The atypical 'hippocampal' glutamate receptor coupled to phospholipase D that controls stretch-sensitivity in primary mechanosensory nerve endings is homomeric purely metabotropic GluK2

ACKNOWLEDGEMENTS We would like to thank: Prof. Christophe Mulle, University of Bordeaux, France for the generous donation of the GluK2-Neo mice; Prof. Roberto Pellicciari and Prof. Maura Marinozzi, University of Perugia, Italy for the generous gift of PCCG-13; the Microscopy and Histology core facility at the Institute of Medical Sciences, University of Aberdeen for their support and assistance in some of the imaging in this work. We would also like to thank Prof. Gernot Riedel, University of Aberdeen UK and Prof. David Jane, University of Bristol UK for helpful comments during the work and discussion about drafts of this manuscript.Peer reviewedPublisher PD

Environmental tracers to evaluate groundwater residence times and water quality risk in shallow unconfined aquifers in sub Saharan Africa

In sub-Saharan Africa, shallow aquifer systems are relied on as the main safe and secure water resource available to rural communities. Information on the sustainability and vulnerability of groundwater abstraction is becoming increasingly important as groundwater development increases. As part of the UpGro Consortium Project- Hidden Crisis, 150 hand pumped boreholes (HPBs), ranging between 15 and 101 m depth were investigated to examine the resilience of aquifer systems in the Ethiopian Highlands, and the crystalline basement rocks of Uganda and Malawi. Environmental tracers (chlorofluorocarbons (CFCs), SF6, chloride and the stable isotopes of water), water quality indicators (nitrate and E. coli), and groundwater-level time series data were used to estimate groundwater residence time and recharge at a regional scale (100–10,000 km2) and investigate the risks to water quality and water supply over different timeframes, and geological and climatic environments. Average estimated recharge rates using three different techniques (CFCs, chloride mass balance, water table fluctuation method) were between 30 and 330, 27–110 and 30–170 mm y−1, for sites in Ethiopia, Uganda and Malawi, respectively. These estimates of recharge suggests abstraction from dispersed low-yielding HPBs is sustainable. Comparison of stable isotopes in rainfall and groundwater indicates that there is little evaporation prior to recharge, and recharge events are biased to months with greater rainfall and more intense rainfall events There was a weak correlation between nitrate and CFCs within all three countries, and no correlation between E. coli and CFCs within Ethiopia or Malawi. The presence of E. coli at a large proportion of the sites (Ethiopia = 38%, Uganda = 65% and Malawi = 47%) suggests rapid transit of contaminated surface water into the borehole and its presence in groundwater that has CFC-12 concentrations less than 75 pg kg−1 indicates mixing of very young water with water >40 years old. The rapid transit pathways are most likely associated with damaged HPB headworks and poor construction. In several monitored HPBs, daily drawdown due to pumping, drew the groundwater levels close to the base of the HPB, indicating that these HPBs were located in parts of the aquifer with low permeability, or were poorly designed, offering limited capacity for increased demand. Improved HPB siting and construction, coupled with groundwater level monitoring are required to capitalise on the more resilient groundwater within the shallow aquifers and safeguard adequate and good quality water supply for rural communities

Influence of the Environment on Participation in Social Roles for Young Adults with Down Syndrome

Background: The concept of disability is now understood as a result of the interaction between the individual, features related to impairment, and the physical and social environment. It is important to understand these environmental influences and how they affect social participation. The purpose of this study is to describe the social participation of young adults with Down syndrome and examine its relationship with the physical and social environment. Methods: Families ascertained from the Down syndrome ‘Needs Opinion Wishes’ database completed questionnaires during 2011. The questionnaires contained two parts, young person characteristics and family characteristics. Young adults’ social participation was measured using the Assessment of Life Habits (LIFE-H) and the influences of environmental factors were measured by the Measure of the Quality of the Environment (MQE). The analysis involved descriptive statistics and linear and logistic regression. Results: Overall, participation in daily activities was higher (mean 6.45) than in social roles (mean 5.17) (range 0 to 9). When the physical and/or social environment was reported as a facilitator, compared to being no influence or a barrier, participation in social roles was greater (coef 0.89, 95%CI 0.28, 1.52, coef 0.83, 95%CI 0.17, 1.49, respectively). The relationships between participation and both the physical (coef 0.60, 95% CI -0.40, 1.24) and social (coef 0.20, 95%CI -0.47, 0.87) environments were reduced when age, gender, behavior and functioning in ADL were taken into account. Conclusion: We found that young adults’ participation in social roles was influenced more by the physical environment than by the social environment, providing a potentially modifiable avenue for intervention

