bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupled weather-biosphere model (WRF-VPRM) response to extreme land cover scenarios over Ganga basin: a cross-component analysis
Authors: Huggannavar Vinayak , Indu J 
Published: July 2023

Abstract
Deforestation can have both biophysical and biochemical effects. In our study we evaluate the impacts of extreme idealized land cover scenarios over Ganga basin, India using an online coupled weather-biosphere model. We present an analysis of the carbon stored, based on introduced afforestation (AFF) and deforestation (DEF) in the Ganga basin of India. WRF-VPRM model simulations were carried out at horizontal resolution of 20 km using optimized downscaling configuration. For DEF case, we found two-fold increase in surface temperatures whereas, AFF scenario exhibited cooling effect. The average carbon sequestration capability for AFF was 0.3 g C m−2 day−1 more than control run (CTL). The CTL simulations exhibited carbon sequestration capability of −0.15 g C m−2 day−1 which for a year accounts for around 59.3 Mt C yr−1. AFF scenario showed relative increase in net sequestration compared to DEF scenario. Most importantly, the model simulations showed that the croplandscan increase net carbon sequestration rather than just deciduous forest type. Our study highlights the possible effects of land use management practices on atmospheric CO2 variability.
Turtling: a time-aware neural topic model on NIH grant data
Authors: Zhang Ruiyi , Duan Ziheng , Lee CheYu , Riffle Dylan , Min Martin Renqiang , Zhang Jing 
Published: July 2023

Abstract

Motivation
Recent initiatives for federal grant transparency allow direct knowledge extraction from large volumes of grant texts, serving as a powerful alternative to traditional surveys. However, its computational modeling is challenging as grants are usually multifaceted with constantly evolving topics.

Results
We propose Turtling, a time-aware neural topic model with three unique characteristics. First, Turtling employs pretrained biomedical word embedding to extract research topics. Second, it leverages a probabilistic time-series model to allow smooth and coherent topic evolution. Lastly, Turtling leverages additional topic diversity loss and funding institute classification loss to improve topic quality and facilitate funding institute prediction. We apply Turtling on publicly available NIH grant text and show that it significantly outperforms other methods on topic quality metrics. We also demonstrate that Turtling can provide insights into research topic evolution by detecting topic trends across decades. In summary, Turtling may be a valuable tool for grant text analysis.

Availability and implementation
Turtling is freely available as an open-source software at https://github.com/aicb-ZhangLabs/Turtling.
CD9 negatively regulates collective electrotaxis of the epidermal monolayer by controlling and coordinating the polarization of leader cells
Authors: Liu Xiaoqiang , Yang Jinrui , Kong Meng , Jiang Min , Liu Luojia , Zhang Jinghong , Chen Ying , Chen Xu , Zhang Ze , Wu Chao , Jiang Xupin , Liu Jie , Zhang Jiaping 
Published: July 2023

Abstract

Background
Endogenous electric fields (EFs) play an essential role in guiding the coordinated collective migration of epidermal cells to the wound centre during wound healing. Although polarization of leadercells is essential for collective migration, the signal mechanisms responsible for the EF-induced polarization of leader cells under electrotactic collective migration remain unclear. This study aims to determine how the leader cells are polarized and coordinated during EF-guided collective migration of epidermal cell sheets.

Methods
Collective migration of the human epidermal monolayer (human immortalized keratinocytes HaCaT) under EFs was observed via time-lapse microscopy. The involvement of tetraspanin-29 (CD9) in EF-induced fibrous actin (F-actin) polarization of leader cells as well as electrotactic migration of the epidermal monolayer was evaluated by genetic manipulation. Blocking, rescue and co-culture experiments were conducted to explore the downstream signalling of CD9.

Results
EFs guided the coordinated collective migration of the epithelial monolayer to the anode, with dynamic formation of pseudopodia in leader cells at the front edge of the monolayer along the direction of migration. F-actin polarization, as expected, played an essential role in pseudopod formation in leader cells under EFs. By confocal microscopy, we found that CD9 was colocalized with F-actin on the cell surface and was particularly downregulated in leader cells by EFs. Interestingly, genetic overexpression of CD9 abolished EF-induced F-actin polarization in leader cells as well as collective migration in the epidermal monolayer. Mechanistically, CD9 determined the polarization of F-actin in leader cells by downregulating a disintegrin and metalloprotease 17/heparin-binding epidermal growth factor-like growth factor/epidermal growth factor receptor (ADAM17/HB-EGF/EGFR) signalling. The abolished polarization of leader cells due to CD9 overexpression could be restored in a co-culture monolayer where normal cells and CD9-overexpressing cells were mixed; however, this restoration was eliminated again by the addition of the HB-EGF-neutralizing antibody.

