Archiving multi-epoch data and the discovery of variables in the near infrared

We present a description of the design and usage of a new synoptic pipeline and database model for time series photometry in the VISTA Data Flow System (VDFS). All UKIRT-WFCAM data and most of the VISTA main survey data will be processed and archived by the VDFS. Much of these data are multi-epoch, useful for finding moving and variable objects. Our new database design allows the users to easily find rare objects of these types amongst the huge volume of data being produced by modern survey telescopes. Its effectiveness is demonstrated through examples using Data Release 5 of the UKIDSS Deep Extragalactic Survey (DXS) and the WFCAM standard star data. The synoptic pipeline provides additional quality control and calibration to these data in the process of generating accurate light-curves. We find that 0.6+-0.1% of stars and 2.3+-0.6% of galaxies in the UKIDSS-DXS with K<15 mag are variable with amplitudes \Delta K>0.015 magComment: 30 pages, 31 figures, MNRAS, in press Minor changes from previous version due to refereeing and proof-readin

Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System

A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has become clear that plants harbor more complex gene regulatory circuits within the core circadian clocks than other organisms, inspiring a fundamental question: are all these regulatory interactions between clock genes equally crucial for the establishment and maintenance of circadian rhythms? Our mechanistic simulation for Arabidopsis thaliana demonstrates that at least half of the total regulatory interactions must be present to express the circadian molecular profiles observed in wild-type plants. A set of those essential interactions is called herein a kernel of the circadian system. The kernel structure unbiasedly reveals four interlocked negative feedback loops contributing to circadian rhythms, and three feedback loops among them drive the autonomous oscillation itself. Strikingly, the kernel structure, as well as the whole clock circuitry, is overwhelmingly composed of inhibitory, rather than activating, interactions between genes. We found that this tendency underlies plant circadian molecular profiles which often exhibit sharply-shaped, cuspidate waveforms. Through the generation of these cuspidate profiles, inhibitory interactions may facilitate the global coordination of temporally-distant clock events that are markedly peaked at very specific times of day. Our systematic approach resulting in experimentally-testable predictions provides insights into a design principle of biological clockwork, with implications for synthetic biology.Comment: Supplementary material is available at the journal websit

Bright light therapy in pregnant women with major depressive disorder: Study protocol for a randomized, double-blind, controlled clinical trial

Background: Depression during pregnancy is a common and high impact disease. Generally, 5-10 % of pregnant women suffer from depression. Children who have been exposed to maternal depression during pregnancy have a higher risk of adverse birth outcomes and more often show cognitive, emotional and behavioural problems. Therefore, early detection and treatment of antepartum depression is necessary. Both psychotherapy and antidepressant medication, first choice treatments in a non-pregnant population, have limitations in treating depression during pregnancy. Therefore, it is urgent and relevant to investigate alternative treatments for antepartum depression. Bright light therapy (BLT) is a promising treatment for pregnant women with depressive disorder, for it combines direct availability, sufficient efficacy, low costs and high safety, taking the safety for the unborn child into account as well. Methods: In this study, 150 pregnant women (12-18 weeks pregnant) with a DSM-V diagnosis of depressive disorder will be randomly allocated in a 1:1 ratio to one of the two treatment arms: treatment with BLT (9.000 lux) or treatment with dim red light therapy (100 lux). Both groups will be treated for 6 weeks at home on a daily basis for 30 min, within 30 min of habitual wake-up time. Follow-up will take place after 6 weeks of therapy, 3 and 10 weeks after end of therapy, at birth and 2, 6 and 18 months postpartum. Primary outcome will be the average change in depressive symptoms between the two groups, as measured by the Structured Interview Guide for the Hamilton Depression Scale - Seasonal Affective Disorder version and the Edinburg Postnatal Depression Scale. Changes in rating scale scores of these questionnaires over time will be analysed using generalized linear mixed models. Secondary outcomes will be the changes in maternal cortisol and melatonin levels, in maternal sleep quality and gestational age, birth weight, infant behaviour, infant cortisol exposure and infant cortisol stress response. Discussion: If BLT reduces depressive symptoms in pregnant women, it will provide a safe, cheap, non-pharmacological and efficacious alternative treatment for psychotherapy and antidepressant medication in treating antepartum depression, without any expected adverse reactions for the unborn child. Trial registration: Netherlands Trial Register NTR5476. Registered 5 November 2015

Correlated long-range mixed-harmonic fluctuations measured in pp, p+Pb and low-multiplicity Pb+Pb collisions with the ATLAS detector

For abstract see published article

Search for large missing transverse momentum in association with one top-quark in proton-proton collisions at √s = 13 TeV with the ATLAS detector

This paper describes a search for events with one top-quark and large missing transverse momentum in the final state. Data collected during 2015 and 2016 by the ATLAS experiment from 13 TeV proton–proton collisions at the LHC corresponding to an integrated luminosity of 36.1 fb−1 are used. Two channels are considered, depending on the leptonic or the hadronic decays of the W boson from the top quark. The obtained results are interpreted in the context of simplified models for dark-matter production and for the single production of a vector-like T quark. In the absence of significant deviations from the Standard Model background expectation, 95% confidence-level upper limits on the corresponding production cross-sections are obtained and these limits are translated into constraints on the parameter space of the models considered

