bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site2Vec: a reference frame invariant algorithm for vector embedding of protein–ligand binding sites
Authors: Bhadra Arnab , Yeturu Kalidas 
Published: August 2020

Abstract
Protein–ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Binding sites would also determine ADMET properties of a drug molecule. Tasks such as assessment of protein functional similarity and detection of side effects of drugs need identification of similar binding sites of disparate proteins across diverse pathways. To this end, methods for computing similarities between binding sites are still evolving and is an active area of research even today. Machine learning methods for similarity assessment require feature descriptors of binding sites. Traditional methods based on hand engineered motifs and atomic configurations are not scalable across several thousands of sites. In this regard, deep neural network algorithms are now deployed which can capture very complex input feature space. However, one fundamental challenge in applying deep learning to structures of binding sites is the input representation and the reference frame. We report here a novel algorithm, Site2Vec, that derives reference frame invariant vector embedding of a protein–ligand binding site. The method is based on pairwise distances between representative points and chemical compositions in terms of constituent amino acids of a site. The vector embedding serves as a locality sensitive hash function for proximity queries and determining similar sites. The method has been the top performer with more than 95% quality scores in extensive benchmarking studies carried over 10 data sets and against 23 other site comparison methods in the field. The algorithm serves for high throughput processing and has been evaluated for stability with respect to reference frame shifts, coordinate perturbations and residue mutations. We also provide the method as a standalone executable and a web service hosted at (http://services.iittp.ac.in/bioinfo/home).
Context Dependence: A Conceptual Approach for Understanding the Habitat Relationships of Coastal Marine Fauna
Authors: Bradley Michael , Nagelkerken Ivan , Baker Ronald , Sheaves Marcus 
Published: August 2020

Abstract
Coastal habitats, such as seagrasses, mangroves, rocky and coral reefs, salt marshes, and kelp forests, sustain many key fish and invertebrate populations around the globe. Our understanding of how animals use these broadly defined habitat types is typically derived from a few well-studied regions and is often extrapolated to similar habitats elsewhere. As a result, a working understanding of their habitat importance is often based on information derived from other regions and environmental contexts. Contexts such as tidal range, rainfall, and local geomorphology may fundamentally alter animal–habitat relationships, and there is growing evidence that broadly defined habitat types such as “mangroves” or “salt marsh” may show predictable spatial and temporal variation in habitat function in relation to these environmental drivers. In the present article, we develop a framework for systematically examining contextual predictability to define the geographic transferability of animal–habitat relationships, to guide ongoing research, conservation, and management actions in these systems.
Greater BOLD Variability is Associated With Poorer Cognitive Function in an Adult Lifespan Sample
Authors: Boylan Maria A , Foster Chris M , Pongpipat Ekarin E , Webb Christina E , Rodrigue Karen M , Kennedy Kristen M 
Published: August 2020

AbstractMoment-to-moment fluctuations in brain signal assessed by functional magnetic resonance imaging blood oxygenation level dependent (BOLD) variability is increasingly thought to represent important “signal” rather than measurement-related “noise.” Efforts to characterize BOLD variability in healthy aging have yielded mixed outcomes, demonstrating both age-related increases and decreases in BOLD variability and both detrimental and beneficial associations. Utilizing BOLD mean-squared-successive-differences (MSSD) during a digit n-back working memory (WM) task in a sample of healthy adults (aged 20–94 years; n = 171), we examined effects of aging on whole-brain 1) BOLD variability during task (mean condition MSSD across 0–2–3-4 back conditions), 2) BOLD variability modulation to incrementally increasing WM difficulty (linear slope from 0–2–3-4 back), and 3) the association of age-related differences in variability with in- and out-of-scanner WM performance. Widespread cortical and subcortical regions evidenced increased mean variability with increasing age, with no regions evidencing age-related decrease in variability. Additionally, posterior cingulate/precuneus exhibited increased variability to WM difficulty. Notably, both age-related increases in BOLD variability were associated with significantly poorer WM performance in all but the oldest adults. These findings lend support to the growing corpus suggesting that brain-signal variability is altered in healthy aging; specifically, in this adult lifespan sample, BOLD-variability increased with age and was detrimental to cognitive performance.
Side-by-Side Comparison of Three Fully Automated SARS-CoV-2 Antibody Assays with a Focus on Specificity
Authors: Perkmann Thomas , Perkmann-Nagele Nicole , Breyer Marie-Kathrin , Breyer-Kohansal Robab , Burghuber Otto C , Hartl Sylvia , Aletaha Daniel , Sieghart Daniela , Quehenberger Peter , Marculescu Rodrig , Mucher Patrick , Strassl Robert , Wagner Oswald F , Binder Christoph J , Haslacher Helmuth 
Published: August 2020

