bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unexpected finding of a rare pathogenic germline BRCA1 variant in an intrahepatic cholangiocarcinoma using the Oncomine Focus DNA assay: clinical and diagnostic implications
Authors: De Bonis Maria , Mannavola Francesco , Salvatore Lisa , De Paolis Elisa , Nero Camilla , Giaco' Luciano , Tortora Giampaolo , Giuliante Felice , Urbani Andrea , Scambia Giovanni , Normanno Nicola , Minucci Angelo 
Published: May 2023

Abstract
Background
Cholangiocarcinoma (CCA) is a malignant tumor arising from the epithelial cells of the bile ducts and is the second most common liver cancer after hepatocellular carcinoma.
Recently, our Institution launched a Comprehensive Genomic Profiling (CGP) program (named FPG500 program), set up to provide a complete molecular characterization through the TruSight Oncology 500 High Throughput (TSO500HT) solution and samples that do not reach pre-set sample quantity and/or quality thresholds required for TSO500HT, are addressed to Oncomine Focus DNA Assay (OFA) and the Archer's FusionPlex Lung Panel (AFL).
Methods and results
Here we report the case of a patient with iCCA enrolled in the FPG500 program and screened by the orthogonal workflow (OFA/AFL). Although BRCA1 is not among the genes declared in the OFA panel, we unexpectedly detected a pathogenic variant in this gene (c.5278-2del, rs878853285).
Conclusions
This case highlights the diagnostic capabilities of CGP, now widely used in both clinical practice and academic setting. The incidental involvement of BRCA1 focuses attention on the role of BRCA genes in biliary tract cancers. Finally, as an orthogonal test confirmed the germline origin of BRCA1 c.5278-2delvariant, the germline implications of CGP need to be considered.
Body image dissatisfaction and its relation to body mass index among female medical students in Sudan: A cross-sectional study 2020-2021
Authors: Mohamed Balqees Abdeen Ahmed , Idrees Malaz Hassan Dafaallah 
Published: May 2023

Abstract
Background Body image is mainly determined by biological, social, psychological and cultural factors thus it is a multifaceted vigorous construct. Body image is an essential aspect of girls' self-definition and individual identity. Excessive concern about body image and body image misconceptions leads to dissatisfaction, disturbed eating patterns, affecting the nutritional status and also leading to depression and anxiety disorder.Methods This is a descriptive cross-sectional university-based study aiming to investigate body image dissatisfaction and its relation to BMI among female medical students at the University of Khartoum, faculty of medicine. The study was carried out between December 2020 and January 2021. Simple random sampling was applied and a two-sectioned questionnaire was used. The first part consisted of socio-demographic data and the second part contained questions to assess body image the data was. A total of 277 participants were enrolled in the study. Data was analyzed using SPSS version 20.Results We enrolled 277 female medical students the majority of participants (53%) were considered of normal weight according to BMI, 7% considered obese, and 18% underweight. Large number of participants thought that they are not in the ideal weight according to their height (62%). (21–17%) of participants always feel pressure from people or society to get to a certain weight. With respect to attitude towards weight, (29%) of participants always wear clothes that don't reveal their body shape, (35%) of them always tend to wear clothes that hide their excess weight.Conclusions The study concluded that participants who were overweight, obese or underweight have significant increase risk for poor body image perception with odd ratio of 39, 11, and 59 respectively. Thus early and proper interventions are necessary to circumvent the impact and future repercussion of body image distortion.
Mechanical Properties of Ply-Lam Cross-Laminated Timbers Fabricated with Lumber and Plywood
Authors: Yang Seungmin , Lee Hyunjae , Choi Gyuwoong , Kang Seoggoo 
Published: May 2023

