bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weight Stigma as a Predictor of Distress and Maladaptive Eating Behaviors During COVID-19: Longitudinal Findings From the EAT Study
Authors: Puhl Rebecca M , Lessard Leah M , Larson Nicole , Eisenberg Marla E , Neumark-Stzainer Dianne 
Published: September 2020

AbstractBackgroundWeight stigma is common for people with obesity and harmful to health. Links between obesity and complications from COVID−19 have been identified, but it is unknown whether weight stigma poses adverse health implications during this pandemic.PurposeWe examined longitudinal associations between prepandemic experiences of weight stigma and eating behaviors, psychological distress, and physical activity during the COVID-19 pandemic in a diverse sample of emerging adults.MethodsParticipants (N = 584, 64% female, mean age = 24.6 ± 2.0 years, mean body mass index [BMI] = 28.2) in the COVID-19 Eating and Activity over Time (C-EAT) study were cohort members of the population-based longitudinal study EAT 2010–2018. Weight stigma reported by participants in 2018 was examined as a predictor of binge eating, eating to cope, physical activity, depressive symptoms, and stress during COVID-19. Data were collected via online surveys during the U.S. outbreak of COVID-19 in 2020.ResultsPrepandemic experiences of weight stigma predicted higher levels of depressive symptoms (β = 0.15, p &lt; .001), stress (β = 0.15, p = .001), eating as a coping strategy (β = 0.16, p &lt; .001), and an increased likelihood of binge eating (odds ratio = 2.88, p &lt; .001) among young adults during the COVID-19 pandemic but were unrelated to physical activity. Although associations remained after accounting for demographic characteristics and BMI, the magnitude of longitudinal associations was attenuated after adjusting for prior levels of the outcome variables.ConclusionsYoung adults who have experienced weight stigma may have increased vulnerability to distress and maladaptive eating during this pandemic. Public health messaging could be improved to support people of diverse body sizes and reduce the harmful consequences of weight stigma.
Microscopic Esophageal Sloughing Is Not Specific to “Sloughing Esophagitis”
Authors: Ettel Mark G , Gonzalez Raul S 
Published: September 2020

Abstract

Objectives
“Sloughing esophagitis” (SE) is characterized by a 2-toned squamous epithelium with superficial necrotic keratinocytes overlying viable epithelium. We compared histologic and clinical findings to determine how cases clinically diagnosed as SE differed from cases with histologic sloughing but a different clinical diagnosis. In addition, we compared cases with inflammatory and noninflammatory histology.

Methods
We searched departmental archives for esophageal biopsies with histologic sloughing features. We compared clinical and histologic findings for cases with and without clinical confirmation of SE and with and without histologic inflammation.

Results
We identified 52 patients, of whom 10 (19%) had clinically diagnosed SE, 18 (35%) had another diagnosis, and 24 (46%) had an unclear diagnosis. Endoscopic sloughing tended to be reported more often in cases with SE (P = .07). Histologic features did not discriminate between SE and other etiologies. Esophagitis resolved in 18 of 31 patients with follow-up, with no difference between sloughing and nonsloughing cases (P = .26). There were no clinical differences based on inflammatory and noninflammatory histology.

Conclusions
SE has a classic microscopic appearance, but its findings are not specific, although endoscopic sloughing helps correlate histologic and clinical findings. In cases with histologic sloughing, pathologists should raise a broad differential diagnosis.
Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information
Authors: Fan Jason , Li Xuan Cindy , Crovella Mark , Leiserson Mark D M 
Published: September 2020

Abstract

Motivation
Mapping genetic interactions (GIs) can reveal important insights into cellular function and has potential translational applications. There has been great progress in developing high-throughput experimental systems for measuring GIs (e.g. with double knockouts) as well as in defining computational methods for inferring (imputing) unknown interactions. However, existing computational methods for imputation have largely been developed for and applied in baker’s yeast, even as experimental systems have begun to allow measurements in other contexts. Importantly, existing methods face a number of limitations in requiring specific side information and with respect to computational cost. Further, few have addressed how GIs can be imputed when data are scarce.

Results
In this article, we address these limitations by presenting a new imputation framework, called Extensible Matrix Factorization (EMF). EMF is a framework of composable models that flexibly exploit cross-species information in the form of GI data across multiple species, and arbitrary side information in the form of kernels (e.g. from protein–protein interaction networks). We perform a rigorous set of experiments on these models in matched GI datasets from baker’s and fission yeast. These include the first such experiments on genome-scale GI datasets in multiple species in the same study. We find that EMF models that exploit side and cross-species information improve imputation, especially in data-scarce settings. Further, we show that EMF outperforms the state-of-the-art deep learning method, even when using strictly less data, and incurs orders of magnitude less computational cost.

