bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae
Authors: Estrada Bonilla Boris , Costa Ana Rita , van den Berg Daan F , van Rossum Teunke , Hagedoorn Stefan , Walinga Hielke , Xiao Minfeng , Song Wenchen , Haas Pieter-Jan , Nobrega Franklin L , Brouns Stan J J 
Published: August 2021

Abstract
Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0–13%) identity to genomic phage sequences deposited in the GenBank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.
Renal function and outcome of patients with non-valvular atrial fibrillation
Authors: Barashi Rami , Hornik-Lurie Tzipi , Gabay Hagit , Haskiah Feras , Minha Saar , Shuvy Mony , Assali Abid , Pereg David 
Published: August 2021

Abstract

Aims
Atrial fibrillation and renal dysfunction are associated with increased cardiovascular risk. We examined the association between renal function and incident ischaemic stroke or myocardial infarction in patients with atrial fibrillation treated with direct oral anticoagulants (DOACs).

Methods and results
This study was conducted using a large health record database. Included were 19 713 patients with first time diagnosis of non-valvular atrial fibrillation treated with DOACs between 2010 and 2018. Patients were categorized into four groups according to the estimated glomerular filtration rate (eGFR) (&lt;30, 30–59, 60–89, and ≥90 mL/min/1.73 m2). Ischaemic stroke and acute myocardial infarction rates were compared between the groups. During 55 086 person-years of follow-up, there were 2295 (11.6%) cases of ischaemic stroke and 1158 (5.9%) cases of acute myocardial infarction. There was a significant inverse association between eGFR and the risk of myocardial infarction. A multivariate analysis using the group with eGFR ≥90 mL/min/1.73 m2 as a reference demonstrated an increased risk of myocardial infarction with lower eGFR [hazard ratio (HR) = 1.2 95% confidence interval (CI) 0.9–1.4, HR = 1.4, 95% CI 1.2–1.7, and HR = 2.5, 95% CI 1.8–3.4 for patients with eGFR 60–89, 30–59, and &lt;30 mL/min/1.73 m2, respectively, P &lt; 0.001]. Each 10 mL decrease in eGFR was associated with an 8% increase in the risk of myocardial infarction. There was no association between eGFR and the risk of ischaemic stroke (HR = 0.9 95% CI 0.8–1.1, HR = 0.93, 95% CI 0.8–1.1, and HR = 1.1, 95% CI 0.8–1.4 for patients with eGFR 60–89, 30–59, and &lt;30 mL/min/1.73 m2, respectively, P = 0.325).

Conclusions
Renal dysfunction is associated with an increased risk of myocardial infarction but not of ischaemic stroke among patients with atrial fibrillation treated with DOACs.
Acute cardiac manifestations under immune checkpoint inhibitors—beware of the obvious: a case report
Authors: Arangalage Dimitri , Pavon Anna Giulia , Özdemir Berna C , Michielin Olivier , Schwitter Jurg , Monney Pierre 
Published: August 2021

Abstract

Background
Immune checkpoint inhibitors (ICI) have revolutionized the management of many cancer types by drastically improving the median survival rate of patients. However, this efficiency comes at the cost of a high rate of immune-related adverse events, including lethal cardiac manifestations. Rapidly fatal cases of ICI-induced myocarditis have been reported and drawn considerable attention over the past years. However, it is essential to bear in mind that not all cardiac events occurring under ICI therapy are necessarily myocarditis.

Case summary
A 61-year-old female treated with pembrolizumab for a stage IV melanoma was admitted for chest pain leading to the diagnosis of ICI-related myocarditis based on the description of a discrete left ventricular subepicardial late gadolinium enhancement (LGE) on cardiac magnetic resonance (CMR) imaging. ICI were suspended and intravenous methylprednisolone initiated. A second line anti-MEK therapy was initiated. After a month of treatment, similar chest pain occurred. CMR revealed a midventricular stress cardiomyopathy and no LGE was detected. A posteriori interrogation revealed emotional stressors preceding both episodes. Review of the first CMR, performed 2 weeks after symptom onset, indicated a pattern compatible with the recovery phase of a stress cardiomyopathy and the presence of LGE was questioned. ICI were reintroduced without recurrence of cardiac events.

