bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between intrauterine foetal growth trajectories and blood pressure in young adults
Authors: Yadav Ashish , Beilin Lawrence J. , Huang Rae-Chi , Vlaskovsky Phil , Newnham John P. , White Scott W. , Mori Trevor A. 
Published: November 2021

Background:
Previous studies have reported an association between low birthweight and elevated blood pressure (BP) in adulthood, but few have examined the relationship between foetal growth and adult BP.

Method:
The study examined the association between intrauterine growth trajectories determined by serial ultrasound and BP of the adult offspring in the Raine Study. Foetal growth trajectories for abdominal circumference, femur length and head circumference z-scores were developed using group-based trajectory modelling from 1440 women with serial ultrasounds from 15-weeks pregnancy to birth. Seven abdominal circumference, five femur length and five head circumference trajectory groups were identified. Longitudinal linear mixed modelling examined the association between trajectory groups and offspring BP at 20 (n = 487), 22 (n = 419) and 27 (n = 436) years.

Results:
Higher SBP in adulthood significantly associated with two abdominal circumference trajectories, one with the most restricted foetal growth [3.52 mmHg, 95% confidence interval (95% CI) = 1.20–5.83] and the other with sustained low-growth (1.92 mmHg, 95% CI = 0.11–3.73) compared with an average growth trajectory, after adjusting for sex, age, alcohol consumption and BMI. Foetal head circumference trajectories with sustained low-growth or average-to-falling growth significantly associated with higher adult systolic (3.45 mmHg, 95% CI = 1.77–5.14 and 1.54 mmHg, 95% CI = 0.30–2.78, respectively) and diastolic (2.28 mmHg, 95% CI = 0.77–3.78 and 1.47 mmHg, 95% CI = 0.54–2.39, respectively) BP compared with average growth. Low femur length growth associated with higher adult DBP after adjusting for sex, but not after accounting for adult BMI.

Conclusion:
Our results show that restricted foetal head and abdominal circumference associated with higher adult SBP over two decades later, reinforcing the importance of the early intrauterine environment and its influence on adult BP.
Smooth muscle tone alters arterial stiffness: the importance of the extracellular matrix to vascular smooth muscle stiffness ratio
Authors: Pewowaruk Ryan J. , Gepner Adam D. 
Published: November 2021

Background:
Recent studies show that vascular smooth muscle (VSM) is more important to elastic artery mechanics than previously believed. It remains unclear whether increased VSM tone increases or decreases arterial stiffness.

Methods and results:
We developed a novel arterial mechanics model based on pressure–diameter relationships that incorporates the contributions of extracellular matrix (ECM) and VSM to arterial stiffness measures. This model is advantageous because it simple enough to use with limited clinical data but has biologically relevant parameters which include ECM stiffness, VSM stiffness, and VSM tone. The model was used to retrospectively analyze the effects of nitroglycerin-induced vasodilation in four clinical studies. Stiffness parameters were modeled for five arterial regions including both elastic and muscular arteries. The model describes complex experimental data with changing VSM tone and blood pressure. Our analysis found that when ECM is less stiff than VSM, increasing VSM tone increases arterial stiffness. The opposite is seen when ECM is stiffer than VSM, increasing VSM tone decreases stiffness. Our results also suggest that VSM tone is a compensatory mechanism for elevated ECM stiffness in hypertensive individuals.

Conclusion:
Based on retrospective analysis of four clinical studies, we propose a simple hypothesis for the role of VSM tone on arterial stiffness: increased VSM tone increases arterial stiffness when VSM is stiffer than ECM and decreases arterial stiffness when ECM is stiffer than VSM. This hypothesis and the methods used in this study could have important implications for understanding arterial physiology in both hypertension and cardiovascular disease and deserve further exploration.
COVID-19 Impact on Students in Physical Therapist and Physical Therapist Assistant Education Programs in New York and New Jersey: Key Issues and Recommended Responses
Authors: Hyland Nannette , Vore Mary Ellen , Chan Clarence , Katz Joanne , Rivers Lynn , Hewson Kyle 
Published: November 2021

Introduction.
In March 2020, after the COVID-19 pandemic surged in New York City, higher education had to either halt or immediately convert to fully online education. Physical therapy program directors in New York (NY) State and New Jersey (NJ) immediately recognized a need to understand the new challenges facing students.

