An analysis of identical single-nucleotide polymorphisms genotyped by two different platforms

The overlap of 94 single-nucleotide polymorphisms (SNP) among the 4,720 and 11,120 SNPs contained in the linkage panels of Illumina and Affymetrix, respectively, allows an assessment of the discrepancy rate produced by these two platforms. Although the no-call rate for the Affymetrix platform is approximately 8.6 times greater than for the Illumina platform, when both platforms make a genotypic call, the agreement is an impressive 99.85%. To determine if disputed genotypes can be resolved without sequencing, we studied recombination in the region of the discrepancy for the most discrepant SNP rs958883 (typed by Illumina) and tsc02060848 (typed by Affymetrix). We find that the number of inferred recombinants is substantially higher for the Affymetrix genotypes compared to the Illumina genotypes. We illustrate this with pedigree 10043, in which 3 of 7 versus 0 of 7 offspring must be double recombinants using the genotypes from the Affymetrix and the Illumina platforms, respectively. Of the 36 SNPs with one or more discrepancies, we identified a subset that appears to cluster in families. Some of this clustering may be due to the presence of a second segregating SNP that obliterates a XbaI site (the restriction enzyme used in the Affymetrix platform), resulting in a fragment too long (>1,000 bp) to be amplified

Earth observation applications for coastal sustainability: potential and challenges for implementation

Copyright remains with the author(s) or their institution(s). The coast is home to unique ecosystems, where complex ecological processes take place through the interaction of terrestrial, aquatic, atmospheric, and human landscapes. However, there are considerable knowledge and data gaps in achieving effective and future change-proof sustainable management of coastal zones around the world due to both technical and social barriers, as well as governance challenges. Currently, the role of Earth observation (EO) in addressing many of the recognised information gaps is small and under-utilised. While EO can provide much of the spatiotemporal information required for historical analysis and current status mapping, and offers the advantage of global coverage; its uptake can be limited by technical and methodological challenges associated mostly with lack of capacity and infrastructure, product accuracy and accessibility, costs, and institutional acceptance. While new initiatives and recent technological progress in the EO and information technology arena aim to tackle some of these issues so that EO products can be more easily used by non-EO experts, uptake is still limited.This paper discusses how EO can potentially inform transformative practices of planning in the coastal water zone, by using examples to demonstrate the EO potential in providing information relevant to decisionmaking framed by international agreements, such as the United Nations Agenda 2030, the Convention on Biological Diversity, and the Sendai Framework for Risk Reduction. By presenting evidence for how EO can contribute to innovative opportunities and data synergies at scale, the paper discusses opportunities and challenges for a more solution-led approach to sustainable coastal management.European Union’s Horizon 2020 research and innovation programme under grant agreement No. 687289 (Co-ReSyF project), the United Kingdom’s Natural Environment Research Council (NERC) under Grant NE/E009328 (GloboLakes project), and the Future Earth Coasts project.European Union’s Horizon 2020 research and innovation programme under grant agreement No. 687289 (Co-ReSyF project); United Kingdom’s Natural Environment Research Council (NERC) under Grant NE/E009328 (GloboLakes project); Future Earth Coasts project

Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease

Extreme obesity (EO, BMI>50) is frequently associated with neuropsychiatric disease (NPD). As both EO and NPD are heritable central nervous system disorders, we assessed the prevalence of protein truncating (PTV) and copy number variants (CNV) in genes/regions previously implicated in NPD, in adults with EO (n=149) referred for weight loss/bariatric surgery. We also assessed the prevalence of CNVs in patients referred to University College London Hospital (UCLH) with EO (n=218) and obesity (O, BMI 35-50, n=374) and a Swedish cohort of participants from the community with predominantly O (n=161). The prevalence of variants was compared to controls in ExAC/gnomAd database. In the discovery cohort (high NPD prevalence: 77%), the cumulative PTV/CNV allele frequency (AF) was 7.7 % vs 2.6% in controls (Odds Ratio (OR) 3.1, (95% CI 2-4.1, p<0.0001). In the UCLH EO cohort (intermediate NPD prevalence: 47%), CNV AF (1.8% vs 0.9% in controls, OR 1.95, 95% CI 0.96-3.93, p=0.06) was lower than the discovery cohort. CNV AF was not increased in the UCLH O cohort (0.8%). No CNVs were identified in the Swedish cohort with no NPD. These findings suggest PTV/CNVs, in genes/regions previously associated with NPD, may contribute to NPD in patients with EO

