bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNAi mediated myosuppressin deficiency affects muscle development and survival in the salmon louse (Lepeophtheirus salmonis)
Authors: Komisarczuk Anna Z. , Kongshaug Heidi , Li Ming , Nilsen Frank 
Published: May 2019

AbstractMuscle activity is regulated by stimulatory and inhibitory neuropeptides allowing for contraction and relaxation. In Arthropods, one of the important myoinhibitors is Myosuppressin, belonging to FMRFamide-like peptides, that was shown to have inhibitory effects on visceral muscle contraction and to regulate vital physiological processes including reproduction or feeding. We have identified myosuppressin in salmon louse Lepeophtheirus salmonis (LsalMS) and systematically characterised its function and complex abnormalities emerging after LsalMS knockdown by RNAi in all developmental stages in this species. Immunohistochemistry analysis localized the LsalMS mainly to the central nervous system, but also to the vital organs within the alimentary tract and the reproductive system. The most striking feature of LsalMS deficiency during lice development was severe reduction of the muscle content, with abnormalities detected in both the visceral and skeletal muscles. Moreover, down-regulation of LsalMS affects moulting, spermatophore deposition and feeding by affecting development of the intestinal wall and increasing its contraction frequency.
Quantile regression analysis reveals widespread evidence for gene-environment or gene-gene interactions in myopia development
Authors: Pozarickij Alfred , Williams Cathy , Hysi Pirro G. , Guggenheim Jeremy A. ,   UK Biobank Eye and Vision Consortium, Aslam Tariq , Barman Sarah A. , Barrett Jenny H. , Bishop Paul , Blows Peter , Bunce Catey , Carare Roxana O. , Chakravarthy Usha , Chan Michelle , Chua Sharon Y.L. , Crabb David P. , Cumberland Philippa M. , Day Alexander , Desai Parul , Dhillon Bal , Dick Andrew D. , Egan Cathy , Ennis Sarah , Foster Paul , Fruttiger Marcus , Gallacher John E.J. , Garway-Heath David F. , Gibson Jane , Gore Dan , Hammond Chris J. , Hardcastle Alison , Harding Simon P. , Hogg Ruth E. , Keane Pearse A. , Khaw Sir Peng T. , Khawaja Anthony P. , Lascaratos Gerassimos , Lotery Andrew J. , Mac Gillivray Tom , Mackie Sarah , Martin Keith , McGaughey Michelle , McGuinness Bernadette , McKay Gareth J. , McKibbin Martin , Mitry Danny , Moore Tony , Morgan James E. , Muthy Zaynah A. , O’Sullivan Eoin , Owen Chris G. , Patel Praveen , Paterson Euan , Peto Tunde , Petzold Axel , Rahi Jugnoo S. , Rudnikca Alicja R. , Self Jay , Sivaprasad Sobha , Steel David , Stratton Irene , Strouthidis Nicholas , Sudlow Cathie , Thomas Dhanes , Trucco Emanuele , Tufail Adnan , Vitart Veronique , Vernon Stephen A. , Viswanathan Ananth C. , Williams Katie , Woodside Jayne V. , Yates Max M. , Yip Jennifer , Zheng Yalin 
Published: May 2019

AbstractA genetic contribution to refractive error has been confirmed by the discovery of more than 150 associated variants in genome-wide association studies (GWAS). Environmental factors such as education and time outdoors also demonstrate strong associations. Currently however, the extent of gene-environment or gene-gene interactions in myopia is unknown. We tested the hypothesis that refractive error-associated variants exhibit effect size heterogeneity, a hallmark feature of genetic interactions. Of 146 variants tested, evidence of non-uniform, non-linear effects were observed for 66 (45%) at Bonferroni-corrected significance (P < 1.1 × 10−4) and 128 (88%) at nominal significance (P < 0.05). LAMA2 variant rs12193446, for example, had an effect size varying from −0.20 diopters (95% CI −0.18 to −0.23) to −0.89 diopters (95% CI −0.71 to −1.07) in different individuals. SNP effects were strongest at the phenotype extremes and weaker in emmetropes. A parsimonious explanation for these findings is that gene-environment or gene-gene interactions in myopia are pervasive.
Engineering quorum quenching enzymes: progress and perspectives
Authors: Murugayah Shereen A. , Gerth Monica L. 
Published: May 2019

