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Estimates of vegetation attributes measured by sampling often inform scientific inference, management actions, and policy decisions. However, different sampling methods and sample sizes (i.e. number of plots) can yield significantly different estimates of vegetation attributes. This occurs because the abundance distributions and spatial distributions of species in the plant community influence their probabilities of detection and estimates of their abundances. We predicted that different sampling methods and sample sizes would produce significantly different estimates not only of vascular plant species diversity, but also of indigenous dominance (the level of indigenous influence) in mixed vegetation where indigenous and exotic floras have different abundance or spatial distributions. To test our predictions we applied three sampling methods to 24 plots in grassland and cushion vegetation in a 1058-ha scientific reserve in the Upper Waitaki (Mackenzie) Basin, New Zealand. Our methods sampled ground areas from 0.65 to 400 m 2 , and included two variants of common 'subsampling' approaches, which assessed only discrete subunits within larger plots. Indigenous plant species were both less abundant on average and more spatially-clustered (i.e. less evenly dispersed across plots) than exotic species. The two subsampling methods were less likely to detect less abundant and more spatially clustered species, leading to lower ratios of indigenous to exotic species recorded, and lower estimates of indigenous dominance of composition (% of species indigenous). Numbers of indigenous species accumulated more rapidly with increasing sample size than numbers of exotic species, so that indigenous dominance also increased with the number of plots sampled. We conclude that properly measuring species diversity and indigenous dominance in mixed indigenous-exotic plant communities requires both the searching of sizeable plots and use of rarefaction rather than plot-averaging of statistics. We suggest greater use of rarefaction and more consideration of species' detection probabilities in sampling New Zealand's mixed indigenous-exotic plant communities should improve the reliability, transparency and comparability of measures of diversity and may also provide new ecological insights.

Defects in PEX3 are associated with a severe neonatal-lethal form of Zellweger spectrum disorder. We report two moderately affected siblings whose clinical and biochemical phenotypes expand the reported spectrum of PEX3-related disease. Genome sequencing of an adolescent male with progressive movement disorder, spasticity and neurodegeneration, and previous non-diagnostic plasma very-long chain fatty acid analysis, revealed a homozygous likely pathogenic missense variant in PEX3 [c.991G > A; p.(Gly331Arg)]. A younger sibling with significant motor decline since the age of three years was also subsequently found to be homozygous for the familial PEX3 variant. A comprehensive review of the scientific literature identified three additional families with non-lethal infantile- or childhood-onset PEX3-related disease, which together with this clinical report illustrate the potential for highly variable disease severity. Our findings demonstrate the diagnostic utility of genome-wide sequencing for identifying clinically and biochemically heterogeneous inherited metabolic disorders such as the peroxisome biogenesis disorders.

Key Points Question What is the diagnostic yield of genome sequencing in children with unexplained medical complexity and prior negative results of genetic testing? Findings In this cohort study that included 138 individuals from 49 families, genome sequencing detected all genomic variation previously identified by conventional genetic testing and resulted in a new diagnosis for 31% of patients. Meaning This study suggests that, because of its high yield, comprehensive nature, and increasingly competitive costs, genome sequencing is a potentially first-tier genetic test for children with unexplained medical complexity., Importance Children with medical complexity (CMC) represent a growing population in the pediatric health care system, with high resource use and associated health care costs. A genetic diagnosis can inform prognosis, anticipatory care, management, and reproductive planning. Conventional genetic testing strategies for CMC are often costly, time consuming, and ultimately unsuccessful. Objective To evaluate the analytical and clinical validity of genome sequencing as a comprehensive diagnostic genetic test for CMC. Design, Setting, and Participants In this cohort study of the prospective use of genome sequencing and comparison with standard-of-care genetic testing, CMC were recruited from May 1, 2017, to November 30, 2018, from a structured complex care program based at a tertiary care pediatric hospital in Toronto, Canada. Recruited CMC had at least 1 chronic condition, technology dependence (child is dependent at least part of each day on mechanical ventilators, and/or child requires prolonged intravenous administration of nutritional substances or drugs, and/or child is expected to have prolonged dependence on other device-based support), multiple subspecialist involvement, and substantial health care use. Review of the care plans for 545 CMC identified 143 suspected of having an undiagnosed genetic condition. Fifty-four families met inclusion criteria and were interested in participating, and 49 completed the study. Probands, similarly affected siblings, and biological parents were eligible for genome sequencing. Exposures Genome sequencing was performed using blood-derived DNA from probands and family members using established methods and a bioinformatics pipeline for clinical genome annotation. Main Outcomes and Measures The primary study outcome was the diagnostic yield of genome sequencing (proportion of CMC for whom the test result yielded a new diagnosis). Results Genome sequencing was performed for 138 individuals from 49 families of CMC (29 male and 20 female probands; mean [SD] age, 7.0 [4.5] years). Genome sequencing detected all genomic variation previously identified by conventional genetic testing. A total of 15 probands (30.6%; 95% CI 19.5%-44.6%) received a new primary molecular genetic diagnosis after genome sequencing. Three individuals had novel diseases and an additional 9 had either ultrarare genetic conditions or rare genetic conditions with atypical features. At least 11 families received diagnostic information that had clinical management implications beyond genetic and reproductive counseling. Conclusions and Relevance This study suggests that genome sequencing has high analytical and clinical validity and can result in new diagnoses in CMC even in the setting of extensive prior investigations. This clinical population may be enriched for ultrarare and novel genetic disorders. Genome sequencing is a potentially first-tier genetic test for CMC., This cohort study evaluates the analytical and clinical validity of genome sequencing as a comprehensive diagnostic genetic test for children with medical complexity.

