bluuebunny/crossref_metadata_2025_split huggingface dataset:
Denoising gravitational-wave signals from binary black holes with a dilated convolutional autoencoder
Authors: Bacon Philippe , Trovato Agata , Bejger Michał 
Published: May 2023

Abstract
The broadband frequency output of gravitational-wave (GW) detectors is a non-stationary and non-Gaussian time series data stream dominated by noise populated by local disturbances and transient artifacts, which evolve on the same timescale as the GW signals and may corrupt the astrophysical information. We study a denoising algorithm dedicated to expose the astrophysical signals by employing a convolutional neural network in the encoder-decoder configuration, i.e. apply the denoising procedure of coalescing binary black hole signals to the publicly available LIGO O1 time series strain data. The denoising convolutional autoencoder neural network is trained on a dataset of simulated astrophysical signals injected into the real detector’s noise and a dataset of detector noise artifacts (‘glitches’), and its fidelity is tested on real GW events from O1 and O2 LIGO-Virgo observing runs.
Mississippi River low-flows: context, causes, and future projections
Authors: Muñoz Samuel E , Dee Sylvia G , Luo Xinyue , Haider M Rezaul , O’Donnell Michelle , Parazin B , Remo Jonathan W F 
Published: May 2023

Abstract
The Mississippi River represents a major commercial waterway, and periods of anomalously low river levels disrupt riverine transport. These low-flow events occur periodically, with a recent event in the fall of 2022 slowing barge traffic and generating sharp increases in riverine transportation costs. Here we combine instrumental river gage observations from the lower Mississippi River with output from the Community Earth System Model v2 Large Ensemble (LENS2) to evaluate historical trends and future projections of Mississippi River low streamflow extremes, place the 2022 low-flow event in a broader temporal context, and assess the hydroclimatic mechanisms that mediate the occurrence of low-flows. We show that the severity and duration of low-flow events gradually decreased between 1950 and 1980 coincident with the establishment of artificial reservoirs. In the context of the last ∼70 years, the 2022 low-flow event was less severe in terms of stage or discharge minima than other low-flow events of the mid- and late-20th century. Model simulations from the LENS2 dataset show that, under a moderate-high emissions scenario (SSP3-7.0), the severity and duration of low-flow events is projected to decrease through to the end of the 21st century. Finally, we use the large sample size afforded by the LENS2 dataset to show that low-flow events on the Mississippi River are associated with cold tropical Pacific forcing (i.e. La Niña conditions), providing support for the hypothesis that the El Niño-Southern Oscillation plays a critical role in mediating Mississippi River discharge extremes. We anticipate that our findings describing the trends in and hydroclimatic mechanisms of Mississippi River low-flow occurrence will aid water resource managers to reduce the negative impacts of low water levels on riverine transport.
Diagnostic Utility of CD200 Immunohistochemistry in Distinguishing EBV-Positive Large B-Cell Lymphoma From Classic Hodgkin Lymphoma
Authors: Batuello Christopher , Mason Emily F 
Published: May 2023

Abstract

Objectives
Epstein-Barr virus–positive large B-cell lymphoma (EBV+ LBCL) is a heterogeneous group of diseases that may resemble classic Hodgkin lymphoma (CHL) both morphologically and immunophenotypically. However, these diseases are treated with different therapies and carry distinct prognoses. We examined CD200 expression by immunohistochemistry in EBV+ LBCL and evaluated its diagnostic utility in the differential diagnosis with CHL.

Methods
CD200 immunohistochemistry was performed on archival material from 20 cases of CHL (11 EBV+, 9 EBV−), 11 cases of EBV+ LBCL, and 10 cases of diffuse large B-cell lymphoma, not otherwise specified (DLBCL NOS). Staining pattern and intensity (0-3+ scale) were recorded.

Results
CD200 positivity was seen in Reed-Sternberg cells in 19 (95%) of 20 cases of CHL, predominantly in a strong (3+, 15/19) and diffuse (&gt;50% of cells, 17/19) pattern. In contrast, CD200 was negative in 8 (73%) of 11 cases of EBV+ LBCL; the 3 positive cases showed 1 to 2+ staining in less than 50% of lesional cells. All cases of DLBCL NOS were negative for CD200.

