Pair densities at contact in the quantum electron gas

The value of the pair distribution function g(r) at contact (r = 0) in a quantum electron gas is determined by the scattering events between pairs of electrons with antiparallel spins. The theoretical results for g(0) as a function of the coupling strength r_s in the paramagnetic electron gas in dimensionality D=2 and 3, that have been obtained from the solution of the two-body scattering problem with a variety of effective scattering potentials embodying many-body effects, are compared with the results of many-body calculations in the ladder approximation and with quantum Monte Carlo data.Comment: 7 pages, 2 figure

Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

We present biallelic SNVs called from 2,548 samples across 26 populationsfrom the 1000 Genomes Project, called directly on GRCh38. We believethis will be a useful reference resource for those using GRCh38,representing an improvement over the “lift-overs” of the 1000 GenomesProject data that have been available to date and providing a resourcenecessary for the full adoption of GRCh38 by the community. Here, wedescribe how the call set was created and provide benchmarking datadescribing how our call set compares to that produced by the final phase ofthe 1000 Genomes Project on GRCh37

Staphylococcus aureus nasal colonization in HIV-seropositive and HIV-seronegative drug users

Nasal colonization plays an important role in the pathogenesis of Staphylococcus aureus infections. To identify characteristics associated with colonization, we studied a cross-section of a well-described cohort of HIV-seropositive and -seronegative active and former drug users considered at risk for staphylococcal infections. Sixty percent of the 217 subjects were Hispanic, 36% were women, 25% actively used injection drugs, 23% actively used inhalational drugs, 23% received antibiotics, and 35% were HIV-seropositive. Forty-one percent of subjects had positive nasal cultures for S. aureus. The antibiotic susceptibility patterns were similar to the local hospital's outpatient isolates and no dominant strain was identified by arbitrarily primed polymerase chain reaction (AB-PCR). Variables significantly and independently associated with colonization included antibiotic use (odds ratio [OR] = 0.37; confidence interval [CI] = 0.18-0.77), active inhalational drug use within the HIV-seropositive population (OR = 2.36; CI = 1.10-5.10) and female gender (OR = 1.97; CI = 1.09-3.57). Characteristics not independently associated included injection drug use, HIV status, and CD4 count. The association with active inhalational drug use, a novel finding, may reflect alterations in the integrity of the nasal mucosa. The lack of association between HIV infection and S. aureus colonization, which is contrary to most previous studies, could be explained by our rigorous control for confounding variables or by a limited statistical power due to the sample sizes

Recognition of skin malignancy by general practitioners: observational study using data from a population-based randomised controlled trial

Skin malignancy is an important cause of mortality in the United Kingdom and is rising in incidence every year. Most skin cancer presents in primary care, and an important determinant of outcome is initial recognition and management of the lesion. Here we present an observational study of interobserver agreement using data from a population-based randomised controlled trial of minor surgery. Trial participants comprised patients presenting in primary care and needing minor surgery in whom recruiting doctors felt to be able to offer treatment themselves or to be able to refer to a colleague in primary care. They are thus relatively unselected. The skin procedures undertaken in the randomised controlled trial generated 491 lesions with a traceable histology report: 36 lesions (7%) from 33 individuals were malignant or pre-malignant. Chance-corrected agreement (κ) between general practitioner (GP) diagnosis of malignancy and histology was 0.45 (0.36–0.54) for lesions and 0.41 (0.32–0.51) for individuals affected with malignancy. Sensitivity of GPs for the detection of malignant lesions was 66.7% (95% confidence interval (CI), 50.3–79.8) for lesions and 63.6% (95% CI, 46.7–77.8) for individuals affected with malignancy. The safety of patients is of paramount importance and it is unsafe to leave the diagnosis and treatment of potential skin malignancy in the hands of doctors who have limited training and experience. However, the capacity to undertake all of the minor surgical demand works demanded in hospitals does not exist. If the capacity to undertake it is present in primary care, then the increased costs associated with enhanced training for general medical practitioners (GPs) must be borne

Many-body aspects of positron annihilation in the electron gas

We investigate positron annihilation in electron liquid as a case study for many-body theory, in particular the optimized Fermi Hypernetted Chain (FHNC-EL) method. We examine several approximation schemes and show that one has to go up to the most sophisticated implementation of the theory available at the moment in order to get annihilation rates that agree reasonably well with experimental data. Even though there is basically just one number to look at, the electron-positron pair distribution function at zero distance, it is exactly this number that dictates how the full pair distribution behaves: In most cases, it falls off monotonously towards unity as the distance increases. Cases where the electron-positron pair distribution exhibits a dip are precursors to the formation of bound electron--positron pairs. The formation of electron-positron pairs is indicated by a divergence of the FHNC-EL equations, from this we can estimate the density regime where positrons must be localized. This occurs in our calculations in the range 9.4 <= r_s <=10, where r_s is the dimensionless density parameter of the electron liquid.Comment: To appear in Phys. Rev. B (2003

Placental Transfer of Lactate, Glucose and 2-deoxyglucose in Control and Diabetic Wistar Rats