Discussion
Not all cardiac manifestations occurring under ICI therapy are drug-related adverse events, therefore differential diagnoses must systematically be considered as the contraindication of ICI may have a major impact on patient prognosis. Cardiac imaging should be performed early and plays a key role in the management strategy.
Intracoronary acetylcholine testing among 746 consecutive Japanese patients with angina-like chest pain and unobstructed coronary artery disease
Authors: Sueda Shozo , Sakaue Tomoki 
Published: August 2021

AbstractAims Intracoronary acetylcholine (ACh) testing is useful for the detection of epicardial spasm (ES) and coronary microvascular spasm (CMS). We retrospectively analysed the incidence of ES and CMS in consecutive Japanese patients with unobstructed coronary artery disease.Methods and resultsFrom January 1991 to February 2019, we performed intracoronary ACh testing of 1864 patients. Among these patients, a total of 746 consecutive patients (254 women, mean age 64 ± 11 years) who underwent first diagnostic angiography for suspected myocardial ischaemia and had unobstructed coronary arteries (&lt;50%) were enrolled. Epicardial spasm was defined as ≥90% stenosis and usual chest symptoms and ischaemic ECG changes, while CMS was defined as &lt;75% stenosis and usual chest symptoms and ischaemic ECG changes. We performed intracoronary ACh testing on both coronary arteries in 96% (716/746) of all subjects. Overall, ES was found in 329 patients (44%), whereas CMS was revealed in 40 patients (5%) including 4 patients with coexisting ES. In patients with ES, women made up 22%, and approximately three-quarters of the patients had resting chest pain. In contrast, women composed 65% (26/40) of those with CMS, and 15 patients with CMS had another chest symptom. Coronary microvascular spasm was frequently observed in the left coronary artery (LCA) but not the right coronary artery. Electrical cardioversion was necessary for two patients.Conclusions Coronary microvascular spasm was recognized in only 5% of consecutive Japanese patients with unobstructed coronary artery disease, whereas ES was revealed in 44% of those patients. Coronary microvascular spasm was often observed in women and in the LCA.
Association of clinical trial participation after myocardial infarction with socioeconomic status, clinical characteristics, and outcomes
Authors: Ohm Joel , Jernberg Tomas , Johansson David , Warnqvist Anna , Leosdottir Margrét , Hambraeus Kristina , Svensson Per 
Published: August 2021

Abstract

Aims
To investigate whether participants in clinical trials after myocardial infarction (MI) are representable for the post-MI population concerning characteristics, secondary prevention, and prognosis.

Methods and results
Cohort study on 31 792 attendants to 1-year revisits after MI throughout Sweden (n = 2941 clinical trial participants) between 2008 and 2013 identified in the Swedish Web-System for Enhancement and Development of Evidence-Based Care in Heart Disease Evaluated According to Recommended Therapies (SWEDEHEART). Individual-level data on socioeconomic status (SES) (disposable income, educational level, and marital status) and outcomes (first recurrent non-fatal MI, coronary heart disease death, fatal or non-fatal stroke until study end 2018) were linked from other national registries. Trial participants were more likely to be men [risk ratio 1.09; 95% confidence interval (CI) 1.07–1.11], and married (1.07; 1.04–1.10), have a highest-quintile income (1.42; 1.36–1.48), and post-secondary education (1.25; 1.18–1.33), while less likely to have a history of MI (0.88; 0.80–0.97), be persistent smokers (0.83; 0.75–0.92) and have left ventricular dysfunction (0.59; 0.44–0.79) compared to non-participants. During a mean 6.7-year follow-up, 5206 outcome events occurred. Risk was lower in trial participants (hazard ratio 0.80; 95% CI 0.72–0.89), also after adjusting for clinical characteristics and post-MI therapies (0.85; 0.77–0.94) and additionally for SES (0.88; 0.79–0.97).

Conclusions
Clinical trial participants post-MI are more often male, have higher SES, a more advantageous risk profile, and better prognosis. Additional unmeasured participation bias was implied. Questionable external validity of post-MI trials highlights the importance of complementary studies using real-world data.
Routine early postoperative computed tomography angiography after coronary artery bypass surgery: clinical value and management implications
Authors: Károlyi Mihály , Eberhard Matthias , Gloor Tobias , Polacin Malgorzata , Manka Robert , Savic Vedran , Plass André R , Vogt Paul Robert , Alkadhi Hatem , Schmiady Martin O 
Published: August 2021

Abstract

OBJECTIVES
Computed tomography angiography (CTA) is broadly used for long-term follow-up of graft patency after coronary artery bypass graft surgery (CABG). However, its clinical value in the early postoperative setting has not been established yet. We evaluated the benefit of adding CTA to the routine clinical work-up after CABG on patient management.

METHODS
A total of 305 consecutive patients (269 males, median age 68 years) underwent CABG and postoperative CTA with a median of 6 days after surgery. Graft patency and additional imaging findings were assessed and their influence on diagnosis and clinical management was evaluated.