Conclusions
CD200 may be a useful immunophenotypic marker in differentiating EBV+ LBCL from CHL, with negative to partial/weak staining favoring a diagnosis of EBV+ LBCL and strong diffuse staining favoring a diagnosis of CHL.
Pathophysiology and treatment of adults with arrhythmias in the emergency department, part 1: Atrial arrhythmias
Authors: Ray Lance , Geier Curtis , DeWitt Kyle M 
Published: May 2023

AbstractPurposeThis article, the first in a 2-part review, aims to reinforce current literature on the pathophysiology of cardiac arrhythmias and various evidence-based treatment approaches and clinical considerations in the acute care setting. Part 1 of this series focuses on atrial arrhythmias.SummaryArrhythmias are prevalent throughout the world and a common presenting condition in the emergency department (ED) setting. Atrial fibrillation (AF) is the most common arrhythmia worldwide and expected to increase in prevalence. Treatment approaches have evolved over time with advances in catheter-directed ablation. Based on historic trials, heart rate control has been the long-standing accepted outpatient treatment modality for AF, but the use of antiarrhythmics is often still indicated for AF in the acute setting, and ED pharmacists should be prepared and poised to help in AF management. Other atrial arrhythmias include atrial flutter (AFL), atrioventricular nodal reentry tachycardia (AVNRT), and atrioventricular reentrant tachycardia (AVRT), which warrant distinction due to their unique pathophysiology and because each requires a different approach to utilization of antiarrhythmics. Atrial arrhythmias are typically associated with greater hemodynamic stability than ventricular arrhythmias but still require nuanced management according to patient subset and risk factors. Since antiarrhythmics can also be proarrhythmic, they may destabilize the patient due to adverse effects, many of which are the focus of black-box label warnings that can be overreaching and limit treatment options. Electrical cardioversion for atrial arrhythmias is generally successful and, depending on the setting and/or hemodynamics, often indicated.ConclusionAtrial arrhythmias arise from a variety of mechanisms, and appropriate treatment depends on various factors. A firm understanding of physiological and pharmacological concepts serves as a foundation for exploring evidence supporting agents, indications, and adverse effects in order to provide appropriate care for patients.
MPI-VGAE: protein–metabolite enzymatic reaction link learning by variational graph autoencoders
Authors: Wang Cheng , Yuan Chuang , Wang Yahui , Chen Ranran , Shi Yuying , Zhang Tao , Xue Fuzhong , Patti Gary J , Wei Leyi , Hou Qingzhen 
Published: May 2023

Abstract
Enzymatic reactions are crucial to explore the mechanistic function of metabolites and proteins in cellular processes and to understand the etiology of diseases. The increasing number of interconnected metabolic reactions allows the development of in silico deep learning-based methods to discover new enzymatic reaction links between metabolites and proteins to further expand the landscape of existing metabolite–protein interactome. Computational approaches to predict the enzymatic reaction link by metabolite–protein interaction (MPI) prediction are still very limited. In this study, we developed a Variational Graph Autoencoders (VGAE)-based framework to predict MPI in genome-scale heterogeneous enzymatic reaction networks across ten organisms. By incorporating molecular features of metabolites and proteins as well as neighboring information in the MPI networks, our MPI-VGAE predictor achieved the best predictive performance compared to other machine learning methods. Moreover, when applying the MPI-VGAE framework to reconstruct hundreds of metabolic pathways, functional enzymatic reaction networks and a metabolite–metabolite interaction network, our method showed the most robust performance among all scenarios. To the best of our knowledge, this is the first MPI predictor by VGAE for enzymatic reaction link prediction. Furthermore, we implemented the MPI-VGAE framework to reconstruct the disease-specific MPI network based on the disrupted metabolites and proteins in Alzheimer’s disease and colorectal cancer, respectively. A substantial number of novel enzymatic reaction links were identified. We further validated and explored the interactions of these enzymatic reactions using molecular docking. These results highlight the potential of the MPI-VGAE framework for the discovery of novel disease-related enzymatic reactions and facilitate the study of the disrupted metabolisms in diseases.
Successful treatment of urticarial vasculitis with omalizumab in children: a case series
Authors: Wang Shan , Fu Libing , Xiang Xin , Zhang Bin , Ma Lin , Xing Huan 
Published: May 2023