Placental transfer of lactate, glucose and 2-deoxyglucose was examined employing the in situ perfused placenta. Control and streptozotocin induced diabetic Wistar rats were infused with [U14C]-glucose and [3H]-2-deoxyglucose (2DG). The fetal side of the placenta was perfuseci with a cell free medium and glucose uptake was calculated in the adjacent fetuses. Despite the 5-fold higher maternal plasma glucose concentration in the diabetic dams the calculated fetal glucose metabolic index was not significantly different between the 2 groups. Placental blood flow was reduced in the diabetic animals compared with controls but reduction of transfer of [U14C]-glucose and [3H]-2-deoxyglucose and endogenously derived [14C]-Lactate to the fetal compartment, could not be accounted for by reduced placental blood flow alone. There was no significant net production or uptake of lactate into the perfusion medium that had perfused the fetal side of the placenta in either group. The plasma lactate levels in the fetuses adjacent to the perfused placenta were found to be higher than in the maternal plasma and significantly higher in the fetuses of the diabetic group compared with control group. In this model the in situ perfused placenta does not secrete significant quantities of lactate into the fetal compartment in either the control or diabetic group

Solonamide B Inhibits Quorum Sensing and Reduces Staphylococcus aureus Mediated Killing of Human Neutrophils

Methicillin-resistant Staphylococcus aureus (MRSA) continues to be a serious human pathogen, and particularly the spread of community associated (CA)-MRSA strains such as USA300 is a concern, as these strains can cause severe infections in otherwise healthy adults. Recently, we reported that a cyclodepsipeptide termed Solonamide B isolated from the marine bacterium, Photobacterium halotolerans strongly reduces expression of RNAIII, the effector molecule of the agr quorum sensing system. Here we show that Solonamide B interferes with the binding of S. aureus autoinducing peptides (AIPs) to sensor histidine kinase, AgrC, of the agr two-component system. The hypervirulence of USA300 has been linked to increased expression of central virulence factors like α-hemolysin and the phenol soluble modulins (PSMs). Importantly, in strain USA300 Solonamide B dramatically reduced the activity of α-hemolysin and the transcription of psma encoding PSMs with an 80% reduction in toxicity of supernatants towards human neutrophils and rabbit erythrocytes. To our knowledge this is the first report of a compound produced naturally by a Gram-negative marine bacterium that interferes with agr and affects both RNAIII and AgrA controlled virulence gene expression in S. aureus

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types

The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide association study across 406,365 CpGs in 52 monozygotic twin pairs discordant for T1D in three immune effector cell types. We observe a substantial enrichment of differentially variable CpG positions (DVPs) in T1D twins when compared with their healthy co-twins and when compared with healthy, unrelated individuals. These T1D-associated DVPs are found to be temporally stable and enriched at gene regulatory elements. Integration with cell type-specific gene regulatory circuits highlight pathways involved in immune cell metabolism and the cell cycle, including mTOR signalling. Evidence from cord blood of newborns who progress to overt T1D suggests that the DVPs likely emerge after birth. Our findings, based on 772 methylomes, implicate epigenetic changes that could contribute to disease pathogenesis in T1D.This work was funded by the EU-FP7 project BLUEPRINT (282510) and the Wellcome Trust (99148). We thank all twins for taking part in this study; Kerra Pearce and Mark Kristiansen (UCL Genomics) for processing the Illumina Infinium HumanMethylation450 BeadChips; Rasmus Bennet for technical assistance; and Laura Phipps for proofreading the manuscript. The BMBF Pediatric Diabetes Biobank recruits patients from the National Diabetes Patient Documentation System (DPV), and is financed by the German Ministry of Education and Research within the German Competence Net Diabetes Mellitus (01GI1106 and 01GI1109B). It was integrated into the German Center for Diabetes Research in January 2015. We thank the Swedish Research Council and SUS Funds for support. We gratefully acknowledge the participation of all NIHR Cambridge BioResource volunteers, and thank the Cambridge BioResource staff for their help with volunteer recruitment. We thank members of the Cambridge BioResource SAB and Management Committee for their support of our study and the NIHR Cambridge Biomedical Research Centre for funding. The Cardiovascular Epidemiology Unit is supported by the UK Medical Research Council (G0800270), BHF (SP/09/002), and NIHR Cambridge Biomedical Research Centre. Research in the Ouwehand laboratory is supported by the NIHR, BHF (PG-0310-1002 and RG/09/12/28096) and NHS Blood and Transplant. K.D. is funded as a HSST trainee by NHS Health Education England. M.F. is supported by the BHF Cambridge Centre of Excellence (RE/13/6/30180). A.D., E.L., L.C. and P.F. receive additional support from the European Molecular Biology Laboratory. A.K.S. is supported by an ADA Career Development Award (1-14-CD-17). B.O.B. and R.D.L. acknowledge support from the Deutsche Forschungsgemeinschaft (DFG) and European Federation for the Study of Diabetes, respectively

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. Results: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. Conclusions: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species