Abstract
The mechanical properties of four ply-lam cross-laminated timbers (CLTs) containing a plywood layer were compared with those of glued laminated timber (GLT) and CLT. The bending, out-of-plane shear, compression strengths were highest in the GLT, which was followed by the ply-lam CLTs and CLT. The modulus of elasticity values for three studied ply-lam CLT samples were 1–2.5 GPa higher than GLT; however, the bending strength of all ply-lam CLTs was 7.3–18.8 MPa lower than GLT. The length of the plywood product is 2,440 mm, and longitudinal bonding is required to manufacture ply-lam CLTs of length > 3m. The prediction of bending capabilities by shear analogy was compared with the bending properties when joints were included. The performances of all the pilot-scale ply-lam CLT samples exceeded the predicted bending performance standards for MOE (10 GPa) and modulus of rupture (30 MPa) All samples exceeded 10 GPa and 30 MPa, based on projected and experimental data.
CFD Uncertainty Quantification using PCE-HDMR – Exemplary Application to a Buoyancy-Driven Mixing Process
Authors: Wenig Philipp J. , Kelm Stephan , Klein Markus 
Published: May 2023

Abstract
For the investigation of uncertainties in high dimensional spaces of computationally expensive engineering applications, reliable Uncertainty Quantification (UQ) methods are needed. These methods should provide accurate and efficient High-Dimensional Model Representations (HDMR) of stochastic results using a reasonable number of calculations. Therefore, the PCE-HDMR approach is utilized to qualify appropriate UQ methods for large-scale computations in the field of Computational Fluid Dynamics (CFD). This technique is a combination of Cut-HDMR, a hierarchical decomposition modeling approach, with Polynomial Chaos Expansion (PCE). To demonstrate its effectiveness, the PCE-HDMR methodology in conjunction with complementary modeling techniques is applied for the UQ analysis of a buoyancy-driven mixing process between two miscible fluids within the Differentially Heated Cavity (DHC) of aspect ratio 4. The results include a thorough probabilistic representation of time-dependent response quantities that comprehensively describe the mixing process. The stochastic models are derived from Large Eddy Simulations (LES) using PCE HDMR and the Sparse Grid Method (SGM), which serves as a reference for the results from PCE-HDMR. The results show that PCE-HDMR provides accurate statistics of the modeled time-dependent stochastic processes and shows good agreement with the SGM reference. Thus, PCE-HDMR indicates great potential for UQ of technical-scale computations due to its efficiency and flexibility in the construction of stochastic models.
Adaptive Growth of the Ductus Arteriosus and Aortic Isthmus in Various Ductus-Dependent Complex Congenital Heart Diseases
Authors: Hashim Liza , Vari Daniel , Bhat Abdul M. , Tsuda Takeshi 
Published: May 2023

Abstract
Background: The ductus arteriosus (DA) is critical in maintaining postnatal circulation in neonates with obstructed systemic circulation (OSC) and pulmonary circulation (OPC). We hypothesized that the size of the DA and aortic isthmus (AoI) undergoes adaptive growth in utero to counteract the hemodynamic challenges in these congenital heart diseases (CHD).
Methods: Postnatal echocardiograms of neonates diagnosed prenatally with ductal-dependent CHD who were started on prostaglandins within 24 hours of birth were reviewed. We assessed the cross-sectional area of the aortic valve opening, pulmonary valve opening, AoI, and DA by calculating (diameter)2/body surface area. Neonates were classified into OSC or OPC then subgrouped depending upon the patency of semilunar valves: OSC with and without aortic atresia (OSC-AA and OSC-nAA, respectively) and OPC with and without pulmonary atresia (OPC-PA and OPC-nPA, respectively).
Results: Ninety-four cases were studied. The DA in OSC was significantly larger than OPC, and the DA in OSC-AA was significantly larger than OSC-nAA. The size of the AoI was significantly larger in OPC than OSC and larger in OSC-AA than OSC-nAA. Within the OSC-nAA group, there was no significant difference in the size of the DA, AoI, or pulmonary valve opening between those with retrograde flow (RF) at the AoI and without (nRF) except the aortic valve opening was significantly larger in nRF. All groups had comparable cross-sectional areas of systemic output.
Conclusions: Our findings suggest that DA and AoI show compensatory growth to maintain critical blood flow to vital organs against primary anatomical abnormalities in ductus-dependent CHD.
Recently Emerging Trends in Big Data Analytic Methods for Modeling and Combating Climate Change Effects
Authors: Ikegwu Anayo , Nweke Henry , Alo Uzoma , Anikwe Chioma , Okonkwo Obikwelu 
Published: May 2023

