bluuebunny/crossref_metadata_2025_split huggingface dataset:
A probabilistic algorithm for optimising the steady-state diffusional flux into a partially absorbing body
Authors: Nicolaou Kyriacos , Mulder Bela M. 
Published: December 2023

AbstractCells in an aqueous environment absorb diffusing nutrient molecules through nanoscale protein channels in their outer membranes. Assuming that there are constraints on the number of such channels a cell can produce, we ask the question: given a nondepleting source of nutrients, what is the optimal distribution of these channels over the cell surface? We coarse-grain this problem, phrasing it as a diffusion problem with position-dependent Robin boundary conditions on the surface. The aim is to maximize the steady-state total flux through the partially absorbing surface under an integral constraint on the local reactivities. We develop an algorithm to tackle this problem that uses the stored and processed results of a particle-based simulation with reflective boundary conditions to a posteriori estimate absorption flux at essentially negligible additional computational cost. We validate the algorithm against a few cases for which analytical or semi-analytical results are available. We apply it to two examples: a spherical cell in the presence of a point source and a spheroidal cell with an isotropic source at infinity. In the former case, there is a significant gain relative to the homogeneous case, while in the latter case the gain is only $$1\%$$

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Inhibition of Drp1 orchestrates the responsiveness of breast cancer cells to paclitaxel but insignificantly relieves paclitaxel-related ovarian damage in mice
Authors: Alalawy Adel I. , Sakran Mohamed , Alzuaibr Fahad M. , Alotaibi Maeidh A. , El-Hefnawy Mohamed E. , Hazazi Abdulelah Y. , El-Gendy Saad M. , Aidy Esraa A. , Effat Heba , Ismail Doha F. , Hessien Mohamed 
Published: December 2023

AbstractChemoresistance and chemotherapy-related ovarian damage are well-reported in breast cancer (BC) young patients. Herein, the inhibition of the mitochondrial fission was invested to explore its chemosensitizing role in Paclitaxel (PTX)-resistant cells, and its ability to restore the ovarian integrity in mice receiving PTX or cisplatin chemotherapy. To establish these aims, PTX-resistance was generated in BC cells, which were treated with PTX in combination with Drp1 deficiency, via mdivi-1, or Drp1-specific siRNA transfection. Furthermore, the alterations in the ovarian structure and the endocrine-related hormones were explored in mice receiving repetitive doses of PTX or cisplatin. We found that combining PTX with mdivi-1 improved cell responsiveness to PTX, induced apoptosis- and autophagy-mediated cell death, and relieved cellular oxidative stress. Additionally, the expression of PCNA1 and cyclin B1 genes were downregulated, meanwhile, p53, p21, and mitochondrial fusion proteins (Mfu1&Mfu2) were increased. The in vivo investigations in mice demonstrated that PTX induced gonadotoxic damage similar to cisplatin, whereas dual treatment of mice with PTX+ mdivi-1 failed to restore their normal follicular count and the circulating levels of E2 and AMH hormones. These results suggested that combining Drp1 inhibition with PTX resensitized breast cancer cells to PTX but failed to offer enough protection against chemotherapy-related gonadotoxicity.
Oxidation differences on Si- versus C-terminated surfaces of SiC during planarization in the fabrication of high-power, high-frequency semiconductor device
Authors: Lee Ganggyu , Lee Yeram , Kim Sungmin , Kim Donghwan , Park Hongjun , Woo Myungju , Song Taeseup , Paik Ungyu 
Published: December 2023

