bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-term and long-term outcomes of patients with anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis
Authors: Ida Tomoaki , Furuta Shunsuke , Fujiwara Michio , Hiraguri Masaki , Hirose Koichi , Ikeda Kei , Iwamoto Taro , Kagami Shin-Ichiro , Kobayashi Yoshihisa , Kurasawa Kazuhiro , Nakagomi Daiki , Oya Yoshihiro , Sanayama Yoshie , Shimizu Toshimasa , Tamachi Tomohiro , Umibe Takeshi , Yasui Masahiro , Nakajima Hiroshi 
Published: January 2024

Abstract

Objectives
Anti-melanoma differentiation-associated gene 5 (MDA5) antibody-positive dermatomyositis (MDA5-DM) is a subtype of dermatomyositis characterized by frequent interstitial lung disease and reduced muscle involvement. This study aimed to determine the short-term and long-term outcomes of patients with MDA5-DM.

Methods
Information on baseline characteristics, treatments and short-term and long-term outcomes of patients with MDA5-DM including survival, relapse and the titre of anti-MDA5 antibody, was retrospectively collected. Descriptive statistics regarding clinical outcomes were calculated, and a comparison of clinical parameters between patients with and without relapse was performed. The short-term survival according to the use of Janus kinase inhibitors (JAKi) was also assessed.

Results
A total of 154 patients with MDA5-DM were included in the study. Forty patients (26.0%) died during the remission induction phase, with respiratory failure being the most common cause of mortality. Among the 114 patients who survived the remission induction phase, the 5-year cumulative survival and relapse-free survival rates were 96.8% and 77.4%, respectively, and 7.9% of patients achieved complete drug-free remission. Fifty-four patients achieved normalization of anti-MDA5 antibody titres and only two of them relapsed after normalization. In the severe patients, the 6-month survival rate became significantly higher after the emergence of the JAKi treatment compared with before its existence (P = 0.03).

Conclusion
Although relapse often occurs, the long-term survival of MDA5-DM patients who survived the remission induction phase is generally favourable. The status of the anti-MDA5 antibody is associated with relapse. JAKi may improve the survival of refractory patients with severe MDA5-DM.
Social support and fear-inhibition: an examination of underlying neural mechanisms
Authors: Hornstein E.A , Leschak C J , Parrish M H , Byrne-Haltom K E , Fanselow M S , Craske M G , Eisenberger N I 
Published: January 2024

Abstract
Recent work has demonstrated that reminders of those we are closest to have a unique combination of effects on fear learning and represent a new category of fear inhibitors, termed prepared fear suppressors. Notably, social-support-figure images have been shown to resist becoming associated with fear, suppress conditional-fear-responding and lead to long-term fear reduction. Due to the novelty of this category, understanding the underlying neural mechanisms that support these unique abilities of social-support-reminders has yet to be investigated. Here, we examined the neural correlates that enable social-support-reminders to resist becoming associated with fear during a retardation-of-acquisition test. We found that social-support-figure-images (vs stranger-images) were less readily associated with fear, replicating prior work, and that this effect was associated with decreased amygdala activity and increased ventromedial prefrontal cortex (VMPFC) activity for social-support-figure-images (vs stranger-images), suggesting that social-support-engagement of the VMPFC and consequent inhibition of the amygdala may contribute to unique their inhibitory effects. Connectivity analyses supported this interpretation, showing greater connectivity between the VMPFC and left amygdala for social-support-figure-images (vs stranger-images).
POSITION STATEMENT: Pass the RESTORE (Re-entry Support Through Opportunities for Resources and Essentials) Act
Authors: LaRowe Lisa R , Frederick Gwyneth , Figueroa Roger , Adams Elizabeth , Bean Melanie , Landry Matthew , Nock Nora 
Published: January 2024

Abstract
Under the Personal Responsibility and Work Opportunity Reconciliation Act (PRWORA), current federal policy mandates a lifetime ban for individuals with a past felony drug conviction from receiving Supplemental Nutrition Assistance Program (SNAP) and Temporary Assistance for Needy Families (TANF) benefits. Denying nutritional and financial assistance to individuals with a past felony conviction will widen existing structural health inequities, set back individuals’ successful re-entry into society, and contribute to recidivism and poorer health outcomes. Therefore, the Society of Behavioral Medicine supports the RESTORE ACT (Re-Entry Support Through Opportunities for Resources and Essentials Act), which would repeal the lifetime ban on receiving SNAP and TANF benefits for individuals convicted of a drug felony.
Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago
Authors: Lebrasseur Ophélie , More Kuldeep Dilip , Orlando Ludovic 
Published: January 2024

