facilitating statistical analysis. For a quantitative description of intracellular response dynamics, we apply alternating time sequences of spatially homogeneous concentration gradients across 300 μm, reorienting on timescales down to a few seconds. Dictyostelium discoideum amoebae respond to gradient switching rates below 0.02 Hz by readapting their migration direction. For faster switching, cellular repolarization ceases and is completely stalled at 0.1 Hz. In this "chemotactically trapped" cell state, external stimuli alternate faster than intracellular feedback is capable to respond by onset of directed migration. To investigate intracellular actin cortex rearrangement during gradient switching, we correlate migratory cell response with actin repolymerization dynamics, quantified by a fluorescence distribution moment of the GFP fusion protein LimEΔcc. We find two fundamentally different cell polarization types and we could reveal the role of PI3-Kinase for cellular repolarization. In the early aggregation phase, PI3-Kinase enhances the capability of D. discoideum cells to readjust their polarity in response to spatially alternating gradient fields, whereas in aggregation competent cells the effect of PI3-Kinase perturbation becomes less relevant.


Revealing hidden states in visual working memory using electroencephalography.
It is often assumed that information in visual working memory (vWM) is maintained via persistent activity. However, recent evidence indicates that information in vWM could be maintained in an effectively "activity-silent" neural state. Silent vWM is consistent with recent cognitive and neural models, but poses an important experimental problem: how can we study these silent states using conventional measures of brain activity? We propose a novel approach that is analogous to echolocation: using a high-contrast visual stimulus, it may be possible to drive brain activity during vWM maintenance and measure the vWM-dependent impulse response. We recorded electroencephalography (EEG) while participants performed a vWM task in which a randomly oriented grating was remembered. Crucially, a high-contrast, task-irrelevant stimulus was shown in the maintenance period in half of the trials. The electrophysiological response from posterior channels was used to decode the orientations of the gratings. While orientations could be decoded during and shortly after stimulus presentation, decoding accuracy dropped back close to baseline in the delay. However, the visual evoked response from the task-irrelevant stimulus resulted in a clear re-emergence in decodability. This result provides important proof-of-concept for a promising and relatively simple approach to decode "activity-silent" vWM content using non-invasive EEG.


IEEE International Symposium on Biomedical Imaging.
The IEEE International Symposium on Biomedical Imaging (ISBI) is a scientific conference dedicated to mathematical, algorithmic, and computational aspects of biological and biomedical imaging, across all scales of observation. It fosters knowledge transfer among different imaging communities and contributes to an integrative approach to biomedical imaging. ISBI is a joint initiative from the IEEE Signal Processing Society (SPS) and the IEEE Engineering in Medicine and Biology Society (EMBS). The 2018 meeting will include tutorials, and a scientific program composed of plenary talks, invited special sessions, challenges, as well as oral and poster presentations of peer-reviewed papers. High-quality papers are requested containing original contributions to the topics of interest including image formation and reconstruction, computational and statistical image processing and analysis, dynamic imaging, visualization, image quality assessment, and physical, biological, and statistical modeling. Accepted 4-page regular papers will be published in the symposium proceedings published by IEEE and included in IEEE Xplore. To encourage attendance by a broader audience of imaging scientists and offer additional presentation opportunities, ISBI 2018 will continue to have a second track featuring posters selected from 1-page abstract submissions without subsequent archival publication.


Prediction of antiarthritic drug efficacies by monitoring active matrix metalloproteinase-3 (MMP-3) levels in collagen-induced arthritic mice using the MMP-3 probe.
Active matrix metalloproteinase-3 (MMP-3) is a prognostic marker of rheumatoid arthritis (RA). We recently developed an MMP-3 probe that can specifically detect the active form of MMP-3. The aim of this study was to investigate whether detection and monitoring of active MMP-3 could be useful to predict therapeutic drug responses in a collagen-induced arthritis (CIA) model. During the period of treatment with drugs such as methotrexate (MTX) or infliximab (IFX), MMP-3 mRNA and protein levels were correlated with fluorescence signals in arthritic joint tissues and in the serum of CIA mice. Also, bone volume density and erosion in the knee joints and the paws of CIA mice were measured with microcomputed tomography (micro-CT), X-ray, and histology to confirm drug responses. In joint tissues and serum of CIA mice, strong fluorescence signals induced by the action of active MMP-3 were significantly decreased when drugs were applied. The decrease in RA scores in drug-treated CIA mice led to fluorescence reductions, mainly as a result of down-regulation of MMP-3 mRNA or protein. The micro-CT, X-ray, and histology results clearly showed marked decreases in bone and cartilage destruction, which were consistent with the reduction of fluorescence by down-regulation of active MMP-3 in drug-treated CIA mice. We suggest that the MMP-3 diagnostic kit could be used to detect and monitor the active form of MMP-3 in CIA mice serum during a treatment course and thereby used to predict the drug response or resistance to RA therapies at an earlier stage. We hope that monitoring of active MMP-3 levels in arthritis patients using the MMP-3 diagnostic kit will be a promising tool for drug discovery, drug development, and monitoring of drug responses in RA therapy.


The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape.
Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [1-7]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [8-11]. Here, using recently described haplotype-based techniques [11], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia.


Gelam honey scavenges peroxynitrite during the immune response.
Monocytes and macrophages are part of the first-line defense against bacterial, fungal, and viral infections during host immune responses; they express high levels of proinflammatory cytokines and cytotoxic molecules, including nitric oxide, reactive oxygen species, and their reaction product peroxynitrite. Peroxynitrite is a short-lived oxidant and a potent inducer of cell death. Honey, in addition to its well-known sweetening properties, is a natural antioxidant that has been used since ancient times in traditional medicine. We examined the ability of Gelam honey, derived from the Gelam tree (Melaleuca spp.), to scavenge peroxynitrite during immune responses mounted in the murine macrophage cell line RAW 264.7 when stimulated with lipopolysaccharide/interferon-γ (LPS/IFN-γ) and in LPS-treated rats. Gelam honey significantly improved the viability of LPS/IFN-γ-treated RAW 264.7 cells and inhibited nitric oxide production-similar to the effects observed with an inhibitor of inducible nitric oxide synthase (1400W). Furthermore, honey, but not 1400W, inhibited peroxynitrite production from the synthetic substrate 3-morpholinosydnonimine (SIN-1) and prevented the peroxynitrite-mediated conversion of dihydrorhodamine 123 to its fluorescent oxidation product rhodamine 123. Honey inhibited peroxynitrite synthesis in LPS-treated rats. Thus, honey may attenuate inflammatory responses that lead to cell damage and death, suggesting its therapeutic uses for several inflammatory disorders.


Effects of B-Active2 on Balance, Gait, Stress, and Well-Being of Adults With Autism Spectrum Disorders and Intellectual Disability: A Controlled Trial.
Effects of B-Active2 (Enjoy Being Physically Active by Walking Safely: A Leisure Education Program) on the risk of falls, stress, and well-being of a sample of 44 adults with ASD (ages M = 36.88; SD =7.31) were examined using a controlled experimental trial. Given the relationship between physical activity and stress reduction to individual well-being, B-Active2 was developed as a multidimensional program involving leisure education and walking designed to create an enjoyable context in which adults with ASD learn about and engage in physical activity. All participants were evaluated on balance, gait, well-being, and stress at baseline and at 1 month postintervention by a team of therapists blind to study objectives. There was a significant difference postintervention on balance, F(1, 40) = 55.63, p < .001, η2 = .58; gait, F(1, 40) = 23.58, p < .001, η 2 =.37; and well-being, F(1, 40) = 34.16, p < .001, η 2 = .47). No statistically significant effect was found for level of stress reduction, F(1, 40) = 0.27, n.s. Results of this study support the conclusion that B-Active2 is a viable leisure education program that promotes physical activity of adults with ASD and has positive effects on their well-being and risk of falls.


Carboxymethyl-starch excipients for gastrointestinal stable oral protein formulations containing protease inhibitors.
The aim of this study was to develop a formulation for bioactive compounds using Carboxymethyl Starch (CMS) as excipient containing protease inhibitors. This formulation provided gastro protection and enhanced stability against pancreatic enzymes. Such stability is needed for formulation of oral vaccines with specific antigens. CMS was synthesized by treatment of starch with monochloroacetic acid in conditions leading to a substitution degree of about 1 meq/g and used as excipient for monolithic devices (300 mg tablets). Pefabloc SC and Aprotinin inhibitors were tested in dissolution media and in formulation to prevent the degradation of released bioactive materials. To evaluate the structural integrity and biological stability of plant proteins in the CMS formulation, albumin and lipase were added to the plant protein extract as protein and respectively as enzyme markers. The amounts of released and recovered proteins were evaluated by SDS-PAGE and densitometric analysis. It was found that 1.6 % (w/w) of Pefabloc SC provides 98 % protection of the released plant proteins for formulations of 30 % alfalfa protein extract (APE) with CMS. In addition, when bovine serum albumin (BSA) added to the plant protein extract as a marker, 90 % protection of the released BSA was observed. Furthermore, a much higher lipase activity was found in the releasing media when the formulations contained Pefabloc SC. Formulations with CM-Starch excipients and containing protease inhibitors prevent protein degradation and protect lipase activity, showing a marked potential to use for orally administered bioactive peptides and therapeutic enzymes.