AbstractSilicon carbide (SiC) wafers have attracted attention as a material for advanced power semiconductor device applications due to their high bandgap and stability at high temperatures and voltages. However, the inherent chemical and mechanical stability of SiC poses significant challenges in the chemical mechanical planarization (CMP) process, an essential step in reducing defects and improving surface flatness. SiC exhibits different mechanical and chemical properties depending on SiC terminal faces, affecting SiC oxidation behavior during the CMP process. Here, we investigate the process of oxide layer formation during the CMP process and how it relates to the SiC terminal faces. The results show that under the same conditions, the C-terminated face (C-face) exhibits higher oxidation reaction kinetics than the Si-terminated face (Si-face), forming an oxide layer of finer particles. Due to the different oxidation kinetic tendencies, the oxide layer formed on the C-face has a higher friction coefficient and more defects than the oxide layer formed on the Si-face. This results in a higher removal rate during CMP for the C-face than the Si-face. Furthermore, by controlling the physicochemical properties of the oxide film, high removal rates can be achieved by friction with the pad alone, without the need for nanoparticle abrasives.
Identification and verification of three autophagy-related genes as potential biomarkers for the diagnosis of psoriasis
Authors: Zou Ailing , Chen Yongjun , Liu Tangsheng , Yang Ting , Zhou Bei 
Published: December 2023

AbstractPsoriasis vulgaris is the most common form of the four clinical types. However, early diagnosis of psoriasis vulgaris is difficult due to the lack of effective biomarkers. The aim of this study was to screen potential biomarkers for the diagnosis of psoriasis. In our study, we downloaded the original data from GSE30999 and GSE41664, and the autophagy-related genes list from human autophagy database to identify differentially expressed autophagy-related genes (DERAGs) by R software. Then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for DERAGs. DERAGs were validated by the other four databases (GSE13355, GSE14905, GSE6710, and GSE55201) to screen biomarkers with high diagnostic value for the early diagnosis of psoriasis vulgaris. Finally, DERAGs were verified in our clinical blood samples by ELISA. A total of 12 DERAGs were identified between 123 paired non-lesional and lesional skin samples from patients with psoriasis vulgaris. GO and KEGG enrichment analysis indicated the TORC2 complex was more enriched and the NOD-like receptor signaling pathway was mostly enriched. Three autophagy-related genes (BIRC5, NAMPT and BCL2) were identified through bioinformatics analysis and verified by ELISA in clinical blood samples. And these genes showed high diagnostic value for the early diagnosis of psoriasis vulgaris. We identified three autophagy-related genes (BIRC5, NAMPT and BCL2) with high diagnostic value for the early diagnosis of psoriasis vulgaris through bioinformatics analysis and clinical samples. Therefore, we proposed that BIRC5, NAMPT and BCL2 may be as potential biomarkers for the early diagnosis of psoriasis vulgaris. In addition, BIRC5, NAMPT and BCL2 may affect the development of psoriasis by regulating autophagy.
Application of response surface methodology for optimization of the test condition of oxygen evolution reaction over La0.8Ba0.2CoO3 perovskite-active carbon composite
Authors: Mahmoudi Elham , Asghari Elnaz , Delibaş Nagihan , Niaei Aligholi 
Published: December 2023

AbstractThe Experimental Design was applied to optimize the electrocatalytic activity of La0.8Ba0.2CoO3 perovskite oxide/Active Carbon composite material in the alkaline solution for the Oxygen Evolution Reaction. After the preparation of La0.8Ba0.2CoO3, and structural characterizations, the experimental design was utilized to determine the optimal amount of the composite material and testing conditions. The overpotential was defined as the response variable, and the mass ratio of perovskite/active carbon, Potassium hydroxide (KOH) concentration, and Poly(vinylidene fluoride) (PVDF) amount were considered effective parameters. The significance of model terms is demonstrated by P-values less than 0.0500. The proposed prediction model determined the optimal amounts of 0.665 mg of PVDF, a KOH concentration of 0.609 M, and A perovskite/Active Carbon mass ratio of 2.81 with 308.22 mV overpotential (2.27% greater than the actual overpotential). The stability test of the optimized electrode material over 24 h suggests that it could be a good candidate electrocatalyst for OER with reusability potential.
Development and evaluation of artificial organ models for ERCP training in patients with surgically altered anatomies
Authors: Koch Kai , Duckworth-Mothes Benedikt , Schweizer Ulrich , Grund Karl-Ernst , Moreels Tom G. , Königsrainer Alfred , Wichmann Dörte 
Published: December 2023

