bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing of intervention in asymptomatic patients with valvular heart disease
Authors: Baumgartner Helmut , Iung Bernard , Otto Catherine M 
Published: May 2020

Abstract
Current management of valvular heart disease (VHD) seeks to optimize long-term outcome by timely intervention. Recommendations for treatment of patients with symptoms due to severe valvular disease are based on a foundation of solid evidence. However, when to intervene in asymptomatic patients remains controversial and decision requires careful individual weighing of the potential benefits against the risk of intervention and its long-term consequences. The primary rationale for earlier intervention is prevention of irreversible left ventricular (LV) myocardial changes that might result in later clinical symptoms and adverse cardiac events. A number of outcome predictors have been identified that facilitate decision-making. This review summarizes current recommendations and discusses recently published data that challenge them suggesting even earlier intervention. In adults with asymptomatic aortic stenosis (AS), emerging risk markers include very severe valve obstruction, elevated serum natriuretic peptide levels, and imaging evidence of myocardial fibrosis or increased extracellular myocardial volume. Currently, transcatheter aortic valve implantation (TAVI) is not recommended for treatment of asymptomatic severe AS although this may change in the future. In patients with aortic regurgitation (AR), the potential benefit of early intervention in preventing LV dilation and dysfunction must be balanced against the long-term risk of a prosthetic valve, a particular concern because severe AR often occurs in younger patients with a congenital bicuspid valve. In patients with mitral stenosis, the option of transcatheter mitral balloon valvotomy tilts the balance towards earlier intervention to prevent atrial fibrillation, embolic events, and pulmonary hypertension. When chronic severe mitral regurgitation is due to mitral valve prolapse, anatomic features consistent with a high likelihood of a successful and durable valve repair favour early intervention. The optimal timing of intervention in adults with VHD is a constantly changing threshold that depends not only on the severity of valve disease but also on the safety, efficacy, and long-term durability of our treatment options.
Orthologous Divergence and Paralogous Anticonvergence in Molecular Evolution of Triplicated Green Opsin Genes in Medaka Fish, Genus Oryzias
Authors: Matsumoto Yoshifumi , Oda Shoji , Mitani Hiroshi , Kawamura Shoji 
Published: May 2020

AbstractGene duplication of green (RH2) opsin genes and their spectral differentiation are well documented in many teleost fish. However, their evolutionary divergence or conservation patterns among phylogenetically close but ecologically diverse species is not well explored. Medaka fish (genus Oryzias) are broadly distributed in fresh and brackish waters of Asia, with many species being laboratory-housed and feasible for genetic studies. We previously showed that a Japan strain (HNI) of medaka (Oryzias latipes) possessed three RH2 opsin genes (RH2-A, RH2-B, and RH2-C) encoding spectrally divergent photopigments. Here, we examined the three RH2 opsin genes from six Oryzias species representing three species groups: the latipes, the celebensis, and the javanicus. Photopigment reconstitution revealed that the peak absorption spectra (λmax) of RH2-A were divergent among the species (447–469 nm), whereas those of RH2-B and RH2-C were conservative (516–519 and 486–493 nm, respectively). For the RH2-A opsins, the largest spectral shift was detected in the phylogenetic branch leading to the latipes group. A single amino acid replacement T94C explained most of the spectral shift. For RH2-B and -C opsins, we detected tracts of gene conversion between the two genes homogenizing them. Nevertheless, several amino acid differences were maintained. We showed that the spectral difference between the two opsins was attributed to largely the E/Q amino acid difference at the site 122 and to several sites with individually small spectral effects. These results depict dynamism of spectral divergence of orthologous and paralogous green opsin genes in phylogenetically close but ecologically diverse species exemplified by medaka.
A Systematic Review of Frailty Trajectories: Their Shape and Influencing Factors
Authors: Welstead Miles , Jenkins Natalie D , Russ Tom C , Luciano Michelle , Muniz-Terrera Graciela 
Published: May 2020

Abstract

Background and Objectives
Frailty describes an increased vulnerability to adverse events such as disease or injury. Combating this state remains a major challenge for geriatric research. By exploring how and why frailty changes throughout later life we will be better positioned to improve ways of identifying and treating those at high risk.

Research Design and Methods
We systematically reviewed publications that captured rate of frailty progression over time and established any associated risk or protective factors that affected this progression. We included longitudinal observational studies which quantified frailty trajectories in adults aged 50+ using any validated continuous frailty measurement tool.