Abstract
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century and continue to be of major concern to the horse industry today. With a seroprevalence of 60–80 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health.
Complete Genome Resource of a Fungal Antagonistic Strain: Pseudomonas tohonis
Authors: Luo Wan-Zhen , Zhu He , Qi Hong-Yue , Song Jian , Zhang Dan-Dan , Dai Xiao-Feng , Mijiti Maihemuti , Chen Jie-Yin , Han Dongfei , Wang Dan 
Published: January 2024

KRS022 was isolated from the rhizosphere soil of a healthy plant in a pathogen-infested cotton field in Xinjiang, China. Previous studies have demonstrated that KRS022 possesses the ability to trigger plant immune responses, inhibit the growth of various pathogenic fungi, including Verticillium dahliae, and promote plant growth. The antagonistic properties of KRS022 primarily stem from its bioactive metabolites. In this study, the high-quality genome of KRS022 was obtained. The KRS022 genome consists of a chromosome of 6,369,026 bp with 67.09% GC content and possesses 5,830 open reading frames, of which 5,186 genes were annotated, and 119 were ncRNA genes. Additionally, 11 gene clusters of secondary metabolites biosynthesis were predicted, involved in polyketide synthase, arylpolyene, NAGGN, beta-lactone, ranthipeptide, PiPP-like, redox cofactor, and non-ribosomal peptide-synthetase clusters. It could be useful to explore the biocontrol potential of P. tohonis, implying promising application of KRS022 to biological control. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Chinese Medicine, Acupuncture and Science
Authors: Eckman Peter 
Published: January 2024

Abstract
Ever since the introduction of Western biomedicine into China, there has been friction between proponents of this new approach, and proponents of the traditional medical practices that had evolved over thousands of years in China. For the most part, this friction has been couched in the unexamined assumption that Western medicine is based on science, while Chinese medicine is not. This article will examine that assumption, which in this author’s opinion is unjustified and incorrect. Having practiced acupuncture for the past 50 years, after receiving my doctoral degrees in medicine and physiology, my thinking on this topic has also evolved over time. I will begin this article with some historical information that bears on the topic under discussion, followed by my personal ideas about how to resolve the conflicts that have arisen.
Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size
Authors: Duncan Maggie C. , Omondi F. Harrison , Kinloch Natalie N. , Lapointe Hope R. , Speckmaier Sarah , Moran-Garcia Nadia , Lawson Tanya , DeMarco Mari L. , Simons Janet , Holmes Daniel T. , Lowe Christopher F. , Bacani Nic , Sereda Paul , Barrios Rolando , Harris Marianne , Romney Marc G. , Montaner Julio S.G. , Brumme Chanson J. , Brockman Mark A. , Brumme Zabrina L. 
Published: January 2024

Objective:The immunogenic nature of coronavirus disease 2019 (COVID-19) mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign.Design:Longitudinal observational cohort and province-wide analysis.Methods:Sixty-two participants were sampled prevaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the intact proviral DNA assay; pVL were measured using the cobas 6800 (lower limit of quantification: 20 copies/ml). The province-wide analysis included all 290 401 pVL performed in British Columbia, Canada between 2012 and 2022.Results:Prevaccination, the median intact reservoir size was 77 [interquartile range (IQR): 20–204] HIV copies/million CD4+T-cells, compared to 74 (IQR: 27–212) and 65 (IQR: 22–174) postfirst and -second dose, respectively (all comparisonsP> 0.07). Prevaccination, 82% of participants had pVL <20 copies/ml (max: 110 copies/ml), compared to 79% postfirst dose (max: 183 copies/ml) and 85% postsecond dose (max: 79 copies/ml) (P > 0.4). There was no evidence that the magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike immune response influenced pVL nor changes in reservoir size (P > 0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART.Conclusion:We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.
Comparative Analysis of Antibacterial and Wound Healing Activities of Chitosan and Povidone-Iodine–Based Hydrogels
Authors: Jeon Sungmi , Kim Iljin , Jeong Yu Jin , Kim Young , Chung Justin J. , Kim Sang Wha 
Published: January 2024

Purpose
This study aimed to compare the antibacterial and wound healing efficacies of chitosan hydrogel with povidone-iodine (PI) hydrogel.

Methods
The in vitro antibacterial activities of chitosan and PI hydrogels against Staphylococcus aureus and Escherichia coli were evaluated. Nine 6- to 8-week-old male Sprague-Dawley rats were divided into plain, PI, and chitosan hydrogel groups. Each rat received two 10-mm full-thickness dorsal wounds using an excisional splinting model. Each wound was treated with 0.2 mL of gel thrice over the course of 3 postoperative weeks. Weekly observations were conducted, and at the end of the third postoperative week, the rats were killed for histopathological and quantitative polymerase chain reaction evaluations. Data analysis included both 2- and 1-way analyses of variance.