Abstract

Background
In the context of the COVID-19 pandemic, numerous new serological test systems for the detection of anti-SARS-CoV-2 antibodies rapidly have become available. However, the clinical performance of many of these is still insufficiently described. Therefore, we compared 3 commercial CE-marked, SARS-CoV-2 antibody assays side by side.

Methods
We included a total of 1154 specimens from pre-COVID-19 times and 65 samples from COVID-19 patients (≥14 days after symptom onset) to evaluate the test performance of SARS-CoV-2 serological assays by Abbott, Roche, and DiaSorin.

Results
All 3 assays presented with high specificities: 99.2% (98.6–99.7) for Abbott, 99.7% (99.2–100.0) for Roche, and 98.3% (97.3–98.9) for DiaSorin. In contrast to the manufacturers’ specifications, sensitivities only ranged from 83.1% to 89.2%. Although the 3 methods were in good agreement (Cohen’s Kappa 0.71–0.87), McNemar tests revealed significant differences between results obtained from Roche and DiaSorin. However, at low seroprevalences, the minor differences in specificity resulted in profound discrepancies of positive predictive values at 1% seroprevalence: 52.3% (36.2–67.9), 77.6% (52.8–91.5), and 32.6% (23.6–43.1) for Abbott, Roche, and DiaSorin, respectively.

Conclusion
We found diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictive values of these tests.
Post-fledging Golden-winged Warblers require forests with multiple stand developmental stages
Authors: Fiss Cameron J , McNeil Darin J , Rodewald Amanda D , Duchamp Joseph E , Larkin Jeffery L 
Published: August 2020

Abstract
Our understanding of songbird habitat needs during the breeding season stems largely from studies of nest success. However, growing evidence shows that nesting habitat and post-fledging habitat often differ. Management guidelines for declining species need to be reevaluated and updated to account for habitat shifts that may occur across the full breeding cycle. The Golden-winged Warbler (Vermivora chrysoptera) is a declining songbird species for which best management practices (BMPs) are based overwhelmingly on nesting habitat. We studied stand-scale habitat selection by fledgling Golden-winged Warblers during May–July, 2014–2017, in 2 landscapes (2 yr of data for each landscape), 200 km apart in Pennsylvania. Across 4 yr, we radio-tagged and tracked 156 fledglings. We used discrete-choice models to evaluate habitat selection during 2 post-fledging time periods (days 1–5, days 6–28). Fledglings used a variety of cover types, but most telemetry relocations (i.e. 85%) occurred in forest in the stand initiation stage, stem exclusion stage, or mature forest upland. Fledglings primarily selected stand initiation forest during the first 5 days, but preferred habitats differed between regions during days 6–28 post-fledging. Fledglings in one landscape favored stands in the stem exclusion stage while fledglings in the other landscape continued to select stands in the initiation stage. Fledglings moved greater distances as they aged and dispersed ~750 m by day 28 post-fledging. These findings suggest the need to update Golden-winged Warbler BMPs to account for the broader habitat needs of fledglings during the breeding season. In addition, these results indicate that regional studies of habitat requirements can help guide management of dynamic forest landscapes for birds.
Clinical correlation and disease phenotype in patients with esophageal achalasia and comorbid autoimmune diseases
Authors: Sara Cassarano , Marcella Pesce , Martina Cargiolli , Marta Andreozzi , Eleonora Efficie , Giovanni Aprea , Marco Milone , Paola Dinuzzi Vincenza , Domenico De Palma Giovanni , Giovanni Sarnelli 
Published: August 2020