Objectives This is a literature review of the published evidence of the benefits and suggested structure of preceptorship programmes for General Practice Nursing, with the aim of informing General Practices and networks who are instituting preceptorship programmes. Design & data sources A literature search was carried out in the CINAHL Plus database of English language papers from the year 2000–2019 using the search terms; (Precept* OR mentor*) AND (“community practice” OR “primary care” OR “general practice” OR “new GPN” OR “new general practice nurse” OR “nurse new to general practice” OR “induction GPN” or “GPN”). Review method A literature review and narrative synthesis of the evidence. Results Our searches produced twelve papers. Seven papers reported on single preceptorship programmes in General Practice or primary care, with qualitative or quantitative evaluation of their effects. Three qualitative papers reported participant experience of preceptorship, or discussed the learning needs that preceptorship must address. Two literature reviews reported the evidence for preceptorship in General Practice or nurse practitioner programmes. Conclusion The quality of the evidence on General Practice Nurse preceptorship is low. There is a lack of robust evidence on the effects, and the benefits. These should be evaluated as preceptorship programmes are implemented. The limited available evidence suggests that a structured preceptorship programme, of more than 4 months duration, which allows the development of peer-to-peer support, is a good model for General Practice Nurse preceptorship. The involvement of doctors and the wider practice team is essential for the success of such a programme. Preceptors require training and support in the role. General Practice Nurse preceptorship should support the development of existing professional competencies, including the ability to make real-time autonomous clinical decisions. The financial costs, and cost of time away from clinical care, should be ameliorated as far as possible, when instituting a national General Practice Nurse preceptorship programme.

Induced pluripotent stem cell (iPSC)-derived cortical neurons are increasingly used as a model to study developmental aspects of Autism Spectrum Disorder (ASD), which is clinically and genetically heterogeneous. To study the complex relationship of rare (penetrant) variant(s) and common (weaker) polygenic risk variant(s) to ASD, “isogenic” iPSC-derived neurons from probands and family-based controls, for modeling, is critical. We developed a standardized set of procedures, designed to control for heterogeneity in reprogramming and differentiation, and generated 53 different iPSC-derived glutamatergic neuronal lines from 25 participants from 12 unrelated families with ASD (14 ASD-affected individuals, 3 unaffected siblings, 8 unaffected parents). Heterozygousde novo(7 families; 16p11.2,NRXN1,DLGAP2,CAPRIN1,VIP,ANOS1,THRA) and rare-inherited (2 families;CNTN5,AGBL4) presumed-damaging variants were characterized in ASD risk genes/loci. In three additional families, functional candidates for ASD (SET), and combinations of putative etiologic variants (GLI3/KIF21AandEHMT2/UBE2Icombinations in separate families), were modeled. We used a large-scale multi-electrode array (MEA) as our primary high-throughput phenotyping assay, followed by patch clamp recordings. Our most compelling new results revealed a consistent spontaneous network hyperactivity in neurons deficient forCNTN5orEHMT2.Our biobank of iPSC-derived neurons and accompanying genomic data are available to accelerate ASD research.

SummaryAutism Spectrum Disorder is phenotypically and genetically heterogeneous, but genomic analyses have identified candidate susceptibility genes. We present a CRISPR gene editing strategy to insert a protein tag and premature termination sites creating an induced pluripotent stem cell (iPSC) knockout resource for functional studies of 10 ASD-relevant genes (AFF2/FMR2, ANOS1, ASTN2, ATRX, CACNA1C, CHD8, DLGAP2, KCNQ2, SCN2A, TENM1). Neurogenin 2 (NEUROG2)-directed differentiation of iPSCs allowed production of cortical excitatory neurons, and mutant proteins were not detectable. RNAseq revealed convergence of several neuronal networks. Using both patch-clamp and multi-electrode array approaches, the electrophysiological deficits measured were distinct for different mutations. However, they culminated in a consistent reduction in synaptic activity, including reduced spontaneous excitatory post-synaptic current frequencies in AFF2/FMR2-, ASTN2-, ATRX-, KCNQ2- and SCN2A-null neurons. Despite ASD susceptibility genes belonging to different gene ontologies, isogenic stem cell resources can reveal common functional phenotypes, such as reduced functional connectivity.

Purpose: RAC3 is an underexamined member of the Rho GTPase gene family that is expressed in the developing brain and linked to key cellular functions. De novo missense variants in the homolog RAC1 were recently associated with developmental disorders. In the RAC subfamily, transforming missense changes at certain shared residues have been observed in human cancers and previously characterized in experimental studies. The purpose of this study was to determine whether constitutional dysregulation of RAC3 is associated with human disease. Methods: We discovered a RAC3 variant in the index case using genome sequencing, and searched for additional variants using international data-sharing initiatives. Functional effects of the variants were assessed using a multifaceted approach generalizable to most clinical laboratory settings. Results: We rapidly identified five individuals with de novo monoallelic missense variants in RAC3, including one recurrent change. Every participant had severe intellectual disability and brain malformations. In silico protein modeling, and prior in vivo and in situ experiments, supported a transforming effect for each of the three different RAC3 variants. All variants were observed in databases of somatic variation in cancer. Conclusions: Missense variants in RAC3 cause a novel brain disorder, likely through a mechanism of constitutive protein activation.