RESULTS
Graft occlusion or high-grade stenosis was found in 15% of the patients. Additional findings were reported in 44% of the patients, including pericardial (2%) and pleural effusion (27%), large pneumothorax (11%), pulmonary infection (4%), cardiac or vascular thrombus (2%), pulmonary embolism (2%), sternal dehiscence (1%) and additional incidental findings requiring follow-up (6%). CT findings initiated new diagnostic and/or therapeutic measures in 15% of the patients, 47% of those with diseased grafts and 19% of patients with non-graft-related findings. No adverse events related to CTA were documented.

CONCLUSIONS
Early routine postoperative assessment of CABG with CTA reveals both cardiac and non-cardiac findings with a high frequency, affecting clinical management in a substantial proportion of patients.
A need for null models in understanding disease transmission: the example ofMycobacterium ulcerans(Buruli ulcer disease)
Authors: Receveur Joseph P , Bauer Alexandra , Pechal Jennifer L , Picq Sophie , Dogbe Magdalene , Jordan Heather R , Rakestraw Alex W , Fast Kayla , Sandel Michael , Chevillon Christine , Guégan Jean-François , Wallace John R , Benbow M Eric 
Published: August 2021

ABSTRACTUnderstanding the interactions of ecosystems, humans and pathogens is important for disease risk estimation. This is particularly true for neglected and newly emerging diseases where modes and efficiencies of transmission leading to epidemics are not well understood. Using a model for other emerging diseases, the neglected tropical skin disease Buruli ulcer (BU), we systematically review the literature on transmission of the etiologic agent, Mycobacterium ulcerans (MU), within a One Health/EcoHealth framework and against Hill's nine criteria and Koch's postulates for making strong inference in disease systems. Using this strong inference approach, we advocate a null hypothesis for MU transmission and other understudied disease systems. The null should be tested against alternative vector or host roles in pathogen transmission to better inform disease management. We propose a re-evaluation of what is necessary to identify and confirm hosts, reservoirs and vectors associated with environmental pathogen replication, dispersal and transmission; critically review alternative environmental sources of MU that may be important for transmission, including invertebrate and vertebrate species, plants and biofilms on aquatic substrates; and conclude with placing BU within the context of other neglected and emerging infectious diseases with intricate ecological relationships that lead to disease in humans, wildlife and domestic animals.
An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets
Authors: Rangel Luiz Thibério , Soucy Shannon M , Setubal João C , Gogarten Johann Peter , Fournier Gregory P 
Published: August 2021

AbstractAssessing the compatibility between gene family phylogenies is a crucial and often computationally demanding step in many phylogenomic analyses. Here, we describe the Evolutionary Similarity Index (IES), a means to assess shared evolution between gene families using a weighted orthogonal distance regression model applied to sequence distances. The utilization of pairwise distance matrices circumvents comparisons between gene tree topologies, which are inherently uncertain and sensitive to evolutionary model choice, phylogenetic reconstruction artifacts, and other sources of error. Furthermore, IES enables the many-to-many pairing of multiple copies between similarly evolving gene families. This is done by selecting non-overlapping pairs of copies, one from each assessed family, and yielding the least sum of squared residuals. Analyses of simulated gene family data sets show that IES’s accuracy is on par with popular tree-based methods while also less susceptible to noise introduced by sequence alignment and evolutionary model fitting. Applying IES to an empirical data set of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. The most cohesive cluster consisted of 62 genes with compatible evolutionary signal, which occur as both single-copy and multiple homologs per genome; phylogenetic analysis of concatenated alignments from this cluster produced a tree closely matching previously published species trees for Archaea. Four other clusters are mainly composed of accessory genes with limited distribution among Archaea and enriched toward specific metabolic functions. Pairwise evolutionary distances obtained from these accessory gene clusters suggest patterns of interphyla horizontal gene transfer. An IES implementation is available at https://github.com/lthiberiol/evolSimIndex.
Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture
Authors: Han Shunhua , Basting Preston J , Dias Guilherme B , Luhur Arthur , Zelhof Andrew C , Bergman Casey M 
Published: August 2021

Abstract
Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabeling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here, we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of long-terminal repeat retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.
An integrative 3-D model of the deep lithospheric structure beneath Dolsk and Odra fault zones as a result of magnetotelluric data interpretation
Authors: Oryński Szymon , Jóźwiak Waldemar , Nowożyński Krzysztof 
Published: August 2021

