bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative prediction of gene expression with chromatin accessibility and conformation data
Authors: Schmidt Florian , Kern Fabian , Schulz Marcel H. 
Published: February 2020

Abstract
Background
Enhancers play a fundamental role in orchestrating cell state and development. Although several methods have been developed to identify enhancers, linking them to their target genes is still an open problem. Several theories have been proposed on the functional mechanisms of enhancers, which triggered the development of various methods to infer promoter–enhancer interactions (PEIs). The advancement of high-throughput techniques describing the three-dimensional organization of the chromatin, paved the way to pinpoint long-range PEIs. Here we investigated whether including PEIs in computational models for the prediction of gene expression improves performance and interpretability.

Results
We have extended our $$\textsc{TEPIC}$$TEPIC framework to include DNA contacts deduced from chromatin conformation capture experiments and compared various methods to determine PEIs using predictive modelling of gene expression from chromatin accessibility data and predicted transcription factor (TF) motif data. We designed a novel machine learning approach that allows the prioritization of TFs binding to distal loop and promoter regions with respect to their importance for gene expression regulation. Our analysis revealed a set of core TFs that are part of enhancer–promoter loops involving YY1 in different cell lines.

Conclusion
We present a novel approach that can be used to prioritize TFs involved in distal and promoter-proximal regulatory events by integrating chromatin accessibility, conformation, and gene expression data. We show that the integration of chromatin conformation data can improve gene expression prediction and aids model interpretability.
The relationship between self-efficacy and instructional practice of in-service soft disciplines, hard disciplines and EFL teachers
Authors: Khanshan Shabnam Kurosh , Yousefi Mohammad Hosssein 
Published: February 2020

AbstractThe present study aimed at investigating the relationship between teachers’ self-efficacy perceptions and their instructional practices. The mediatory role of the teachers’ occupational characteristics such as their disciplines was also examined. For this purpose, a total of 70 teachers from the soft science, hard science and English language teaching (ELT) disciplines were compared. This study was situated within a mixed-methods design in which questionnaires as well as observation and semi-structured interviews were used to measure the efficacy-teaching practice. Results of Pearson correlation coefficients revealed that the self-efficacy of soft science and hard science teachers was significantly correlated with their teaching practice, with the ELT teachers’ efficacy-teaching relation not reaching a statistical significance. Results obtained from the observation and interviews further explained the teachers’ practices and the challenges that they faced in their classroom practices. Findings are discussed in light of both individual and societal perspective, offering important implications for the classrooms.
Safety of Influenza Vaccine in Patients With Cancer Receiving Pembrolizumab
Authors: Failing Jarrett J. , Ho Thanh P. , Yadav Siddhartha , Majithia Neil , Riaz Irbaz Bin , Shin John Y. , Schenk Erin L. , Xie Hao 
Published: February 2020

PURPOSE: There is a concern that influenza vaccination could increase the incidence of immune-related adverse events (irAEs) in patients with cancer receiving immune checkpoint inhibitors. The aim of our study was to determine the safety of influenza vaccination in this patient population. PATIENTS AND METHODS: We retrospectively identified patients who received at least 1 dose of pembrolizumab during any influenza season from September 2014 to August 2017 and reviewed medical records for irAEs. The primary endpoint was the incidence of irAEs. We used multivariable logistic regression and cumulative incidence curve with competing risks for comparison. RESULTS: Among 162 patients with cancer included in this study, 70 patients (43.2%) received at least 1 influenza vaccination. The vaccinated group was significantly older ( P = .002) and received more cycles of pembrolizumab ( P = .006). The incidence of any grade irAEs in the vaccinated group trended toward being lower (25.7% v 40.2%; P = .07) compared with the nonvaccinated group. Influenza vaccination was independently associated with fewer irAEs, with an odds ratio of 0.4 (95% CI, 0.2 to 0.9; P = .03) in multivariable analyses. The vaccinated group was less likely to have irAEs compared with the nonvaccinated group (24.7% v 34.4% at 12 months; P = .05), with death as a competing risk. The median irAE-free duration in the vaccinated group was longer than the nonvaccinated group (not reached v 28 months; P = .037). CONCLUSION: Influenza vaccination in patients with cancer receiving immune checkpoint inhibitor therapy was not associated with increased irAEs. This supports the safety of influenza vaccination in this patient population.
Gender Differences in Faculty Rank and Leadership Positions Among Hematologists and Oncologists in the United States
Authors: Riaz Irbaz Bin , Siddiqi Rabbia , Zahid Umar , Durani Urshila , Fatima Kaneez , Sipra Qurat-ul-Ain Riaz , Raina Ammad I. , Farooq Muhammad Zain , Chamberlain Alanna M. , Wang Zhen , Go Ronald S. , Marshall Ariela L. , Khosa Faisal 
Published: February 2020