Chitayat-Hall syndrome, initially described in 1990, is a rare condition characterised by distal arthrogryposis, intellectual disability, dysmorphic features and hypopituitarism, in particular growth hormone deficiency. The genetic aetiology has not been identified., Background Chitayat-Hall syndrome, initially described in 1990, is a rare condition characterised by distal arthrogryposis, intellectual disability, dysmorphic features and hypopituitarism, in particular growth hormone deficiency. The genetic aetiology has not been identified. Methods and results We identified three unrelated families with a total of six affected patients with the clinical manifestations of Chitayat-Hall syndrome. Through whole exome or whole genome sequencing, pathogenic variants in the MAGEL2 gene were identified in all affected patients. All disease-causing sequence variants detected are predicted to result in a truncated protein, including one complex variant that comprised a deletion and inversion. Conclusions Chitayat-Hall syndrome is caused by pathogenic variants in MAGEL2 and shares a common aetiology with the recently described Schaaf-Yang syndrome. The phenotype of MAGEL2-related disorders is expanded to include growth hormone deficiency as an important and treatable complication, he McLaughlin Centre, University of Toronto, Toronto, Canada, and Fondation Jeanne et Jean- Louis Lévesque (JLM). The Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada. FDL has a fellowship funded by FCT - Fundação para a Ciência e a Tecnologia (SFRH/BD/84650/2010), info:eu-repo/semantics/publishedVersion

AimTo explore, in a general practice setting, the concerns, beliefs and attitudes about intrauterine contraception (IUC) reported by women, who had never used the methods.MethodsWe used a sequential mixed-method (QUAL/quant) approach. A pragmatic, self-selecting sample of 30 women, aged 18–46 years, who had never used IUC), was recruited through seven general practices in South East England. Themes arising from qualitative interviews were used to construct a quantitative survey, completed by a pragmatic sample of 1195 women, aged 18–49 years, attending 32 general practices in the same region, between February and August 2015.ResultsQualitative themes were concerns about the long-acting nature of IUC, concerns about body boundaries, and informal knowledge of IUC, especially ‘friend of a friend’ stories. Women were not sure if the devices can be removed before their full 5- or 10-year duration of use, and felt that these timeframes did not fit with their reproductive intentions. Quantitative survey data showed that the most commonly endorsed concerns among never-users were painful fitting (55.8%), unpleasant removal of the device (60.1%), and concern about having a device ’inside me' (60.2%).ConclusionsTo facilitate fully informed contraceptive choice, information provided to women considering IUC should be tailored to more fully address the concerns expressed by never-users, particularly around the details of insertion and removal, and concerns about the adverse, long-term effects of the device. Women need to be reassured that IUC can be removed and fertility restored at any time following insertion.Trial registrationTrial registration NIHR CRN portfolio; 15912.

ObjectivesIntrauterine contraception (IUC) is highly effective, safe and long-lasting, but is not a popular method of contraception among British women. This study examined barriers to the uptake of IUC in general practice in England.MethodA sequential mixed-method approach to explore the views of practitioners regarding the provision of IUC. We e-surveyed 208 practitioners from 69 practices in a region of England and subsequently interviewed 14 practitioners from eight practices.ResultsJust under half of general practitioners (GPs) (46.8%; 58/124), and only 8.2% (4/49) of nurses reported being trained to fit IUC. Lack of knowledge of IUC was a barrier to fitting, and also to recommending IUC, especially by practitioners who were not trained to fit. There was discordance between reported knowledge of eligibility for IUC and the likelihood of recommending IUC. Respondents were less likely to recommend IUC to young, nulliparous women, women who had experienced a previous ectopic pregnancy, a recent sexually transmitted infection (STI), or an abnormal cervical smear. The qualitative data indicate that risk aversion and limited training, together with practitioners’ assessments that women are uninterested, may lead to IUC being precluded as a suitable method.ConclusionsIncreased practitioner education, for those not trained to fit IUC, may remove a barrier to the uptake of IUC in general practice. More research is required on the discordance between the practitioners’ views on the characteristics of women considered suitable for IUC, and the criteria set out in the UK Medical Eligibility Criteria (UKMEC) guidelines.

Introduction.Based on extensive piloting work, we adapted the Incredible Years (IY) teacher-training programme to the Jamaican preschool setting and evaluated this adapted version through a cluster-randomised trial.Methods.Twenty-four community preschools in Kingston, Jamaica were randomly assigned to intervention (12 schools, 37 teachers) or control (12 schools, 36 teachers). The intervention involved training teachers in classroom management through eight full-day training workshops and four individual 1-h in-class support sessions. Outcome measurements included direct observation of teachers’ positive and negative behaviours to the whole class and to high-risk children and four observer ratings: two measures of class-wide child behaviour and two measures of classroom atmosphere. Measures were repeated at a six-month follow-up.Results.Significant benefits of intervention were found for teachers’ positive [effect size (ES) = 3.35] and negative (ES = 1.29) behaviours to the whole class and to high-risk children (positive: ES = 0.83; negative: ES = 0.50) and for observer ratings of class-wide child behaviour (ES = 0.73), child interest and enthusiasm (ES = 0.98), teacher warmth (ES = 2.03) and opportunities provided to share and help (ES = 5.72). At 6-month follow-up, significant benefits of intervention were sustained: positive behaviours (ES = 2.70), negative behaviours (ES = 0.98), child behaviour (ES = 0.50), child interest and enthusiasm (ES = 0.78), teacher warmth (ES = 0.91), opportunities to share and help (ES = 1.42).Conclusions.The adapted IY teacher-training programme produced large benefits to teacher's behaviour and to class-wide measures of children's behaviour, which were sustained at 6-month follow-up. Benefits were of a similar magnitude to those found in a pilot study of the minimally adapted version that required significantly more in-class support for teachers.