Global, regional, and national progress towards Sustainable Development Goal 3.2 for neonatal and child health: all-cause and cause-specific mortality findings from the Global Burden of Disease Study 2019.
Sustainable Development Goal 3.2 has targeted elimination of preventable child mortality, reduction of neonatal death to less than 12 per 1000 livebirths, and reduction of death of children younger than 5 years to less than 25 per 1000 livebirths, for each country by 2030. To understand current rates, recent trends, and potential trajectories of child mortality for the next decade, we present the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 findings for all-cause mortality and cause-specific mortality in children younger than 5 years of age, with multiple scenarios for child mortality in 2030 that include the consideration of potential effects of COVID-19, and a novel framework for quantifying optimal child survival. We completed all-cause mortality and cause-specific mortality analyses from 204 countries and territories for detailed age groups separately, with aggregated mortality probabilities per 1000 livebirths computed for neonatal mortality rate (NMR) and under-5 mortality rate (U5MR). Scenarios for 2030 represent different potential trajectories, notably including potential effects of the COVID-19 pandemic and the potential impact of improvements preferentially targeting neonatal survival. Optimal child survival metrics were developed by age, sex, and cause of death across all GBD location-years. The first metric is a global optimum and is based on the lowest observed mortality, and the second is a survival potential frontier that is based on stochastic frontier analysis of observed mortality and Healthcare Access and Quality Index. Global U5MR decreased from 71·2 deaths per 1000 livebirths (95% uncertainty interval [UI] 68·3-74·0) in 2000 to 37·1 (33·2-41·7) in 2019 while global NMR correspondingly declined more slowly from 28·0 deaths per 1000 live births (26·8-29·5) in 2000 to 17·9 (16·3-19·8) in 2019. In 2019, 136 (67%) of 204 countries had a U5MR at or below the SDG 3.2 threshold and 133 (65%) had an NMR at or below the SDG 3.2 threshold, and the reference scenario suggests that by 2030, 154 (75%) of all countries could meet the U5MR targets, and 139 (68%) could meet the NMR targets. Deaths of children younger than 5 years totalled 9·65 million (95% UI 9·05-10·30) in 2000 and 5·05 million (4·27-6·02) in 2019, with the neonatal fraction of these deaths increasing from 39% (3·76 million [95% UI 3·53-4·02]) in 2000 to 48% (2·42 million; 2·06-2·86) in 2019. NMR and U5MR were generally higher in males than in females, although there was no statistically significant difference at the global level. Neonatal disorders remained the leading cause of death in children younger than 5 years in 2019, followed by lower respiratory infections, diarrhoeal diseases, congenital birth defects, and malaria. The global optimum analysis suggests NMR could be reduced to as low as 0·80 (95% UI 0·71-0·86) deaths per 1000 livebirths and U5MR to 1·44 (95% UI 1·27-1·58) deaths per 1000 livebirths, and in 2019, there were as many as 1·87 million (95% UI 1·35-2·58; 37% [95% UI 32-43]) of 5·05 million more deaths of children younger than 5 years than the survival potential frontier. Global child mortality declined by almost half between 2000 and 2019, but progress remains slower in neonates and 65 (32%) of 204 countries, mostly in sub-Saharan Africa and south Asia, are not on track to meet either SDG 3.2 target by 2030. Focused improvements in perinatal and newborn care, continued and expanded delivery of essential interventions such as vaccination and infection prevention, an enhanced focus on equity, continued focus on poverty reduction and education, and investment in strengthening health systems across the development spectrum have the potential to substantially improve U5MR. Given the widespread effects of COVID-19, considerable effort will be required to maintain and accelerate progress. Bill & Melinda Gates Foundation.


Reversal of autoimmune diabetes by restoration of antigen-specific tolerance using genetically modified Lactococcus lactis in mice.
Current interventions for arresting autoimmune diabetes have yet to strike the balance between sufficient efficacy, minimal side effects, and lack of generalized immunosuppression. Introduction of antigen via the gut represents an appealing method for induction of antigen-specific tolerance. Here, we developed a strategy for tolerance restoration using mucosal delivery in mice of biologically contained Lactococcus lactis genetically modified to secrete the whole proinsulin autoantigen along with the immunomodulatory cytokine IL-10. We show that combination therapy with low-dose systemic anti-CD3 stably reverted diabetes in NOD mice and increased frequencies of local Tregs, which not only accumulated in the pancreatic islets, but also suppressed immune response in an autoantigen-specific way. Cured mice remained responsive to disease-unrelated antigens, which argues against excessive immunosuppression. Application of this therapeutic tool achieved gut mucosal delivery of a diabetes-relevant autoantigen and a biologically active immunomodulatory cytokine, IL-10, and, when combined with a low dose of systemic anti-CD3, was well tolerated and induced autoantigen-specific long-term tolerance, allowing reversal of established autoimmune diabetes. Therefore, we believe this method could be an effective treatment strategy for type 1 diabetes in humans.


Demographic history of european populations of Arabidopsis thaliana.
The model plant species Arabidopsis thaliana is successful at colonizing land that has recently undergone human-mediated disturbance. To investigate the prehistoric spread of A. thaliana, we applied approximate Bayesian computation and explicit spatial modeling to 76 European accessions sequenced at 876 nuclear loci. We find evidence that a major migration wave occurred from east to west, affecting most of the sampled individuals. The longitudinal gradient appears to result from the plant having spread in Europe from the east approximately 10,000 years ago, with a rate of westward spread of approximately 0.9 km/year. This wave-of-advance model is consistent with a natural colonization from an eastern glacial refugium that overwhelmed ancient western lineages. However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition.


Similar nociceptive afferents mediate psychophysical and electrophysiological responses to heat stimulation of glabrous and hairy skin in humans.
The ability to perceive and withdraw rapidly from noxious environmental stimuli is crucial for survival. When heat stimuli are applied to primate hairy skin, first pain sensation is mediated by type-II A-fibre nociceptors (II-AMHs). In contrast, the reported absence of first pain and II-AMH microneurographical responses when heat stimuli are applied to the hand palm has led to the notion that II-AMHs are lacking in this primate glabrous skin. The aim of this study was to assess the effect of hairy and glabrous skin stimulation on neural transmission of nociceptive inputs elicited by different kinds of thermal heating. We recorded psychophysical and EEG brain responses to radiant (laser-evoked potentials, LEPs) and contact heat stimuli (contact heat-evoked potentials, CHEPs) delivered to the dorsum and the palm of the hand in normal volunteers. Brain responses were analysed at a single-trial level, using an automated approach based on multiple linear regression. Laser stimulation of hairy and glabrous skin at the same energy elicited remarkably similar psychophysical ratings and LEPs. This finding provides strong evidence that first pain to heat does exist in glabrous skin, and suggests that similar nociceptive afferents, with the physiological properties of II-AMHs, mediate first pain to heat stimulation of glabrous and hairy skin in humans. In contrast, when contact heat stimuli were employed, a significantly higher nominal temperature had to be applied to glabrous skin in order to achieve psychophysical ratings similar to those obtained following hairy skin stimulation, and CHEPs following glabrous skin stimulation had significantly longer latencies (N2 wave, +25%; P2 wave, +24%) and smaller amplitudes (N2 wave, -40%; P2 wave, -44%) than CHEPs following hairy skin stimulation. Irrespective of the stimulated territory, CHEPs always had significantly longer latencies (hairy skin N2 wave, +75%; P2 wave, +56%) and smaller amplitudes (hairy skin N2 wave, -42%; P2 wave, -19%) than LEPs. These findings are consistent with the thickness-dependent delay and attenuation of the temperature waveform at nociceptor depth when conductive heating is applied, and suggest that the previously reported lack of first pain and microneurographical II-AMH responses following glabrous skin stimulation could have been the result of a search bias consequent to the use of long-wavelength radiant heating (i.e. CO(2) laser) as stimulation procedure.


Pain, sleep disturbance, and fatigue in patients with cancer: using a mediation model to test a symptom cluster.
To test whether sleep disturbance mediates the effect of pain on fatigue. Cross-sectional. Radiation therapy clinic, oncology ambulatory clinic, and inpatient oncology unit in an urban teaching hospital. 84 patients with cancer with multiple primary diagnoses who were experiencing pain. Fifty-three percent were female and 92% were Caucasian, with a mean age of 54 years. All participants completed a symptom questionnaire that included the Brief Pain Inventory-Short Form, the Pittsburgh Sleep Quality Index, and the fatigue subscale of the Profile of Mood States questionnaire. Multistage linear regression was used to test a mediation model. Fatigue, pain, and sleep disturbance. Mediation analyses indicate that pain influences fatigue directly as well as indirectly by its effect on sleep. About 20% (adjusted R2 = 0.20) of the variation in fatigue is explained by pain. Thirty-five percent of the variance in fatigue explained by pain was accounted for by the mediation pathway. Some of the effect of pain on fatigue is mediated by sleep disturbance, but pain has a direct effect on fatigue as well. Although the relationship can be explained only partially by the commonsense point of view that people who are in pain lose sleep and naturally report more fatigue, this finding is important and leads to a potential intervention opportunity. Strategies to improve sleep by better pain management may contribute to decreased fatigue.