Purpose.
The purpose of this paper was to identify the challenges that students in physical therapist (PT)/physical therapist assistant (PTA) programs in NY and NJ were experiencing and how institutions could respond to those challenges.

Subjects.
Students enrolled in a PT or PTA program in NY or NJ; N = 934 (861 PT and 73 PTA).

Methods.
An online survey was distributed to PT/PTA programs in NY/NJ. The survey consisted of open-ended and closed-ended questions related to academic, financial, and nonacademic issues, transition to online learning, and how institutions could respond to student challenges. Descriptive statistics and thematic analysis were used.

Results.
The most important challenges that students identified were quality/quantity of hands-on experiences, lack of contact with classmates, personal physical and mental health/wellness, and affording tuition and fees. Some differences were found across geographical regions and graduating cohorts. Physical therapist and PTA student cohorts had the same top concerns. Five major themes emerged from open-ended questions: communication; safe return to campus for psychomotor skills; additional academic resources; recognition of students' financial, mental, and physical health concerns; and, financial support.

Discussion and Conclusion.
Students in physical therapy education in NY and NJ faced similar challenges because of COVID-19 as observed by other universities worldwide. Physical therapy education can be stressful, and these additional challenges made this time extremely difficult. The findings of this survey can be used to develop a crisis management plan for university emergencies that require program modifications.
Intravitreal vascular endothelial growth factors hypertension, proteinuria, and renal injury: a concise review
Authors: Hanna Ramy M. , Ahdoot Rebecaa S. , Kim Matthew S. , Jhaveri Kenar D. , Kalantar-Zadeh Kamyar , Kurtz Ira B. 
Published: November 2021

Purpose of review
Nearly 20 years ago, vascular endothelial growth factor (VEGF)inhibitors (VEGFi) were adapted from systemic use from antiangiogenesis roles to intravitreal uses. Initially bevacizumab a murine immunoglobulin was injected ‘off label’ as a treatment for diabetic macular edema and age-related macular degeneration. Throughout the following decade aflibercept and finally ranibizumab were adapted and obtained Food and Drug Administration approval for intravitreal use. Initially systemic absorption was thought to be quite low after intravitreal injections and was quoted as being 200-fold lower than levels postulated to induce significant VEGF inhibition. Pharmacodynamic studies obtained in 2014 and again in 2017 revealed significant systemic absorption and detectable VEGF inhibition, this has since been confirmed in multiple subsequent studies.

Recent findings
A few case reports of renal dysfunction and glomerular disease related to VEGFi were initially identified. Mixed findings on effects on blood pressure were noted in studies. More recently, 32 cases of de-novo glomerular disease and/or proteinuria exacerbation were identified. New studies have corroborated increased blood pressure, proteinuria exacerbation in patients with pre-existing nephrotic syndrome, and systemic VEGF depletion. Further, the most common lesion of systemic VEGFi nephrotoxicity, thrombotic microangiopathy, has recently been reported by our group.

Summary
We will review the pharmacokinetic, translational, and epidemiological data that year upon year establish the finite-yet real risk of intravitreal VEGFi.
Mycophenolate-Induced Colitis in Autoimmune Polyendocrinopathy-Candidiasis-Ectodermal Dystrophy Patients
Authors: Schmitt Monica M. , Ferré Elise M. N. , Sampaio De Melo Michelly , Cooper Megan A. , Quezado Martha M. , Heller Theo , Lionakis Michail S. 
Published: November 2021

Introduction:
Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a prototypic monogenic autoimmune disorder caused by AIRE deficiency-mediated impaired central immune tolerance. Although multiple endocrine and nonendocrine tissues are affected in APECED, the colon is an uncommon target of autoimmune attack. Mycophenolate is a potent immunomodulatory medication that is used to treat autoimmune manifestations in patients with APECED and other autoimmune diseases.