Purpose Hemiplegia is a subtype of cerebral palsy (CP) in which one side of the body is affected. Our earlier study of unselected children with CP demonstrated de novo and clinically relevant rare inherited genomic copy-number variations (CNVs) in 9.6% of participants. Here, we examined the prevalence and types of CNVs specifically in hemiplegic CP. Methods We genotyped 97 unrelated probands with hemiplegic CP and their parents. We compared their CNVs to those of 10,851 population controls, in order to identify rare CNVs (

Objective To determine a molecular diagnosis for a large multigenerational family of South Asian ancestry with seizures, hyperactivity, and episodes of tongue biting. Methods Two affected individuals from the family were analyzed by whole-genome sequencing on the Illumina HiSeq X platform, and rare variants were prioritized for interpretation with respect to the phenotype. Results A previously undescribed, 1-kb homozygous deletion was identified in both individuals sequenced, which spanned 2 exons of the VPS13A gene, and was found to segregate in other family members. Conclusions VPS13A is associated with autosomal recessive chorea-acanthocytosis, a diagnosis consistent with the phenotype observed in this family. Whole-genome sequencing presents a comprehensive and agnostic approach for detecting diagnostic mutations in families with rare neurologic disorders.

We are entering an era of unprecedented quantities of data from current and planned survey telescopes. To maximise the potential of such surveys, automated data analysis techniques are required. Here we implement a new methodology for variable star classification, through the combination of Kohonen Self Organising Maps (SOM, an unsupervised machine learning algorithm) and the more common Random Forest (RF) supervised machine learning technique. We apply this method to data from the K2 mission fields 0-4, finding 154 ab-type RR Lyraes (10 newly discovered), 377 Delta Scuti pulsators, 133 Gamma Doradus pulsators, 183 detached eclipsing binaries, 290 semi-detached or contact eclipsing binaries and 9399 other periodic (mostly spot-modulated) sources, once class significance cuts are taken into account. We present lightcurve features for all K2 stellar targets, including their three strongest detected frequencies, which can be used to study stellar rotation periods where the observed variability arises from spot modulation. The resulting catalogue of variable stars, classes, and associated data features are made available online. We publish our SOM code in Python as part of the open source PyMVPA package, which in combination with already available RF modules can be easily used to recreate the method., Accepted for publication in MNRAS, 16 pages, 13 figures. Updated with proof corrections. Full catalogue tables available at https://www2.warwick.ac.uk/fac/sci/physics/research/astro/people/armstrong/ or at the CDS

Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family. All 56 GntR proteins of M145 strain were classified into FadR, HutC, MocR, YtrA, and DevA subfamilies according to their secondary structure. We then checked for the presence of GntR orthologs in six other sequenced Streptomyces and one Kitasatospora genomes, revealing that 12 GntRs were conserved in all analyzed strains. Genomic analysis of the less studied YtrA type regulators revealed 160 sequences present in 88 members of Coriobacteridae, Rubrobacteridae, and Actinobacteridae subclasses. These proteins form seven dense clusters on the consensus phylogenetic tree and their genes are usually co-located with the genes for transport proteins. Probable operator sites were identified for orthologous groups of Sco0823 and Sco3812 proteins. All S. coelicolor YtrA-like regulatory genes (SCO0823, SCO1728, SCO3812) were analyzed at transcriptional level, knocked out, and introduced on moderate copy number plasmid in M145 strain. Also, gene SCO0824, a part of putative SCO0823 operon, was studied. Results of these experiments are discussed here.

Background Nonalcoholic fatty liver disease and nonalcoholic steatohepatitis (NASH) are serious conditions and are being diagnosed at an increased rate. The etiology of these hepatic disorders is not clear but involves insulin resistance and oxidative stress. Remogliflozin etabonate (Remo) is an inhibitor of the sodium glucose-dependent renal transporter 2 (SGLT2), and improves insulin sensitivity in type 2 diabetics. In the current study, we examined the effects of Remo in a diet-induced obese mouse model of NAFLD. Methods After 11-weeks on High-Fat-Diet 32 (HFD32), C57BL/6J mice were obese and displayed characteristics consistent with NAFLD. Cohorts of obese animals were continued on HFD32 for an additional 4-week treatment period with or without Remo. Results Treatment with Remo for 4 weeks markedly lowered both plasma alanine aminotransferase (76%) and aspartate aminotransferase (48%), and reduced both liver weight and hepatic triglyceride content by 42% and 40%, respectively. Remo also reduced hepatic mRNA content for tumor necrosis factor (TNF)-α (69%), and monocyte chemoattractant protein (MCP)-1 (69%). The diet-induced increase in thiobarbituric acid-reactive substances, a marker of oxidative stress, was reduced following treatment with Remo, as measured in both liver homogenates (22%) and serum (37%). Finally, the oxygen radical absorbance capacity (ORAC) in three different SGLT2 inhibitors was determined: remogliflozin, canagliflozin and dapagliflozin. Only remogliflozin had any significant ORAC activity. Conclusions Remo significantly improved markers associated with NAFLD in this animal model, and may be an effective compound for the treatment of NASH and NAFLD due to its insulin-sensitizing and antioxidant properties.