Use of residue pairs in protein sequence-sequence and sequence-structure alignments.
Two new sets of scoring matrices are introduced: H2 for the protein sequence comparison and T2 for the protein sequence-structure correlation. Each element of H2 or T2 measures the frequency with which a pair of amino acid types in one protein, k-residues apart in the sequence, is aligned with another pair of residues, of given amino acid types (for H2) or in given structural states (for T2), in other structurally homologous proteins. There are four types, corresponding to the k-values of 1 to 4, for both H2 and T2. These matrices were set up using a large number of structurally homologous protein pairs, with little sequence homology between the pair, that were recently generated using the structure comparison program SHEBA. The two scoring matrices were incorporated into the main body of the sequence alignment program SSEARCH in the FASTA package and tested in a fold recognition setting in which a set of 107 test sequences were aligned to each of a panel of 3,539 domains that represent all known protein structures. Six procedures were tested; the straight Smith-Waterman (SW) and FASTA procedures, which used the Blosum62 single residue type substitution matrix; BLAST and PSI-BLAST procedures, which also used the Blosum62 matrix; PASH, which used Blosum62 and H2 matrices; and PASSC, which used Blosum62, H2, and T2 matrices. All procedures gave similar results when the probe and target sequences had greater than 30% sequence identity. However, when the sequence identity was below 30%, a similar structure could be found for more sequences using PASSC than using any other procedure. PASH and PSI-BLAST gave the next best results.


ERAD components in organisms with complex red plastids suggest recruitment of a preexisting protein transport pathway for the periplastid membrane.
The plastids of cryptophytes, haptophytes, and heterokontophytes (stramenopiles) (together once known as chromists) are surrounded by four membranes, reflecting the origin of these plastids through secondary endosymbiosis. They share this trait with apicomplexans, which are alveolates, the plastids of which have been suggested to stem from the same secondary symbiotic event and therefore form a phylogenetic clade, the chromalveolates. The chromists are quantitatively the most important eukaryotic contributors to primary production in marine ecosystems. The mechanisms of protein import across their four plastid membranes are still poorly understood. Components of an endoplasmic reticulum-associated degradation (ERAD) machinery in cryptophytes, partially encoded by the reduced genome of the secondary symbiont (the nucleomorph), are implicated in protein transport across the second outermost plastid membrane. Here, we show that the haptophyte Emiliania huxleyi, like cryptophytes, stramenopiles, and apicomplexans, possesses a nuclear-encoded symbiont-specific ERAD machinery (SELMA, symbiont-specific ERAD-like machinery) in addition to the host ERAD system, with targeting signals that are able to direct green fluorescent protein or yellow fluorescent protein to the predicted cellular localization in transformed cells of the stramenopile Phaeodactylum tricornutum. Phylogenies of the duplicated ERAD factors reveal that all SELMA components trace back to a red algal origin. In contrast, the host copies of cryptophytes and haptophytes associate with the green lineage to the exclusion of stramenopiles and alveolates. Although all chromalveolates with four membrane-bound plastids possess the SELMA system, this has apparently not arisen in a single endosymbiotic event. Thus, our data do not support the chromalveolate hypothesis.


South African HIV-1 vaccine candidates - the journey from the bench to clinical trials.
Around 2.5 million people become infected with human immunodeficiency virus (HIV) each year. This extraordinary toll in human life and public health worldwide will only be reversed with effective prevention. Vaccination is regarded as the most effective way to prevent infectious disease. However, there are many challenges to overcome before a successful prophylactic HIV vaccine will be available. We are participating in a global effort to develop and test candidate HIV vaccines. Two candidate prophylactic HIV vaccines that were designed and developed at the University of Cape Town (UCT) entered phase 1 clinical trials in the USA and South Africa in 2009, after a 9-year development period. In addition to the vaccines in clinical trial, there is a pipeline of candidate HIV-1 subtype C vaccines including virus-like particles, novel DNA vaccines, capripoxvirus and Bacillus Calmette-Guérin (BCG)-vectored vaccines. This article describes the history of HIV vaccine research at UCT, and the partnerships that made the project possible.


Performance- and stimulus-dependent oscillations in monkey prefrontal cortex during short-term memory.
Short-term memory requires the coordination of sub-processes like encoding, retention, retrieval and comparison of stored material to subsequent input. Neuronal oscillations have an inherent time structure, can effectively coordinate synaptic integration of large neuron populations and could therefore organize and integrate distributed sub-processes in time and space. We observed field potential oscillations (14-95 Hz) in ventral prefrontal cortex of monkeys performing a visual memory task. Stimulus-selective and performance-dependent oscillations occurred simultaneously at 65-95 Hz and 14-50 Hz, the latter being phase-locked throughout memory maintenance. We propose that prefrontal oscillatory activity may be instrumental for the dynamical integration of local and global neuronal processes underlying short-term memory.


Autoantibodies at the neuromuscular junction - link to the central nervous system.
Antibodies to different membrane proteins, namely acetylcholine receptor, muscle specific kinase and low density lipoprotein receptor-related protein 4, at the neuromuscular junction are well recognised in myasthenia gravis, although the mechanisms responsible for the muscle distribution and fluctuations in function are still not very clear, and some of the issues are discussed below. In addition, the involvement of antibodies to the potassium channel complex proteins in neuromyotonia, help to lead to a better understanding of immunotherapy-responsive central nervous system diseases.


Randomized trial to compare bilateral vs. single internal mammary coronary artery bypass grafting: 1-year results of the Arterial Revascularisation Trial (ART).
Observational data suggest that the use of bilateral internal mammary arteries (BIMA) during coronary artery bypass graft surgery provides superior revascularization to a single internal mammary artery (SIMA), but concerns about safety have prevented the widespread use of BIMA. The Arterial Revascularisation Trial (ART) is a randomized trial of BIMA vs. SIMA, with a primary outcome of survival at 10 years. This paper reports mortality, morbidity, and resource use data at 1 year. Coronary artery bypass graft patients were enrolled in 28 hospitals in seven countries. Three thousand one hundred and two patients were randomly assigned to SIMA (n = 1554) or BIMA (n = 1548). The mean number of grafts was 3 for both groups. Forty per cent of the SIMA procedures and 42% of the BIMA were performed off-pump. Mortality at 30 days was 18 of 1548 (1.2%) for SIMA and 19 of 1537 (1.2%) for BIMA, and at 1 year was 36 of 1540 (2.3%) and 38 of 1529 (2.5%), respectively. The rates of stroke, myocardial infarction, and repeat revascularization were all ≤2% at 1 year and similar between the two groups. Sternal wound reconstruction was required in 0.6 and 1.9% of the SIMA and BIMA groups, respectively. Data from ART demonstrate similar clinical outcomes for SIMA and BIMA at 1 year but BIMA grafts are associated with a small absolute increase (1.3%) in the need for sternal wound reconstruction. The results suggest that the use of BIMA grafts is feasible on a routine basis. The 10-year results of the ART will confirm whether BIMA grafting results in lower mortality and the need for repeat intervention. Controlled-trials.com (ISRCTN46552265).


How effective are added constraints in improving TKR kinematics?
Newer designs of total knee arthroplasty (TKA), through the use of added degrees of constraint, attempt to provide a "guided motion" to restore more normal and predictable kinematics. Two such design philosophies are the posterior stabilised (PS) using a cam-post and the medial pivot (MP) concepts. Knee kinematics of 12 patients with a PS TKA, 13 subjects with a MP TKA and 10 normal subjects were compared. For kinematic assessment, patients underwent fluoroscopic assessment of the knee during a step-up exercise and deep knee bend. Fluoroscopic images were corrected for distortion and assessed using 3D model fitting to determine relative 3D motion, and a 2D method to measure the patellar tendon angle (PTA) as function of knee flexion. For the PS design the cam-post mechanism engaged between 70 degrees and 100 degrees flexion. Between extension and 50 degrees there was forward motion of the contact points. Beyond 60 degrees both condyles rolled moved posteriorly. The majority of the external rotation of the femur occurred between 50 degrees and 80 degrees . The PTA was lower than normal in extension and higher than normal in flexion. The MP exhibited no anterior movement throughout the rage of motion. The medial condyle moved minimally. The lateral contact point moved posteriorly from extension to flexion. The femur rotated externally throughout the range of flexion analysed. The PTA was similar to normal from extension to mid flexion and then higher than normal beyond to high flexion. The PS design fails to fully restrain paradoxical anterior movement and although the cam engages, it does not contribute significantly to overall rollback. The MP knee does not show significant anterior movement, the medial pivot concept appears to achieve near normal kinematics from extension to 50 degrees of knee flexion. However, the results show that at high flexion this design does not achieve normal knee kinematics.