Conclusion
CD9 functions as a key regulator in the EF-guided collective migration of the epidermal monolayer by controlling and coordinating the polarization of leader cells through ADAM17/HB-EGF/EGFR signalling.
Cultivating Trauma-Informed Educational Practices for Students with Refugee Backgrounds
Authors: Bailey Megan , Kim Wooksoo , Koury Samantha P , Green Susan A , Kim Isok 
Published: July 2023

Abstract
Schools provide spaces for academic knowledge while also addressing children’s social and emotional developmental needs. Because of the holistic development occurring within the education system, it is important to have an awareness of students’ experiences and challenges both inside and outside of the classroom. Students with refugee backgrounds represent diverse cultures, languages, and experiences but often share some common challenges and traumas. While trauma can impact students’ ability to learn and develop, classroom expectations, procedures, and rhythms can be adjusted to be trauma informed. Trauma-informed educational practices allow for a universal precautionary model for teachers and school staff to neutralize the environment for possible retraumatization, contributing to the creation of better educational experiences for students with refugee backgrounds as well as the rest of the student body. The aim of this article is to provide primary and secondary school staff—including teachers, administrators, and social workers—with practical information about trauma-informed educational practices to help them address the specific and unique needs of students with refugee backgrounds. Authors include examples of how school social workers, teachers, staff, and administrators can think about trauma-informed practices in the context of education and students with refugee backgrounds.
Myocardial infarction induced by caseous mitral annular calcification: a case report
Authors: Cosma Joseph , Wain-Hobson Julien , Gobbi Cecilia , Zuffi Andrea , Joret Cédric 
Published: July 2023

AbstractBackgroundCaseous mitral annular calcification (CMAC) is a rare variant of mitral annular calcification. Symptoms can be related to mitral valvular dysfunction, arterial embolization, and transient aortic outflow tract obstruction. CMAC usually affects the posterior fibrous mitral annulus and is commonly diagnosed in elderly patients with a history of hypertension, dyslipidaemia, and renal failure.Case summaryA 68-year-old patient was transferred to our department for late presenting acute myocardial infarction and acute heart failure. Coronary angiography revealed a significant extrinsic compression of the circumflex artery. Transthoracic echocardiography revealed an ovoid calcified mass of 3.6 cm × 2 cm originating from the posterior mitral annulus causing moderate mitral stenosis as well as akinesia of the inferolateral wall, reduced left ventricle ejection fraction (35%), and a low-flow low-gradient severe aortic stenosis. Cardiac computed tomography scan confirmed the presence of a large calcified mass, inserted to the posterior mitral annulus evocating caseous necrosis. The patient underwent a double valve replacement with implantation of both aortic and mitral bioprostheses. Histopathology of the excised mass revealed a chronic mitral valve fibrocalcification with aseptic necrosis, consistent with a caseous calcification of the posterior mitral annulus.DiscussionExtrinsic coronary artery compression is a rare disease entity. We report a rather peculiar cause of extrinsic artery compression: CMAC inducing significant mitral stenosis and compressing the circumflex artery leading to myocardial infarction. To the best of our knowledge, this is the first case of extrinsic artery compression caused by CMAC.
Sutureless repair for vena cava bleeding using an elastomeric sealant in a porcine model
Authors: Nakahara Yoshinori , Tateishi Retsu , Ono Shunya , Kanemura Takeyuki 
Published: July 2023

Abstract
To address the issue of bleeding from the vena cava, a common complication of cardiac and aortic surgeries, we developed a sutureless repair technique using Hydrofit, an elastomeric sealant. In a porcine model, we surgically incised the inferior vena cava and applied the elastomeric sealant with a pericardial patch, achieving complete haemostasis through manual compression. This simple and rapid technique demonstrates effective sutureless haemostasis for the vena cava.
Heterogeneity in the gene regulatory landscape of leiomyosarcoma
Authors: Belova Tatiana , Biondi Nicola , Hsieh Ping-Han , Lutsik Pavlo , Chudasama Priya , Kuijjer Marieke L 
Published: July 2023