Abstract

Big climate change data have become a pressing issue that organizations faced with methods to analyse data generated from various data types. However, storage, processing, and analysis of data generated from climate change activities are massive, which is challenging for the current algorithms to handle. Therefore, big data analytics methods are designed for significant data that is required to enhance seasonal change monitoring and understanding, ascertain the health risk of climate change, and improve the allocation, and utilisation of natural resources. This paper provides an outlook on big data analytic methods and describes how climate change and sustainability issues can be analysed through these methods. We extensively discuss big data analytic methods, strengths, and weaknesses. The purpose of analysing big climate change using these methods, the common datasets and implementation frameworks for climate change modeling using the big data analytics approach was also discussed. This big data analytics method is well timed to solve the inherent issues of data analysis and easy realization of sustainable development goals.
miRNA profiling of lumpy skin disease virus infected primary lamb testicle cells
Authors: Pandita Sakshi , Verma Assim , kamboj Himanshu , Kumar Ram , Chander Yogesh , Yadav Devender , Barua Sanjay , Kumar Naveen 
Published: May 2023

Abstract
In this study, miRNA profiling of cells infected with lumpy skin disease virus (LSDV) was conducted for the first time. As compared to the mock-infected cells, LSDV-infected primary lamb testicle (LT) cells revealed dysregulation of 64, 85, and 85 miRNAs at 12 hours post-infection (hpi), 48 hpi and 72 hpi, respectively. While some of these miRNAs were found to be specifically dysregulated at a particular time point following LSDV infection, others were commonly dysregulated across all three time points. The analysis of the differentially expressed miRNA-mRNA interaction networks, Gene ontology analysis of the predicted targets and KEGG analysis of the highly enriched pathways revealed several cellular factors/pathways involved in protein/ion/enzyme binding, cell differentiation, movement of subcellular component, calcium reabsorption, aldosterone synthesis and secretion and, melanogenesis. Besides understanding virus replication, virus-host interactions and disease pathogenesis, these miRNAs and their cellular targets may serve as biomarkers as well as novel targets for therapeutic intervention against LSDV.
Fever and syndrome of inappropriate antidiuretic hormone secretion in a patient with multiple system atrophy after treatment with duloxetine
Authors: Zhao Wen , Shi Jinyu , Zhang Haitao , Sarma Anand Karthik , Lin Jianwen , Zhang Yuhua , Xie Lushuang , Liu Yi 
Published: May 2023

Abstract
Background: Multiple system atrophy (MSA) is characterized by involvement of the extrapyramidal system, cerebellum and autonomic nervous system. Hypothalamus can also be affected with fever and hyponatremia, and is more vulnerable when combined with certain conditions, such as infection. Duloxetine was prescribed for chronic pain as a dual inhibitor of serotonin (5-HT) and norepinephrine reuptake, resulting in the rare side effects of fever and syndrome of inappropriate antidiuretic hormone secretion (SIADH).
Case presentation: This article reports a rare case of fever and SIADH in a patient with multiple system atrophy after treatment with duloxetine, and analyzes potential pathophysiological mechanism.
Conclusions: For MSA patients with suspected hypothalamic involvement, drugs such as duloxetine that could potentially exacerbate the hypothalamic burden through neurotransmitters involved neural circuits should be evaluated carefully before prescription.
Mortality Risk Factor Stratification in a Retrospective Cohort of Hospitalized Patients with Community Acquired Pneumonia
Authors: Sloan Meredith , Owings Anna , Glover Sarah , Liu Julia , Abraham George E. , Claggett Brian , Senitko Michal 
Published: May 2023

Abstract
Purpose A retrospective cohort was used to investigate the conditions that affected mortality in hospitalized community-acquired pneumonia (CAP) patients.Methods 1223 patients were identified based on diagnostic codes. T-tests, chi-squared tests, and logistic regression models were used to evaluate the data.Results There were 613 (50%) patients on proton pump inhibitors (PPIs) with a mortality rate of 26.3% vs 13.4% in non-PPI users (P < 0.001). Variables that increased the risk of death included: each decade of age, odds ratio (OR) = 1.15 (95% confidence interval 1.07 to 1.23), congestive heart failure OR = 2.06 (1.46 to 2.91), cancer OR = 1.66 (1.20 to 2.23), cardiovascular disease OR = 2.04 (1.19 to 3.49), and stroke OR = 1.53 (1.05 to 2.23). Statin use was associated with improved mortality, OR = 0.28 (0.13 to 0.59).Conclusion Statin use may improve and PPIs may worsen mortality in CAP.
Evaluation of patient safety competencies: Findings of the psychometric properties of the H-PEPSS in France and French-speaking Switzerland
Authors: Boloré Sylvain , Sovet Laurent , Guirimand Nicolas 
Published: May 2023