Autism spectrum disorder (ASD) is genetically heterogeneous, with evidence for hundreds of susceptibility loci. Previous microarray and exome-sequencing studies have examined portions of the genome in simplex families (parents and one ASD-affected child) having presumed sporadic forms of the disorder. We used whole-genome sequencing (WGS) of 85 quartet families (parents and two ASD-affected siblings), consisting of 170 individuals with ASD, to generate a comprehensive data resource encompassing all classes of genetic variation (including noncoding variants) and accompanying phenotypes, in apparently familial forms of ASD. By examining de novo and rare inherited single-nucleotide and structural variations in genes previously reported to be associated with ASD or other neurodevelopmental disorders, we found that some (69.4%) of the affected siblings carried different ASD-relevant mutations. These siblings with discordant mutations tended to demonstrate more clinical variability than those who shared a risk variant. Our study emphasizes that substantial genetic heterogeneity exists in ASD, necessitating the use of WGS to delineate all genic and non-genic susceptibility variants in research and in clinical diagnostics.

Chitayat-Hall syndrome, initially described in 1990, is a rare condition characterised by distal arthrogryposis, intellectual disability, dysmorphic features and hypopituitarism, in particular growth hormone deficiency. The genetic aetiology has not been identified.We identified three unrelated families with a total of six affected patients with the clinical manifestations of Chitayat-Hall syndrome. Through whole exome or whole genome sequencing, pathogenic variants in theChitayat-Hall syndrome is caused by pathogenic variants in

Background Autism spectrum disorder (ASD), a developmental disorder of early childhood onset, affects males four times more frequently than females, suggesting a role for the sex chromosomes. In this study, we describe a family with ASD in which a predicted pathogenic nonsense mutation in the X-chromosome gene RAB39B segregates with ASD phenotype. Methods Clinical phenotyping, microarray, and whole genome sequencing (WGS) were performed on the five members of this family. Maternal and female sibling X inactivation ratio was calculated, and phase was investigated. Mutant-induced pluripotent stem cells engineered for an exon 2 nonsense mutation were generated and differentiated into cortical neurons for expression and pathway analyses. Results Two males with an inherited RAB39B mutation both presented with macrocephaly, intellectual disability (ID), and ASD. Their female sibling with the same mutation presented with ID and a broad autism phenotype. In contrast, their transmitting mother has no neurodevelopmental diagnosis. Our investigation of phase indicated maternal preferential inactivation of the mutated allele, with no such bias observed in the female sibling. We offer the explanation that this bias in X inactivation may explain the absence of a neurocognitive phenotype in the mother. Our cellular knockout model of RAB39B revealed an impact on expression in differentiated neurons for several genes implicated in brain development and function, supported by our pathway enrichment analysis. Conclusions Penetrance for ASD is high among males but more variable among females with RAB39B mutations. A critical role for this gene in brain development and function is demonstrated. Electronic supplementary material The online version of this article (10.1186/s13229-017-0175-3) contains supplementary material, which is available to authorized users.

A remaining hurdle to whole-genome sequencing (WGS) becoming a first-tier genetic test has been accurate detection of copy-number variations (CNVs). Here, we used several datasets to empirically develop a detailed workflow for identifying germline CNVs >1 kb from short-read WGS data using read depth-based algorithms. Our workflow is comprehensive in that it addresses all stages of the CNV-detection process, including DNA library preparation, sequencing, quality control, reference mapping, and computational CNV identification. We used our workflow to detect rare, genic CNVs in individuals with autism spectrum disorder (ASD), and 120/120 such CNVs tested using orthogonal methods were successfully confirmed. We also identified 71 putative genic de novo CNVs in this cohort, which had a confirmation rate of 70%; the remainder were incorrectly identified as de novo due to false positives in the proband (7%) or parental false negatives (23%). In individuals with an ASD diagnosis in which both microarray and WGS experiments were performed, our workflow detected all clinically relevant CNVs identified by microarrays, as well as additional potentially pathogenic CNVs < 20 kb. Thus, CNVs of clinical relevance can be discovered from WGS with a detection rate exceeding microarrays, positioning WGS as a single assay for genetic variation detection.

Obesity is a multifactorial condition that is highly heritable. There have been ~60 susceptibility loci identified, but they only account for a fraction of cases. As copy number variations (CNVs) have been implicated in the etiology of a multitude of human disorders including obesity, here, we investigated the contribution of rare (

This article is a personal narrative by Ronnie Walker, MS, LCPC about the suicide of her stepson, Channing, in 1995. It describes the particular journey of shock, despair, disorientation, guilt, and anger that Walker began after the death. It also describes the remarkable personal growth and restoration of meaning that emerged for the author as she began what is now the largest online community of suicide loss survivors in the world, the Alliance of Hope ( www.allianceofhope.org ). The article also provides numerous examples of the power of supportive community in helping survivors of suicide loss to not only cope but also to demonstrate posttraumatic growth after the suicide of a loved one.