Methods:
We reviewed the clinical, laboratory, genetic, histological, and treatment data of mycophenolate-induced colitis in our cohort of 104 APECED patients.

Results:
Among 10 mycophenolate-treated APECED patients, 4 (40%) developed reversible biopsy-proven mycophenolate-induced colitis characterized by an inflammatory bowel disease-like and/or graft-versus-host disease-like histological pattern.

Conclusion:
Mycophenolate-induced colitis appears to be a common complication in patients with APECED for which clinicians should maintain a high index of suspicion.
Sex differences in type 2 diabetes mellitus prevalence among persons with HIV
Authors: Birabaharan Morgan , Strunk Andrew , Kaelber David C. , Smith Davey M. , Martin Thomas C.S. 
Published: November 2021

Objective:
To examine whether type 2 diabetes mellitus (T2DM) is more common among women with HIV (WWH) than men with HIV (MWH).

Design:
A cross-sectional analysis of a demographically heterogenous population-based sample of more than 64 million patients in the United States.

Methods:
Using the Explorys (IBM) database, compare the prevalence of T2DM among men and women without HIV and influence of HIV on T2DM by sex controlling for confounding factors.

Results:
From 19 182 775 persons included in the study, 39 485 were with HIV. Rates of obesity was higher among WWH than MWH (58 vs. 35%). Prevalence of T2DM among WWH was 23% compared with 16% among MWH (P < 0.001). In sex-stratified adjusted analysis, WWH had 1.31 [95% confidence interval (CI), 1.24–1.38] times the odds of having T2DM than women without HIV. Women with HIV was associated with T2DM across all demographic subgroups. In contrast, no association between HIV and T2DM was observed among men (OR 1.01; 95% CI 0.98–1.05).

Conclusion:
These data suggest that HIV confers a sex-specific increase in odds of T2DM among women but not men.
Paenihalocynthiibacter styelae gen. nov., sp. nov., isolated from stalked sea squirt Styela clava
Authors: Kim Young-Ok , Noh Jae Koo , Kim Dong-Gyun , Park In-Suk , Park Sooyeon , Yoon Jung-Hoon 
Published: November 2021

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, MYP1-1T, was isolated from the intestine of a stalked sea squirt (Styela clava) of the South Sea in the Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP1-1T clustered with the type strains of

Halocynthiibacter

species and

Pseudohalocynthiibacter aestuariivivens

. Strain MYP1-1T exhibited 16S rRNA gene sequence similarity values of 97.0–97.6 % to the type strains of

Halocynthiibacter namhaensis

,

Halocynthiibacter arcticus

and

P. aestuariivivens

. The phylogenetic tree based on genomic sequences showed that strain MYP1-1T formed a distinct branch separating it from the type strains of two

Halocynthiibacter

species and

P. aestuariivivens

and other taxa. The DNA G+C content of strain MYP1-1T from its genomic sequence was 55.0 mol%. Strain MYP1-1T contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c as the major fatty acid. The major polar lipids of strain MYP1-1T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The differences in fatty acid and polar lipid profiles and other differential phenotypic properties made it reasonable to distinguish strain MYP1-1T from the genera

Halocynthiibacter

and

Pseudohalocynthiibacter

. On the basis of the polyphasic taxonomic investigations, we conclude that strain MYP1-1T constitutes a new genus and species within the class

Alphaproteobacteria

, for which the name Paenihalocynthiibacter styelae gen. nov., sp. nov. is proposed. The type strain is MYP1-1T (=KCTC 82143T=NBRC 114355T).
DOCKGROUND Membrane Protein-Protein Set
Authors: Kotthoff Ian , Kundrotas Petras J. , Vakser Ilya A. 
Published: November 2021