AbstractEndoscopy training models (ETM) using artificial organs are practical, hygienic and comfortable for trainees. However, few models exist for training endoscopic retrograde cholangiopancreatography (ERCP) in patients with surgically altered anatomy. This training is necessary as the number of bariatric surgeries performed worldwide increases. ETM with human-like anatomy were developed to represent the postoperative anatomy after Billroth II (BII) reconstruction for a standard duodenoscope and the situs of a long-limbed Roux-en-Y (RY) for device-assisted enteroscopy (DAE). In three independent workshops, the models were evaluated by international ERCP experts. In RY model, a simulation for small bowel behavior in endoscopy was created. Thirty-three experts rated the ETM in ERCP expert courses. The BII model was evaluated as suitable for training (school grades 1.36), with a haptic and visual impression rating of 1.73. The RY model was rated 1.50 for training suitability and 2.06 for overall impression. Animal tissue-free ETMs for ERCP in surgically altered anatomy were successfully created. Evaluation by experienced endoscopists indicated that the models are suitable for hands-on ERCP training, including device-assisted endoscopy. It is expected that patient care will improve with appropriate training in advanced procedures.
Comparative effects of a calcium chelator (BAPTA-AM) and melatonin on cryopreservation-induced oxidative stress and damage in ovarian tissue
Authors: Najafi Atefeh , Asadi Ebrahim , Benson James D. 
Published: December 2023

AbstractOncology treatments cause infertility, and ovarian tissue cryopreservation and transplantation (OTCT) is the only option for fertility preservation in prepubertal girls with cancer. However, OTCT is associated with massive follicle loss. Here, we aimed to determine the effect of supplementation of slow freezing and vitrification media with BAPTA-AM and melatonin alone and in combination on ovarian tissue viability, reactive oxygen species (ROS) levels, total antioxidant capacity (TAC), and follicular morphology and viability. Our results indicated that BAPTA-AM and melatonin can significantly improve ovarian tissue viability and the TAC/ROS ratio and reduce ROS generation in frozen-thawed ovarian tissues in slow freezing and vitrification procedures. BAPTA-AM was also found to be less effective on TAC compared to melatonin in vitrified ovarian tissue. While supplementation of slow freezing and vitrification media with BAPTA-AM and/or melatonin could increase the percentage of morphologically intact follicles in cryopreserved ovarian tissues, the differences were not significant. In conclusion, supplementation of cryopreservation media with BAPTA-AM or melatonin improved the outcome of ovarian tissue cryopreservation in both vitrification and slow freezing methods. Our data provide some insight into the importance of modulating redox balance and intracellular Ca2+ levels during ovarian tissue cryopreservation to optimize the current cryopreservation methods.
On a potential morpho-mechanical link between the gluteus maximus muscle and pelvic floor tissues
Authors: Siess Maximilian , Steinke Hanno , Zwirner Johann , Hammer Niels 
Published: December 2023