Availability
Implementations of models and experiments are available at: https://github.com/lrgr/EMF.

Supplementary information
Supplementary data are available at Bioinformatics online.
IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation
Authors: Li Hong-Dong , Yang Changhuo , Zhang Zhimin , Yang Mengyun , Wu Fang-Xiang , Omenn Gilbert S , Wang Jianxin 
Published: September 2020

AbstractMotivationHigh resolution annotation of gene functions is a central goal in functional genomics. A single gene may produce multiple isoforms with different functions through alternative splicing. Conventional approaches, however, consider a gene as a single entity without differentiating these functionally different isoforms. Towards understanding gene functions at higher resolution, recent efforts have focused on predicting the functions of isoforms. However, the performance of existing methods is far from satisfactory mainly because of the lack of isoform-level functional annotation.ResultsWe present IsoResolve, a novel approach for isoform function prediction, which leverages the information from gene function prediction models with domain adaptation (DA). IsoResolve treats gene-level and isoform-level features as source and target domains, respectively. It uses DA to project the two domains into a latent variable space in such a way that the latent variables from the two domains have similar distribution, which enables the gene domain information to be leveraged for isoform function prediction. We systematically evaluated the performance of IsoResolve in predicting functions. Compared with five state-of-the-art methods, IsoResolve achieved significantly better performance. IsoResolve was further validated by case studies of genes with isoform-level functional annotation.Availability and implementationIsoResolve is freely available at https://github.com/genemine/IsoResolve.Supplementary informationSupplementary data are available at Bioinformatics online.
On the phase transition of Wilks’ phenomenon
Authors: He Yinqiu , Meng Bo , Zeng Zhenghao , Xu Gongjun 
Published: September 2020

Summary
Wilks’ theorem, which offers universal chi-squared approximations for likelihood ratio tests, is widely used in many scientific hypothesis testing problems. For modern datasets with increasing dimension, researchers have found that the conventional Wilks’ phenomenon of the likelihood ratio test statistic often fails. Although new approximations have been proposed in high-dimensional settings, there still lacks a clear statistical guideline regarding how to choose between the conventional and newly proposed approximations, especially for moderate-dimensional data. To address this issue, we develop the necessary and sufficient phase transition conditions for Wilks’ phenomenon under popular tests on multivariate mean and covariance structures. Moreover, we provide an in-depth analysis of the accuracy of chi-squared approximations by deriving their asymptotic biases. These results may provide helpful insights into the use of chi-squared approximations in scientific practices.
Targeting of BCR-ABL1 and IRE1α induces synthetic lethality in Philadelphia-positive acute lymphoblastic leukemia
Authors: Vieri Margherita , Preisinger Christian , Schemionek Mirle , Salimi Azam , Patterson John B , Samali Afshin , Brümmendorf Tim H , Appelmann Iris , Kharabi Masouleh Behzad 
Published: September 2020