ABSTRACTMembrane proteins play essential role in cellular mechanisms. Despite that and the major progress in experimental structure determination, they are still significantly underrepresented in Protein Data Bank. Thus, computational approaches to protein structure determination, which are important in general, are especially valuable in the case of membrane proteins and protein-protein assemblies. Due to a number of reasons, not the least of which is much greater availability of structural data, the main focus of structure prediction techniques has been on soluble proteins. Structure prediction of protein-protein complexes is a well-developed field of study. However, because of the differences in physicochemical environment in the membranes and the spatial constraints of the membranes, the generic protein-protein docking approaches are not optimal for the membrane proteins. Thus, specialized computational methods for docking of the membrane proteins must be developed. Development and benchmarking of such methods requires high-quality datasets of membrane protein-protein complexes. In this study we present a new dataset of 456 non-redundant alpha helical binary complexes. The set is significantly larger and more representative than previously developed ones. In the future, this set will become the basis for the development of docking and scoring benchmarks, similar to the ones developed for soluble proteins in the DOCKGROUND resource http://dockground.compbio.ku.edu.
The Immune Signatures Data Resource: A compendium of systems vaccinology datasets
Authors: Diray-Arce Joann , Miller Helen E.R. , Henrich Evan , Gerritsen Bram , Mulè Matthew P. , Fourati Slim , Gygi Jeremy , Hagan Thomas , Tomalin Lewis , Rychkov Dmitry , Kazmin Dmitri , Chawla Daniel G. , Meng Hailong , Dunn Patrick , Campbell John ,   The Human Immunology Project Consortium (HIPC), Sarwal Minnie , Tsang John S. , Levy Ofer , Pulendran Bali , Sekaly Rafick , Floratos Aris , Gottardo Raphael , Kleinstein Steven H. , Suárez-Fariñas Mayte 
Published: November 2021

AbstractVaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern ‘omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines, including those targeting seasonal influenza, yellow fever, and hepatitis B. These data are made available to the broader scientific community through the ImmuneSpace data portal and analysis engine leveraging the NIH/NIAID ImmPort repository1,2. However, a barrier to progress in this area is that comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines and includes transcriptional profiles and antibody response measurements. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses.
Distribution And Population Of Chukar Partrigde (Alectoris chukar) In District Bajuar, KPK, Pakistan
Authors: Shahwar Durr e , Kawan Atufa , Mukhtar Hina , Ullah Inam 
Published: November 2021

AbstractThe Chukar Partridge (Alectoris chukar) is a wild bird of the Phasianidae family. In Pakistan, it occurs in a wide range of rugged, sloping and dry areas, rising to the interior of the Himalayas, the western Himalayas and plains, the higher piedmont valleys on the dry slopes of the Baluchistan provinces and Punjab and Sindh provinces. It is the “national bird” of Pakistan, however, little is known about its ecology and reproduction in the northern part of the country. This study investigated the existence, distribution and population of birds in the Bajaur region of Khyber Pakhtunkhwa (KP) Province from December 2019 to August 2020. Usually in the early morning (5 to 78 AM) and evening (4 to 9 pm). The areas occupied by Alectoris chukar mainly include Mulberry, Ficus banyan, Gum arabic, Arabian acacia, Barberes lycium, Dilberia sisso, Melia azedarach, Ailanthus, Alalthus altissima, Zanthoxylum alatum, Olea europaea, Olea europaea, Ingres, Celtis eriocarpa and Pinus wallichiana. Habitat destruction (overgrazing, mowing and landslides) caused by hunting, shooting, capture, explosives, excavation, and road construction is the main threat to existing wildlife (including Alectoris chukar).
Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332
Authors: Li Jian , Lin Cheng , Zhou Xuelan , Zhong Fanglin , Zeng Pei , Yang Yang , Zhang Yuting , Yu Bo , Fan Xiaona , McCormick Peter J. , Fu Rui , Fu Yang , Jiang Haihai , Zhang Jin 
Published: November 2021