Abstract
Quorum sensing is a key contributor to the virulence of many important plant, animal and human pathogens. The disruption of this signalling—a process referred to as ‘quorum quenching’—is a promising new approach for controlling microbial pathogens. In this mini-review, we have focused on efforts to engineer enzymes that disrupt quorum sensing by inactivating acyl-homoserine lactone signalling molecules. We review different approaches for protein engineering and provide examples of how these engineering approaches have been used to tailor the stability, specificity and activities of quorum quenching enzymes. Finally, we grapple with some of the issues around these approaches—including the disconnect between in vitro biochemistry and potential in vivo applications.
Efficacy of Intratympanic Steroid on Idiopathic Sudden Sensorineural Hearing Loss: An Analysis of Cases With Negative Prognostic Factors
Authors: Suzuki Hideaki , Kawaguchi Rintaro , Wakasugi Tetsuro , Do Ba Hung , Kitamura Takuro , Ohbuchi Toyoaki 
Published: May 2019

Purpose
We retrospectively studied the efficacy of intratympanic steroid administration in comparison with hyperbaric oxygen (HBO) therapy for idiopathic sudden sensorineural hearing loss (ISSNHL) with negative prognostic factors.

Method
We enrolled 301 patients (302 ears) with ISSNHL (average hearing level at 250–4000 Hz ≥ 40 dB; time from onset to treatment ≤ 30 days). From August 2002 to March 2009, 174 patients (174 ears) received systemic steroid plus HBO therapy (HBO group), and from June 2015 to January 2018, 127 patients (128 ears) received systemic plus intratympanic steroid (IT group). Hearing outcomes were evaluated by 6 indices: cure rate, marked-recovery rate (percent of patients with hearing gain ≥ 30 dB), recovery rate (percent of patients with hearing gain ≥ 10 dB), hearing gain, hearing level after treatment, and percent hearing improvement compared to the unaffected contralateral ear.

Results

The recovery rate was significantly higher in the IT group than in the HBO group (80.5% vs. 68.4%,
p
= .019). The IT group showed a higher recovery rate than the HBO group in patients aged ≥ 60 years (
p
= .010), patients with early (≤ 7 days from onset) treatment (
p
= .005), patients with initial hearing levels ≥ 90 dB (
p
= .037), and patients with vertigo/dizziness (
p
= .040). The IT group also showed higher hearing gain and percent hearing improvement than the HBO group in patients with vertigo/dizziness (
p
= .046 and
p
= .026, respectively).

Conclusions
Systemic plus intratympanic steroid is more effective for ISSNHL than systemic steroid plus HBO, particularly in patients with negative prognostic factors, such as old age, profound hearing loss, and/or presence of vertigo/dizziness.
New technique to measure the cavity defects of Fabry–Perot interferometers
Authors: Greco V. , Sordini A. , Cauzzi G. , Reardon K. , Cavallini F. 
Published: May 2019

Context. Several astronomical instruments, for both nighttime and solar use, rely on tunable Fabry–Perot interferometers (FPIs). Knowing the exact shape of the etalons’ cavity is crucial for assessing the overall instrumental transmission profile and its possible variations during the tuning process.Aims. We aim to define and test a technique to accurately measure the cavity defects of air-spaced FPIs, including distortions due to the spectral tuning process that are typical of astronomical observations. We further aim to develop a correction technique to maintain the shape of the cavity as constant as possible during the spectral scan. These are necessary steps to optimize the spectral transmission profile of a two-dimensional spectrograph (polarimeter) using one or more FPIs in series, and to ensure that the spectral transmission profile remains constant during typical observing conditions.Methods. We devised a generalization of the techniques developed for the so-called phase-shifting interferometry to the case of FPI. This measuring technique is applicable to any given FPI that can be tuned via changing the cavity spacing (z-axis), and can be used for any etalon regardless of the coating’ reflectivity. The major strength of our method is the ability to fully characterize the cavity during a spectral scan, allowing for the determination of scan-dependent modifications of the plates. We have applied the measuring technique to three 50 mm diameter interferometers, with cavity gaps ranging between 600μm and 3 mm, coated for use in the visible range.Results. The technique developed in this paper allows us to accurately and reliably measure the cavity defects of air-spaced FPIs, and of their evolution during the entire spectral scan. Our main, and unexpected, result is that the relative tilt between the two FPI plates varies significantly during the spectral scan, and can dominate the cavity defects; in particular, we observe that the tilt component at the extremes of the scan is sensibly larger than that at the center of the scan. Exploiting the capability of the electronic controllers to set the reference plane at any given spectral step, we then develop a correction technique that allows the minimization of the tilt during a complete spectral scan. The correction remains highly stable over long periods, well beyond the typical duration of astronomical observations.
Census of ρ Ophiuchi candidate members from Gaia Data Release 2
Authors: Cánovas H. , Cantero C. , Cieza L. , Bombrun A. , Lammers U. , Merín B. , Mora A. , Ribas Á. , Ruíz-Rodríguez D. 
Published: May 2019