Abstract
BCR-ABL1-positive acute lymphoblastic leukemia (ALL) cell survival is dependent on the inositol-requiring enzyme 1 alpha (IRE1α) branch of the unfolded protein response. In the current study, we have focused on exploring the efficacy of a simultaneous pharmacological inhibition of BCR-ABL1 and IRE1α in Philadelphia-positive (Ph+) ALL using tyrosine kinase inhibitor (TKI) nilotinib and the IRE1α inhibitor MKC-8866. The combination of 0.5 µM nilotinib and 30 µM MKC-8866 in Ph+ ALL cell lines led to a synergistic effect on cell viability. To mimic this dual inhibition on a genetic level, pre-B-cells from conditional Xbp1+/fl mice were transduced with a BCR-ABL1 construct and with either tamoxifen-inducible cre or empty vector. Cells showed a significant sensitization to the effect of TKIs after the induction of the heterozygous deletion. Finally, we performed a phosphoproteomic analysis on Ph+ ALL cell lines treated with the combination of nilotinib and MKC-8866 to identify potential targets involved in their synergistic effect. An enhanced activation of p38 mitogen-activated protein kinase α (p38α MAPK) was identified. In line with this findings, p38 MAPK and, another important endoplasmic reticulum-stress-related kinase, c-Jun N-terminal kinase (JNK) were found to mediate the potentiated cytotoxic effect induced by the combination of MKC-8866 and nilotinib since the targeting of p38 MAPK with its specific inhibitor BIRB-796 or JNK with JNK-in-8 hindered the synergistic effect observed upon treatment with nilotinib and MKC-8866. In conclusion, the identified combined action of nilotinib and MKC-8866 might represent a successful therapeutic strategy in high-risk Ph+ ALL.
Multidose Priming and Delayed Boosting ImprovePlasmodium falciparumSporozoite Vaccine Efficacy Against HeterologousP. falciparumControlled Human Malaria Infection
Authors: Lyke Kirsten E , Singer Alexandra , Berry Andrea A , Reyes Sharina , Chakravarty Sumana , James Eric R , Billingsley Peter F , Gunasekera Anusha , Manoj Anita , Murshedkar Tooba , Laurens Matthew B , Church W Preston , Garver Baldwin Lindsey S , Sedegah Martha , Banania Glenna , Ganeshan Harini , Guzman Ivelese , Reyes Anatalio , Wong Mimi , Belmonte Arnel , Ozemoya Amelia , Belmonte Maria , Huang Jun , Villasante Eileen , Sim B Kim Lee , Hoffman Stephen L , Richie Thomas L , Epstein Judith E ,   Warfighter II Study Team
Published: September 2020

AbstractBackgroundA live-attenuated Plasmodium falciparum sporozoite (SPZ) vaccine (PfSPZ Vaccine) has shown up to 100% protection against controlled human malaria infection (CHMI) using homologous parasites (same P. falciparum strain as in the vaccine). Using a more stringent CHMI, with heterologous parasites (different P. falciparum strain), we assessed the impact of higher PfSPZ doses, a novel multi-dose prime regimen, and a delayed vaccine boost upon vaccine efficacy (VE).MethodsWe immunized 4 groups that each contained 15 healthy, malaria-naive adults. Group 1 received 5 doses of 4.5 x 105 PfSPZ (Days 1, 3, 5, and 7; Week 16). Groups 2, 3, and 4 received 3 doses (Weeks 0, 8, and 16), with Group 2 receiving 9.0 × 105/doses; Group 3 receiving 18.0 × 105/doses; and Group 4 receiving 27.0 × 105 for dose 1 and 9.0 × 105 for doses 2 and 3. VE was assessed by heterologous CHMI after 12 or 24 weeks. Volunteers not protected at 12 weeks were boosted prior to repeat CHMI at 24 weeks.ResultsAt 12-week CHMI, 6/15 (40%) participants in Group 1 (P = .04) and 3/15 (20%) participants in Group 2 remained aparasitemic, as compared to 0/8 controls. At 24-week CHMI, 3/13 (23%) participants in Group 3 and 3/14 (21%) participants in Group 4 remained aparasitemic, versus 0/8 controls (Groups 2–4, VE not significant). Postboost, 9/14 (64%) participants versus 0/8 controls remained aparasitemic (3/6 in Group 1, P = .025; 6/8 in Group 2, P = .002).ConclusionsAdministering 4 stacked priming injections (multi-dose priming) resulted in 40% VE against heterologous CHMI, while dose escalation of PfSPZ using single-dose priming was not significantly protective. Boosting unprotected subjects improved VE at 24 weeks, to 64%.Clinical Trials RegistrationNCT02601716.
Antibiotic Overuse After Hospital Discharge: A Multi-hospital Cohort Study
Authors: Vaughn Valerie M , Gandhi Tejal N , Chopra Vineet , Petty Lindsay A , Giesler Daniel L , Malani Anurag N , Bernstein Steven J , Hsaiky Lama M , Pogue Jason M , Dumkow Lisa , Ratz David , McLaughlin Elizabeth S , Flanders Scott A 
Published: September 2020

Abstract

Background
Antibiotics are commonly prescribed to patients as they leave the hospital. We aimed to create a comprehensive metric to characterize antibiotic overuse after discharge among hospitalized patients treated for pneumonia or urinary tract infection (UTI), and to determine whether overuse varied across hospitals and conditions.