Longitudinal COVID-19 profiling associates IL-1RA and IL-10 with disease severity and RANTES with mild disease.
Identifying immune correlates of COVID-19 disease severity is an urgent need for clinical management, vaccine evaluation, and drug development. Here, we present a temporal analysis of key immune mediators, cytokines, and chemokines in blood of hospitalized COVID-19 patients from serial sampling and follow-up over 4 weeks. A total of 71 patients with laboratory-confirmed COVID-19 admitted to Beijing You'an Hospital in China with either mild (53 patients) or severe (18 patients) disease were enrolled with 18 healthy volunteers. We measured 34 immune mediators, cytokines, and chemokines in peripheral blood every 4-7 days over 1 month per patient using a bioplex multiplex immunoassay. We found that the chemokine RANTES (CCL5) was significantly elevated, from an early stage of the infection, in patients with mild but not severe disease. We also found that early production of inhibitory mediators including IL-10 and IL-1RA were significantly associated with disease severity, and a combination of CCL5, IL-1 receptor antagonist (IL-1RA), and IL-10 at week 1 may predict patient outcomes. The majority of cytokines that are known to be associated with the cytokine storm in virus infections such as IL-6 and IFN-γ were only significantly elevated in the late stage of severe COVID-19 illness. TNF-α and GM-CSF showed no significant differences between severe and mild cases. Together, our data suggest that early intervention to increase expression of CCL5 may prevent patients from developing severe illness. Our data also suggest that measurement of levels of CCL5, as well as IL-1RA and IL-10 in blood individually and in combination, might be useful prognostic biomarkers to guide treatment strategies.


Prebiotic administration normalizes lipopolysaccharide (LPS)-induced anxiety and cortical 5-HT2A receptor and IL1-β levels in male mice.
The manipulation of the enteric microbiota with specific prebiotics and probiotics, has been shown to reduce the host's inflammatory response, alter brain chemistry, and modulate anxiety behaviour in both rodents and humans. However, the neuro-immune and behavioural effects of prebiotics on sickness behaviour have not been explored. Here, adult male CD1 mice were fed with a specific mix of non-digestible galacto-oligosaccharides (Bimuno®, BGOS) for 3 weeks, before receiving a single injection of lipopolysaccharide (LPS), which induces sickness behaviour and anxiety. Locomotor and marble burying activities were assessed 4h after LPS injection, and after 24h, anxiety in the light-dark box was assessed. Cytokine expression, and key components of the serotonergic (5-Hydroxytryptamine, 5-HT) and glutamatergic system were evaluated in the frontal cortex to determine the impact of BGOS administration at a molecular level. BGOS-fed mice were less anxious in the light-dark box compared to controls 24h after the LPS injection. Elevated cortical IL-1β concentrations in control mice 28 h after LPS were not observed in BGOS-fed animals. This significant BGOS×LPS interaction was also observed for 5HT2A receptors, but not for 5HT1A receptors, 5HT, 5HIAA, NMDA receptor subunits, or other cytokines. The intake of BGOS did not influence LPS-mediated reductions in marble burying behaviour, and its effect on locomotor activity was equivocal. Together, our data show that the prebiotic BGOS has an anxiolytic effect, which may be related to the modulation of cortical IL-1β and 5-HT2A receptor expression. Our data suggest a potential role for prebiotics in the treatment of neuropsychiatric disorders where anxiety and neuroinflammation are prominent clinical features.


Juxtaglomerular cell tumour of the kidney: a rare cause of resistant hypertension.
Juxtaglomerular cell tumour (JGCT) is an unusually encountered clinical entity. A 33-year-old man with severe long-standing hypertension and hypokalaemia is described. The patient also suffered from polyuria, polydipsia, nocturia and severe headaches. On admission, laboratory investigation revealed hypokalaemia, kaliuresis, high aldosterone and renin levels, and the abdomen CT identified a mass of 4 cm at the right kidney. Kidney function was normal. Following nephrectomy, the histological investigation revealed the presence of a JGCT. Immunostaining was positive for CD34 as well as for smooth muscle actin and vimentin. Following surgery, a marked control of his hypertension with calcium channel blockers and normalization of the serum potassium, renin or aldosterone levels were reached. According to our findings, JGCT could be included in the differential diagnosis of secondary hypertension as it consists of a curable cause. The association of JGCT with hypertension and hypokalaemia focusing on the clinical presentation, diagnostic evaluation and management is herein discussed and a brief review of the existing literature is provided. Juxtaglomerular cell tumours (JGCT), despite their rarity, should be included in the differential diagnosis of secondary hypertension as they consist of a curable cause of hypertension. JGCT could be presented with resistant hypertension along with hypokalaemia, kaliuresis and metabolic alkalosis. Early recognition and management can help to prevent cardiovascular complications. Imaging (enhanced CT scans) may be considered as the primary diagnostic tool for the detection of renal or JGCT. For the confirmation of the diagnosis, a histopathologic examination is needed.


Functional neuronal cells generated by human parthenogenetic stem cells.
Parent of origin imprints on the genome have been implicated in the regulation of neural cell type differentiation. The ability of human parthenogenetic (PG) embryonic stem cells (hpESCs) to undergo neural lineage and cell type-specific differentiation is undefined. We determined the potential of hpESCs to differentiate into various neural subtypes. Concurrently, we examined DNA methylation and expression status of imprinted genes. Under culture conditions promoting neural differentiation, hpESC-derived neural stem cells (hpNSCs) gave rise to glia and neuron-like cells that expressed subtype-specific markers and generated action potentials. Analysis of imprinting in hpESCs and in hpNSCs revealed that maternal-specific gene expression patterns and imprinting marks were generally maintained in PG cells upon differentiation. Our results demonstrate that despite the lack of a paternal genome, hpESCs generate proliferating NSCs that are capable of differentiation into physiologically functional neuron-like cells and maintain allele-specific expression of imprinted genes. Thus, hpESCs can serve as a model to study the role of maternal and paternal genomes in neural development and to better understand imprinting-associated brain diseases.


Silencing of the HER2/neu gene by siRNA inhibits proliferation and induces apoptosis in HER2/neu-overexpressing breast cancer cells.
In eukaryotes, double-stranded (ds) RNA induces sequence-specific inhibition of gene expression referred to as RNA interference (RNAi). We exploited RNAi to define the role of HER2/neu in the neoplastic proliferation of human breast cancer cells. We transfected SK-BR-3, BT-474, MCF-7, and MDA-MB-468 breast cancer cells with short interfering RNA (siRNA) targeted against human HER2/neu and analyzed the specific inhibition of HER2/neu expression by Northern and Western blots. Transfection with HER2/neu-specific siRNA resulted in a sequence-specific decrease in HER2/neu mRNA and protein levels. Moreover, transfection with HER2/neu siRNA caused cell cycle arrest at G0/G1 in the breast cancer cell lines SK-BR-3 and BT-474, consistent with a powerful RNA silencing effect. siRNA treatment resulted in an antiproliferative and apoptotic response in cells overexpressing HER2/neu, but had no influence in cells with almost no expression of HER2/neu proteins like MDA-MB-468 cells. These data indicate that HER2/neu function is essential for the proliferation of HER2/neu-overexpressing breast cancer cells. Our observations suggest that siRNA targeted against human HER2/neu may be valuable tools as antiproliferative agents that display activity against neoplastic cells at very low doses.


Marathon of eponyms: 7 Gorlin-Goltz syndrome (Naevoid basal-cell carcinoma syndrome).
The use of eponyms has long been contentious, but many remain in common use, as discussed elsewhere (Editorial: Oral Diseases. 2009: 15; 185). The use of eponyms in diseases of the head and neck is found mainly in specialties dealing with medically compromised individuals (paediatric dentistry, special care dentistry, oral and maxillofacial medicine, oral and maxillofacial pathology, oral and maxillofacial radiology and oral and maxillofacial surgery) and particularly by hospital-centred practitioners. This series has selected some of the more recognized relevant eponymous conditions and presents them alphabetically. The information is based largely on data available from MEDLINE and a number of internet websites as noted below: the authors would welcome any corrections. This document summarizes data about Gorlin-Goltz syndrome.


The schizotypal ambivalence scale as a marker of schizotypy.
The present study examined the psychometric properties of the Schizotypal Ambivalence Scale (SAS) in a sample of 1798 young adults. The study also investigated the concurrent validity of the measure for identifying schizophrenic-like symptoms in a sample of 43 high scorers on the scale and 43 control participants. Previous findings indicated that high scores on the SAS were associated with schizophrenia-spectrum pathology in a sample of schizotypic young adults selected with other measures. However, this is the first study to assess schizophrenic-like psychopathology in a sample selected using the SAS. The SAS has good internal consistency (coefficient alpha = 0.84) and test-retest reliability (intraclass correlation = 0.74 across 9 weeks). As hypothesized, the ambivalence group exceeded the control group on interview ratings of schizotypal, schizoid, paranoid, psychotic-like, and negative symptoms, as well as exhibiting poorer overall functioning. The SAS seems to be a promising measure of schizotypy in young adults.


Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease.
Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are complex chronic inflammatory conditions of the gastrointestinal tract that are driven by perturbed cytokine pathways. Anti-tumor necrosis factor-α (TNF) antibodies are mainstay therapies for IBD. However, up to 40% of patients are nonresponsive to anti-TNF agents, which makes the identification of alternative therapeutic targets a priority. Here we show that, relative to healthy controls, inflamed intestinal tissues from patients with IBD express high amounts of the cytokine oncostatin M (OSM) and its receptor (OSMR), which correlate closely with histopathological disease severity. The OSMR is expressed in nonhematopoietic, nonepithelial intestinal stromal cells, which respond to OSM by producing various proinflammatory molecules, including interleukin (IL)-6, the leukocyte adhesion factor ICAM1, and chemokines that attract neutrophils, monocytes, and T cells. In an animal model of anti-TNF-resistant intestinal inflammation, genetic deletion or pharmacological blockade of OSM significantly attenuates colitis. Furthermore, according to an analysis of more than 200 patients with IBD, including two cohorts from phase 3 clinical trials of infliximab and golimumab, high pretreatment expression of OSM is strongly associated with failure of anti-TNF therapy. OSM is thus a potential biomarker and therapeutic target for IBD, and has particular relevance for anti-TNF-resistant patients.


The activation mechanism of Irga6, an interferon-inducible GTPase contributing to mouse resistance against Toxoplasma gondii.
The interferon-inducible immunity-related GTPases (IRG proteins/p47 GTPases) are a distinctive family of GTPases that function as powerful cell-autonomous resistance factors. The IRG protein, Irga6 (IIGP1), participates in the disruption of the vacuolar membrane surrounding the intracellular parasite, Toxoplasma gondii, through which it communicates with its cellular hosts. Some aspects of the protein's behaviour have suggested a dynamin-like molecular mode of action, in that the energy released by GTP hydrolysis is transduced into mechanical work that results in deformation and ultimately rupture of the vacuolar membrane. Irga6 forms GTP-dependent oligomers in vitro and thereby activates hydrolysis of the GTP substrate. In this study we define the catalytic G-domain interface by mutagenesis and present a structural model, of how GTP hydrolysis is activated in Irga6 complexes, based on the substrate-twinning reaction mechanism of the signal recognition particle (SRP) and its receptor (SRα). In conformity with this model, we show that the bound nucleotide is part of the catalytic interface and that the 3'hydroxyl of the GTP ribose bound to each subunit is essential for trans-activation of hydrolysis of the GTP bound to the other subunit. We show that both positive and negative regulatory interactions between IRG proteins occur via the catalytic interface. Furthermore, mutations that disrupt the catalytic interface also prevent Irga6 from accumulating on the parasitophorous vacuole membrane of T. gondii, showing that GTP-dependent Irga6 activation is an essential component of the resistance mechanism. The catalytic interface of Irga6 defined in the present experiments can probably be used as a paradigm for the nucleotide-dependent interactions of all members of the large family of IRG GTPases, both activating and regulatory. Understanding the activation mechanism of Irga6 will help to explain the mechanism by which IRG proteins exercise their resistance function. We find no support from sequence or G-domain structure for the idea that IRG proteins and the SRP GTPases have a common phylogenetic origin. It therefore seems probable, if surprising, that the substrate-assisted catalytic mechanism has been independently evolved in the two protein families.


High-resolution analysis of cis-acting regulatory networks at the α-globin locus.
We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the α-globin cluster.


A comparison between acupuncture versus zolpidem in the treatment of primary insomnia.
To determine the relative efficacy of acupuncture and zolpidem in the treatment of primary insomnia, we administered a sleep quality scale to thirty-three patients with primary insomnia randomly chosen to receive one of the two therapies at a psychosomatic clinic. A study in the psychosomatic clinic at a teaching hospital in southern Taiwan from November 2007 to November 2008. The 19 patients in acupuncture group underwent one acupuncture session a week. The 14 patients in the control group took zolpidem 1# (10mg) every night. Members of both groups returned to our clinic once a week for four weeks. The main outcome measure was the Pittsburgh Sleep Quality Index (PSQI). Both groups were found to have improved significantly. Using generalized estimating equation analysis to test the variance with group and time as factors, we found both groups improved over time at a similar rate (p=0.79). In regression analysis, setting the fourth total PSQI score to zero, the baseline PSQI score was 4.13 (p<0.001), the second score 1.32 (p=0.005), and the third 1.49 (p=0.03); men had a higher PSQI score 1.56 than women (p=0.02); the increasing age of one year would have lower PSQI score 0.08 (p<0.001) and increasing educational level of one year which would decrease PSQI score 0.25 (p=0.007). Acupuncture might be used as an alternative strategy compared to zolpidem for the treatment of primary insomnia.


Cell-mediated immunity in pigeon breeders' lung: the effect of removal from antigen exposure.
Eighteen precipitin-positive pigeon breeders, thirteen symptomatic (SPB), with extrinsic allergic alveolitis (EAA), and five asymptomatic (APB), without lung disease, underwent bronchoalveolar lavage (BAL). Cytospins were prepared on which differential cell counts were performed. Immunocytological methods, using monoclonal antibodies, were performed to identify lymphocyte and macrophage subsets. Marked abnormalities in cell populations were observed in both groups but with no suggestion of differences between the groups. All subjects had a lymphocytosis in BAL (SPB 45%; APB 29%). These lymphocytes were almost exclusively T-cells. The cluster designation CD4/CD8 ratio was decreased (SPB 0.86; APB 1.13) and a significantly higher proportion of these cells than normal expressed UCHL1 (an antigen associated with the common leucocyte antigen complex) indicating immune commitment. In the macrophage population increased proportions of cells expressing antigens associated with interdigitating cells (RFD1+) and mature macrophages (RFD7+) were also abnormal. When six SPB patients were relavaged after isolation from pigeons for three weeks, there was a significant reduction in the lymphocytosis and in the proportion of UCHL1+ lymphocytes. This was accompanied by reductions in the percentage of macrophages expressing RFD1 and UCHL1. We suggest that EAA in pigeon breeders is associated with a cell-mediated immune response which is down-regulated by isolating patients from exposure to pigeon derived antigens.


MiR-142-3p controls the specification of definitive hemangioblasts during ontogeny.
Hematopoietic stem cells (HSCs) emerge during embryogenesis from hemogenic endothelium, but it remains unclear how the HSC lineage is initially established from mesoderm during ontogeny. In Xenopus, the definitive hemangioblast precursors of the HSC lineage have been identified in dorsal lateral plate (DLP) mesoderm, and a transcriptional gene regulatory network (GRN) controlling hemangioblast programming has been elucidated. Herein, we identify an essential role for microRNAs (miRNAs) in establishing the mesodermal lineage leading to both HSC emergence and vasculogenesis and determine that a single miRNA, miR-142-3p, is primarily responsible for initiation of definitive hemangioblast specification. miR-142-3p forms a double-negative gate unlocking entry into the hemangioblast program, in part by inhibiting TGFβ signaling. Our results table miR-142-3p as a master regulator of HSC lineage specification, sitting at the apex of the hierarchy programming the adult hemangioblast, thus illustrating that miRNAs can act as instructive determinants of cell fate during development.


Divergent effects of glucose and fructose on hepatic lipogenesis and insulin signaling.
Overconsumption of high-fat diet (HFD) and sugar-sweetened beverages are risk factors for developing obesity, insulin resistance, and fatty liver disease. Here we have dissected mechanisms underlying this association using mice fed either chow or HFD with or without fructose- or glucose-supplemented water. In chow-fed mice, there was no major physiological difference between fructose and glucose supplementation. On the other hand, mice on HFD supplemented with fructose developed more pronounced obesity, glucose intolerance, and hepatomegaly as compared to glucose-supplemented HFD mice, despite similar caloric intake. Fructose and glucose supplementation also had distinct effects on expression of the lipogenic transcription factors ChREBP and SREBP1c. While both sugars increased ChREBP-β, fructose supplementation uniquely increased SREBP1c and downstream fatty acid synthesis genes, resulting in reduced liver insulin signaling. In contrast, glucose enhanced total ChREBP expression and triglyceride synthesis but was associated with improved hepatic insulin signaling. Metabolomic and RNA sequence analysis confirmed dichotomous effects of fructose and glucose supplementation on liver metabolism in spite of inducing similar hepatic lipid accumulation. Ketohexokinase, the first enzyme of fructose metabolism, was increased in fructose-fed mice and in obese humans with steatohepatitis. Knockdown of ketohexokinase in liver improved hepatic steatosis and glucose tolerance in fructose-supplemented mice. Thus, fructose is a component of dietary sugar that is distinctively associated with poor metabolic outcomes, whereas increased glucose intake may be protective.