AbstractThe high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.
A Descriptive Analysis of Chairs of Academic Neurology Departments in the United States
Authors: Patel Kajol K. , Patel Parth A. 
Published: November 2021

AbstractThere remains a limited understanding of the characteristics of academic leaders within neurology departments, despite similar research in other fields. This investigation characterized the demographics, academic background, and scholarly productivity of United States (U.S.) neurology department chairs. Here, 131 chairs at Accreditation Council for Graduate Medical Education (ACGME)-certified neurology programs were identified. Publicly accessible demographic and academic data available online were collected in March 2021. Among the 131 neurology chairs analyzed, 84.7% were male. On average, these faculty were 60.5 years old and were appointed at a mean age of 52.0 years. 74.8% of chairs graduated from an American medical school, although a notable proportion of department heads received medical training internationally. A substantial cohort also acquired an additional graduate degree, of which Doctor of Philosophy (PhD; 22.1%) and master’s degree (21.4%) were most common. 82.4% completed a post-residency fellowship, which were most frequently in vascular neurology (24.1%) and clinical neurophysiology (17.6%). The mean h-index, m-quotient, and lifetime NIH grant funding received were 39.2 ± 29.4, 1.2 ± 0.8, and $20,021,594 ± $31,861,816, respectively. No between-gender differences were observed. Overall, neurology chairs are predominantly male, most often completing fellowships in vascular neurology or clinical neurophysiology. Research productivity is a notable component of these chairs’ careers, although certain programs place less emphasis on these metrics. Finally, substantial effort remains to address disparities in female representation at this leadership position. These findings serve as a benchmark to evaluate demographic trends among neurology department chairs.
An interactome landscape of SARS-CoV-2 virus-human protein-protein interactions by protein sequence-based multi-label classifiers
Authors: Lee Ho-Joon 
Published: November 2021

ABSTRACTThe new coronavirus species, SARS-CoV-2, caused an unprecedented global pandemic of COVID-19 disease since late December 2019. A comprehensive characterization of protein-protein interactions (PPIs) between SARS-CoV-2 and human cells is a key to understanding the infection and preventing the disease. Here we present a novel approach to predict virus-host PPIs by multi-label machine learning classifiers of random forests and XGBoost using amino acid composition profiles of virus and human proteins. Our models harness a large-scale database of Viruses.STRING with >80,000 virus-host PPIs along with evidence scores for multi-level evidence prediction, which is distinct from predicting binary interactions in previous studies. Our multi-label classifiers are based on 5 evidence levels binned from evidence scores. Our best model of XGBoost achieves 74% AUC and 68% accuracy on average in 10-fold cross validation. The most important amino acids are cysteine and histidine. In addition, our model predicts experimental PPIs with higher accuracy than text mining-based PPIs by 4% despite their smaller data size by more than 6-fold. We then predict evidence levels of ∼2,000 SARS-CoV-2 virus-human PPIs from public experimental proteomics data. Interactions with SARS-CoV-2 Nsp7b show high evidence. We also predict evidence levels of all pairwise PPIs of ∼550,000 between the SARS-CoV-2 and human proteomes to provide a draft virus-host interactome landscape for SARS-CoV-2 infection in humans in a comprehensive and unbiased wayin silico. Most human proteins from 140 highest evidence predictions interact with SARS-CoV-2 Nsp7, Nsp1, and ORF14, with significant enrichment in the top 2 pathways of vascular smooth muscle contraction (CALD1, NPR2, CALML3) and Myc targets (CBX3, PES1). Our prediction also suggests that histone H2A components are targeted by multiple SARS-CoV-2 proteins.