Naturopathic Care for Anxiety: A Randomized Controlled Trial ISRCTN78958974

BACKGROUND: Anxiety is a serious personal health condition and represents a substantial burden to overall quality of life. Additionally anxiety disorders represent a significant cost to the health care system as well as employers through benefits coverage and days missed due to incapacity. This study sought to explore the effectiveness of naturopathic care on anxiety symptoms using a randomized trial. METHODS: Employees with moderate to severe anxiety of longer than 6 weeks duration were randomized based on age and gender to receive naturopathic care (NC) (n = 41) or standardized psychotherapy intervention (PT) (n = 40) over a period of 12 weeks. Blinding of investigators and participants during randomization and allocation was maintained. Participants in the NC group received dietary counseling, deep breathing relaxation techniques, a standard multi-vitamin, and the herbal medicine, ashwagandha (Withania somnifera) (300 mg b.i.d. standardized to 1.5% with anolides, prepared from root). The PT intervention received psychotherapy, and matched deep breathing relaxation techniques, and placebo. The primary outcome measure was the Beck Anxiety Inventory (BAI) and secondary outcome measures included the Short Form 36 (SF-36), Fatigue Symptom Inventory (FSI), and Measure Yourself Medical Outcomes Profile (MY-MOP) to measure anxiety, mental health, and quality of life respectively. Participants were blinded to the placebo-controlled intervention. RESULTS: Seventy-five participants (93%) were followed for 8 or more weeks on the trial. Final BAI scores decreased by 56.5% (p<0.0001) in the NC group and 30.5% (p<0.0001) in the PT group. BAI group scores were significantly decreased in the NC group compared to PT group (p = 0.003). Significant differences between groups were also observed in mental health, concentration, fatigue, social functioning, vitality, and overall quality of life with the NC group exhibiting greater clinical benefit. No serious adverse reactions were observed in either group. RELEVANCE: Many patients seek alternatives and/or complementary care to conventional anxiety treatments. To date, no study has evaluated the potential of a naturopathic treatment protocol to effectively treat anxiety. Knowledge of the efficacy, safety or risk of natural health products, and naturopathic treatments is important for physicians and the public in order to make informed decisions. INTERPRETATION: Both NC and PT led to significant improvements in patients' anxiety. Group comparison demonstrated a significant decrease in anxiety levels in the NC group over the PT group. Significant improvements in secondary quality of life measures were also observed in the NC group as compared to PT. The whole system of naturopathic care for anxiety needs to be investigated further including a closer examination of the individual components within the context of their additive effect. TRIAL REGISTRATION: Controlled-Trials.com ISRCTN78958974

Smad4 promotes diabetic nephropathy by modulating glycolysis and OXPHOS

Diabetic nephropathy (DN) is the leading cause of end‐stage kidney disease. TGF‐β1/Smad3 signalling plays a major pathological role in DN; however, the contribution of Smad4 has not been examined. Smad4 depletion in the kidney using anti‐Smad4 locked nucleic acid halted progressive podocyte damage and glomerulosclerosis in mouse type 2 DN, suggesting a pathogenic role of Smad4 in podocytes. Smad4 is upregulated in human and mouse podocytes during DN. Conditional Smad4 deletion in podocytes protects mice from type 2 DN, independent of obesity. Mechanistically, hyperglycaemia induces Smad4 localization to mitochondria in podocytes, resulting in reduced glycolysis and oxidative phosphorylation and increased production of reactive oxygen species. This operates, in part, via direct binding of Smad4 to the glycolytic enzyme PKM2 and reducing the active tetrameric form of PKM2. In addition, Smad4 interacts with ATPIF1, causing a reduction in ATPIF1 degradation. In conclusion, we have discovered a mitochondrial mechanism by which Smad4 causes diabetic podocyte injury

Promoting patient engagement with self-management support information: a qualitative meta-synthesis of processes influencing uptake