Methods
In a retrospective cohort study of hospitalized patients treated for pneumonia or UTI in 46 hospitals between 1 July 2017–30 July 2019, we quantified the proportion of patients discharged with antibiotic overuse, defined as unnecessary antibiotic use, excess antibiotic duration, or suboptimal fluoroquinolone use. Using linear regression, we assessed hospital-level associations between antibiotic overuse after discharge in patients treated for pneumonia versus a UTI.

Results
Of 21 825 patients treated for infection (12 445 with pneumonia; 9380 with a UTI), nearly half (49.1%) had antibiotic overuse after discharge (56.9% with pneumonia; 38.7% with a UTI). For pneumonia, 63.1% of overuse days after discharge were due to excess duration; for UTIs, 43.9% were due to treatment of asymptomatic bacteriuria. The percentage of patients discharged with antibiotic overuse varied 5-fold among hospitals (from 15.9% [95% confidence interval, 8.7%–24.6%] to 80.6% [95% confidence interval, 69.4%–88.1%]) and was strongly correlated between conditions (regression coefficient = 0.85; P &lt; .001).

Conclusions
Antibiotic overuse after discharge was common and varied widely between hospitals. Antibiotic overuse after discharge was associated between conditions, suggesting that the prescribing culture, physician behavior, or organizational processes contribute to overprescribing at discharge. Multifaceted efforts focusing on all 3 types of overuse and multiple conditions should be considered to improve antibiotic prescribing at discharge.
Estimation of dynamic models of recurrent events with censored data
Authors: Lee Sanghyeok , Gørgens Tue 
Published: September 2020

Summary
In this paper, we consider estimation of dynamic models of recurrent events (event histories) in continuous time using censored data. We develop maximum simulated likelihood estimators where missing data are integrated out using Monte Carlo and importance sampling methods. We allow for random effects and integrate out this unobserved heterogeneity using a quadrature rule. In Monte Carlo experiments, we find that maximum simulated likelihood estimation is practically feasible and performs better than both listwise deletion and auxiliary modelling of initial conditions. In an empirical application, we study ischaemic heart disease events for male Maoris in New Zealand.
Non-ST-elevation myocardial infarction after complex percutaneous coronary intervention and transcatheter aortic valve implantation: a case report of bioprosthesis-related delayed coronary obstruction and its difficult diagnosis
Authors: Rudziński Piotr Nikodem , Mach Markus , Gross Christoph , Andreas Martin 
Published: September 2020

Abstract

Background
There is a high coincidence of significant coronary artery disease and severe aortic stenosis. Coronary revascularization should be performed prior to transcatheter aortic valve implantation (TAVI). We report a case of non-ST-elevation myocardial infarction (NSTEMI) after complex percutaneous coronary intervention (PCI) prior to TAVI, where differential diagnosis between coronary stent failure and bioprosthesis-related sinus obstruction was substantial.

Case summary
A 79-year-old woman was re-admitted to the hospital 5 days after TAVI due to troponin-negative new-onset angina. She underwent complex PCI 3 days before TAVI and was not compliant to medications. Symptoms initially resolved after re-establishment of anti-hypertensive treatment. There were no signs of aortic bioprosthesis failure, paravalvular leak, or myocardial ischaemia. After 1 month, the symptoms re-occurred. Due to elevated troponins, myocardial ischaemia in electrocardiogram and new contractility disorders, NSTEMI was diagnosed. Because it was impossible to intubate the left coronary artery (LCA), cardiac surgery was performed. Calcified native coronary leaflet was pushed by the stent frame of aortic bioprosthesis towards LCA ostium causing its subtotal occlusion. Transcatheter heart valve (THV) was removed and the new surgical aortic bioprosthesis was implanted. Further hospitalization and 1-month follow-up were uneventful.

Discussion
Pre-procedural assessment is crucial prior to THV interventions. Delayed coronary obstruction caused by the native leaflet is extremely rare and potentially fatal complication of TAVI. The diagnosis is difficult and high clinical suspicion is required to detect this pathology. Given our experience, the indication towards interventional or surgical repair should be established faster to avoid coronary ischaemia.
Case report of non-ST-segment elevation myocardial infarction diagnosed in spectral detector-based computed tomography performed for the diagnosis of acute pulmonary embolism
Authors: Aoyama Rie , Murata Teppei , Ishikawa Joji , Harada Kazumasa 
Published: September 2020

Abstract

Background
Contrast-enhanced spectral detector-based computed tomography (SDCT) allows for the comprehensive and retrospective analysis. We report a case of pulmonary thromboembolism (PE) accompanied by non-ST-segment elevation myocardial infarction (NSTEMI) diagnosed by SDCT.