Effectiveness and feasibility of virtual reality and gaming system use at home by older adults for enabling physical activity to improve health-related domains: a systematic review.
use of virtual reality and commercial gaming systems (VR/gaming) at home by older adults is receiving attention as a means of enabling physical activity. to summarise evidence for the effectiveness and feasibility of VR/gaming system utilisation by older adults at home for enabling physical activity to improve impairments, activity limitations or participation. a systematic review searching 12 electronic databases from 1 January 2000-10 July 2012 using key search terms. Two independent reviewers screened yield articles using pre-determined selection criteria, extracted data using customised forms and applied the Cochrane Collaboration Risk of Bias Tool and the Downs and Black Checklist to rate study quality. fourteen studies investigating the effects of VR/gaming system use by healthy older adults and people with neurological conditions on activity limitations, body functions and physical impairments and cognitive and emotional well-being met the selection criteria. Study quality ratings were low and, therefore, evidence was not strong enough to conclude that interventions were effective. Feasibility was inconsistently reported in studies. Where feasibility was discussed, strong retention (≥70%) and adherence (≥64%) was reported. Initial assistance to use the technologies, and the need for monitoring exertion, aggravation of musculoskeletal symptoms and falls risk were reported. existing evidence to support the feasibility and effectiveness VR/gaming systems use by older adults at home to enable physical activity to address impairments, activity limitations and participation is weak with a high risk of bias. The findings of this review may inform future, more rigorous research.


Dopamine modulates risk-taking as a function of baseline sensation-seeking trait.
Trait sensation-seeking, defined as a need for varied, complex, and intense sensations, represents a relatively underexplored hedonic drive in human behavioral neuroscience research. It is related to increased risk for a range of behaviors including substance use, gambling, and risky sexual practice. Individual differences in self-reported sensation-seeking have been linked to brain dopamine function, particularly at D2-like receptors, but so far no causal evidence exists for a role of dopamine in sensation-seeking behavior in humans. Here, we investigated the effects of the selective D2/D3 agonist cabergoline on performance of a probabilistic risky choice task in healthy humans using a sensitive within-subject, placebo-controlled design. Cabergoline significantly influenced the way participants combined different explicit signals regarding probability and loss when choosing between response options associated with uncertain outcomes. Importantly, these effects were strongly dependent on baseline sensation-seeking score. Overall, cabergoline increased sensitivity of choice to information about probability of winning; while decreasing discrimination according to magnitude of potential losses associated with different options. The largest effects of the drug were observed in participants with lower sensation-seeking scores. These findings provide evidence that risk-taking behavior in humans can be directly manipulated by a dopaminergic drug, but that the effectiveness of such a manipulation depends on baseline differences in sensation-seeking trait. This emphasizes the importance of considering individual differences when investigating manipulation of risky decision-making, and may have relevance for the development of pharmacotherapies for disorders involving excessive risk-taking in humans, such as pathological gambling.


Disaster planning and risk communication with vulnerable communities: lessons from Hurricane Katrina.
We studied the experience of Hurricane Katrina evacuees to better understand factors influencing evacuation decisions in impoverished, mainly minority communities that were most severely affected by the disaster. We performed qualitative interviews with 58 randomly selected evacuees living in Houston's major evacuation centers from September 9 to 12, 2005. Transcripts were content analyzed using grounded theory methodology. Participants were mainly African American, had low incomes, and were from New Orleans. Participants' strong ties to extended family, friends, and community groups influenced other factors affecting evacuation, including transportation, access to shelter, and perception of evacuation messages. These social connections cut both ways, which facilitated and hindered evacuation decisions. Effective disaster plans must account for the specific obstacles encountered by vulnerable and minority communities. Removing the more apparent obstacles of shelter and transportation will likely be insufficient for improving disaster plans for impoverished, minority communities. The important influence of extended families and social networks demand better community-based communication and preparation strategies.


Orienting attention to instants in time.
My colleagues and I have investigated whether the temporal framework can be used to guide selective attention, and have applied non-invasive methodology to reveal the brain systems and mechanisms involved. Our findings show that we are able to orient attention selectively to different points in time, enhancing behavioral performance. These effects are mediated by a left-hemisphere dominant parietal-frontal system, which partially overlaps with the networks involved in spatial orienting. The neural system for temporal orienting also includes brain areas associated with motor preparation and anticipation, suggesting that sensorimotor areas with different specializations can contribute to attentional orienting depending on the stimulus attributes guiding selection. The optimization of behavior by temporal orienting involves enhancement of the latency and amplitude of event-related potentials that are associated with motor responses and decisions. The effects are distinct from those during visual spatial attention, indicating that behavioral advantages can be conferred by multiple types of neural mechanisms. Taken together, the findings illustrate the flexibility of attentional functions in the human brain.


Fluid Intake and Dietary Factors and the Risk of Incident Kidney Stones in UK Biobank: A Population-based Prospective Cohort Study.
Fluid intake and diet are thought to influence kidney stone risk. However, prospective studies have been limited to small samples sizes and/or restricted measures. To investigate whether fluid intake and dietary factors are associated with the risk of developing a first kidney stone. Participants were selected from UK Biobank, a population-based prospective cohort study. Cox proportional hazards models were used to investigate the association between fluid intake and dietary factors and the risk of a first incident kidney stone, ascertained from hospital inpatient records. After exclusion, 439 072 participants were available for the analysis, of whom 2057 had hospital admission with an incident kidney stone over a mean of 6.1 yr of follow-up. For every additional drink (200 ml) consumed per day of total fluid, the risk of kidney stones declined by 13% (hazard ratio [HR] = 0.87, 95% confidence interval [CI] 0.85-0.89). Similar patterns of associations were observed for tea, coffee, and alcohol, although no association was observed for water intake. Fruit and fibre intake was also associated with a lower risk (HR per 100 g increase of fruits per day = 0.88, 95% CI 0.83-0.93, and HR per 10 g fibre per day = 0.82, 95% CI 0.77-0.87), whereas meat and salt intake was associated with a higher risk (HR per 50 g increase in meat per week = 1.17, 95% CI 1.05-1.29, and HR for always vs never/rarely added salt to food = 1.33, 95% CI 1.12-1.58). Vegetable, fish, and cheese intake was not associated with kidney stone risk. The finding that high intake of total fluid, fruit, and fibre was associated with a lower risk of hospitalisation for a first kidney stone suggests that modifiable dietary factors could be targeted to prevent kidney stone development. We found that higher intake of total fluid, specifically tea, coffee, and alcohol (but not water), and consumption of fruit and foods high in fibre are linked with a reduced likelihood of developing kidney stones.


Quinine treatment of severe falciparum malaria in African children: a randomized comparison of three regimens.
The pharmacokinetics and effectiveness of three dosage regimens of quinine were studied in a group of 59 children with severe malaria. The children were randomized to receive high-dose intravenous or intramuscular quinine (20 mg salt/kg loading, then 10 mg salt/kg every 12 hr), or low-dose intravenous quinine (10 mg salt/kg loading, then 5 mg salt/kg every 12 hr). In the group receiving the high-dose intravenous regimen, mean high and low quinine concentrations were consistently greater than 10 and 6.5 mg/l, respectively. Peak concentrations as well as the time required to achieve them were similar in the intramuscular and high-dose intravenous groups. The low-dose intravenous quinine regimen resulted in mean peak concentrations greater than 6 mg/l and mean low concentrations greater than 3.5 mg/l. All blood concentrations exceeded the 99% in vitro inhibitory concentration (EC99) of 0.89 mg/l or less of quinine for 60 isolates of Plasmodium falciparum, which were taken from children with malaria during the same period. Judged by a number of clinical criteria, the response was better in patients receiving the high-dose than the low-dose intravenous regimen. The time taken to clear parasites with both the high-dose intravenous and intramuscular regimens were significantly shorter than those obtained in the low-dose group. We have also shown for the first time that the rate of parasite clearance can be directly related to the area under the quinine concentration versus time curve. This applied to all three quinine regimens (r = 0.4252, P less than 0.02; n less than or equal to 35). Five patients, two on the low-dose regimen, two on the intramuscular regimen, and one on the high-dose regimen, developed hypoglycemia after admission, but in these cases, insulin concentrations were correspondingly low. No significant quinine toxicity was observed in any of the cases. The high-dose intravenous quinine regimen described here may be optimal for treatment of severe falciparum malaria in areas of chloroquine resistance in Africa. Our data provide no justification for reducing the dose of quinine in the treatment of severe malaria in Africa. The intramuscular regimen could provide a satisfactory alternative in areas where intravenous administration might be delayed or is impossible.