Abstract
Urticarial vasculitis (UV) is a small vessel leucocytoclastic vasculitis, which often needs to be distinguished from urticaria and other dermatoses. Treatment of UV in children is challenging because of the unsatisfying efficacy of antihistamines and the safety concern of long-term systemic corticosteroids or immunosuppressive agents. As a classic biological agent widely used in chronic spontaneous urticaria, omalizumab might also be a potential therapeutic option in the treatment of children with UV. This report presented four children, aged 4–6 years, with glucocorticoid-unresponsive UV successfully treated by omalizumab, thus providing evidence that omalizumab can be used to treat UV with good efficacy and tolerability in the paediatric population.
Fecal Calprotectin in Gastrointestinal Disease
Authors: Murray Jennifer , Kok Klaartje B , Ayling Ruth M 
Published: May 2023

Abstract

Background
Inflammatory bowel disease (IBD) comprises a group of chronic conditions characterized by relapsing and remitting inflammation of the gastrointestinal tract. The incidence is increasing worldwide, and the therapeutic options for management are expanding. Endoscopy is the gold standard investigation for diagnosis of IBD and for assessing mucosal healing, which is increasingly being used as a measure of disease control. However, it is an invasive procedure that is unpleasant for patients and expensive and time-consuming for hospitals. Fecal calprotectin has been shown to be an accurate surrogate marker of gastrointestinal inflammation in IBD.

Content
Fecal calprotectin was initially used for the diagnosis of IBD but is now recognized as having a role in assisting in assessment of disease activity, prediction of relapse, and informing decisions around therapy and may help to minimize requirement for endoscopy. However, there are various preanalytical and analytical factors that can affect interpretation of the results; these need to be understood to optimize clinical care.

Summary
Preanalytical and analytical factors that can potentially influence fecal calprotectin concentrations are examined, and an overview is provided of clinical situations in which fecal calprotectin is commonly measured.
A Comparative Evaluation of the Measurement Properties of Three Histological Indices of Mucosal Healing in Ulcerative Colitis: Geboes Score, Robarts Histopathology Index and Nancy Index
Authors: Peyrin-Biroulet Laurent , Arenson Ethan , Rubin David T , Siegel Corey A , Lee Scott , Stephen Laroux F , Zhou Wen , Finney-Hayward Tricia , Sanchez Gonzalez Yuri , Shields Alan L 
Published: May 2023

Abstract

Background and Aims
To inform their future use in regulated clinical trials to evaluate treatment efficacy hypotheses, the measurement properties of three histological indices, Geboes Score [GS], Robarts Histopathology Index [RHI] and Nancy Index [NI], were evaluated among patients with ulcerative colitis.

Methods
Analyses were conducted on data from a Phase 3 clinical trial of adalimumab [M14-033, n = 491] and focused on evaluating the measurement properties of the GS, RHI and NI. Specifically, internal consistency and inter-rater reliability, convergent, discriminant and known-group validity, and sensitivity to change were assessed at Baseline, and at Weeks 8 and 52.

Results
Internal consistency for the RHI showed lower alpha [α] values at Baseline [α = 0.62] relative to Weeks 8 [α = 0.82] and 52 [α = 0.81]. The inter-rater reliability values of RHI [0.91], NI [0.64] and GS [0.53] were excellent, good and fair, respectively. Regarding validity, Week 52 correlations were moderate to strong between full and partial Mayo scores and Mayo subscale scores and the RHI and GS, and were weak to moderate for the NI. Significant differences between mean scores of all three histological indices were observed across known-groups based on Mayo endoscopy subscores and full Mayo scores at Weeks 8 and 52 [p &lt; 0.001].

Conclusions
The GS, RHI and NI are each capable of producing reliable and valid scores that are sensitive to changes in disease activity over time, in patients with moderately to severely active ulcerative colitis. While all three indices demonstrated relatively acceptable measurement properties, the GS and RHI performed better than the NI.
Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis
Authors: Bruggeling Carlijn E , te Groen Maarten , Garza Daniel R , van Heeckeren tot Overlaer Famke , Krekels Joyce P M , Sulaiman Basma-Chick , Karel Davy , Rulof Athreyu , Schaaphok Anne R , Hornikx Daniel L A H , Nagtegaal Iris D , Dutilh Bas E , Hoentjen Frank , Boleij Annemarie 
Published: May 2023