Results
After screening 8,318 publications, 25 met our criteria. Findings show that despite a great degree of heterogeneity in the literature, progression of frailty is unquestionably affected by numerous risk and protective factors, with particular influence exhibited by social demographics, brain pathology, and physical comorbidities.

Discussion and Implications
Findings that the gradient of frailty progression is affected by various influencing factors are valuable to clinicians and policymakers as they will help identify those at highest frailty risk and inform prevention strategies. However, the heterogeneous methodological approaches of the publications included in this review highlight the need for consensus within the field to promote more coordinated research. Improved consistency of methods will enable further data synthesis and facilitate a greater understanding of the shape of frailty over time and the influencing factors contributing to change, the results of which could have crucial implications for frailty risk reduction.
TinderMIX: Time-dose integrated modelling of toxicogenomics data
Authors: Serra Angela , Fratello Michele , del Giudice Giusy , Saarimäki Laura Aliisa , Paci Michelangelo , Federico Antonio , Greco Dario 
Published: May 2020

Abstract

Background
Omics technologies have been widely applied in toxicology studies to investigate the effects of different substances on exposed biological systems. A classical toxicogenomic study consists in testing the effects of a compound at different dose levels and different time points. The main challenge consists in identifying the gene alteration patterns that are correlated to doses and time points. The majority of existing methods for toxicogenomics data analysis allow the study of the molecular alteration after the exposure (or treatment) at each time point individually. However, this kind of analysis cannot identify dynamic (time-dependent) events of dose responsiveness.

Results
We propose TinderMIX, an approach that simultaneously models the effects of time and dose on the transcriptome to investigate the course of molecular alterations exerted in response to the exposure. Starting from gene log fold-change, TinderMIX fits different integrated time and dose models to each gene, selects the optimal one, and computes its time and dose effect map; then a user-selected threshold is applied to identify the responsive area on each map and verify whether the gene shows a dynamic (time-dependent) and dose-dependent response; eventually, responsive genes are labelled according to the integrated time and dose point of departure.

Conclusions
To showcase the TinderMIX method, we analysed 2 drugs from the Open TG-GATEs dataset, namely, cyclosporin A and thioacetamide. We first identified the dynamic dose-dependent mechanism of action of each drug and compared them. Our analysis highlights that different time- and dose-integrated point of departure recapitulates the toxicity potential of the compounds as well as their dynamic dose-dependent mechanism of action.
Bacterial Mucosa-associated Microbiome in Inflamed and Proximal Noninflamed Ileum of Patients With Crohn’s Disease
Authors: Olaisen Maya , Flatberg Arnar , Granlund Atle van Beelen , Røyset Elin Synnøve , Martinsen Tom Christian , Sandvik Arne Kristian , Fossmark Reidar 
Published: May 2020

Abstract

Background
Microbiota is most likely essential in the pathogenesis of Crohn’s disease (CD). Fecal diversion after ileocecal resection (ICR) protects against CD recurrence, whereas infusion of fecal content triggers inflammation. After ICR, the majority of patients experience endoscopic recurrence in the neoterminal ileum, and the ileal microbiome is of particular interest. We have assessed the mucosa-associated microbiome in the inflamed and noninflamed ileum in patients with CD.

Methods
Mucosa-associated microbiome was assessed by 16S rRNA sequencing of biopsies sampled 5 and 15 cm orally of the ileocecal valve or ileocolic anastomosis.

Results
Fifty-one CD patients and forty healthy controls (HCs) were included in the study. Twenty CD patients had terminal ileitis, with endoscopic inflammation at 5 cm, normal mucosa at 15 cm, and no history of upper CD involvement. Crohn’s disease patients (n = 51) had lower alpha diversity and separated clearly from HC on beta diversity plots. Twenty-three bacterial taxa were differentially represented in CD patients vs HC; among these, Tyzzerella 4 was profoundly overrepresented in CD. The microbiome in the inflamed and proximal noninflamed ileal mucosa did not differ according to alpha diversity or beta diversity. Additionally, no bacterial taxa were differentially represented.