Case summary
A 72-year-old man with diabetes mellitus, hypertension, and prostate cancer suddenly developed chest and back pain and had difficulty in breathing at rest. Electrocardiography showed a right bundle branch block without significant ST-segment change. The initial serum troponin I level was 0.05 ng/mL, and the d-dimer level was 14.7 μg/mL. Spectral detector-based computed tomography showed bilateral scattered PE. After admission, his chest pain persisted, and the serum troponin I level 3 h after admission was elevated to 0.90 ng/mL. Reconstruction of SDCT images showed a perfusion defect of the posterolateral left ventricle myocardium. A coronary angiogram showed total occlusion of the obtuse marginal branch (OM); percutaneous coronary intervention was performed. Furthermore, we administered him with oral anticoagulants (OACs) for PE. Spectral detector-based computed tomography tests performed 6 months after the treatment was initiated, until when the dual antiplatelet therapy and OAC therapy were continued, showed improvement in perfusion defects of both pulmonary fields and the myocardium. His treatment was deescalated to single antiplatelet therapy and OAC, and the patient has had a good course.

Discussion
Non-ST-segment elevation myocardial infarction is sometimes difficult to diagnose accurately, especially in the hyper-acute phase or in the OM branch. The reconstruction of spectral images from enhanced SDCT was helpful to diagnose this unique combination of PE and NSTEMI and may be useful for evaluating therapeutic effects in such patients.
Pericardial effusion in patients with COVID-19: case series
Authors: Sauer François , Dagrenat Charlotte , Couppie Philippe , Jochum Gaelle , Leddet Pierre 
Published: September 2020

AbstractBackgroundSARS-coronavirus-2 [coronavirus disease 2019 (COVID-19)] infection is a public health issue affecting millions of people. It started in Wuhan in China in December 2019 spreading rapidly worldwide.Case summaryThree patients aged 51–84 developed a pericarditis related to COVID-19, associated for two of them with a myocarditis. Case 1 was a COVID-19 cardiac tamponade without myocarditis, confirmed by a positive chest computed tomography (CT) scan. Case 2 showed a COVID-19 myopericarditis, confirmed by a positive chest CT scan and a SARS-coronavirus-2 positive swab. Case 3 was a cardiac tamponade due to COVID-19 pericarditis, with a positive polymerase chain reaction on pericardial fluid. They were all treated by colchicine and their condition improved rapidly.DiscussionPresumably rare, we reported three cases of pericardial effusions (PEs) occurring in a single cardiology centre. There is a higher incidence of COVID-19-related cardiac diseases such as pericarditis that can manifest as a minimal PE to a cardiac tamponade, which should result in a higher awareness of cardiologists. A systematic measure of the high-sensitivity troponin kinetic in patients affected by COVID-19 could be interesting in order to screen for potential myocarditis. Any unexplained haemodynamic failure or increased cardiac biomarkers should make the medical team search for myopericarditis by a transthoracic echocardiography.
A new method of superior vena cava isolation without phrenic nerve injury by longitudinal ablation parallel to the phrenic nerve: a case report
Authors: Arai Tomoyuki , Hojo Rintaro , Kitamura Takeshi , Fukamizu Seiji 
Published: September 2020

Abstract

Background
Superior vena cava (SVC) isolation has improved the outcomes of paroxysmal atrial fibrillation (AF) originating from the SVC. However, right phrenic nerve (PN) injury is a major complication of this procedure. Therefore, in cases where the right atrium (RA)-SVC conduction site is near the PN, tremendous care is required to prevent PN injury.

Case summary
Repeated SVC isolation was performed due to the recurrence of SVC-triggered AF. The RA-SVC activation map revealed that the partial conduction block line was detected, and the propagation broke through the gap at the course of the PN site from the RA to the SVC. Since the course of the PN identified at high-output pacing was wide, the SVC was isolated by making longitudinal lines on both sides of the PN in a cranial direction, except for where low-output pacing captured, confirming compound muscle action potential to detect PN injury. Eventually, the SVC was successfully isolated without PN injury, and the sinus rhythm was maintained without antiarrhythmic drugs during a 14-month follow-up period.

Conclusion
Superior vena cava isolation was difficult depending on the course of the PN, and some methods to avoid PN injury were reported. However, this method can facilitate safe and effective SVC isolation with the conventional system, including the cases with AF foci located on the course of the PN.