AbstractBackground and AimsColonic bacterial biofilms are frequently present in ulcerative colitis [UC] and may increase dysplasia risk through pathogens expressing oncotraits. This prospective cohort study aimed to determine [1] the association of oncotraits and longitudinal biofilm presence with dysplasia risk in UC, and [2] the relation of bacterial composition with biofilms and dysplasia risk.MethodsFaeces and left- and right-sided colonic biopsies were collected from 80 UC patients and 35 controls. Oncotraits [FadA of Fusobacterium, BFT of Bacteroides fragilis, colibactin [ClbB] and Intimin [Eae] of Escherichia coli] were assessed in faecal DNA with multiplex quantitative polymerase chain reaction [qPCR]. Biopsies were screened for biofilms [n = 873] with 16S rRNA fluorescent in situ hybridiation. Shotgun metagenomic sequencing [n = 265], and ki67-immunohistochemistry were performed. Associations were determined with a mixed-effects regression model.ResultsBiofilms were highly prevalent in UC patients [90.8%] with a median persistence of 3 years (interquartile range [IQR] 2–5 years). Biofilm-positive biopsies showed increased epithelial hypertrophy [p = 0.025] and a reduced Shannon diversity independent of disease status [p = 0.015], but were not significantly associated with dysplasia in UC: adjusted odds ratio [aOR] 1.45, 95% confidence interval [CI] 0.63–3.40. In contrast, ClbB independently associated with dysplasia [aOR 7.16, 95% CI 1.75–29.28], and FadA and Fusobacteriales were associated with a decreased dysplasia risk in UC [aOR 0.23, 95% CI 0.06–0.83, p &lt;0.01].ConclusionsBiofilms are a hallmark of UC; however, because of their high prevalence are a poor biomarker for dysplasia. In contrast, colibactin presence and FadA absence independently associate with dysplasia in UC and might therefore be valuable biomarkers for future risk stratification and intervention strategies.
Transcatheter tricuspid valve edge-to-edge repair after a heart transplant: a single-centre experience with a novel therapy
Authors: Kerbel Tillmann , Uyanik-Ünal Keziban , Mach Markus , Bartunek Anna , Gökler Johannes , Osorio Emilio , Bartko Philipp , Zuckermann Andreas , Andreas Martin 
Published: May 2023

Abstract

OBJECTIVES
Tricuspid regurgitation (TR) in patients who had heart transplants is associated with poor outcome. The increased risk for surgical and postoperative complications might be reduced in these vulnerable patients by transcatheter therapies.

METHODS
All patients with a prior heart transplant (HTX) undergoing transcatheter edge-to-edge repair in the tricuspid position (T-TEER) were prospectively enrolled in an institutional registry.

RESULTS
Seven patients who had heart transplants (5/7 female) at a mean age of 53 [48; 64] and median TRI-SCORE of 14 [7; 22] underwent T-TEER to treat symptomatic TR ≥ IV in an elective (n = 6) and urgent (n = 1) setting, respectively. The median time from HTX to T-TEER was 13 years. A total of 2 (n = 4) and 3 (n = 3) clips were implanted with a technical success in 6/7 (one single- device detachment). TR reduction was effective and durable within a median echocardiographic follow-up time of 10 months (TR baseline vs last follow-up: P = 0.03). Further, significant right ventricular remodelling (right ventricular end-diastolic diameter: 50 mm–36 mm, P = 0.02), decrease in the inferior vena cava diameter (24 mm–18 mm, P = 0.04) and in the gamma-glutamyl-transferase (255 U/l–159 U/l, P = 0.04) was found. Four of 7 patients were free of cardiovascular death (n = 1, 267 days after T-TEER), cardiac redo surgery (n = 1) and heart failure hospitalization (n = 2) and had no further clinical signs of right heart failure.