AbstractCharacterizing inter-tumor heterogeneity is crucial for selecting suitable cancer therapy, as the presence of diverse molecular subgroups of patients can be associated with disease outcome or response to treatment. While cancer subtypes are often characterized by differences in gene expression, the mechanisms driving these differences are generally unknown. We set out to model the regulatory mechanisms driving sarcoma heterogeneity based on patient-specific, genome-wide gene regulatory networks. We developed a new computational framework, PORCUPINE, which combines knowledge on biological pathways with permutation-based network analysis to identify pathways that exhibit significant regulatory heterogeneity across a patient population. We applied PORCUPINE to patient-specific leiomyosarcoma networks modeled on data from The Cancer Genome Atlas and validated our results in an independent dataset from the German Cancer Research Center. PORCUPINE identified 37 heterogeneously regulated pathways, including pathways representing potential targets for treatment of subgroups of leiomyosarcoma patients, such as FGFR and CTLA4 inhibitory signaling. We validated the detected regulatory heterogeneity through analysis of networks and chromatin states in leiomyosarcoma cell lines. We showed that the heterogeneity identified with PORCUPINE is not associated with methylation profiles or clinical features, thereby suggesting an independent mechanism of patient heterogeneity driven by the complex landscape of gene regulatory interactions.
Engineering confined fluids to autonomously assemble hierarchical 3D structures
Authors: Shklyaev Oleg E , Laskar Abhrajit , Balazs Anna C 
Published: July 2023

Abstract
The inherent coupling of chemical and mechanical behavior in fluid-filled microchambers enables the fluid to autonomously perform work, which in turn can direct the self-organization of objects immersed in the solution. Using theory and simulations, we show that the combination of diffusioosmotic and buoyancy mechanisms produce independently controlled, respective fluid flows: one generated by confining surfaces and the other in the bulk of the solution. With both flows present, the fluid can autonomously join 2D, disconnected pieces to a chemically active, “sticky” base and then fold the resulting layer into regular 3D shapes (e.g. pyramids, tetrahedrons, and cubes). Here, the fluid itself performs the work of construction and thus, this process does not require extensive external machinery. If several sticky bases are localized on the bottom surface, the process can be parallelized, with the fluid simultaneously forming multiple structures of the same or different geometries. Hence, this approach can facilitate the relatively low-cost, mass production of 3D micron to millimeter-sized structures. Formed in an aqueous solution, the assembled structures could be compatible with biological environments, and thus, potentially useful in medical and biochemical applications.
Orchestration of Mesenchymal Stem/Stromal Cells and Inflammation During Wound Healing
Authors: Zhu Mengting , Cao Lijuan , Melino Sonia , Candi Eleonora , Wang Ying , Shao Changshun , Melino Gerry , Shi Yufang , Chen Xiaodong 
Published: July 2023

Abstract
Wound healing is a complex process and encompasses a number of overlapping phases, during which coordinated inflammatory responses following tissue injury play dominant roles in triggering evolutionarily highly conserved principals governing tissue repair and regeneration. Among all nonimmune cells involved in the process, mesenchymal stem/stromal cells (MSCs) are most intensely investigated and have been shown to play fundamental roles in orchestrating wound healing and regeneration through interaction with the ordered inflammatory processes. Despite recent progress and encouraging results, an informed view of the scope of this evolutionarily conserved biological process requires a clear understanding of the dynamic interplay between MSCs and the immune systems in the process of wound healing. In this review, we outline current insights into the ways in which MSCs sense and modulate inflammation undergoing the process of wound healing, highlighting the central role of neutrophils, macrophages, and T cells during the interaction. We also draw attention to the specific effects of MSC-based therapy on different pathological wound healing. Finally, we discuss how ongoing scientific advances in MSCs could be efficiently translated into clinical strategies, focusing on the current limitations and gaps that remain to be overcome for achieving preferred functional tissue regeneration.
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations
Authors: Pagnoni Saul , Oufensou Safa , Balmas Virgilio , Bulgari Daniela , Gobbi Emanuela , Forgia Marco , Migheli Quirico , Turina Massimo 
Published: July 2023