Conclusions
The microbiome is similar in the inflamed and proximal noninflamed ileal mucosa within the same patients. Our results support the concept of CD-specific microbiota alterations and demonstrate that neither ileal sublocation nor endoscopic inflammation influence the mucosa-associated microbiome.
Dynamic Distribution and Postmortem Redistribution of Tramadol in Poisoned Rats
Authors: Su Hongliang , Li Yongjun , Wu Miaomiao , Sun Tingting , Niu Weifen , Jia Juan , Wei Zhiwen , Yun Keming 
Published: May 2020

Abstract
In the past dozen years, the cases of tramadol intoxication have become frequent in many countries. Most previous studies focused on tramadol’s pharmacology, such as pharmacokinetics, pharmacodynamics and pharmacogenetics. However, the dynamic distribution and postmortem redistribution (PMR) of tramadol remain unclear. Our study aimed to investigate these two issues systematically in various specimens of 216 poisoned male rats. A validated gas chromatography–mass spectrometry method was used in this study to measure the concentrations of tramadol. In the first part, 66 tramadol poisoned rats were sacrificed at 11 different time points and their organs were collected separately for the study of tramadol’s dynamic distribution, which made it feasible to investigate its PMR later on. The results of this part showed that tramadol’s concentrations varied according to the organ and time, and peaked 2 h after intragastric administration in the specimens of liver, kidney, spleen, lung, brain and heart-blood (except stomach and heart). Based on the results of the first part, the concentration of tramadol peaked 2 h in most tissues. Therefore, this time point was used for the study of tramadol’s PMR. In the second part, the remaining 150 rats were sacrificed 2 h after intragastric administration of tramadol, and the carcasses were stored under three different conditions (−20, 4 and 20°C). The autopsy was carried out at eight different time points and their organs were collected separately. The results of this part showed that under storage temperatures of −20 and 4°C, the concentrations of tramadol in individual organs showed no significant changes at different time points whereas under a storage temperature of 20°C, the concentrations in certain organs (liver, kidney, spleen, lung, brain and heart-blood) increased significantly at the last few time points. PMR of tramadol was therefore confirmed. The process of PMR of tramadol could be slowed or stopped at lower storage temperatures (−20 or 4°C), which is significant in cases of suspected tramadol poisoning.
Dynamic localization of αB-crystallin at the microtubule cytoskeleton network in beating heart cells
Authors: Ohto-Fujita Eri , Hayasaki Saaya , Atomi Aya , Fujiki Soichiro , Watanabe Toshiyuki , Boelens Wilbert C , Shimizu Miho , Atomi Yoriko 
Published: May 2020

AbstractαB-crystallin is highly expressed in the heart and slow skeletal muscle; however, the roles of αB-crystallin in the muscle are obscure. Previously, we showed that αB-crystallin localizes at the sarcomere Z-bands, corresponding to the focal adhesions of cultured cells. In myoblast cells, αB-crystallin completely colocalizes with microtubules and maintains cell shape and adhesion. In this study, we show that in beating cardiomyocytes α-tubulin and αB-crystallin colocalize at the I- and Z-bands of the myocardium, where it may function as a molecular chaperone for tubulin/microtubules. Fluorescence recovery after photobleaching (FRAP) analysis revealed that the striated patterns of GFP-αB-crystallin fluorescence recovered quickly at 37°C. FRAP mobility assay also showed αB-crystallin to be associated with nocodazole-treated free tubulin dimers but not with taxol-treated microtubules. The interaction of αB-crystallin and free tubulin was further confirmed by immunoprecipitation and microtubule sedimentation assay in the presence of 1–100 μM calcium, which destabilizes microtubules. Förster resonance energy transfer analysis showed that αB-crystallin and tubulin were at 1–10 nm apart from each other in the presence of colchicine. These results suggested that αB-crystallin may play an essential role in microtubule dynamics by maintaining free tubulin in striated muscles, such as the soleus or cardiac muscles.
Clinical Utility of Buccal Swabs for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Coronavirus Disease 2019–Infected Children
Authors: Kam Kai-qian , Yung Chee Fu , Maiwald Matthias , Chong Chia Yin , Soong Han Yang , Loo Liat Hui , Tan Natalie Woon Hui , Li Jiahui , Nadua Karen Donceras , Thoon Koh Cheng 
Published: May 2020

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected from at least 1 buccal specimen in 9 of 11 coronavirus disease 2019 (COVID-19)–infected children (81.8%). Viral loads in buccal specimens were substantially lower than those in nasopharyngeal specimens. Buccal swabs are not good as COVID-19 screening specimens in children.
Oxford Nanopore sequencing: new opportunities for plant genomics?
Authors: Dumschott Kathryn , Schmidt Maximilian H-W , Chawla Harmeet Singh , Snowdon Rod , Usadel Björn 
Published: May 2020

Abstract
DNA sequencing was dominated by Sanger’s chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
Authors: Brealey Jaelle C , Leitão Henrique G , van der Valk Tom , Xu Wenbo , Bougiouri Katia , Dalén Love , Guschanski Katerina 
Published: May 2020