SUMMARY
Long-period magnetotelluric soundings were carried out in the eastern part of the Fore-Sudetic Monocline in central Europe to determine the deep geoelectrical structure. It is an important area in the contact zone of the Palaeozoic terranes of Western Europe and the Proterozoic East European Craton. The research area includes the Dolsk fault zone and the Odra fault zone, which are essential geological boundaries of a regional nature separating crustal blocks of various origins. There were conducted 51 soundings on the quasi-regular mesh 150 km in SE and 225 km in NE. The research region is highly urbanized, and hence some of the data were strongly disturbed. Careful processing of data was required, and sometimes measurements had to be repeated at other locations. The collected data allow constructing 3-D models of the electrical conductivity distribution. A parallel version of the ModEM 3-D inversion code was used for modelling. The information contained in each used transfer function was also examined by performing a separate inversion of these functions. The obtained resistivity distribution models confirm the Dolsk and Odra faults' location as postulated previously by geologists. They also show that these very deep faults are reaching the lower crust. However, they do not clearly state how far the contemporary lowering of the Baltica reaches under cover of younger Palaeozoic sediments.
The influence of trawl efficiency assumptions on survey-based population metrics
Authors: Dean Micah J , Hoffman William S , Buchan Nicholas C , Cadrin Steven X , Grabowski Jonathan H 
Published: August 2021

Abstract
Catch data from bottom trawl surveys are used in various ways (e.g. stock assessments, fisheries management, and ecosystem studies) to represent trends in fish populations across space, time, season, or size. Relative abundance indices assume constant capture efficiency, and area-swept abundance requires an estimate of capture efficiency. Therefore, it is important to develop a predictive understanding of the interaction between fish and survey gear. We conducted experiments to test two primary factors that influence the efficiency of survey trawls at capturing demersal groundfish: (1) footrope escapement—estimated by attaching a collection bag beneath the primary trawl, and (2) herding of the sweeps/doors—estimated by varying sweep length. Random forest models were used to disentangle the herding effect from patterns caused by environmental variables. Contrary to common assumptions, footrope efficiency was incomplete (&lt; 100%) and herding was non-trivial (&gt; 0%), which introduces a bias in population metrics that rely on such assumptions. This bias varied by species and depended upon the relative strength of the counteracting effects of footrope escapement and herding. Our findings suggest that trawl efficiency should be estimated (not assumed) to derive area-swept abundance, and relative abundance indices should account for size-based efficiency and changing size compositions.
Applying Bayesian model selection to determine ecological covariates for recruitment and natural mortality in stock assessment
Authors: Trochta John T , Branch Trevor A 
Published: August 2021

AbstractIncorporating ecological covariates into fishery stock assessments may improve estimates, but most covariates are estimated with error. Model selection criteria are often used to identify support for covariates, have some limitations and rely on assumptions that are often violated. For a more rigorous evaluation of ecological covariates, we used four popular selection criteria to identify covariates influencing natural mortality or recruitment in a Bayesian stock assessment of Pacific herring (Clupea pallasii) in Prince William Sound, Alaska. Within this framework, covariates were incorporated either as fixed effects or as latent variables (i.e. covariates have associated error). We found most support for pink salmon increasing natural mortality, which was selected by three of four criteria. There was ambiguous support for other fixed effects on natural mortality (walleye pollock and the North Pacific Gyre Oscillation) and recruitment (hatchery-released juvenile pink salmon and a 1989 regime shift). Generally, similar criteria values among covariates suggest no clear evidence for a consistent effect of any covariate. Models with covariates as latent variables were sensitive to prior specification and may provide potentially very different results. We recommend using multiple criteria and exploring different statistical assumptions about covariates for their use in stock assessment.
Converging Lexicography and Neology
Authors: Klosa-Kückelhaus Annette , Kernerman Ilan 
Published: August 2021

Abstract:
This introduction summarizes general issues combining lexicography and neology in the context of the Globalex Workshop on Lexicography and Neology series. We present each of the six papers composing this Special Issue, featuring two Slavic languages (Czech and Slovak) and two Romance ones (Brazilian Portuguese and Spanish in its European and Latin American varieties) and their diverse lexicographic research and representation, in specialized dictionaries of neologisms or general language ones, in monolingual, bilingual and multilingual lexical resources, and in print and digital dictionaries.
Non-uniform ISS small-gain theorem for infinite networks
Authors: Mironchenko Andrii 
Published: August 2021

Abstract
We introduce the concept of non-uniform input-to-state stability for networks. It combines the uniform global stability with the uniform attractivity of any subnetwork while it allows for non-uniform convergence of all components. For an infinite network consisting of input-to-state stable subsystems, which do not necessarily have a uniform $\mathscr{K}\mathscr{L}$-bound on the transient behaviour, we show the following: if the gain operator satisfies the uniform small-gain condition, then the whole network is non-uniformly input-to-state stable and all its finite subnetworks are input-to-state stable.