PURPOSE: Gender disparity persists in academic medicine. Female faculty are underrepresented in leadership positions and have lower research output. We studied gender differences in faculty rank and departmental leadership and contributing factors among academic hematologists and oncologists in the United States. METHODS: For clinical faculty at 146 hematology or oncology fellowship programs listed in the Fellowship and Residency Electronic Interactive Database, we collected data on demographics, academic rank, and research output using the Doximity and Scopus databases. We compared unadjusted characteristics of men and women by using 2-sided t tests and χ2 tests where appropriate. To predict probability of full professorship or leadership position among men versus women, we performed multivariable logistic regression analysis adjusted for clinical experience in years, number of publications, h-index, clinical trial investigator status, National Institutes of Health funding, and workplace ranking (top 20 v not). RESULTS: Two thousand one hundred sixty academic hematologists and oncologists were included. Women composed 21.9% (n = 142) of full professors, 35.7% (n = 169) of associate professors, and 45.4% (n = 415) of assistant professors. Thirty percent (n = 70) of departmental leaders were women. Female faculty, compared with male faculty, had a lower mean h-index (12.1 v 20.9, respectively; P < .001) and fewer years of professional experience since fellowship (10 v 16 years, respectively; P < .001). After adjusting for duration of clinical experience, academic productivity, and workplace ranking, the odds of obtaining professorship (odds ratio [OR], 1.05; 95% CI, 0.71 to 1.57; P = .85) or divisional leadership (OR, 0.57; 95% CI, 0.20 to 1.58; P = .28) for female physicians were not different compared with male physicians. CONCLUSION: Gender disparity exists in senior ranks of academic hematology and oncology; however, gender is not a significant predictor in achieving professorship or department leadership position.
Quantification of T Cell Binding Polyclonal Rabbit Anti-thymocyte Globulin in Human Plasma with Liquid Chromatography Tandem-Mass Spectrometry
Authors: Amrani Mohsin El , Admiraal Rick , Willaert Lobke , Ebskamp-van Raaij Lysette J. C. , Lacna Amelia M. , Hack C. Erik , Huitema Alwin D. R. , Nierkens Stefan , van Maarseveen Erik M. 
Published: February 2020

AbstractThe addition of rabbit anti-human thymocyte globulin (ATG) to the conditioning regimen prior to allogeneic hematopoietic cell transplantation has significantly reduced the risk of graft-versus-host disease (GvHD) and graft failure. However, ATG has a small therapeutic window. Overexposure of ATG post-HCT hampers T cell immune reconstitution and has been associated with increased relapse rates and viral reactivations, whereas underexposure has been associated with an increased incidence of GvHD, both of which lead to increased mortality. Therapeutic drug monitoring of T cell binding ATG plasma levels provides a means to optimize dosing for patients at high risk for graft failure to ensure timely T cell immune reconstitution and subsequently increase survival chances. This manuscript describes the first liquid chromatography tandem-mass spectrometry (LC-MS/MS) method to quantify the pharmacologically active fraction of polyclonal ATG in plasma. This was achieved through immunoaffinity purification of active ATG from plasma with Jurkat T cells. After the binding and washing, samples were eluted, denatured, and trypsin-digested. Signature peptides originating from the IgG constant chain were measured with LC-MS/MS. Critical method parameters were optimized, and the method was successfully validated following European Medicines Agency (EMA) guidelines. The method covered the therapeutic range of ATG and was validated at a lower limit of quantification (LLOQ) of 1 AU/mL with an overall CV and bias of 11.8% and − 2.5%, respectively. In conclusion, we developed a LC-MS/MS-based method to quantify active polyclonal rabbit ATG in human plasma. We suggest that this novel assay can be used to monitor and optimize dosing of ATG in clinical practice.
Distribution of Body Hair in Young Australian Women and Associations With Serum Androgen Concentrations
Authors: Skiba Marina A , Bell Robin J , Islam Rakibul M , Karim Md Nazmul , Davis Susan R 
Published: February 2020

Abstract

Context
An important element of the diagnosis of polycystic ovary syndrome is hyperandrogenism.