Abstract
Trichoderma genus includes soil-inhabiting fungi that provide important ecosystem services in their interaction with plants and other fungi, as well as biocontrol of fungal plant diseases. A collection of Trichoderma isolates from Sardinia has been previously characterized, but here we selected 113 isolates, representatives of the collection, and characterized their viral components. We carried out high-throughput sequencing of ribosome-depleted total RNA following a bioinformatics pipeline that detects virus-derived RNA-directed RNA polymerases (RdRps) and other conserved viral protein sequences. This pipeline detected seventeen viral RdRps with two of them corresponding to viruses already detected in other regions of the world and the remaining fifteen representing isolates of new putative virus species. Surprisingly, eight of them are from new negative-sense RNA viruses, a first in the genus Trichoderma. Among them is a cogu-like virus, closely related to plant-infecting viruses. Regarding the positive-sense viruses, we report the presence of an ‘ormycovirus’ belonging to a recently characterized group of bisegmented single-stranded RNA viruses with uncertain phylogenetic assignment. Finally, for the first time, we report a bisegmented member of Mononegavirales which infects fungi. The proteins encoded by the second genomic RNA of this virus were used to re-evaluate several viruses in the Penicillimonavirus and Plasmopamonavirus genera, here shown to be bisegmented and encoding a conserved polypeptide that has structural conservation with the nucleocapsid domain of rhabdoviruses.
The Association of Lumbar Plexus Lengthening With Neurological Deficit After Adult Spinal Deformity Surgery
Authors: Nakarai Hiroyuki , Lovecchio Francis C. , Kim David N. , Zhang Bo , Clohisy John C. , Merrill Robert K. , Pajak Anthony , Du Jerry , Kazarian Gregory S. , Kaidi Austin C. , Samuel Justin T. , Knopp Rachel L. , Kim Han Jo 
Published: July 2023

Study Design:
Retrospective cohort study.

Objective:
This study aimed to evaluate the association between nerve lengthening after adult deformity correction and motor deficits dervied from the upper lumbar plexus or femoral nerve.

Summary of Background Data:
Adult spinal deformity (ASD) surgery is associated with high rates of neurological deficits. Certain postoperative deficits may be related to lengthening of the upper lumbar plexus (ULP) and/or femoral nerve (FN) after correction of lumbar deformity.

Methods:
Patients with ASD who underwent posterior-only corrective surgery from the sacrum to L3 or above were included. The length of each lumbar nerve root was calculated geometrically using the distance from the foramen to the midpoint between the anterosuperior iliac crest and pubic symphysis on AP and lateral radiographs. The mean lengths of the L1 to 3 and L2 to 4 nerve roots were used to define the lengths of the ULP and FN, respectively. Preoperative to postoperative changes in nerve length were calculated. Neurological examination was performed at discharge. Proximal weakness (PW) was defined as the presence of weakness compared with baseline in either hip flexors or knee extensors. Multiple linear regression analysis was used for estimating the postoperative lengthening according to the magnitude of preoperative curvature and postoperative correction angles.

Results:
A total of 202 sides were analyzed in 101 patients, and PW was present on 15 (7.4%) sides in 10 patients. Excluding the 10 cases with three-column osteotomies, those with PW had a significantly higher rate of pure sagittal deformity (P<.001) and greater nerve lengthening than those without PW (ULP 24 vs. 15 mm, P=0.02; FN 18 vs. 11 mm, P=0.05). No patient had advanced imaging showing neural compression, and complete recovery of PW occurred in eight patients at one-year follow-up.

Conclusions:
After ASD surgery, lengthening of the ULP was associated with PW. In preoperative planning, surgeons must consider how the type of correction may influence the risk for nerve lengthening, which may contribute to postoperative neurological deficit.
Using Machine Learning (ML) Models to Predict Risk of Venous Thromboembolism (VTE) Following Spine Surgery
Authors: Katiyar Prerana , Chase Herbert , Lenke Lawrence G. , Weidenbaum Mark , Sardar Zeeshan M. 
Published: July 2023

Study Design:
A retrospective cohort study.