CONCLUSIONS
T-TEER after HTX is feasible and effective regarding TR reduction in a short-term follow-up. The initial results may pave the way for a novel approach in TR management in patients having HTX.
Strategies for avoiding misunderstanding in English L2 conversations
Authors: McDonough Kim , Liu Chen , Trofimovich Pavel 
Published: May 2023

Abstract
To contribute to existing research that describes how L2 speakers avoid misunderstanding during conversation, the current study examines the strategies used by university students in Canada. The students (N = 104) were audio-recorded while carrying out two communicative tasks in pairs: exchanging personal experiences about moving to Canada, and discussing academic research studies. Transcripts were coded for the occurrence of speaker strategies (e.g. comprehension check, elaboration) and listener strategies (e.g. confirmation check, clarification request) for avoiding misunderstanding. Their use of speaker and listener strategies was compared overall and by conversational topic (i.e. personal or academic). The results indicated that the students used more speaker strategies than listener strategies and produced more speaker strategies during the academic discussion than the personal topic. Implications for L2 teaching are highlighted.
Sex-related differences in the impact of nutritional status on in-hospital mortality in heart failure: a retrospective cohort study
Authors: Kwaśny Adrian , Uchmanowicz Izabella , Juárez-Vela Raúl , Młynarska Agnieszka , Łokieć Katarzyna , Czapla Michał 
Published: May 2023

Abstract

Aims
A nutritional status is related to the length of hospitalization and in-hospital mortality of patients with heart failure (HF). The aim of this study is to assess the prognostic impact of nutritional status and body mass index (BMI) on in-hospital mortality among patients with HF relative to their sex.

Methods and results
We conducted a retrospective study and analysis of 809 medical records of patients admitted to the Institute of Heart Disease of the University Clinical Hospital in Wroclaw (Poland). Women were statistically significantly older than men (74.67 ± 11.15 vs. 66.76 ± 17.78; P &lt; 0.001). In unadjusted model, significant predictors of the odds of in-hospital mortality for men were underweight (OR = 14.81, P = 0.001) and the risk of malnutrition (OR = 8.979, P &lt; 0.001). In the case of women, none of the traits analysed was significant. In age-adjusted model, significant independent predictors of the odds of in-hospital mortality in the case of men were BMI &lt; 18.5 (OR = 15.423, P = 0.001) and risk of malnutrition (OR = 5.557, P = 0.002). In the case of women, none of the nutritional status traits analysed were significant. In multivariable-adjusted model in men, significant independent predictors of the odds of in-hospital mortality were BMI &lt; 18.5 (OR = 15.978, P = 0.007) compared with having normal body weight and the risk of malnutrition (OR = 4.686, P = 0.015). In the case of women, none of the nutritional status traits analysed were significant.

Conclusion
Both underweight and the risk of malnutrition are direct predictors of the odds of in-hospital mortality in men, but not in women. The study did not find a relationship between nutritional status and in-hospital mortality in women.
Relation of Life’s Essential 8 to the genetic predisposition for cardiovascular outcomes and all-cause mortality: results from a national prospective cohort
Authors: Zhang Junguo , Chen Ge , Habudele Zierdi , Wang Xiaojie , Cai Miao , Li Haitao , Gao Yanhui , Lip Gregory Y H , Lin Hualiang 
Published: May 2023

AbstractAimsTo evaluate the independent, mediating, interactive, and associated effects of Life's Essential 8 (LE8) and genetic predisposition on the risk of cardiovascular outcomes and all-cause mortality.Methods and resultsWe retrieved a total of 254 783 individuals from the UK Biobank. LE8 was determined by eight metrics (nicotine exposure, physical activity, diet, sleep, body mass index, blood pressure, blood glucose, and blood lipids), and was characterized as low, moderate, and high cardiovascular health (CVH). Genetic predisposition was estimated using the polygenic risk score (PRS). Cox regressions were performed to evaluate the associations between LE8, PRS, and outcomes. During a median follow-up of 12.53 years, all-cause mortality occurred in 10 257 of 197 473 participants, cardiovascular mortality in 2074 of 215 675, and incident cardiovascular disease (CVD) in 71 774 of 215 675. Individuals with moderate or high CVH experienced a lower risk [hazard ratios (HRs) 0.33 to 0.81] of adverse health outcomes compared with their counterparts with low CVH. A substantial proportion (16.1∼69.8%) of health outcomes could be attributable to moderate or high LE8, and up to 51.2% of the associations between PRS and adverse outcomes were mediated by LE8. In high PRS group, individuals with high CVH had lower CVD mortality (HR: 0.26, 95% confidence interval: 0.18, 0.39), compared to those with low CVH.ConclusionIdeal CVH was associated with lower risks of cardiovascular outcomes and all-cause mortality, with a more pronounced association observed in individuals with high PRS for CVD. Improving CVH according to LE8 guidelines should be encouraged, especially for those with PRS that indicate high CVD risk.