Abstract
Background Several initiatives have been implemented to develop, manage, and assess patient safety competencies, which are considered as a serious public health issue across the world. The Health Professional Education in Patient Safety Survey (H-PEPSS) is widely used as a psychometric scale for evaluating perceived patient safety competencies. The purpose of the study was to investigate the psychometric properties of the French version of H-PEPSS.Methods A total of 449 students enrolled in nursing and physiotherapy schools in France and French-speaking Switzerland completed a self-administered questionnaire.Results The 6-factor model demonstrated adequate goodness-of-fit statistics. The total score can be used as an overall measure of patient safety competence. In contrast to previous studies, the use of McDonald's omega was preferred to Cronbach's alpha to measure the composite reliability of the scale. Contrary to the original study, the “Understanding Human and Environmental Factors” Subscale showed inadequate reliability. This subscale has often been reported with the lowest reliability in previous studies. Scalar invariance between countries and partial scalar invariance between majors were observed.Conclusion Perceived patient safety competencies can be assessed and fairly compared across France and Switzerland as well as across nursing and physiotherapy students. Practical and research implications of the H-PEPSS are discussed.
INES: INteractive tool for construction and Extrapolation of partitioned Survival models
Authors: Gimeno-Ballester Vicente , Perez-Troncoso Daniel , Olry-Labry Antonio , Epstein David 
Published: May 2023

Abstract
Background
INES (INteractive model for Extrapolation of Survival and cost) provides an open-access tool powered by R that implements partitioned survival models (PSM). This article describes the properties of the tool, and the situations where INES may or may not be suitable.
Methods
INES is designed to be used by investigators or healthcare professionals who have a good grasp of the principles of economic evaluation and understand the strengths and weaknesses of partitioned survival models, but are not sufficiently familiar with a statistical package such as Excel or R to be able to construct and test a de-novo PSM themselves.
INES is delivered to the user via a batch file. Once downloaded to the user’s hard drive, it interacts with the user via a portable version of R with web interactivity built in shiny. INES requires absolutely no knowledge of R and the user does not need to have R or any of its dependences installed. Hence the user will deal with a standalone shiny app. Inputs (digitalized survival curves, unit costs, posology, hazard ratios, discount rate) can be uploaded from a template spreadsheet.
Results
An example of the inputs and outputs of INES are given that may serve as a tutorial.
Conclusion
INES offers a rapid, flexible, robust open access tool for calculating a PSM that can be used in many different contexts.
Formation and Stability of Nanoscrolls Composed of Graphene and Hexagonal Boron Nitride Nanoribbons: Insights from Molecular Dynamics Simulations
Authors: Lima Kleuton Antunes Lopes , Junior Luiz Antonio Ribeiro 
Published: May 2023