Context. The Ophiuchus cloud complex is one of the best laboratories to study the earlier stages of the stellar and protoplanetary disc evolution. The wealth of accurate astrometric measurements contained in the Gaia Data Release 2 can be used to update the census of Ophiuchus member candidates.
Aims. We seek to find potential new members of Ophiuchus and identify those surrounded by a circumstellar disc.
Methods. We constructed a control sample composed of 188 bona fide Ophiuchus members. Using this sample as a reference we applied three different density-based machine learning clustering algorithms (DBSCAN, OPTICS, and HDBSCAN) to a sample drawn from the Gaia catalogue centred on the Ophiuchus cloud. The clustering analysis was applied in the five astrometric dimensions defined by the three-dimensional Cartesian space and the proper motions in right ascension and declination.
Results. The three clustering algorithms systematically identify a similar set of candidate members in a main cluster with astrometric properties consistent with those of the control sample. The increased flexibility of the OPTICS and HDBSCAN algorithms enable these methods to identify a secondary cluster. We constructed a common sample containing 391 member candidates including 166 new objects, which have not yet been discussed in the literature. By combining the Gaia data with 2MASS and WISE photometry, we built the spectral energy distributions from 0.5 to 22 μm for a subset of 48 objects and found a total of 41 discs, including 11 Class II and 1 Class III new discs.
Conclusions. Density-based clustering algorithms are a promising tool to identify candidate members of star forming regions in large astrometric databases. By combining the Gaia data with infrared catalogues, it is possible to discover new protoplanetary discs. If confirmed, the candidate members discussed in this work would represent an increment of roughly 40–50% of the current census of Ophiuchus.
Hämophagozytische Lymphohistiozytose – eine seltene, aber
schwere Komplikation
Authors: Lachmann Gunnar , Brunkhorst Frank M. 
Published: May 2019

ZusammenfassungPatienten mit Multiorganversagen oder Sepsis, die nur unzureichend auf eine
antiinfektive Therapie ansprechen oder bei denen keine infektiöse Ursache
erkennbar ist, könnten als Ursache das Hyperinflammationssyndrom
Hämophagozytische Lymphohistiozytose entwickelt haben. Dieses syndromale
Krankheitsbild verläuft klinisch ähnlich der Sepsis und endet aufgrund der
verzögerten Diagnosestellung mit irreversiblem Organversagen oft letal, wobei
die Erkrankung auch im Rahmen einer Sepsis entstehen kann. Die Kenntnis dieses
Syndroms ist für das Überleben der Patienten von herausragender Bedeutung.
Vom Betroffenen zum Helfer
Authors: Trumann Arne 
Published: May 2019

ZusammenfassungAutor Arne Trumann erlitt im Alter von 44 Jahren einen septischen Schock. Obwohl
jeder Verlauf einer Sepsis anders ist, macht sein Fall in vielerlei Hinsicht
deutlich, dass sich an bestimmten Punkten der medizinischen Versorgung einiges
bessern muss, damit Sepsispatienten keine so schwerwiegenden Folgeschäden
davontragen müssen.
ntEdit: scalable genome sequence polishing
Authors: Warren René L , Coombe Lauren , Mohamadi Hamid , Zhang Jessica , Jaquish Barry , Isabel Nathalie , Jones Steven J M , Bousquet Jean , Bohlmann Joerg , Birol Inanç 
Published: May 2019

Abstract

Motivation
In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing utility that scales to large mammalian and conifer genomes.