Objective
To determine the distribution of modified Ferriman-Gallwey (mF-G) scores, as a measure of facial and body hair growth, and associations between the mF-G scores and serum androgen concentrations, including 11-oxygenated androgens.

Design
Cross-sectional study of non-health-care-seeking women, aged 18 to 39 years, recruited from the eastern states of Australia from November 2016 to July 2017.

Participants and measurements
Participants provided an mF-G self-assessment that corresponded to their appearance when not using treatment for excess hair. Androgens were measured in 710 women by liquid chromatography and tandem mass spectrometry.

Results
The distribution of the mF-G scores was right-skewed. The median (range) mF-G score of all participants (73.1% Caucasian) was 5 (0–36). The mF-G scores were negatively associated with age (rs = 0.124; P &lt; 0.0001) and positively associated with body mass index (BMI) (rs = 0.073; P &lt; 0.0001). Only androstenedione remained significantly associated with mF-G scores when controlling for age and BMI. Cluster analysis identified 2 groups with mF-G score of &lt; 10 and ≥ 10. Repeating the cluster analysis using the combined vector of mF-G score and androstenedione returned a similar cluster structure, and again separated the 2 groups at a mF-G score &lt; 10 versus ≥ 10.

Conclusions
A self-assessed mF-G score ≥ 10 is indicative of excess body hair. Androstenedione, as well as testosterone, should be measured when hyperandrogenism is being evaluated. The lack of association between mF-G scores and the 11-oxygenated androgens highlights the need for a better understanding of these steroids.
Lipid Emulsion Restoration of Myocardial Contractions After Bupivacaine-Induced Asystole In Vitro: A Benefit of Long- and Medium-Chain Triglyceride Over Long-Chain Triglyceride
Authors: Kim Hyun Joo , Kim Hyun Soo , Jung Ja Rang , Kim Ha Yan , Lynch Carl , Park Wyun Kon 
Published: February 2020

BACKGROUND:
The relative efficacies of a long- and medium-chain triglyceride (LCT/MCT) emulsion and an LCT emulsion for treatment of bupivacaine (BPV)-induced cardiac toxicity are poorly defined.

METHODS:
After inducing asystole by BPV, varied concentrations (1%–12%) of either LCT/MCT (Lipofundin; B. Braun, Melsungen, Germany) or LCT emulsion (Intralipid; Fresenius Kabi, Upsala, Sweden) were applied to observe the recovery of stimulated contractile responses and contractile forces in either a recirculating or washout condition for 60 minutes, using guinea pig papillary muscles. The recirculation condition was used to demonstrate BPV binding by lipid emulsion. The washout condition was used to determine whether the time-dependent recovery of contraction is due to their metabolic enhancement. Oxfenicine, an inhibitor of carnitine palmitoyltransferase I in heart mitochondria, was used to evaluate the effect of each lipid emulsion on mitochondrial metabolic inhibition by BPV. To examine the effect of the lipid emulsion alone on contractility, either lipid emulsion was examined. BPV concentrations in solution and myocardial tissues were measured.

RESULTS:
In the recirculating condition, LCT/MCT emulsions (2%–12%) restored regular stimulated contractile responses in all muscles. Eight percent and 12% LCT/MCT emulsions led to complete recovery of contractile forces after 30 minutes. Meanwhile, LCT emulsions (4%–12%) did not restore regular stimulated contractile responses in some muscles (6, 3, and 2 in 9 muscles each in 4%, 8%, and 12% emulsions, respectively). Partial recovery, approximately 60%, of contractile forces was observed with 8% and 12% LCT emulsions. In the washout experiments, after asystole, LCT/MCT emulsions (1%–12%) restored contractility to baseline levels earlier and greater than LCT emulsion. Partial recovery, approximately 60%, was observed with a high concentration of LCT emulsion (12%). In the oxfenicine-pretreated group, the contractile recovery was enhanced with LCT/MCT emulsion but showed no change with LCT emulsion. Contractile depression by 40% was observed with high concentrations of LCT emulsion alone (8% and 12%), whereas no depression or enhanced contraction was observed with LCT/MCT emulsion (1%–12%) alone. Both types of lipid emulsions (2%–12%) caused concentration-related reductions of tissue BPV levels; LCT/MCT emulsions reduced tissue BPV levels slightly greater than LCT emulsion in a recirculating condition.