Semi-rigid solution structures of heparin by constrained X-ray scattering modelling: new insight into heparin-protein complexes.
The anionic polysaccharides heparin and heparan sulphate play essential roles in the regulation of many physiological processes. Heparin is often used as an analogue for heparan sulphate. Despite knowledge of an NMR solution structure and 19 crystal structures of heparin-protein complexes for short heparin fragments, no structures for larger heparin fragments have been reported up to now. Here, we show that solution structures for six purified heparin fragments dp6-dp36 (where dp stands for degree of polymerisation) can be determined by a combination of analytical ultracentrifugation, synchrotron X-ray scattering, and constrained modelling. Analytical ultracentrifugation velocity data for dp6-dp36 showed sedimentation coefficients that increased linearly from 1.09 S to 1.84 S with size. X-ray scattering of dp6-dp36 gave radii of gyration R(G) that ranged from 1.33 nm to 3.12 nm and maximum lengths that ranged from 3.0 nm to 12.3 nm. The higher resolution of X-ray scattering revealed an increased bending of heparin with increased size. Constrained molecular modelling of 5000 randomised heparin conformers resulted in 9-15 best-fit structures for each of dp18, dp24, dp30, and dp36 that indicated flexibility and the presence of short linear segments in mildly bent structures. Comparisons of these solution structures with crystal structures of heparin-protein complexes revealed similar ranges of phi (phi) and psi (psi) angles between iduronate and glucosamine rings. We conclude that heparin in solution has a semi-rigid and extended conformation that is preformed for its optimal binding to protein targets without major conformational changes.


Comparing routine administrative data with registry data for assessing quality of hospital care in patients with myocardial infarction using deterministic record linkage.
Assessment of quality of care in patients with myocardial infarction (MI) should be based on data that effectively enable determination of quality. With the need to simplify measurement techniques, the question arises whether routine data can be used for this purpose. We therefore compared data from a German sickness fund (AOK) with data from the Berlin Myocardial Infarction Registry (BMIR). We included patients hospitalised for treatment of MI in Berlin from 2009-2011. We matched 2305 patients from AOK and BMIR by using deterministic record linkage with indirect identifiers. For matched patients we compared the frequency in documentation between AOK and BMIR for quality assurance variables and calculated the kappa coefficient (KC) as a measure of agreement. There was almost perfect agreement in documentation between AOK and BMIR data for matched patients for: catheter laboratory (KC: 0.874), ST elevation MI (KC: 0.826), diabetes (KC: 0.818), percutaneous coronary intervention (KC: 0.860) and hospital mortality (KC: 0.952). The remaining variables compared showed moderate or less than moderate agreement (KC < 0.6), and were grouped in Category II with less frequent documentation in AOK for risk factors and aspects of patients' history; in Category III with more frequent documentation in AOK for comorbidities; and in Category IV for medication at and after hospital discharge. Routine data are primarily collected and defined for reimbursement purposes. Quality assurance represents merely a secondary use. This explains why only a limited number of variables showed almost perfect agreement in documentation between AOK and BMIR. If routine data are to be used for quality assessment, they must be constantly monitored and further developed for this new application. Furthermore, routine data should be complemented with registry data by well-established methods of record linkage to realistically reflect the situation - also for those quality-associated variables not collected in routine data.


The effects of an aerobic training intervention on cognition, grey matter volumes and white matter microstructure.
While there is strong evidence from observational studies that physical activity is associated with reduced risk of cognitive decline and dementia, the extent to which aerobic training interventions impact on cognitive health and brain structure remains subject to debate. In a pilot study of 46 healthy older adults (66.6 years ± 5.2 years, 63% female), we compared the effects of a twelve-week aerobic training programme to a waitlist control condition on cardiorespiratory fitness, cognition and magnetic resonance imaging (MRI) outcomes. Cardiorespiratory fitness was assessed by VO2 max testing. Cognitive assessments spanned executive function, memory and processing speed. Structural MRI analysis included examination of hippocampal volume, and voxel-wise assessment of grey matter volumes using voxel-based morphometry. Diffusion tensor imaging analysis of fractional anisotropy, axial diffusivity and radial diffusivity was performed using tract-based spatial statistics. While the intervention successfully increased cardiorespiratory fitness, there was no evidence that the aerobic training programme led to changes in cognitive functioning or measures of brain structure in older adults. Interventions that are longer lasting, multi-factorial, or targeted at specific high-risk populations, may yield more encouraging results.


Treatment of cannabis use among people with psychotic or depressive disorders: a systematic review.
This article systematically reviews the evidence from randomized controlled trials (RCTs) for pharmacologic and psychological approaches to the treatment of cannabis use among individuals with psychotic or depressive disorders. A systematic literature search was conducted using the PubMed and PsychINFO databases from inception to December 2008. Individual searches in cannabis use (search terms: marijuana, cannabis, marijuana abuse, cannabis abuse, marijuana usage, cannabis usage), mental disorders (search terms: mood disorders, affective disorders, anxiety disorders, anxiety, depressive disorder, depression, psychotic disorders, psychosis, mental disorders), and pharmacotherapy (search terms: medication, drug therapy, pharmacotherapy, psychopharmacology, clinical trials, drug trial, treatment trial) were conducted and limited to humans, adolescents and adults. A search combining the individual cannabis use, mental disorder and pharmacotherapy searches produced 1,713 articles (PubMed = 1,398; PsychINFO = 315). Combining the cannabis use and mental disorder searches while limiting them to English articles and RCTs produced a total of 286 articles (PubMed = 228; PsychINFO = 58). From this literature, there were 7 RCTs conducted among mental health clients that reported cannabis use outcomes using pharmacologic or psychological interventions. While few RCTs have been conducted, there is evidence that pharmacologic and psychological interventions are effective for reducing cannabis use in the short-term among people with psychotic disorders or depression. Although it is difficult to make evidence-based treatment recommendations due to the paucity of research in this area, available studies indicate that effectively treating the mental health disorder with standard pharmacotherapy may be associated with a reduction in cannabis use and that longer or more intensive psychological interventions rather than brief interventions may be required, particularly among heavier users of cannabis and those with more chronic mental disorders. Specific recommendations regarding the type and length of specific psychological treatments cannot be made at this time, although motivational interviewing and cognitive-behavioral therapy approaches appear most promising.


Lift and drag performance of odontocete cetacean flippers.
Cetaceans (whales, dolphins and porpoises) have evolved flippers that aid in effective locomotion through their aquatic environments. Differing evolutionary pressures upon cetaceans, including hunting and feeding requirements, and other factors such as animal mass and size have resulted in flippers that are unique among each species. Cetacean flippers may be viewed as being analogous to modern engineered hydrofoils, which have hydrodynamic properties such as lift coefficient, drag coefficient and associated efficiency. Field observations and the collection of biological samples have resulted in flipper geometry being known for most cetacean species. However, the hydrodynamic properties of cetacean flippers have not been rigorously examined and thus their performance properties are unknown. By conducting water tunnel testing using scale models of cetacean flippers derived via computed tomography (CT) scans, as well as computational fluid dynamic (CFD) simulations, we present a baseline work to describe the hydrodynamic properties of several cetacean flippers. We found that flippers of similar planform shape had similar hydrodynamic performance properties. Furthermore, one group of flippers of planform shape similar to modern swept wings was found to have lift coefficients that increased with angle of attack nonlinearly, which was caused by the onset of vortex-dominated lift. Drag coefficient versus angle of attack curves were found to be less dependent on planform shape. Our work represents a step towards the understanding of the association between performance, ecology, morphology and fluid mechanics based on the three-dimensional geometry of cetacean flippers.


The survival advantage of milk and dairy consumption: an overview of evidence from cohort studies of vascular diseases, diabetes and cancer.
To conduct a detailed evaluation, with meta-analyses, of the published evidence on milk and dairy consumption and the incidence of vascular diseases and diabetes. Also to summarise the evidence on milk and dairy consumption and cancer reported by the World Cancer Research Fund and then to consider the relevance of milk and dairy consumption to survival in the UK, a typical Western community. Finally, published evidence on relationships with whole milk and fat-reduced milks was examined. Prospective cohort studies of vascular disease and diabetes with baseline data on milk or dairy consumption and a relevant disease outcome were identified by searching MEDLINE, and reference lists in the relevant published reports. Meta-analyses of relationships in these reports were conducted. The likely effect of milk and dairy consumption on survival was then considered, taking into account the results of published overviews of relationships of these foods with cancer. From meta-analysis of 15 studies the relative risk of stroke and/or heart disease in subjects with high milk or dairy consumption was 0.84 (95% CI 0.76, 0.93) and 0.79 (0.75, 0.82) respectively, relative to the risk in those with low consumption. Four studies reported incident diabetes as an outcome, and the relative risk in the subjects with the highest intake of milk or diary foods was 0.92 (0.86, 0.97). Set against the proportion of total deaths attributable to the life-threatening diseases in the UK, vascular disease, diabetes and cancer, the results of meta-analyses provide evidence of an overall survival advantage from the consumption of milk and dairy foods.