The April issue of the BJGP discussed the ongoing issues of alcohol and opiate misuse in our society.1,2 We wish to highlight a less well-recognised drug of abuse with potentially devastating consequences, namely nitrous oxide. This drug can have significant adverse effects on the nervous system by causing vitamin B12 deficiency. Sliney argues that it should not be the doctor’s role to distinguish between genuine and fraudulent claims of pain and that doing so …

Atypical brain connectivity is a major contributor to the pathophysiology of neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASDs). TAOK2 is one of several genes in the 16p11.2 microdeletion region, but whether it contributes to NDDs is unknown. We performed behavioral analysis on Taok2 heterozygous (Het) and knockout (KO) mice and found gene dosage-dependent impairments in cognition, anxiety, and social interaction. Taok2 Het and KO mice also have dosage-dependent abnormalities in brain size and neural connectivity in multiple regions, deficits in cortical layering, dendrite and synapse formation, and reduced excitatory neurotransmission. Whole-genome and -exome sequencing of ASD families identified three de novo mutations in TAOK2 and functional analysis in mice and human cells revealed that all the mutations impair protein stability, but they differentially impact kinase activity, dendrite growth, and spine/synapse development. Mechanistically, loss of Taok2 activity causes a reduction in RhoA activation, and pharmacological enhancement of RhoA activity rescues synaptic phenotypes. Together, these data provide evidence that TAOK2 is a neurodevelopmental disorder risk gene and identify RhoA signaling as a mediator of TAOK2-dependent synaptic development.

Intestinal dysbiosis is implicated in alcoholic hepatitis (AH). However, changes in the circulating microbiome, its association with the presence and severity of AH and its functional relevance in AH is unknown. Qualitative and quantitative assessment of changes in the circulating microbiome were performed by sequencing bacterial DNA in subjects with moderate (n=18) or severe AH (n=19). These data were compared to heavy drinking controls (HDC) without obvious liver disease (n=19) and non-alcohol consuming controls (NAC, n=20). The data were related to endotoxin levels and markers of monocyte activation. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis, inferred metagenomics and predictive functional analysis using PICRUSt were performed. There was a significant increase in 16S copies/ng DNA both in MAH (p

We are performing whole genome sequencing (WGS) of families with Autism Spectrum Disorder (ASD) to build a resource, named MSSNG, to enable the sub-categorization of phenotypes and underlying genetic factors involved. Here, we report WGS of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible in a cloud platform, and through an internet portal with controlled access. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertion/deletions (indels) or copy number variations (CNVs) per ASD subject. We identified 18 new candidate ASD-risk genes such as MED13 and PHF3, and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (p=6×10−4). In 294/2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried CNV/chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.

This document will serve as a guide for the servicewoman who wants to transition to a civilian positon in the security field. Transitions are never easy. If you are currently in the US Military, you are used to discipline, doctrine, and regulations. Sometimes in the civilian world, you get some of the above, and sometimes you do not. I was in the Army for 25 years, so this document will reflect my experience with the Army; I hope you can see the similarities if you are in another branch of the military.

We report three newly discovered exoplanets from the SuperWASP survey. WASP-127b is a heavily inflated super-Neptune of mass 0.18 +/- 0.02 M_J and radius 1.37 +/- 0.04 R_J. This is one of the least massive planets discovered by the WASP project. It orbits a bright host star (Vmag = 10.16) of spectral type G5 with a period of 4.17 days. WASP-127b is a low-density planet that has an extended atmosphere with a scale height of 2500 +/- 400 km, making it an ideal candidate for transmission spectroscopy. WASP-136b and WASP-138b are both hot Jupiters with mass and radii of 1.51 +/- 0.08 M_J and 1.38 +/- 0.16 R_J, and 1.22 +/- 0.08 M_J and 1.09 +/- 0.05 R_J, respectively. WASP-136b is in a 5.22-day orbit around an F9 subgiant star with a mass of 1.41 +/- 0.07 M_sun and a radius of 2.21 +/- 0.22 R_sun. The discovery of WASP-136b could help constrain the characteristics of the giant planet population around evolved stars. WASP-138b orbits an F7 star with a period of 3.63 days. Its radius agrees with theoretical values from standard models, suggesting the presence of a heavy element core with a mass of ~10 M_earth. The discovery of these new planets helps in exploring the diverse compositional range of short-period planets, and will aid our understanding of the physical characteristics of both gas giants and low-density planets., Comment: 10 pages, 12 figures, 6 tables, accepted for publication in A&A

Projects attempting the direct detection of WIMP dark matter share the common problem of eliminating sources of background or using techniques to distinguish background events from true signals. Although experiments such as DarkSide have achieved essentially background free exposures through careful choice of materials and application of efficient veto techniques, there will still be a high burden of proof to convince the greater scientific community when a discovery is claimed. A directional signature in the data would provide extremely strong evidence to distinguish a true WIMP signal from that of an isotropic background. Two-phase argon time projection chambers (TPCs) provide an experimental apparatus which can both be scaled to the ton-scale size required to accommodate the low cross-section expected for WIMP interactions and have an anisotropy that could be exploited to evaluate the polar angles of the resulting nuclear recoils from WIMP collisions with target nuclei. Our studies show that even a modest resolution in the polar angle reconstruction would offer a powerful tool to detect a directional signature. In this contribution, the status of the ReD experiment, which is under construction at Naples University, will be also shown. The aim of the project is to assess and enhance the directionality of two-phase argon TPCs. ReD will use a small TPC exposed to a beam of mono-energetic neutrons to study the so called “columnar recombination” in liquid argon. This development could have high impact on the future experiments in the field, opening up the potential to find conclusive evidence for dark matter or disprove the WIMP hypothesis at and above the mass range explored by planned accelerator experiments.