Results
We first tested ntEdit and the state-of-the-art assembly improvement tools GATK, Pilon and Racon on controlled Escherichia coli and Caenorhabditis elegans sequence data. Generally, ntEdit performs well at low sequence depths (&lt;20×), fixing the majority (&gt;97%) of base substitutions and indels, and its performance is largely constant with increased coverage. In all experiments conducted using a single CPU, the ntEdit pipeline executed in &lt;14 s and &lt;3 m, on average, on E.coli and C.elegans, respectively. We performed similar benchmarks on a sub-20× coverage human genome sequence dataset, inspecting accuracy and resource usage in editing chromosomes 1 and 21, and whole genome. ntEdit scaled linearly, executing in 30–40 m on those sequences. We show how ntEdit ran in &lt;2 h 20 m to improve upon long and linked read human genome assemblies of NA12878, using high-coverage (54×) Illumina sequence data from the same individual, fixing frame shifts in coding sequences. We also generated 17-fold coverage spruce sequence data from haploid sequence sources (seed megagametophyte), and used it to edit our pseudo haploid assemblies of the 20 Gb interior and white spruce genomes in &lt;4 and &lt;5 h, respectively, making roughly 50M edits at a (substitution+indel) rate of 0.0024.

Availability and implementation
https://github.com/bcgsc/ntedit

Supplementary information
Supplementary data are available at Bioinformatics online.
Homogeneity tests of covariance matrices with high-dimensional longitudinal data
Authors: Zhong Ping-Shou , Li Runze , Santo Shawn 
Published: May 2019

Summary
This paper deals with the detection and identification of changepoints among covariances of high-dimensional longitudinal data, where the number of features is greater than both the sample size and the number of repeated measurements. The proposed methods are applicable under general temporal-spatial dependence. A new test statistic is introduced for changepoint detection, and its asymptotic distribution is established. If a changepoint is detected, an estimate of the location is provided. The rate of convergence of the estimator is shown to depend on the data dimension, sample size, and signal-to-noise ratio. Binary segmentation is used to estimate the locations of possibly multiple changepoints, and the corresponding estimator is shown to be consistent under mild conditions. Simulation studies provide the empirical size and power of the proposed test and the accuracy of the changepoint estimator. An application to a time-course microarray dataset identifies gene sets with significant gene interaction changes over time.
Duodenojejunal Bypass and Strictureplasty for Diffuse Small Bowel Crohn’s Disease with a Step-by-Step Visual Guide
Authors: Lee Chun Hin Angus , Rieder Florian , Holubar Stefan D 
Published: May 2019

Lay Summary
Crohn’s disease is an inflammatory condition of the intestine with an unknown cause and can result in inflammation, narrowing (stricuture) or penetrating disease (fistula that inflammation goes through the wall of the bowel and into another structure). Unfortunately Crohn’s disease can affect anywhere in the gastrointestinal tract, all the way from the mouth to the anus. Sometimes Crohn’s disease can affect the duodenum, the portion of the small intestine just after the stomach. When Crohn’s disease is in the duodenum and causes narrowing, it is difficult to treat medically, and often needs a surgical intervention. When the narrowing is short, less than a few centimeters, the surgeon can do a strictureplasty which means opening the intestine across the stricture and sewing it back shut in the horitzontal direction to make the opening larger. When the narrowing, or stricture, is longer, then the surgeon may have to connect the stomach to another part of the small intestine (gastrojejunostomy) to avoid or bypass the duodenum, or may have to perform a large reconstructive operation to remove that portion of the small intestine. the challenge is that those operations have significant potential complications associated with them. Therefore, sometimes a bypass operation can be done instead to connect the duodenum to the next part of the small intestine, the jejunum. In this manuscript the authors describe this surgical technique is a 38 year old male with Crohn’s disease who was referred with multiple areas of narrowing in his intestine.
Clinical use of intracoronary imaging. Part 2: acute coronary syndromes, ambiguous coronary angiography findings, and guiding interventional decision-making: an expert consensus document of the European Association of Percutaneous Cardiovascular Interventions
Authors: Johnson Thomas W , Räber Lorenz , di Mario Carlo , Bourantas Christos , Jia Haibo , Mattesini Alessio , Gonzalo Nieves , de la Torre Hernandez Jose M , Prati Francesco , Koskinas Konstantinos , Joner Michael , Radu Maria D , Erlinge David , Regar Evelyn , Kunadian Vijay , Maehara Akiko , Byrne Robert A , Capodanno Davide , Akasaka Takashi , Wijns William , Mintz Gary S , Guagliumi Giulio 
Published: May 2019