AbstractStress urinary incontinence presents a condition not only found in female elderlies, but also in young athletes participating in high-impact sports such as volleyball or trampolining. Repeated jumps appear to be a predisposing factor. Yet the pathophysiology remains incompletely elucidated to date; especially with regard to the influence of the surrounding buttock tissues including gluteus maximus. The present study assessed the morpho-mechanical link between gluteus maximus and the pelvic floor female bodies. 25 pelves obtained from Thiel embalmed females were studied in a supine position. Strands of tissues connecting gluteus maximus with the pelvic floor obtained from 20 sides were assessed mechanically. Plastinates were evaluated to verify the dissection findings. In total, 49 hemipelves were included for data acquisition. The fascia of gluteus maximus yielded connections to the subcutaneous tissues, the fascia of the external anal sphincter and that of obturator internus and to the fascia of the urogenital diaphragm. The connection between gluteus maximus and the urogenital diaphragm withstood an average force of 23.6 ± 17.3 N. Cramér φ analyses demonstrated that the connections of the fasciae connecting gluteus maximus with its surroundings were consistent in the horizontal and sagittal planes, respectively. In conclusion, gluteus maximus is morphologically densely linked to the pelvic floor via strands of connective tissues investing the adjacent muscles. Though gluteus maximus has also been reported to facilitate urinary continence, the here presented morpho-mechanical link suggests that it may also have the potential to contribute to urinary stress incontinence. Future research combining clinical imaging with in-situ testing may help substantiate the potential influence from a clinical perspective.
Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella
Authors: Srivastava Subodh K. , Parker Carolyn , O’Brien Celia N. , Tucker Matthew S. , Thompson Peter C. , Rosenthal Benjamin M. , Dubey Jitender P. , Khan Asis , Jenkins Mark C. 
Published: December 2023

AbstractEimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, “ERR296879”) share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development.
A complete morphological characterization of all life stages of the phorid fly Megaselia scalaris
Authors: Pallavi Jayakumar , Snehal Harshita , Kolipakala Rakshita Sukruth , Salazar Daniela , Hanbar Mrunal , Chiramel Larina Bejoy , Alok Jha Khushi , Venkatesh Sai Bhumica Lakshmi , Shetty Tanishka Dayanand , Madhusudan Navya , Mohan Amrutha , John Amulia , D’souza Naomi Deep , Sheet Priyanka , Nagarajan Deepesh 
Published: December 2023

AbstractMegaselia scalaris, commonly known as the scuttle fly, is a cosmopolitan species in the family Phoridae. It is an easily cultured fly species that is an emerging model organism in the fields of genetics and developmental biology. Its affinity for carrion and its predictable life cycle makes it useful in the field of forensic science for estimating the post-mortem interval (PMI) of human remains. Cases of human myasis caused by M. scalaris have also been reported in the medical literature. Despite its ubiquitous prevalence and its relevance across multiple fields, its morphology has not been adequately characterized. Here, we report the complete morphological characterization of all lifestages of M. scalaris, ranging from egg to adult. Scanning electron microscopy has enabled us to uncover morphological features and developmental processes that have previously not been reported in the literature. Our data lays the groundwork for future genetic studies: a morphological characterization of the wild type must be performed before mutants displaying different phenotypes can be identified. In this vein, we also report the observation of a acephalic, or 'headless’, adult phenotype whose study could yield insights into the process of cephalogenesis. Finally, all morphological features observed have been compiled into an ’atlas’ that should be of use to all workers in the field.
Reactivity-based identification of oxygen containing functional groups of chemicals applied as potential classifier in non-target analysis
Authors: Latz Milena , Böhme Alexander , Ulrich Nadin 
Published: December 2023

AbstractIn this work, we developed a reactivity-based strategy to identify functional groups of unknown analytes, which can be applied as classifier in non-target analysis with gas chromatography. The aim of this strategy is to reduce the number of potential candidate structures generated for a molecular formula determined by high resolution mass spectrometry. We selected an example of 18 isomers with the molecular formula C12H10O2 to test the performance of different derivatization reagents, whereas our aim was to select mild and fast reaction conditions. Based on the results for the isomers, we developed a four-step workflow for the identification of functional groups containing oxygen.
The emotion prediction of college students with attention LSTM during the COVID19 epidemic
Authors: Wu Mengwei , Lin Shaodan , Xiao Chenhan , Xiao Xiulin , Xu Siwei , Yu Shuhan 
Published: December 2023