Performance of top-quark and W -boson tagging with ATLAS in Run 2 of the LHC

The performance of identification algorithms (“taggers”) for hadronically decaying top quarks and W bosons in pp collisions at √s=13 TeV recorded by the ATLAS experiment at the Large Hadron Collider is presented. A set of techniques based on jet shape observables are studied to determine a set of optimal cut-based taggers for use in physics analyses. The studies are extended to assess the utility of combinations of substructure observables as a multivariate tagger using boosted decision trees or deep neural networks in comparison with taggers based on two-variable combinations. In addition, for highly boosted top-quark tagging, a deep neural network based on jet constituent inputs as well as a re-optimisation of the shower deconstruction technique is presented. The performance of these taggers is studied in data collected during 2015 and 2016 corresponding to 36.1 fb −1 for the tt ¯ and γ+jet and 36.7 fb −1 −1 for the dijet event topologies

Multi-exon deletions of the FBN1 gene in Marfan syndrome

BACKGROUND: Mutations in the fibrillin -1 gene (FBN1) cause Marfan syndrome (MFS), an autosomal dominant multi-system connective tissue disorder. The 200 different mutations reported in the 235 kb, 65 exon-containing gene include only one family with a genomic multi-exon deletion. METHODS: We used long-range RT-PCR for mutation detection and long-range genomic PCR and DNA sequencing for identification of deletion breakpoints, allele-specific transcript analyses to determine stability of the mutant RNA, and pulse-chase studies to quantitate fibrillin synthesis and extracellular matrix deposition in cultured fibroblasts. Southern blots of genomic DNA were probed with three overlapping fragments covering the FBN1 coding exons RESULTS: Two novel multi-exon FBN1 deletions were discovered. Identical nucleotide pentamers were found at or near the intronic breakpoints. In a Case with classic MFS, an in-frame deletion of exons 42 and 43 removed the C-terminal 24 amino acids of the 5(th) LTBP (8-cysteine) domain and the adjacent 25(th) calcium-binding EGF-like (6-cysteine) domain. The mutant mRNA was stable, but fibrillin synthesis and matrix deposition were significantly reduced. A Case with severe childhood-onset MFS has a de novo deletion of exons 44–46 that removed three EGF-like domains. Fibrillin protein synthesis was normal, but matrix deposition was strikingly reduced. No genomic rearrangements were detected by Southern analysis of 18 unrelated MFS samples negative for FBN1 mutation screening. CONCLUSIONS: Two novel deletion cases expand knowledge of mutational mechanisms and genotype/phenotype correlations of fibrillinopathies. Deletions or mutations affecting an LTBP domain may result in unstable mutant protein cleavage products that interfere with microfibril assembly

Current view: indications for extracorporeal lipid apheresis treatment

One of the first investigations concerning extracorporeal treatment of hypercholesterolemia was performed in 1967 by plasma exchange in patients with homozygous or severe heterozygous familial hypercholesterolemia (FH). In the following decades, several specific lipid apheresis systems were developed to efficiently eliminate low-density lipoprotein (LDL) cholesterol and Lp(a) cholesterol in hypercholesterolemic patients. In the early 1980s, the main clinical indication has been homozygous FH including mainly children and pregnant women. In consideration of the current development of lipid-lowering regimens and scientific knowledge of preventing progression of cardiovascular diseases, the spectrum of indications to initiate lipid apheresis was extended due to still insufficient lipid-lowering therapy in some clinical cases. However, a generally accepted indication for lipid apheresis treatment is still under discussion. In Germany, the target-oriented distribution of increasingly limited healthcare resources demand data which support the benefit of established treatment procedures such as lipid apheresis. In recent years, the Federal Joint Committee (G-BA), a paramount decision-making body of the German Healthcare System, issued to reassess the approval of chronic lipid apheresis therapy for regular reimbursement. Therefore, in 2005, an interdisciplinary German Apheresis Working Group has been established by members of both the German societies of nephrology. One of the first goals of this working group was a revision of the indications for lipid apheresis corresponding to current guidelines and recommendations for the treatment of lipid disorders. In addition, recently new pathophysiological perceptions of the impact of lipoproteins on atherogenesis and thrombosis were also considered.Since 2005, the working group met on a regular basis to substantiate the first defined goals. The indications for lipid apheresis were critically revised with respect to actual results from clinical investigations, cardiovascular guidelines, and scientific knowledge and were accepted by the members of the apheresis working group.There is consensus between the medical societies and health insurance funds regarding the need for general accepted guidelines for lipid apheresis. Recommendations for the indications of lipid apheresis were developed, but additionally these results should be confirmed by medical societies to transform them to guidelines. However, due to limited data showing that lipid apheresis has effects on the progression of cardiovascular diseases all members of the apheresis working group support a project for creating a lipid apheresis registry. This apheresis registry has been developed and recently started. The primary goal is to substantiate prospective long-term data on clinical outcome of chronic lipid apheresis treatment and to support additional clinical research activities in this field. In addition, this registry should comply with the actual requests of the Federal Joint Committee (G-BA)