Alteration of Forkhead Box O (Foxo4) Acetylation Mediates Apoptosis of Podocytes in Diabetes Mellitus

The number of kidney podocytes is reduced in diabetic nephropathy. Advanced glycation end products (AGEs) accumulate in patients with diabetes and promote the apoptosis of podocyte by activating the forkhead box O4 (Foxo4) transcription factor to increase the expression of a pro-apoptosis gene, Bcl2l11. Using chromatin immunoprecipitation we demonstrate that AGE-modified bovine serum albumin (AGE-BSA) enhances Foxo4 binding to a forkhead binding element in the promoter of Bcl2lll. AGE-BSA also increases the acetylation of Foxo4. Lysine acetylation of Foxo4 is required for Foxo4 binding and transcription of Bcl2l11 in podocytes treated with AGE-BSA. The expression of a protein deacetylase that targets Foxo4 for deacetylation, sirtuin (Sirt1), is down regulated in cultured podocytes by AGE-BSA treatment and in glomeruli of diabetic patients. SIRT1 over expression in cultured murine podocytes prevents AGE-induced apoptosis. Glomeruli isolated from diabetic db/db mice have increased acetylation of Foxo4, suppressed expression of Sirt1, and increased expression of Bcl2l11 compared to non-diabetic littermates. Together, our data provide evidence that alteration of Foxo4 acetylation and down regulation of Sirt1 expression in diabetes promote podocyte apoptosis. Strategies to preserve Sirt1 expression or reduce Foxo4 acetylation could be used to prevent podocyte loss in diabetes

Breast cancer management pathways during the COVID-19 pandemic: outcomes from the UK ‘Alert Level 4’ phase of the B-MaP-C study

Abstract: Background: The B-MaP-C study aimed to determine alterations to breast cancer (BC) management during the peak transmission period of the UK COVID-19 pandemic and the potential impact of these treatment decisions. Methods: This was a national cohort study of patients with early BC undergoing multidisciplinary team (MDT)-guided treatment recommendations during the pandemic, designated ‘standard’ or ‘COVID-altered’, in the preoperative, operative and post-operative setting. Findings: Of 3776 patients (from 64 UK units) in the study, 2246 (59%) had ‘COVID-altered’ management. ‘Bridging’ endocrine therapy was used (n = 951) where theatre capacity was reduced. There was increasing access to COVID-19 low-risk theatres during the study period (59%). In line with national guidance, immediate breast reconstruction was avoided (n = 299). Where adjuvant chemotherapy was omitted (n = 81), the median benefit was only 3% (IQR 2–9%) using ‘NHS Predict’. There was the rapid adoption of new evidence-based hypofractionated radiotherapy (n = 781, from 46 units). Only 14 patients (1%) tested positive for SARS-CoV-2 during their treatment journey. Conclusions: The majority of ‘COVID-altered’ management decisions were largely in line with pre-COVID evidence-based guidelines, implying that breast cancer survival outcomes are unlikely to be negatively impacted by the pandemic. However, in this study, the potential impact of delays to BC presentation or diagnosis remains unknown

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Accuracy Of Thinprep Imaging System In Detecting Atypical Glandular Cells