Objectives:
Venous thromboembolism (VTE) is a potentially high-risk complication for patients undergoing spine surgery. Although guidelines for assessing VTE risk in this population have been established, development of new techniques that target different aspects of the medical history may prove to be of further utility. The goal of this study was to develop a predictive machine learning (ML) model to identify nontraditional risk factors for predicting VTE in spine surgery patients.

Summary of Background Data:
A cohort of 63 patients was identified who had undergone spine surgery at a single center from 2015 to 2021. Thirty-one patients had a confirmed VTE, while 32 had no VTE. A total of 113 attributes were defined and collected via chart review. Attribute categories included demographics, medications, labs, past medical history, operative history, and VTE diagnosis.

Methods:
The Waikato Environment for Knowledge Analysis (WEKA) software was used in creating and evaluating the ML models. Six classifier models were tested with 10-fold cross-validation and statistically evaluated using t tests.

Results:
Comparing the predictive ML models to the control model (ZeroR), all predictive models were significantly better than the control model at predicting VTE risk, based on the 113 attributes (P<0.001). The Random Forest model had the highest accuracy of 88.89% with a positive predictive value of 93.75%. The Simple Logistic algorithm had an accuracy of 84.13% and defined risk attributes to include calcium and phosphate laboratory values, history of cardiac comorbidity, history of previous VTE, anesthesia time, selective serotonin reuptake inhibitor use, antibiotic use, and antihistamine use. The J48 model had an accuracy of 80.95% and it defined hemoglobin laboratory values, anesthesia time, beta-blocker use, dopamine agonist use, history of cancer, and Medicare use as potential VTE risk factors.

Conclusion:
Further development of these tools may provide high diagnostic value and may guide chemoprophylaxis treatment in this setting of high-risk patients.
Correlates of Sexual Lifestyles Among Older Adults Living With HIV in China: Findings From the Sexual Well-being (SWELL) Study
Authors: Wang Bingyi , Peng Xin , Fu Leiwen , Li Xinyi , Shi Tongxin , Liang Bowen , Tian Tian , Fitzpatrick Thomas , Lu Zhen , Zhang Weijie , Bian Junye , Xiao Xin , Wang Ying , Ao Yunlong , Ouyang Lin , Cai Yong , Yu Maohe , Wu Guohui , Li Linghua , Meng Xiaojun , Zou Huachun 
Published: July 2023

Abstract
Sexual lifestyles are closely related to overall human health and well-being. Few studies have focused on sexual lifestyles among older adults living with HIV (OALHIV), especially in low- and middle-income countries. This study is a part of the sexual well-being among older adults in China (SWELL) study, which is a multi-centre cross-sectional study focused on sexual health among older adults aged 50 years and older. Participants were 680 OALHIV (≥ 50 years old) from the SWELL study conducted from June 2020 to December 2022. Data were collected through one-on-one interviews. We used logistic regression to assess the correlates of sexual activity and sexual satisfaction. Among all participants, 37.1% were sexually active. Being older, male, in a steady relationship, and employed were associated with being sexually active. The prevalence of sexual satisfaction was 69.8% among sexually active OALHIV. Being homosexual and reporting a better general health status were associated with sexual satisfaction. OALHIV who have depressive symptoms were less likely to report sexual satisfaction. To support holistic healthy ageing among OALHIV, it is important for healthcare providers to be educated about the importance of enquiring about sexual activity, satisfaction and problems, and addressing concerns whilst conveying sex-positive attitudes during clinical reviews, as these are still critical aspects of their health and well-being.
PSMA Uptake in a Subdural Hematoma
Authors: Lawson Tristan R. , O’Brien Sophia R. , Pantel Austin R. 
Published: July 2023

Abstract
An 81-year-old man with known metastatic prostate cancer with recent biochemical progression underwent a PSMA PET/CT (18F-piflufolastat) for restaging. Review of the images demonstrated an acute or chronic left cerebral convexity subdural hematoma on CT with corresponding radiotracer activity throughout the collection on PET. Analysis of the patient’s prior imaging showed that this subdural hematoma had significantly increased in size when compared with a head CT obtained 2 months prior. The patient was referred to a nearby emergency department and underwent repeat imaging and subdural drain placement. Unfortunately, the patient died secondary to rapid reaccumulation of subdural blood products after intervention.