Maintaining a balance: a focus group study on living and coping with chronic whiplash-associated disorder

<p>Abstract</p> <p>Background</p> <p>There is little qualitative insight into how persons with chronic Whiplash-Associated Disorder cope on a day to day basis. This study seeks to identify the symptoms persons with Whiplash-Associated Disorder describe as dominating and explore their self-initiated coping strategies.</p> <p>Methods</p> <p>Qualitative study using focus groups interviews. Fourteen Norwegian men and women with Whiplash-Associated Disorder (I or II) were recruited to participate in two focus groups. Data were analyzed according to a phenomenological approach, and discussed within the model of Cognitive Activation Theory of Stress (CATS).</p> <p>Results</p> <p>Participants reported neck and head pain, sensory hypersensitivity, and cognitive dysfunction following their whiplash injury. Based on the intensity of symptoms, participants divided everyday life into good and bad periods. In good periods the symptoms were perceived as manageable. In bad periods the symptoms intensified and took control of the individual. Participants expressed a constant notion of trying to balance their three main coping strategies; rest, exercise, and social withdrawal. In good periods participants experienced coping by expecting good results from the strategies they used. In bad periods they experienced no or negative relationships between their behavioral strategies and their complaints.</p> <p>Conclusions</p> <p>Neck and head pain, sensory hypersensitivity, and cognitive dysfunction were reported as participants' main complaints. A constant notion of balancing between their three main coping strategies; rest, exercise, and social withdrawal, was described.</p

Seleção recorrente para produtividade e qualidade de frutos em abobrinha braquítica

Considerando-se que abobrinha (Cucurbita moschata) geralmente não apresenta perda de vigor pela endogamia, a seleção recorrente pode ser um método adequado para o melhoramento desta espécie. O objetivo deste trabalho foi avaliar a eficiência da seleção recorrente em abobrinha, cultivar Piramoita, visando aumento de produtividade e melhoria da qualidade de frutos. Foram realizados três ciclos de seleção recorrente a partir da cultivar Piramoita (população P0), com avaliação e seleção de progênies S1. Em todos os ciclos de seleção, os experimentos foram conduzidos em blocos ao acaso, com parcelas de cinco plantas, tendo a cultivar Piramoita como testemunha. O espaçamento foi de 2,0 x 1,0 m. Após cada ciclo de seleção, as sementes remanescentes das progênies selecionadas foram empregadas no ciclo seguinte de recombinação, cada progênie contribuindo em média com dez plantas tomadas ao acaso. As quatro populações (P0, PI, PII e PIII) foram avaliadas em blocos ao acaso, com oito repetições de cinco plantas por parcela. Foram avaliados número e massa total e comercial (retos, com pescoço comprido e sem defeitos aparentes) de frutos imaturos por planta e a proporção de frutos comerciais. Foram realizadas as análises de variância e regressão. Foram observados aumentos de produção lineares significativos ao longo dos ciclos de seleção. Na população PIII, os números de frutos total (17) e comercial (11) por planta, assim como a massa total (3,7) e comercial (2,6 kg planta-1), superaram a população inicial em 32, 63, 24 e 57%, respectivamente. Essas diferenças correspondem a um aumento superior a 11 t ha-1 ou mais de 36.000 frutos ha-1 em apenas três ciclos de seleção recorrente.Since squash (Cucurbita moschata) usually does not have inbreeding depression, recurrent selection may be an adequate method for squash breeding. In this study the recurrent selection efficiency was evaluated in squash, cultivar Piramoita, aiming to improving fruit yield and quality. Three generations were produced out of cultivar Piramoita (population P0), with evaluation and selection of S1 progenies. In all selection cycles, experiments were set up in randomized blocks design, with five plants per plot, with cultivar Piramoita as control. Spacing was 2.0 x 1.0 m. After each cycle, the remaining seeds of selected progenies were used in the following cycle of recombination, and each progeny was represented, on average, by ten random plants. The four populations (P0, PI, PII and PIII) were evaluated in randomized blocks design, with eight replicates and five-plant plots. Number and weight of total and commercial (straight fruits, with long neck and without visible defects) fruits per plant and the rate of commercial fruits were evaluated. Variance and regression analysis was performed and indicated a linear increase in yield due to selection cycles. In population PIII, total (17) and commercial (11) fruit number plant-1, and total (3.7) and commercial (2.6 kg) weight of fruits plant-1, overcame initial population in 32; 63; 24, and 57%, respectively. These differences correspond to an increase larger than 11 t ha-1 or more than 36000 fruits ha-1 in only three recurrent selection cycles