AbstractDental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
Benchmarking of long-read correction methods
Authors: Dohm Juliane C , Peters Philipp , Stralis-Pavese Nancy , Himmelbauer Heinz 
Published: May 2020

AbstractThird-generation sequencing technologies provided by Pacific Biosciences and Oxford Nanopore Technologies generate read lengths in the scale of kilobasepairs. However, these reads display high error rates, and correction steps are necessary to realize their great potential in genomics and transcriptomics. Here, we compare properties of PacBio and Nanopore data and assess correction methods by Canu, MARVEL and proovread in various combinations. We found total error rates of around 13% in the raw datasets. PacBio reads showed a high rate of insertions (around 8%) whereas Nanopore reads showed similar rates for substitutions, insertions and deletions of around 4% each. In data from both technologies the errors were uniformly distributed along reads apart from noisy 5′ ends, and homopolymers appeared among the most over-represented kmers relative to a reference. Consensus correction using read overlaps reduced error rates to about 1% when using Canu or MARVEL after patching. The lowest error rate in Nanopore data (0.45%) was achieved by applying proovread on MARVEL-patched data including Illumina short-reads, and the lowest error rate in PacBio data (0.42%) was the result of Canu correction with minimap2 alignment after patching. Our study provides valuable insights and benchmarks regarding long-read data and correction methods.
Characteristics of Nontuberculous Mycobacterial Infections at a Midwestern Tertiary Hospital: A Retrospective Study of 365 Patients
Authors: Hannah Claire E , Ford Bradley A , Chung Jina , Ince Dilek , Wanat Karolyn A 
Published: May 2020

Abstract

Background
The prevalence of infections due to nontuberculous mycobacteria (NTM) is increasing worldwide, yet little is known about the epidemiology and pathophysiology of these ubiquitous environmental organisms. Pulmonary disease due to Mycobacterium avium complex is most prevalent, but many other NTM species can cause disease in virtually any organ system. As NTM becomes an increasingly common cause of morbidity and mortality, more information is needed about the epidemiology of NTM disease.

Methods
We conducted a retrospective chart review of all patients with cultures that grew NTM at a Midwestern tertiary hospital from 1996 to 2017. Information on demographics, medical history, clinical findings, treatment, and outcome was obtained from medical records of all NTM isolates. American Thoracic Society/Infectious Diseases Society of America criteria were used to define pulmonary NTM infections.

Results
We identified 1064 NTM isolates, 365 of which met criteria for NTM infection. Pulmonary cases predominated (185 of 365; 50.7%), followed by skin/soft tissue (56 of 365; 15.3%), disseminated (40 of 365; 11%), and lymphatic (28 of 365; 7.7%) disease. Mycobacterium avium complex was the most common species (184 of 365; 50.4%). Individuals aged &gt;50 years were most affected (207 of 365; 56.7%). Common comorbidities included structural lung disease (116 of 365; 31.8%), use of immunosuppressive medications (78 of 365; 21.4%), malignancy (59 of 365; 16.2%), and human immunodeficiency virus (42 of 365; 11.5%).

Conclusions
This large cohort provides information on the demographics, risk factors, and disease course of patients with pulmonary and extrapulmonary NTM infections. Most patients had medical comorbidities that resulted in anatomic, genetic, or immunologic risk factors for NTM infection. Further population-based studies and increased disease surveillance are warranted to further characterize NTM infection prevalence and trends.
The IGNITE Trial: Participant Recruitment Lessons Prior to SARS-CoV-2
Authors: Vidoni Eric D. , Szabo-Reed Amanda , Kang Chaeryon , Perales-Puchalt Jaime , Shaw Ashley R. , Grove George , Hamill Morgan , Henry Donovan , Burns Jeffrey M. , Hillman Charles , Kramer Arthur F. , McAuley Edward , Erickson Kirk I. 
Published: May 2020

AbstractFull and diverse participant enrollment is critical to the success and generalizability of all large-scale Phase III trials. Recruitment of sufficient participants is among the most significant challenges for many studies. The novel SARS-CoV-2 coronavirus pandemic has further changed and challenged the landscape for clinical trial execution, including screening and randomization. The Investigating Gains in Neurocognition in an Intervention Trial of Exercise (IGNITE) study has been designed as the most comprehensive test of aerobic exercise effects on cognition and brain health. Here we assess recruitment into IGNITE prior to the increased infection rates in the United States, and examine new challenges and opportunities for recruitment with a goal of informing the remaining required recruitment as infection containment procedures are lifted. The results may assist the design and implementation of recruitment for future exercise studies, and outline opportunities for study design that are flexible in the face of emerging threats.