Results
Chitosan hydrogel exhibited comparable in vitro antibacterial activity and a significantly enhanced in vivo wound closure rate compared with PI hydrogel. Three weeks after the surgery, the chitosan hydrogel group demonstrated marked differences in wound repair (P < 0.01). Histologically, increased collagen deposition was observed with chitosan hydrogel treatment. Immunohistochemistry for CD68 revealed a lower number of macrophages in the wounds treated with chitosan hydrogel. Quantitative polymerase chain reaction analysis indicated a superior collagen 1 to 3 ratio and reduced expression of proinflammatory cytokine mRNAs (interleukin 1b, interleukin 6, tumor necrosis factor α, and interferon γ) in the chitosan hydrogel group.

Conclusion
Chitosan hydrogel demonstrates the potential to serve as an effective alternative to PI hydrogel, providing enhanced wound healing capabilities while maintaining comparable antimicrobial properties.
Is the h-Index Enough? A Comprehensive Bibliometric Analysis of 871 Academic Plastic Surgeons and Their Departments/Divisions
Authors: Persad-Paisley Elijah M. , Gopal Jay R. , Menville Jesse E. , Baranwal Navya , McIntire Damon R. T. , Zeyl Victoria G. , Kalliainen Loree K. 
Published: January 2024

BackgroundIn plastic surgery academia, research output is heavily used as a metric of accreditation, from assessing residency applicants to evaluating faculty for promotion. Thehindex, defined as an author'shpapers with at leasthcitations, is commonly used as a measure of academic success. However, the index itself disfavors junior researchers, favors publication quantity, and discounts highly cited works. Given the importance of bibliometrics within plastic surgery, there is a paramount need to adopt additional metrics to measure research productivity. The authors sought to validate the use of time-independent bibliometrics to complement thehindex in measuring citation impact.MethodsThe genders and academic titles of plastic surgeons affiliated with US plastic surgery programs were recorded. Author publications were retrieved from Scopus. Bibliometrics software was used to calculate the following metrics per surgeon:hindex,eindex, andgindex. Time-adjusted versions of these indices were used to correct for the number of years since first publication. Medians and interquartile ranges (IQRs) are reported. Departmental ranks were determined using the cumulative sum of time-corrected indices and compared with Doximity departmental research rankings.P< 0.05 was deemed significant.ResultsIndices were calculated for 871 academic plastic surgeons in 85 departments/divisions. Men had statistically greaterhindex (median, 13.0 [IQR, 7.0–21.0] vs 6.0 [IQR, 3.0–13];P< 0.001),eindex (18.3 [IQR, 10.0–28.7] vs 11.1 [IQR, 5.5–18.4];P< 0.001), andgindex (23.0 [IQR, 11.0–39.0] vs 11.0 [IQR, 5.0–22.0];P< 0.001) than women. Professors had the highest median time-uncorrected indices. After adjusting for the number of years since an author's first publication, there were no significant differences inmquotient (men: 0.66 [IQR, 0.40–0.98] vs women: 0.57 [IQR, 0.33–0.90];P= 0.05) andecindex (men: 0.93 [IQR, 0.62–1.3] vs women: 0.87 [IQR, 0.50–1.3];P= 0.08) between genders. Departmental chairs had significantly higher indices than other faculty after correcting for time. The calculated program rankings were low to moderately correlated with that of Doximity (correlation coefficient τ = 0.49 [95% confidence interval, 0.37–0.59;P< 0.001]).ConclusionsMen and women have statistically similar citation patterns after correcting for the time. Citation differences between academic levels are less pronounced when controlling for time, suggesting comparable research quality between academic roles.
Shear stress-induced restoration of pulmonary endothelial barrier function following ischaemia reperfusion injury requires VEGFR2 signalling
Authors: Walsh Don , Kostyunina Daria S. , Boylan John , McLoughlin Paul 
Published: January 2024

AbstractNormal physiological shear stress produced by blood flow is sensed by the vascular endothelium and required for the maintenance of both the normal structure and barrier function of the endothelium. Many common, critical illnesses are characterised by periods of abnormally reduced or absent shear stress e.g. haemorrhagic shock, myocardial infarction and pulmonary embolism and are complicated by oedema formation following restoration of normal perfusion (IRI).We tested the hypothesis that, in lungs injured by a period of ischaemia and reperfusion (IRI), reduced shear stress contributes to increased endothelial barrier permeability and oedema formation following the restoration of perfusion. Furthermore, we examined the role of VEGFR2 as a mechanosensor in the response of the pulmonary endothelium to altered shear stress in this condition.Following IRI, we perfused isolated ventilated mouse lungs with a low viscosity solution (LVS) or a higher, physiological viscosity solution (PVS) at constant flow to produce differing shear stresses on the endothelium of the intact pulmonary circulation. Lungs perfused with LVS developed pulmonary oedema due to increased endothelial permeability whereas those perfused with PVS were protected from oedema formation by reduced endothelial permeability. This effect of PVS required normal VEGFR2 tyrosine kinase activity but was unaffected by blocking VEGFA binding to the receptor.These data show for the first time that shear stress has an important role in restoring endothelial barrier function in the pulmonary circulation following injury and have important implications for the treatment of pulmonary oedema in critically ill patients following ischaemia reperfusion injury.
Elucidating an implicit-statistical learning brain network: Coordinate-based meta-analyses and functional connectivity profiles of artificial grammar learning in healthy adults
Authors: Ramage Amy E. , Cote Kaila , Thorson Jill C. , Lerner Katelyn , Reidel Michael C. , Laird Angela R. 
Published: January 2024