SummaryBackgroundThere is evidence that idiopathic achalasia has an autoimmune component and a significant association with several autoimmune comorbidities has been described. However, data regarding the prevalence of autoimmune diseases in achalasia are not well established, and few studies have explored this association.ObjectiveOur primary aim was to prospectively investigate the type and frequency of autoimmune comorbidities in a large cohort of consecutive achalasia patients. Our secondary aim was to investigate the effects of autoimmune comorbidities on achalasia phenotype (clinical features and manometric pattern).MethodsThe study population consisted of 375 consecutive patients (215 females—median age 55 ± 17 years), referred at our tertiary referral center from January 2008 to January 2018, with clinical and instrumental (EGDS, barium esophagogram, and manometry) diagnosis of idiopathic achalasia. Gender- and age-matched subjects undergoing manometry and pH-impedance monitoring for typical gastroesophageal reflux (GERD) complaints served as controls. In all patients a detailed history taking was carried out, recording the presence and type of autoimmune comorbidities.ResultsThe overall prevalence of autoimmune comorbidities was two times higher in achalasia than in control patients (12.3 vs. 5%, respectively). The presence of comorbidities did not significantly affect disease’s phenotype, as the age of disease onset was similar in achalasia patients with and without comorbidities (50.13 ± 14.47 and 48.3 ± 18.71, respectively, P = NS).ConclusionsAlthough larger epidemiologic studies are needed to confirm our data, our findings likely suggest that achalasia has a complex multifactorial pathophysiology with an autoimmune component.
The echocardiographic ratio tricuspid annular plane systolic excursion/pulmonary arterial systolic pressure predicts short-term adverse outcomes in acute pulmonary embolism
Authors: Lyhne Mads D , Kabrhel Christopher , Giordano Nicholas , Andersen Asger , Nielsen-Kudsk Jens Erik , Zheng Hui , Dudzinski David M 
Published: August 2020

Abstract

Aims
Right ventricular (RV) failure causes death from acute pulmonary embolism (PE), due to a mismatch between RV systolic function and increased RV afterload. We hypothesized that an echocardiographic ratio of this mismatch [RV systolic function by tricuspid annular plane systolic excursion (TAPSE) divided by pulmonary arterial systolic pressure (PASP)] would predict adverse outcomes better than each measurement individually, and would be useful for risk stratification in intermediate-risk PE.

Methods and results
This was a retrospective analysis of a single academic centre Pulmonary Embolism Response Team registry from 2012 to 2019. All patients with confirmed PE and a formal transthoracic echocardiogram performed within 2 days were included. All echocardiograms were analysed by an observer blinded to the outcome. The primary endpoint was a 7-day composite outcome of death or haemodynamic deterioration. Secondary outcomes were 7- and 30-day all-cause mortality. A total of 627 patients were included; 135 met the primary composite outcome. In univariate analysis, the TAPSE/PASP was associated with our primary outcome [odds ratio = 0.028, 95% confidence interval (CI) 0.010–0.087; P &lt; 0.0001], which was significantly better than either TAPSE or PASP alone (P = 0.017 and P &lt; 0.0001, respectively). A TAPSE/PASP cut-off value of 0.4 was identified as the optimal value for predicting adverse outcome in PE. TAPSE/PASP predicted both 7- and 30-day all-cause mortality, while TAPSE and PASP did not.

Conclusion
A combined echocardiographic ratio of RV function to afterload is superior in prediction of adverse outcome in acute intermediate-risk PE. This ratio may improve risk stratification and identification of the patients that will suffer short-term deterioration after intermediate-risk PE.
Tofacitinib, an Oral Janus Kinase Inhibitor: Analysis of Malignancy (Excluding Nonmelanoma Skin Cancer) Events Across the Ulcerative Colitis Clinical Program
Authors: Lichtenstein Gary R , Rogler Gerhard , Ciorba Matthew A , Su Chinyu , Chan Gary , Pedersen Ronald D , Lawendy Nervin , Quirk Daniel , Nduaka Chudy I , Thorpe Andrew J , Panés Julian 
Published: August 2020

Abstract

Background
Tofacitinib is an oral, small molecule Janus kinase inhibitor for the treatment of ulcerative colitis (UC). Here, we performed an integrated analysis of malignancy events from the tofacitinib phase 3 UC clinical development program (excluding nonmelanoma skin cancer [NMSC]).

Methods
Data (up to May 2019) were pooled from two phase 3 induction studies, a phase 3 maintenance study, and an ongoing, open-label, long-term extension (OLE) study, and analyzed as 3 cohorts: induction (N = 1139), maintenance (N = 592), and overall (induction, maintenance, and ongoing OLE study; N = 1124). Proportions and incidence rates (IRs; unique patients with events per 100 patient-years [PY] of exposure) for malignancies confirmed by adjudication were calculated.