<p>Abstract</p> <p>Background</p> <p>Patient information has been viewed as a key component of self-management. However, little attention has been given to methods of dissemination or implementation of effective information strategies. Previous problems identified with the use and implementation of patient information point to the need to explore the way in which patients engage with and use information to support self-management for chronic conditions.</p> <p>Methods</p> <p>Four published qualitative studies from a programme of research about self-management were analysed as a group; these included studies of the management of inflammatory bowel disease (IBD); self-help in anxiety and depression (SHADE); menorrhagia, treatment, information, and preference (MENTIP) study; and self-help for irritable bowel syndrome (IBS). For the analysis, we used an adapted meta-ethnographic approach to the synthesis of qualitative data in order to develop an evidence base.</p> <p>Results</p> <p>The ontological status and experience of the condition in everyday life was the most dominant theme to emerge from this synthesis. This, coupled with access to and experience of traditional health services responses, shaped the engagement with and use of information to support self-management. Five key elements were found which were likely to influence this: the perception and awareness of alternative self-management possibilities; the prior extent and nature of engagement with information; the extent of and ability to self-manage; opportunities for use of the information and the stage of the illness career; and congruence and synergy with the professional role.</p> <p>Conclusion</p> <p>People with chronic conditions need support from providers in both supply and engagement with information, in a way which gives legitimacy to the person's own self-management strategies and possible alternatives. Thus, a link could usefully be made between information offered, as well as patients' past experiences of self-management and engagement with services for their condition. The timeliness of the information should be considered, both in terms of the illness career and the type of condition (<it>i.e</it>., before depression gets too bad or time to reflect on existing knowledge about a condition and how it is to be managed) and in terms of the pre-existing relationship with services (<it>i.e</it>., options explored and tried).</p> <p>More considered use of information (how it is provided, by whom, and at what point it should be introduced) is key to facilitating patients' engagement with and therefore use of information to support self-management.</p

Characterization of CTX-M ESBLs in Enterobacter cloacae, Escherichia coli and Klebsiella pneumoniae clinical isolates from Cairo, Egypt

<p>Abstract</p> <p>Background</p> <p>A high rate of resistance to 3^rdgeneration cephalosporins among Enterobacteriaceae isolates from Egypt has been previously reported. This study aims to characterize the resistance mechanism (s) to extended spectrum cephalosporins among resistant clinical isolates at a medical institute in Cairo, Egypt.</p> <p>Methods</p> <p>Nonconsecutive <it>Klebsiella pneumoniae </it>(Kp), <it>Enterobacter cloacae </it>(ENT) and <it>Escherichia coli </it>(EC) isolates were obtained from the clinical laboratory at the medical institute. Antibiotic susceptibility was tested by CLSI disk diffusion and ESBL confirmatory tests. MICs were determined using broth microdilution. Isoelectric focusing (IEF) was used to determine the pI values, inhibitor profiles, and cefotaxime (CTX) hydrolysis by the β-lactamases. PCR and sequencing were performed using <it>bla</it>_CTX-Mand IS<it>Ecp1</it>-specific primers, with DNA obtained from the clinical isolates. Conjugation experiments were done to determine the mobility of <it>bla</it>_CTX-M.</p> <p>Results</p> <p>All five clinical isolates were resistant to CTX, and were positive for ESBL screening. IEF revealed multiple β-lactamases produced by each isolate, including a β-lactamase with a pI of 8.0 in Kp and ENT and a β-lactamase with a pI of 9.0 in EC. Both β-lactamases were inhibited by clavulanic acid and hydrolyzed CTX. PCR and sequence analysis identified <it>bla</it>_CTX-M-14in Kp and ENT and a <it>bla</it>_CTX-M-15in EC. Both <it>bla</it>_CTX-M-14and <it>bla</it>_CTX-M-15were preceded by IS<it>Ecp1 </it>elements as revealed by partial sequence analysis of the upstream region of the <it>bla</it>_CTX-Mgenes. <it>bla</it>_CTX-M-15 was transferable but not <it>bla</it>_CTX-M-14.</p> <p>Conclusion</p> <p>This is the first report of CTX-M-14 in Kp and ENT isolates from Egypt, the Middle East and North Africa.</p

Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium

Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database ‘BraMi’ (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot–dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s)

Attentional Performance, Age and Scholastic Achievement in Healthy Children

Attentional processes in children play a critical role in daily school demands and accomplishments. Studies on the association of attentional processes with school achievement and age in healthy school children are scarce. The aim of the present study was to identify correlations between dimensions of attentional performance, scholastic achievement and age.An extensive testing battery was used to assess a wide range of attentional dimensions. A principal component analysis revealed three factors that are related to attentional performance (distractibility, lapses of attention, cognitive speed). Age was negatively associated with distractibility, lapses of attention and cognitive speed, indicating that distractibility and lapses of attention decreased with age in healthy children and resulted in lower cognitive speed.Attentional processes in healthy children should be measured in relation to distractibility, lapses of attention and cognitive speed