Copy number variation has emerged as an important cause of phenotypic variation, particularly in relation to some complex disorders. Autism spectrum disorder (ASD) is one such disorder, in which evidence is emerging for an etiological role for some rare penetrant de novo and rare inherited copy number variants (CNVs). De novo variation, however, does not always explain the familial nature of ASD, leaving a gap in our knowledge concerning the heritable genetic causes of this disorder. Extended pedigrees, in which several members have ASD, provide an opportunity to investigate inherited genetic risk factors. In this current study, we recruited 19 extended ASD pedigrees, and, using the Illumina HumanOmni2.5 BeadChip, conducted genome-wide CNV interrogation. We found no definitive evidence of an etiological role for segregating CNVs in these pedigrees, and no evidence that linkage signals in these pedigrees are explained by segregating CNVs. However, a small number of putative de novo variants were transmitted from BAP parents to their ASD offspring, and evidence emerged for a rare duplication CNV at 11p13.3 harboring two putative 'developmental/neuropsychiatric' susceptibility gene(s), GSTP1 and NDUFV1.

Synaptic function is central to brain function. Understanding the synapse is aided by studies of patients lacking individual synaptic proteins. Common neurological diseases are genetically complex. Their understanding is likewise simplified by studies of less common monogenic forms. We detail the disease caused by absence of the synaptic protein CNKSR2 in 8 patients ranging from 6 to 62 years old. The disease is characterized by intellectual disability, attention problems, and abrupt lifelong language loss following a brief early childhood epilepsy with continuous spike-waves in sleep. This study describes the phenotype of CNKSR2 deficiency and its involvement in systems underlying common neurological disorders. Ann Neurol 2014;76:758–764

The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome sequencing, here we show that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR) < 0.05, plus a set of 107 autosomal genes strongly enriched for those likely to affect risk (FDR < 0.30). These 107 genes, which show unusual evolutionary constraint against mutations, incur de novo loss-of-function mutations in over 5% of autistic subjects. Many of the genes implicated encode proteins for synaptic formation, transcriptional regulation and chromatin-remodelling pathways. These include voltage-gated ion channels regulating the propagation of action potentials, pacemaking and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodellers-most prominently those that mediate post-translational lysine methylation/demethylation modifications of histones.

Live-shearing of wild guanacos Lama guanicoe may affect their reproductive success and population resilience, and therefore it is important to assess the biological sustainability of obtaining their wool. We evaluated effects of capture and shearing on survival and reproduction, population parameters, daily movements, ranging behaviour and spatial distribution in sedentary and migratory populations. We assessed population variables by radio-telemetry and line-transect surveys before and after capture. We estimated high post-shearing survival rates in both populations and similar yearling production in shorn and non-shorn females in the migratory population. We did not find significant variations in density and population structure before and after shearing in the sedentary population, whereas in the migratory population density decreased and the population structure changed significantly after assembly of the capture structure, returning to pre-assembly levels 1 month later. The mean daily distance moved by radio-collared guanacos during the first 2 days after shearing was three times longer than during the following 30 days. There was a 25% decrease in the mean home-range size of shorn guanacos between the first and second month after shearing but this decline appeared to be associated with a seasonal change in movement, because a similar reduction occurred during the same period the following year, when the guanacos were not shorn. Live-shearing modified the spatial distribution pattern in the sedentary population but did not have a significant effect on the migratory population.Management of guanacos may contribute towards developing a biologically sustainable economic activity that promotes conservation of wildlife and habitats. Fil: Carmanchahi, Pablo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación En Biodiversidad y Medioambiente; Argentina Fil: Schroeder, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza. Instituto Argentino de Investigaciones de Zonas Aridas; Argentina Fil: Bolgeri, María José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación En Biodiversidad y Medioambiente; Argentina Fil: Walker, R. Susan. Wildlife Conservation Society. Programa Estepa Patagónica y Andina, Junín de los Andes, Neuquén; Argentina Fil: Funes, Martín. Wildlife Conservation Society. Programa Estepa Patagónica y Andina, Junín de los Andes, Neuquén; Argentina Fil: Berg, Jodi. Wildlife Conservation Society. Programa Estepa Patagónica y Andina, Junín de los Andes, Neuquén; Argentina Fil: Taraborelli, Paula Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza. Instituto Argentino de Investigaciones de Zonas Aridas; Argentina Fil: Ovejero Aguilar, Ramiro Jose Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza. Instituto Argentino de Investigaciones de Zonas Aridas; Argentina Fil: Gregorio, Pablo Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación En Biodiversidad y Medioambiente; Argentina Fil: Moreno, Pablo Gastón. Universidad Nacional del Litoral. Facultad de Ciencias Veterinarias; Argentina Fil: Novaro, Andres Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación En Biodiversidad y Medioambiente; Argentina