CONCLUSIONS:
An LCT/MCT emulsion was more beneficial than an LCT emulsion in terms of local anesthetic-binding and metabolic enhancement for treating acute BPV toxicity. The metabolic benefit of MCT, combined with the local anesthetic-binding effect of LCT, in an LCT/MCT emulsion may improve contractile function better than an LCT emulsion in an isolated in vitro animal myocardium model.
Exposure to General Anesthesia for Cesarean Delivery and Odds of Severe Postpartum Depression Requiring Hospitalization
Authors: Guglielminotti Jean , Li Guohua 
Published: February 2020

BACKGROUND:
Previous research suggests that, compared with regional anesthesia, general anesthesia is associated with increased odds of postoperative depressive disorders. No study has specifically evaluated the possible protective effect of neuraxial anesthesia for cesarean delivery on maternal mental health compared with general anesthesia. This exploratory study was designed to test the hypothesis that general anesthesia for cesarean delivery is associated with increased odds of severe postpartum depression (PPD) requiring hospitalization compared with neuraxial anesthesia.

METHODS:
This retrospective cohort study included cesarean delivery cases performed in New York State hospitals between January 2006 and December 2013. Exclusion criteria were as follows: (1) having >1 cesarean delivery during the study period; (2) residing outside of New York State; (3) having a general anesthetic for other surgery or delivery in the previous year or in the year after the index case. The primary outcome was the occurrence of PPD, and the secondary outcomes were: (1) the composite of suicidal ideation or self-inflicted injury (ie, suicidality); (2) anxiety disorders; and (3) posttraumatic stress disorders (PTSD). Primary and secondary outcomes were identified during the delivery hospitalization and up to 1 year after delivery. Adjusted odds ratios (aORs) and 95% confidence interval (CI) of adverse psychiatric outcomes associated with general anesthesia were estimated using propensity score matching.

RESULTS:
Of the 428,204 cesarean delivery cases included, 34,356 had general anesthesia (8.0%). Severe PPD requiring hospitalization was recorded in 1158 women (2.7/1000; 95% CI, 2.5–2.9); of them, 60% were identified during readmission, with a median of 164 days after discharge. Relative to neuraxial anesthesia, general anesthesia in cesarean delivery was associated with a 54% increased odds of PPD (aOR, 1.54; 95% CI, 1.21–1.95) and a 91% increased odds of suicidal ideation or self-inflicted injury (aOR, 1.91; 95% CI, 1.12–3.25). There was insufficient evidence in these data that general anesthesia was associated with anxiety disorders (aOR, 1.37; 95% CI, 0.97–1.95) or PTSD (aOR, 1.50; 95% CI, 0.50–4.47).

CONCLUSIONS:
General anesthesia for cesarean delivery is associated with increased odds of severe PPD requiring hospitalization, suicidal ideation, and self-inflicted injury. If confirmed, these preliminary findings underscore the need to avoid the use of general anesthesia for cesarean delivery whenever possible, and to provide mental health screening, counseling, and other follow-up services to obstetric patients exposed to general anesthesia.
Canting Antiferromagnetic Spin-Order (TN = 102 K) in a Monomer Mott Insulator (ET)Ag4(CN)5 with a Diamond Spin-Lattice
Authors: Otsuka Akihiro , Shimizu Yasuhiro , Saito Gunzi , Maesato Mitsuhiko , Kiswandhi Andhika , Hiramatsu Takaaki , Yoshida Yukihiro , Yamochi Hideki , Tsuchiizu Masahisa , Nakamura Yuto , Kishida Hideo , Ito Hiroshi 
Published: February 2020