Results
The overall cohort consisted of patients who received at least 1 dose of tofacitinib at 5 or 10 mg twice daily, for up to 6.8 years, with an exposure of 2576.4 PY. Of the 1124 overall cohort tofacitinib-treated patients, 20 developed a malignancy (excluding NMSC; IR, 0.75; 95% confidence interval, 0.46–1.16), of which 17 occurred in patients treated with tofacitinib 10 mg twice daily; importantly, more than 80% of patients predominantly received this dose. Furthermore, there was no apparent clustering of malignancy types, and IRs were stable over time.

Conclusions
In the tofacitinib UC clinical development program, malignancy events were infrequent, and rates were comparable with those in the tofacitinib rheumatoid arthritis and psoriatic arthritis clinical development programs, and for biologic UC treatments. ClinicalTrials.gov: NCT01465763, NCT01458951, NCT01458574, and NCT01470612.
Association of continuity of care with readmission, mortality and suicide after hospital discharge among psychiatric patients
Authors: Choi Young , Nam Chung Mo , Lee Sang Gyu , Park Sohee , Ryu Hwang-Gun , Park Eun-Cheol 
Published: August 2020

Abstract

Objectives
The objective of this study was to identify the association between continuity of ambulatory psychiatric care after hospital discharge among psychiatric patients and readmission, mortality and suicide.

Design
Nationwide nested case-control study.

Settings
South Korea.

Participants
Psychiatric inpatients.

Interventions
Continuity of psychiatric outpatient care was measured from the time of hospital discharge until readmission or death occurred, using the continuity of care index.

Main Outcome Measures
Readmission, all-cause mortality and suicides within 1-year post-discharge.

Results
Of 18 702 psychiatric inpatients in the study, 8022 (42.9%) were readmitted, 355 (1.9%) died, and 108 (0.6%) died by suicide within 1 year after discharge. Compared with the psychiatric inpatients with a high continuity-of-care score, a significant increase in the readmission risk within 1 year after discharge was found in those with medium and low continuity of care scores. An increased risk of all-cause mortality within 1 year after hospital discharge was shown in the patients in the low continuity group, relative to those in the high-continuity group. The risk of suicide within 1 year after hospital discharge was higher in those with medium and low continuity of care than those with high continuity of care.

Conclusion
The results of this study provide empirical evidence of the importance of continuity of care when designing policies to improve the quality of mental health care, such as increasing patient awareness of the importance of continuity and implementation of policies to promote continuity.
Crisis standards of care in a pandemic: navigating the ethical, clinical, psychological and policy-making maelstrom
Authors: Hertelendy Attila J , Ciottone Gregory R , Mitchell Cheryl L , Gutberg Jennifer , Burkle Frederick M 
Published: August 2020

Abstract
The COVID-19 pandemic has caused clinicians at the frontlines to confront difficult decisions regarding resource allocation, treatment options and ultimately the life-saving measures that must be taken at the point of care. This article addresses the importance of enacting crisis standards of care (CSC) as a policy mechanism to facilitate the shift to population-based medicine. In times of emergencies and crises such as this pandemic, the enactment of CSC enables concrete decisions to be made by governments relating to supply chains, resource allocation and provision of care to maximize societal benefit. This shift from an individual to a population-based societal focus has profound consequences on how clinical decisions are made at the point of care. Failing to enact CSC may have psychological impacts for healthcare providers particularly related to moral distress, through an inability to fully enact individual beliefs (individually focused clinical decisions) which form their moral compass.
Histochemical assessment on the cellular interplay of vascular endothelial cells and septoclasts during endochondral ossification in mice
Authors: Tsuchiya Erika , Hasegawa Tomoka , Hongo Hiromi , Yamamoto Tomomaya , Abe Miki , Yoshida Taiji , Zhao Shen , Tsuboi Kanako , Udagawa Nobuyuki , Henrique Luiz de Freitas Paulo , Li Minqi , Kitagawa Yoshimasa , Amizuka Norio 
Published: August 2020