Abstract
Context Nanoscrolls are tube-like structures formed when a sheet or ribbon of material is rolled up into a cylinder, creating a hollow tube with a diameter on the nanoscale - much like papyrus. Carbon nanoscrolls have unique properties that make them useful in various applications, such as energy storage, catalysis, and drug delivery. In this study, we employed classical molecular dynamics simulations to investigate the formation and stability of nanoscrolls composed of graphene and hexagonal boron nitride (hBN) nanoribbons. Using a carbon nanotube (CNT) as a template to trigger their collapsing, we found that graphene/graphene, graphene/hBN, and hBN/hBN could form CNT-wrapped nanoscrolls at ultrafast speeds. We also confirmed that these nanoscrolls are thermally stable and discussed the other products formed from the interaction of these complexes and their temperature dependence. Gr/Gr and hBN/Gr nanoscrolls exhibit similar interlayer distances, while hBN/hBN nanoscrolls have wider interlayer distances than the other two types of composite nanoscrolls. These features suggest that hBN/hBN composite nanoscrolls could more efficiently capture small molecules due to their greater interlayer spacing.
Methods We conducted molecular dynamics (MD) simulations using the Forcite package in the Biovia Materials Studio software, which employs the Universal (UFF) and Dreiding (DFF) Force Fields. UFF models bonded interactions with a harmonic approximation for bond stretching, a three-term Fourier cosine expansion for angle bending, and Cosine-Fourier expansion terms for torsions and inversions. Non-bonded interactions are modeled using the Lennard-Jones potential for VDW interactions and atomic monopoles with a screened coulomb term for electrostatic interactions that vary with distance. DFF employs a rule-based approach to derive explicit parameters for its general force constants and geometry parameters based on simple hybridization rules instead of relying on specific atom combinations as UFF does. Unlike UFF, it does not generate parameters automatically. The force field is diagonal and includes harmonic valence terms and a cosine-Fourier expansion torsion term, while inversions follow the umbrella functional form defined by the Wilson out-of-plane definition. The Lennard-Jones potential describes van der Waals interactions, while atomic monopoles and a screened Coulombic term dependent on distance describe electrostatic interactions. Hydrogen bonding is described using an explicit Lennard-Jones 12-10 potential.
General, Open-Source Vertex Modeling in Biological Applications Using Tissue Forge
Authors: Sego T.J. , Comlekoglu Tien , Peirce Shayn M. , Desimone Douglas , Glazier James A. 
Published: May 2023

Abstract
Vertex models are a widespread approach for describing the biophysics and behaviors of multicellular systems, especially of epithelial tissues. Vertex models describe a wide variety of developmental scenarios and behaviors like cell rearrangement and tissue folding. Often, these models are implemented as single-use or closed-source software, which inhibits reproducibility and decreases accessibility for researchers with limited proficiency in software development and numerical methods. We developed a physics-based vertex model methodology in Tissue Forge, an open-source, particle-based modeling and simulation environment. Our methodology describes the properties and processes of vertex model objects on the basis of vertices, which allows integration of vertex modeling with the particle-based formalism of Tissue Forge, enabling an environment for developing mixed-method models of multicellular systems. Our methodology in Tissue Forge inherits all features provided by Tissue Forge, delivering open-source, extensible vertex modeling with interactive simulation, real-time simulation visualization and model sharing in the C, C + + and Python programming languages and a Jupyter Notebook. Demonstrations show a vertex model of cell sorting and a mixed-method model of cell migration combining vertex- and particle-based models. Our methodology provides accessible vertex modeling for a broad range of scientific disciplines, and we welcome community-developed contributions to our open-source software implementation.
Dual targeting ovarian cancer by Muc16 CAR-T cells secreting a bispecific T cell engager antibody for an intracellular tumor antigen WT1
Authors: Mun Sung Soo , Peraro Leila , Meyerberg Jeremy , Korontsvit Tatyana , Malviya Manish , Gardner Thomas , Kyi Chrisann , O’Cearbhaill Roisin E. , Liu Cheng , Dao Tao , Scheinberg David A. 
Published: May 2023

Abstract
Epithelial ovarian cancer is the most lethal of gynecological cancers. The therapeutic efficacy of chimeric antigen receptor (CAR) T cell directed against single antigens is limited by the heterogeneous target antigen expression in epithelial ovarian tumors. To overcome this limitation, we describe an engineered cell with both dual targeting and orthogonal cytotoxic modalities directed against two tumor antigens that are highly expressed on ovarian cancer cells: cell surface Muc16 and intracellular WT1. Muc16-specific CAR-T cells (4H11) were engineered to secrete a bispecific T cell engager (BiTE) constructed from a TCR mimic antibody (ESK1) reactive with the WT1-derived epitope RMFPNAPYL (RMF) presented by HLA-A2 molecules. The secreted ESK1 BiTE recruited and redirected other T cells to WT1 on the tumor cells. We show that ESK1 BiTE-secreting 4H11 CAR-T cells exhibited enhanced anticancer activity against cancer cells with low Muc16 expression, compared to 4H11 CAR-T cells alone, both in vitro and in mouse tumor models. Dual orthogonal cytotoxic modalities with different specificities targeting both surface and intracellular tumor-associated antigens present a promising strategy to overcome resistance to CAR-T cell therapy in epithelial ovarian cancer and other cancers.