Abstract
This consensus document is the second of two reports summarizing the views of an expert panel organized by the European Association of Percutaneous Cardiovascular Interventions (EAPCI) on the clinical use of intracoronary imaging including intravascular ultrasound (IVUS), optical coherence tomography (OCT), and near infrared spectroscopy (NIRS)-IVUS. Beyond guidance of stent selection and optimization of deployment, invasive imaging facilitates angiographic interpretation and may guide treatment in acute coronary syndrome. Intravascular imaging can provide additional important diagnostic information when confronted with angiographically ambiguous lesions and allows assessment of plaque morphology enabling identification of vulnerability characteristics. This second document focuses on useful imaging features to identify culprit and vulnerable coronary plaque, which offers the interventional cardiologist guidance on when to adopt an intracoronary imaging-guided approach to the treatment of coronary artery disease and provides an appraisal of intravascular imaging-derived metrics to define the haemodynamic significance of coronary lesions.
Association of Sarcopenia With Performance on Multiple Cognitive Domains: Results From the ELSA-Brasil Study
Authors: Szlejf Claudia , Suemoto Claudia K , Lotufo Paulo A , Benseñor Isabela M 
Published: May 2019

Abstract

Background
Sarcopenia and cognitive impairment share pathophysiological paths and risk factors. Our aim was to investigate the association of sarcopenia and its defining components with cognitive performance in middle-aged and older adults.

Methods
This cross-sectional analysis included 5,038 participants from the ELSA-Brasil Study, aged ≥ 55 years. Muscle mass was evaluated by bioelectrical impedance analysis and muscle strength by handgrip strength. Sarcopenia was defined according to the Foundation for the National Institutes of Health. Cognition was evaluated using delayed word recall test, semantic verbal fluency test, and trail making test version B. Possible confounders included sociodemographic characteristics, lifestyle, and clinical comorbidities.

Results
The frequencies of sarcopenia, low muscle mass, and low muscle strength were 1.8%, 23.3%, and 4.4%, respectively. After adjustment for possible confounders, poorer performance on the verbal fluency test was associated with sarcopenia (β = −0.20, 95% confidence interval [CI] = −0.38; −0.01, p = .03) and low muscle mass (β = −0.08, 95% CI = −0.14; −0.01, p = .02). Low muscle strength was associated with poorer performance in the delayed word recall test (β = −0.14, 95% CI = −0.27; −0.02, p = .02), verbal fluency test (β = −0.14, 95% CI = −0.26; −0.02, p = .03), and trail making test (β = −0.15, 95% CI = −0.27; −0.03, p = .01).

Conclusions
Sarcopenia was associated with poorer performance on the verbal fluency test, and low muscle strength was associated with poorer performance in all cognitive tests in middle-aged and older adults.
The Devil is in the Details: Identifying Aspects of Temperature Variation that Underlie Sex Determination in Species with TSD
Authors: Carter A W , Paitz R T , Bowden R M 
Published: May 2019

AbstractMost organisms experience thermal variability in their environment; however, our understanding of how organisms cope with this variation is under-developed. For example, in organisms with temperature-dependent sex determination (TSD), an inability to predict sex ratios under fluctuating incubation temperatures in the field hinders predictions of how species with TSD will fare in a changing climate. To better understand how sex determination is affected by thermal variation, we incubated Trachemys scripta eggs using a “heat wave” design, where embryos experienced a male-producing temperature of 25 ± 3°C for the majority of development and varying durations at a female-producing temperature of 29.5 ± 3°C during the window of development when sex is determined. We compared the sex ratios from these incubation conditions with a previous data set that utilized a similar heat wave design, but instead incubated eggs at a male-producing temperature of 27 ± 3°C but utilized the same female-producing temperature of 29.5 ± 3°C. We compared the sex ratio reaction norms produced from these two incubation conditions and found that, despite differences in average temperatures, both conditions produced 50:50 sex ratios after ∼8 days of exposure to female-producing conditions. This emphasizes that sex can be determined in just a few days at female-producing conditions and that sex determination is relatively unaffected by temperatures outside of this short window. Further, these data demonstrate the reduced accuracy of the constant temperature equivalent model (the leading method of predicting sex ratios) under thermally variable temperatures. Conceptualizing sex determination as the number of days spent incubating at female-producing conditions rather than an aggregate statistic is supported by the mechanistic underpinnings of TSD, helps to improve sex ratio estimation methods, and has important consequences for predicting how species with TSD will fare in a changing climate.