We report changes in guanaco Lama guanicoe density, recruitment, and social structure associated with increased access of poachers along an extensive network of hydrocarbon-exploration roads in northern Patagonia, and conservation measures taken in response. Mean guanaco densities declined 93?96% and mean group size declined from 9.8 to 5.0 guanacos per group at three sites surveyed during 1982?1983 and 2002?2007, whereas yearling proportions did not change significantly. Additional surveys during 2002?2007 suggest population declines and fragmentation have occurred over a wide area of intense hydrocarbon exploration and extraction. Guanaco densities in 2002?2007 showed a strong negative association with the density of access points along hydrocarbon-exploration roads and, to a lesser degree, with livestock densities. The increase in poaching in recent decades, resulting from increased access and an urban population that has appropriate vehicles, has probably been the main cause of the decline of the guanaco population, although overgrazing by livestock and decreased plant productivity may also be contributing factors. Closing of exploration roads with levees and ditches in 2006 and 2010 by a hydrocarbon company, under supervision by the local government and scientists, restricted access by unauthorized vehicles to a 220,000-ha area, including two of the sites where guanaco numbers collapsed. This action, in combination with increased ranger patrols, may allow guanaco recovery in the coming years. Fil: Radovani, Natalia Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentina. Wildlife Conservation Society; Estados Unidos Fil: Funes, Martin Cristian. Wildlife Conservation Society; Estados Unidos Fil: Walker, R. Susan. Wildlife Conservation Society; Estados Unidos Fil: Gader, Reinaldo. Provincia del Neuquen. Subsecretaria de Produccion y Recursos Naturales. Centro de Ecologia Aplicada del Neuquen; Argentina Fil: Novaro, Andres Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentina. Wildlife Conservation Society; Estados Unidos

A half-life-sized copper-alloy head of a bearded man was published in the Portable Antiquities Scheme's report of finds from Roman Britain in 2009.1 The head was purchased by the Ashmolean Museum in 2011. In this paper evidence for the identification of the subject as a portrait of the emperor Marcus Aurelius is reviewed by comparison with metropolitan and other certainly identified heads of deities and portraits of the emperor. The technique and likely function of the head are compared with those of similarly worked Roman copper-alloy heads of emperors and deities found in South-East Britain. Finally, a brief account is given of geophysical survey and trial excavation conducted in 2012–13 in the field where the head was found. This offers a unique opportunity to explore the head's archaeological context.

Background Morvan’s syndrome is a rare disorder, characterized by peripheral nerve hyperexcitability, dysautonomia and encephalopathy with marked insomnia. About three quarters of patients have voltage gated potassium channel (VGKC) antibodies. A significant proportion of patients have associated tumours and the majority of these are thymomas. Introduction A 53 year-old man presented with a history of pain, cramps and twitching of the muscles of the chest and limbs, insomnia, hyperhidrosis, hypersalivation and cognitive impairment with hallucinations. Examination revealed fasciculations of the proximal upper limbs, piloerection of the forearms and mild postural hypotension. Investigations The patient underwent a number of electrophysiological studies: (1) EMG demonstrated spontaneous and frequent irregularly occurring neuromyotonic activity as doublet, triplet and multiplet single motor unit discharges firing at a high intraburst frequency (133–200 Hz), consistent with peripheral nerve hyperexcitability. (2) Paired-pulse transcranial magnetic stimulation revealed reduction in the short-interval intracortical inhibition (SICI) suggestive of central hyperexcitability. (3) EEG demonstrated left temporal slowing on an otherwise normal background. (4) autonomic testing showed a generalized sudomotor impairment consistent with autonomic dysfunction. Neuroimaging of the brain with PET demonstrated bilateral temporal lobe hypometabolism. Whole body PET revealed a hypermetabolic thyroid lesion, which was subsequently confirmed histologically to be a multifocal papillary thyroid carcinoma. Discussion The clinical and electrophysiological presentation was consistent with a diagnosis of Morvan’s syndrome in the context of a paraneoplastic phenomenon secondary to papillary thyroid cancer. The patient underwent a thyroidectomy and adjuvant radiotherapy. In addition, monthly intravenous methylprednisolone and intravenous immunoglobulin was instituted. Subsequently, the patient experienced significant symptomatic improvement with resolution of muscle fasciculations and cramps, hyperhidrosis and visual hallucinations. Insomnia and pain although improved did not completely resolve. Conclusion This case reviews the clinical and neurophysiological findings of Morvan’s syndrome. The case adds to the small number of non-thymomatous tumours associated with this syndrome and highlights the importance of a thorough search for malignancy in this clinical context.

The underpinnings of mild to moderate neurodevelopmental delay remain elusive, often leading to late diagnosis and interventions. Here, we present data on exome and genome sequencing as well as array analysis of 13 individuals that point to pathogenic, heterozygous, mostly de novo variants in WDFY3 (significant de novo enrichment P = 0.003) as a monogenic cause of mild and non-specific neurodevelopmental delay. Nine variants were protein-truncating and four missense. Overlapping symptoms included neurodevelopmental delay, intellectual disability, macrocephaly, and psychiatric disorders (autism spectrum disorders/attention deficit hyperactivity disorder). One proband presented with an opposing phenotype of microcephaly and the only missense-variant located in the PH-domain of WDFY3. Findings of this case are supported by previously published data, demonstrating that pathogenic PH-domain variants can lead to microcephaly via canonical Wnt-pathway upregulation. In a separate study, we reported that the autophagy scaffolding protein WDFY3 is required for cerebral cortical size regulation in mice, by controlling proper division of neural progenitors. Here, we show that proliferating cortical neural progenitors of human embryonic brains highly express WDFY3, further supporting a role for this molecule in the regulation of prenatal neurogenesis. We present data on Wnt-pathway dysregulation in Wdfy3-haploinsufficient mice, which display macrocephaly and deficits in motor coordination and associative learning, recapitulating the human phenotype. Consequently, we propose that in humans WDFY3 loss-of-function variants lead to macrocephaly via downregulation of the Wnt pathway. In summary, we present WDFY3 as a novel gene linked to mild to moderate neurodevelopmental delay and intellectual disability and conclude that variants putatively causing haploinsufficiency lead to macrocephaly, while an opposing pathomechanism due to variants in the PH-domain of WDFY3 leads to microcephaly.