AbstractDuring the COVID19 pandemic, there is a pronounced collective mental health issue among college students. Forecasting the trend of emotional changes in on-campus students is crucial to effectively address this issue. This study proposes an Attention-LSTM neural network model that performs deep learning on key input sequence information, so as to predict the distribution of emotional states in college students. By testing 60 consecutive days of emotional data, the model successfully predicts students' emotional distribution, triggers and resolution strategies, with an accuracy rate of no less than 99%. Compared with models such as ARIMA, SARIMA and VAR, this model shows significant advantages in accuracy, operational efficiency, and data collection requirements. The integration of deep learning technology with student management in this study offers a novel approach to address emotional issues among students under exceptional circumstances.
Time-resolved optical shadowgraphy of solid hydrogen jets as a testbed to benchmark particle-in-cell simulations
Authors: Yang Long , Huang Lingen , Assenbaum Stefan , Cowan Thomas E. , Goethel Ilja , Göde Sebastian , Kluge Thomas , Rehwald Martin , Pan Xiayun , Schramm Ulrich , Vorberger Jan , Zeil Karl , Ziegler Tim , Bernert Constantin 
Published: December 2023

AbstractParticle-in-cell (PIC) simulations are a widely-used tool to model kinetics-dominated plasmas in ultrarelativistic laser-solid interactions (dimensionless vectorpotential a0 > 1). However, interactions approaching subrelativistic laser intensities (a0 ≲ 1) are governed by correlated and collisional plasma physics, calling for benchmarks of available modeling capabilities and the establishment of standardized testbeds. Here, we propose such a testbed to experimentally benchmark PIC simulations of laser-solid interactions using a laser-irradiated micron-sized cryogenic hydrogen-jet target. Time-resolved optical shadowgraphy of the expanding plasma density, complemented by hydrodynamics and ray-tracing simulations, is used to determine the bulk-electron-temperature evolution after laser irradiation. We showcase our testbed by studying isochoric heating of solid hydrogen induced by laser pulses with a dimensionless vectorpotential of a0 ≈ 1. Our testbed reveals that the initial surface-density gradient of the target is decisive to reach quantitative agreement at 1 ps after the interaction, demonstrating its suitability to benchmark controlled parameter scans at subrelativistic laser intensities.
Large-scale data reveal disparate associations between leisure time physical activity patterns and mental health
Authors: Zhou Ying , Li Chenshuang , Wang Wei , Ding Lieyun 
Published: December 2023

Abstract
Background
Leisure time physical activity (LTPA) is known to be associated with a lower risk for mental health burden, while whether the underlying mechanisms vary across populations is unknown. We aimed to explore the disparate associations between LTPA and mental health based on large-scale data.

Methods
In this study, we analyzed data including 711,759 individuals aged 15 years or above from the latest four rounds (2003, 2008, 2013, and 2018) of the National Health Service Survey (NHSS) in China. We used multiple logistic regression models adjusted for potential confounders to investigate associations between LTPA and mental health in the total population and subgroups by measuring a diverse set of activity frequencies, intensities, and types. To examine the dose-response associations between total activity volume and mental health, we conducted restricted cubic splines to investigate possible nonlinearity.

Results
LTPA was associated with remarkably lower self-reported mental health burden (OR 0.56, 95% CI 0.54–0.58). The dose-response relationship between total activity volume and mental health was highly nonlinear (p < 0.001), presenting L-shaped with first 1200 metabolic equivalents of task (METs)-min/week for significant risk reduction (OR 0.58, 95% CI 0.56–0.60). Notably, merely exercising 3–5 times per week with moderate swimming was significantly associated with lower mental health burden among younger people, while the association was strongly large in older adults aged 60 years or above doing 55-min moderate apparatus exercise at least six times a week.

Conclusions
In a large Chinese sample, LTPA was meaningfully and disparately associated with mental health burden across different people. Policy targeted at prompting activity may be effective for reducing mental health burden, but importantly, tailored strategies are needed based on population contexts.