AbstractLanguage rehabilitation centers on modifying its use through experience-based neuroplasticity. Implicit statistical learning of language is essential to its acquisition and likely its rehabilitation following brain injury, but its corresponding brain networks remain elusive. Coordinate-based meta-analyses were conducted to identify common and distinct brain activity across 25 studies coded for meta-data and experimental contrasts (grammatical or non-grammatical). The resultant brain regions served as seeds for profiling functional connectivity in large task-independent and task-dependent data sets. Hierarchical clustering of these profiles grouped brain regions into three subnetworks associated with grammatical/non-grammatical processes. Functional decoding clarified the mental operations associated with those subnetworks. Results support a left-dominant language sub-network and two cognitive control networks as scaffolds for grammar rule identification, maintenance, and application in healthy adults. These data suggest that cognitive control is necessary to track regularities across stimuli and imperative for rule identification and application of grammar. Future empirical investigation of these brain networks in language learning in individuals with brain injury will clarify their prognostic role in language recovery.
Spatial interactions modulate tumor growth and immune infiltration
Authors: Marzban Sadegh , Srivastava Sonal , Kartika Sharon , Bravo Rafael , Safriel Rachel , Zarski Aidan , Anderson Alexander , Chung Christine H. , Amelio Antonio L. , West Jeffrey 
Published: January 2024

ABSTRACTDirect observation of immune cell trafficking patterns and tumor-immune interactions is unlikely in human tumors with currently available technology, but computational simulations based on clinical data can provide insight to test hypotheses. It is hypothesized that patterns of collagen formation evolve as a mechanism of immune escape, but the exact nature of the interaction between immune cells and collagen is poorly understood. Spatial data quantifying the degree of collagen fiber alignment in squamous cell carcinomas indicates that late stage disease is associated with highly aligned fibers. Here, we introduce a computational modeling framework (called Lenia) to discriminate between two hypotheses: immune cell migration that moves 1) parallel or 2) perpendicular to collagen fiber orientation. The modeling recapitulates immune-ECM interactions where collagen patterns provide immune protection, leading to an emergent inverse relationship between disease stage and immune coverage. We also illustrate the capabilities of Lenia to model the evolution of tumor progression and immune predation. Lenia provides a flexible framework for considering a spectrum of local (cell-scale) to global (tumor-scale) dynamics by defining a kernel cell-cell interaction function that governs tumor growth dynamics under immune predation with immune cell migration. Mathematical modeling provides important mechanistic insights into cell interactions. Short-range interaction kernels provide a mechanism for tumor cell survival under conditions with strong Allee effects, while asymmetric tumor-immune interaction kernels lead to poor immune response. Thus, the length scale of tumor-immune interactions drives tumor growth and infiltration.
How many specimens make a sufficient training set for automated 3D feature extraction?
Authors: Mulqueeney James M. , Searle-Barnes Alex , Brombacher Anieke , Sweeney Marisa , Goswami Anjali , Ezard Thomas H. G. 
Published: January 2024

AbstractDeep learning has emerged as a robust tool for automating feature extraction from 3D images, offering an efficient alternative to labour-intensive and potentially biased manual image segmentation methods. However, there has been limited exploration into the optimal training set sizes, including assessing whether artificial expansion by data augmentation can achieve consistent results in less time and how consistent these benefits are across different types of traits. In this study, we manually segmented 50 planktonic foraminifera specimens from the genus Menardella to determine the minimum number of training images required to produce accurate volumetric and shape data from internal and external structures. The results reveal unsurprisingly that deep learning models improve with a larger number of training images and that data augmentation can enhance network accuracy by up to 8.0%. Notably, predicting both volumetric and shape measurements for the internal structure poses a greater challenge compared to the external structure, due to low contrast between different materials and increased geometric complexity. These results provide novel insight into optimal training set sizes for precise image segmentation of diverse traits and highlight the potential of data augmentation for enhancing multivariate feature extraction from 3D images.Subject CategoryLife Sciences – Computer ScienceSubject Areascomputational biology, Artificial Intelligence