The aim of this study was to evaluate the accuracy of the ThinPrep Imaging System (Imager) in detecting atypical glandular cells (AGC) or adenocarcinoma in the 22 selected fields. All cases reported as AGC or adenocarcinoma from January 2005 to December 2006 that had been initially screened by the Imager were retrospectively reviewed to determine whether the most diagnostically relevant groups/cells were within the 22 selected fields. A total of 39 cases were reviewed. The cases were divided into two groups: the group with diagnostic cells detected within the 22 selected fields (accurately detected group) and the group with upgraded diagnosis following rescreening process (underdetected group). The Imager accurately detected 32 (82%) of cases with abnormal glandular cells, including six cases reported as adenocarcinoma, one case as adenocarcinoma in situ (AIS), and 25 cases as AGC. In seven (18%) cases, the Imager failed to detect the most abnormal cells within the 22 selected fields. Among these, one case was adenocarcinoma, while the rest were reported as AGC. Overall, four cases were assessed as atypical during quality control (QC) rescreening even though the Imager detected abnormal groups in most. Fourteen of 32 cases had abnormalities proven by histologic follow-up. Overall, the Imager was effective in detecting most AGC, AIS and invasive adenocarcinomas. In a minority (18%) of cases, the Imager failed to detect the cells of interest within the 22 selected fields. However, full manual review of cases with potential atypical/reactive groups or endometrial groups in women ≥ 40 and QC rescreening of selected cases may help to minimize the underdetected cases. © 2009 Wiley-Liss, Inc

Optimising EEG-fMRI for Localisation of Focal Epilepsy in Children

Early surgical intervention in children with drug resistant epilepsy has benefits but requires using tolerable and minimally invasive tests. EEG-fMRI studies have demonstrated good sensitivity for the localization of epileptic focus but a poor yield although the reasons for this have not been systematically addressed. While adults EEG-fMRI studies are performed in the "resting state"; children are commonly sedated however, this has associated risks and potential confounds. In this study, we assessed the impact of the following factors on the tolerability and results of EEG-fMRI in children: viewing a movie inside the scanner; movement; occurrence of interictal epileptiform discharges (IED); scan duration and design efficiency. This work's motivation is to optimize EEG-fMRI parameters to make this test widely available to paediatric population.Forty-six children with focal epilepsy and 20 controls (6-18) underwent EEG-fMRI. For two 10 minutes sessions subjects were told to lie still with eyes closed, as it is classically performed in adult studies ("rest sessions"), for another two sessions, subjects watched a child friendly stimulation i.e. movie ("movie sessions"). IED were mapped with EEG-fMRI for each session and across sessions. The resulting maps were classified as concordant/discordant with the presumed epileptogenic focus for each subject.Movement increased with scan duration, but the movie reduced movement by ~40% when played within the first 20 minutes. There was no effect of movie on the occurrence of IED, nor in the concordance of the test. Ability of EEG-fMRI to map the epileptogenic region was similar for the 20 and 40 minute scan durations. Design efficiency was predictive of concordance.A child friendly natural stimulus improves the tolerability of EEG-fMRI and reduces in-scanner movement without having an effect on IED occurrence and quality of EEG-fMRI maps. This allowed us to scan children as young as 6 and obtain localising information without sedation. Our data suggest that ~20 minutes is the optimal length of scanning for EEG-fMRI studies in children with frequent IED. The efficiency of the fMRI design derived from spontaneous IED generation is an important factor for producing concordant results

The human inactive X chromosome modulates expression of the active X chromosome

The inactive X chromosome (Xi) has been assumed to have little impact, in , on the active X (Xa). To test this, we quantified Xi and Xa gene expression in individuals with one Xa and zero to three Xis. Our linear modeling revealed modular Xi and Xa transcriptomes and significant Xi-driven expression changes for 38% (162/423) of expressed X chromosome genes. By integrating allele-specific analyses, we found that modulation of Xa transcript levels by Xi contributes to many of these Xi-driven changes (≥121 genes). By incorporating metrics of evolutionary constraint, we identified 10 X chromosome genes most likely to drive sex differences in common disease and sex chromosome aneuploidy syndromes. We conclude that human X chromosomes are regulated both in , through Xi-wide transcriptional attenuation, and in , through positive or negative modulation of individual Xa genes by Xi. The sum of these and effects differs widely among genes