Abstract
The ET•+ molecules in a charge-transfer salt (ET)Ag4(CN)5 form a three-dimensional diamond spin-lattice with S = 1/2 (ET: bis(ethylenedithio)tetrathiafulvalene), where a geometrical spin-frustration is expected when an appropriate spin interaction is realized. A metallic nature has been proposed for this salt based on both band calculation and electron paramagnetic resonance measurements. We studied the crystal and band structures, optical spectra, resistivity, magnetic, and NMR measurements and found the salt to be a three-dimensional monomer Mott insulator with a resistivity of 1.8 × 102 Ω cm at room temperature (// c), though the calculated band structure showed a Dirac-like semimetallic dispersion. 1H NMR and magnetic susceptibility measurements reveal an antiferromagnetic spin ordering at TN = 102 K, above which characteristic temperature insensitive behaviors of T1−1 and spin susceptibility are observed. A weak ferromagnetism is detected below TN with a spin canting angle of ∼0.01°, possibly arising from a Dzyaloshinskii-Moriya interaction due to a lowering of the crystal symmetry. This is the first example of a weak ferromagnetic three-dimensional diamond spin-lattice among the organic charge-transfer solids.
Establishing a Global Standard for Wearable Devices in Sport and Fitness: Perspectives from the New England Chapter of the American College of Sports Medicine Members
Authors: Ash Garrett I. , Stults-Kolehmainen Matthew , Busa Michael A. , Gregory Robert , Garber Carol Ewing , Liu Jason , Gerstein Mark , Casajus José Antonio , Gonzalez-Aguero Alex , Constantinou Demitri , Geistlinger Michael , Guppy Fergus M. , Pigozzi Fabio , Pitsiladis Yannis P. 
Published: February 2020

Abstract
The recent explosion of wearable technology and the associated concerns prompted the International Federation of Sports Medicine (FIMS) to create a quality assurance standard for wearable devices, which provides commissioned testing of marketing claims and endorsement of commercial wearables that test favorably. An open forum as announced in the conference advertising was held at the Annual Meeting of the New England Regional Chapter of the American College of Sports Medicine (NEACSM) November 7 to 8, 2019, in Providence, Rhode Island, USA for attending NEACSM members to voice their input on the process. Herein, we report the proceedings. The round table participants perceived the quality assurance standard to be important, but identified some practical process challenges that included the broad scope and complexity of the device universe, the need for a multiphase testing pathway, and the associated fees for product evaluation. The participants also supported the evaluation of device data analysis, behavioral influences, and user experience in the overall evaluation. Looking forward, the FIMS quality assurance standard faces the challenge of balancing these broader perspectives with practical constraints of budget, facilities, time, and human resources.
Musculoskeletal Preparticipation Physical Evaluation—Does it Lead to Decreased Musculoskeletal Morbidity?
Authors: Andujo Victor D. , Fletcher Ian E. , McGrew Christopher 
Published: February 2020

Abstract
A preparticipation physical evaluation (PPE) is a requirement that many athletes must complete before participating in organized sports. Currently, the traditional musculoskeletal (MSK) portion of the PPE lacks robust evidence to support its ability to accurately predict those at greater risk for MSK injury. Functional movement testing has garnered attention for potential use in the PPE having shown some promise for greater sensitivity at identifying those at greater risk for MSK injury. Despite the widespread use of MSK PPE screening to identify athletes at greater risk for MSK injury, there is no significant evidence demonstrating that subsequent interventions result in decreased MSK injury.
Shifting Focus: A Clinician's Guide to Understanding Neuroplasticity for Anterior Cruciate Ligament Rehabilitation
Authors: Faltus John , Criss Cody Ryan , Grooms Dustin Robert 
Published: February 2020

AbstractNeuroplasticity after anterior cruciate ligament (ACL) injury has lingering effects throughout rehabilitation and can influence reinjury risk upon returning to sport if not addressed. Various neural compensatory strategies have been identified following ACL injury, which appear to not be rectified with typical therapy. Thus, further consideration is warranted, addressing the neurophysiologic and neurocognitive aspects of injury when developing a rehabilitation program. Integration of external focus of control strategies, neurocognition, motor planning, unanticipated sensory processing, and load management provide an efficient and effective method for improving motor learning and control throughout the rehabilitation process. Rehabilitation exercises that incorporate unique sports-specific challenges can target the visual processing and anticipatory reaction components of motor control to reduce motor errors that increase injury risk when returning to activity. The neurocognitive demands of returning to sport of efficient decision making and motor patterning amid a rapidly changing competitive environment require novel and clinically implemental strategies.