Abstract

This study was aimed to verify the cellular interplay between vascular endothelial cells and surrounding cells in the chondro-osseous junction of murine tibiae. Many CD31-positive endothelial cells accompanied with Dolichos Biflorus Agglutinin lectin-positive septoclasts invaded into the hypertrophic zone of the tibial epiphyseal cartilage. MMP9 immunoreactive cytoplasmic processes of vascular endothelial cells extended into the transverse partitions of cartilage columns. In contrast, septoclasts included several large lysosomes which indicate the incorporation of extracellular matrices despite no immunopositivity for F4/80—a hallmark of macrophage/monocyte lineage. In addition, septoclasts were observed in c-fos-/- mice but not in Rankl-/- mice. Unlike c-fos-/- mice, Rankl-/- mice showed markedly expanded hypertrophic zone and the irregular shape of the chondro-osseous junction. Immunoreactivity of platelet-derived growth factor-bb, which involved in angiogenic roles in the bone, was detected in not only osteoclasts but also septoclasts at the chondro-osseous junction. Therefore, septoclasts appear to assist the synchronous vascular invasion of endothelial cells at the chondro-osseous junction. Vascular endothelial cells adjacent to the chondro-osseous junction possess endomucin but not EphB4, whereas those slightly distant from the chondro-osseous junction were intensely positive for both endomucin and EphB4, while being accompanied with ephrinB2-positive osteoblasts. Taken together, it is likely that vascular endothelial cells adjacent to the chondro-osseous junction would interplay with septoclasts for synchronous invasion into the epiphyseal cartilage, while those slightly distant from the chondro-osseous junction would cooperate with osteoblastic activities presumably by mediating EphB4/ephrinB2.

Mini-abstract
Our original article demonstrated that vascular endothelial cells adjacent to the chondro-osseous junction would interplay with septoclasts for synchronous invasion into the epiphyseal cartilage, while those slightly distant from the chondro-osseous junction would cooperate with osteoblastic activities presumably by mediating EphB4/ephrinB2. (A figure that best represents your paper is Fig. 5c)
Validation of selection function, sample contamination and mass calibration in galaxy cluster samples
Authors: Grandis S , Klein M , Mohr J J , Bocquet S , Paulus M , Abbott T M C , Aguena M , Allam S , Annis J , Benson B A , Bertin E , Bhargava S , Brooks D , Burke D L , Carnero Rosell A , Carrasco Kind M , Carretero J , Capasso R , Costanzi M , da Costa L N , De Vicente J , Desai S , Dietrich J P , Doel P , Eifler T F , Evrard A E , Flaugher B , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Gerdes D W , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hartley W G , Hinton S R , Hollowood D L , Honscheid K , James D J , Jeltema T , Kuehn K , Kuropatkin N , Lima M , Maia M A G , Marshall J L , Melchior P , Menanteau F , Miquel R , Ogando R L C , Palmese A , Paz-Chinchón F , Plazas A A , Romer A K , Roodman A , Sanchez E , Saro A , Scarpine V , Schubnell M , Serrano S , Sheldon E , Smith M , Stark A A , Suchyta E , Swanson M E C , Tarle G , Thomas D , Tucker D L , Varga T N , Weller J , Wilkinson R 
Published: August 2020

ABSTRACT
We construct and validate the selection function of the MARD-Y3 galaxy cluster sample. This sample was selected through optical follow-up of the 2nd ROSAT faint source catalogue with Dark Energy Survey year 3 data. The selection function is modelled by combining an empirically constructed X-ray selection function with an incompleteness model for the optical follow-up. We validate the joint selection function by testing the consistency of the constraints on the X-ray flux–mass and richness–mass scaling relation parameters derived from different sources of mass information: (1) cross-calibration using South Pole Telescope Sunyaev-Zel'dovich (SPT-SZ) clusters, (2) calibration using number counts in X-ray, in optical and in both X-ray and optical while marginalizing over cosmological parameters, and (3) other published analyses. We find that the constraints on the scaling relation from the number counts and SPT-SZ cross-calibration agree, indicating that our modelling of the selection function is adequate. Furthermore, we apply a largely cosmology independent method to validate selection functions via the computation of the probability of finding each cluster in the SPT-SZ sample in the MARD-Y3 sample and vice versa. This test reveals no clear evidence for MARD-Y3 contamination, SPT-SZ incompleteness or outlier fraction. Finally, we discuss the prospects of the techniques presented here to limit systematic selection effects in future cluster cosmological studies.