Turkish propolis supresses MCF-7 cell death induced by homocysteine.
Elevated plasma homocysteine (Hcy) level is a most important risk factor for various vascular diseases including coronary, cerebral and peripheral arterial and venous thrombosis. Propolis is produced by honeybee from various oils, pollens and wax materials. Therefore, it has various biological properties including antioxidant, antitumor and antimicrobial activities. This study investigated the effects of propolis and Hcy on apoptosis in cancer cells. According to our findings, Hcy induced apoptosis in human breast adenocarcinoma (MCF-7) cells by regulating numerous genes and proteins involved in the apoptotic signal transduction pathway. In contrast, treatment with propolis inhibited caspase- 3 and -9 induced by Hcy in MCF-7 cells. It can be concluded that Hcy may augment the activity of anticancer agents that induce excessive reactive oxygen species (ROS) generation and apoptosis in their target cells. In contrast to the previous studies herein we found that propolis in low doses protected cancer cells inhibiting cellular apoptosis mediated by intracellular ROS-dependent mitochondrial pathway.


miR-126 regulates angiogenic signaling and vascular integrity.
Precise regulation of the formation, maintenance, and remodeling of the vasculature is required for normal development, tissue response to injury, and tumor progression. How specific microRNAs intersect with and modulate angiogenic signaling cascades is unknown. Here, we identified microRNAs that were enriched in endothelial cells derived from mouse embryonic stem (ES) cells and in developing mouse embryos. We found that miR-126 regulated the response of endothelial cells to VEGF. Additionally, knockdown of miR-126 in zebrafish resulted in loss of vascular integrity and hemorrhage during embryonic development. miR-126 functioned in part by directly repressing negative regulators of the VEGF pathway, including the Sprouty-related protein SPRED1 and phosphoinositol-3 kinase regulatory subunit 2 (PIK3R2/p85-beta). Increased expression of Spred1 or inhibition of VEGF signaling in zebrafish resulted in defects similar to miR-126 knockdown. These findings illustrate that a single miRNA can regulate vascular integrity and angiogenesis, providing a new target for modulating vascular formation and function.


Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm.
The finite mixture (FM) model is the most commonly used model for statistical segmentation of brain magnetic resonance (MR) images because of its simple mathematical form and the piecewise constant nature of ideal brain MR images. However, being a histogram-based model, the FM has an intrinsic limitation--no spatial information is taken into account. This causes the FM model to work only on well-defined images with low levels of noise; unfortunately, this is often not the the case due to artifacts such as partial volume effect and bias field distortion. Under these conditions, FM model-based methods produce unreliable results. In this paper, we propose a novel hidden Markov random field (HMRF) model, which is a stochastic process generated by a MRF whose state sequence cannot be observed directly but which can be indirectly estimated through observations. Mathematically, it can be shown that the FM model is a degenerate version of the HMRF model. The advantage of the HMRF model derives from the way in which the spatial information is encoded through the mutual influences of neighboring sites. Although MRF modeling has been employed in MR image segmentation by other researchers, most reported methods are limited to using MRF as a general prior in an FM model-based approach. To fit the HMRF model, an EM algorithm is used. We show that by incorporating both the HMRF model and the EM algorithm into a HMRF-EM framework, an accurate and robust segmentation can be achieved. More importantly, the HMRF-EM framework can easily be combined with other techniques. As an example, we show how the bias field correction algorithm of Guillemaud and Brady (1997) can be incorporated into this framework to achieve a three-dimensional fully automated approach for brain MR image segmentation.


The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity.
Forkhead box N1 (FOXN1) is a member of the forkhead box family of transcription factors and plays an important role in thymic epithelial cell differentiation and development. FOXN1 mutations in humans and mice give rise to the "nude" phenotype, which is marked by athymia. FOXN1 belongs to a subset of the FOX family that recognizes an alternative forkhead-like (FHL) consensus sequence (GACGC) that is different from the more widely recognized forkhead (FKH) sequence RYAAAYA (where R is purine, and Y is pyrimidine). Here, we present the FOXN1 structure in complex with DNA containing an FHL motif at 1.6 Å resolution, in which the DNA sequence is recognized by a mixture of direct and water-mediated contacts provided by residues in an α-helix inserted in the DNA major groove (the recognition helix). Comparisons with the structure of other FOX family members revealed that the FKH and FHL DNA sequences are bound in two distinct modes, with partially different registers for the protein DNA contacts. We identified a single alternative rotamer within the recognition helix itself as an important determinant of DNA specificity and found protein sequence features in the recognition helix that could be used to predict the specificity of other FOX family members. Finally, we demonstrate that the C-terminal region of FOXN1 is required for high-affinity DNA binding and that FOXN1 has a significantly reduced affinity for DNA that contains 5'-methylcytosine, which may have implications for the role of FOXN1 in thymic involution.


T- and B-cell responses and previous exposure to hepatitis B virus in 'anti-HBc alone' patients.
A serologic response to hepatitis B virus (HBV) defined as 'anti-HBc alone' is commonly observed, but its significance remains unclear. This study aimed to define the relationship between 'anti-HBc alone' serostatus and HBV infection, including HBV-specific T- and B-cell memory responses. We enrolled 31 'anti-HBc alone' patients. Total HBV DNA and cccDNA were tested by nested polymerase chain reaction (PCR) analysis in liver samples from 22 'anti-HBc alone' patients vs controls (chronic or resolved HBV infection), followed by HBsAg/HBcAg immunohistochemical (IHC) staining. IFN-γ secretion by HBV-specific T cells was compared in individuals who were 'anti-HBc alone' (n = 27), resolved HBV (n = 21), chronic HBV (n = 24) and 12 healthy controls using enzyme-linked immunospot (ELISpot) assays. An HBsAg-IgG B-cell ELISpot assay was performed in 'anti-HBc alone' patients before and after one dose of recombinant HBsAg vaccine. The majority (23/31, 74.2%) of the 'anti-HBc alone' individuals were co-infected with HCV. Infrequent intrahepatic total HBV DNA (2/22, 9.1%) and cccDNA (1/22, 4.5%) were detected in biopsies; HBsAg and HBcAg IHC staining was negative. HBV-specific T-cell responses were similar between 'anti-HBc alone' individuals and HBV resolvers. Circulating HBV-memory B-cell responses were detected in all 'anti-HBc alone' individuals, consistent with an HBsAg-specific memory pool. After one HBV vaccine dose, increased anti-HBs antibody levels were observed, accompanied by an expansion of HBsAg-specific memory B cells (P = 0.0226). 'Anti-HBc alone' individuals showed HBV-specific T-cell and memory B-cell responses typical of previous viral exposure and protective memory, suggesting a resolved infection.


TIM23-mediated insertion of transmembrane α-helices into the mitochondrial inner membrane.
While overall hydrophobicity is generally recognized as the main characteristic of transmembrane (TM) α-helices, the only membrane system for which there are detailed quantitative data on how different amino acids contribute to the overall efficiency of membrane insertion is the endoplasmic reticulum (ER) of eukaryotic cells. Here, we provide comparable data for TIM23-mediated membrane protein insertion into the inner mitochondrial membrane of yeast cells. We find that hydrophobicity and the location of polar and aromatic residues are strong determinants of membrane insertion. These results parallel what has been found previously for the ER. However, we see striking differences between the effects elicited by charged residues flanking the TM segments when comparing the mitochondrial inner membrane and the ER, pointing to an unanticipated difference between the two insertion systems.


Deaths: leading causes for 2007.
This report presents final 2007 data on the 10 leading causes of death in the United States by age, race, sex, and Hispanic origin. Leading causes of infant, neonatal, and postneonatal death are also presented. This report supplements the Division of Vital Statistics' annual report of final mortality statistics. Data in this report are based on information from all death certificates filed in the 50 states and the District of Columbia in 2007. Causes of death classified by the International Classification of Diseases, Tenth Revision (ICD-10) are ranked according to the number of deaths assigned to rankable causes. Cause-of-death statistics are based on the underlying cause of death. In 2007, the 10 leading causes of death were, in rank order: Diseases of heart; Malignant neoplasms; Cerebrovascular diseases; Chronic lower respiratory diseases; Accidents (unintentional injuries); Alzheimer's disease; Diabetes mellitus; Influenza and pneumonia; Nephritis, nephrotic syndrome and nephrosis; and Septicemia. They accounted for approximately 76 percent of all deaths occurring in the United States. Differences in the rankings are evident by age, sex, race, and Hispanic origin. Leading causes of infant death for 2007 were, in rank order: Congenital malformations, deformations and chromosomal abnormalities; Disorders related to short gestation and low birth weight, not elsewhere classified; Sudden infant death syndrome; Newborn affected by maternal complications of pregnancy; Accidents (unintentional injuries); Newborn affected by complications of placenta, cord and membranes; Bacterial sepsis of newborn; Respiratory distress of newborn; Diseases of the circulatory system; and Neonatal hemorrhage. Important variations in the leading causes of infant death are noted for the neonatal and postneonatal periods.