bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of embryo production method on the quality of embryos produced by Nguni, Bonsmara, Boran beef cattle breeds
Authors: Mapeka Mohleko Helen Mohleko , Pilane Cyril Mpho , Molomo Karabo , Banga Cuthbert Baldwin , Ng’ambi Jones Wilfred 
Published: October 2022

Abstract
The objective of this study was to compare the quality of in vivo and in vitro produced embryos in Bonsmara, Nguni and Boran cattle. Hormonal supplements were used to produce in vivo embryos while ovum pickup and ovarian follicle aspiration were used to produce in vitro embryos. Embryos produced by both methods in all the three breeds were evaluated for morphological appearence based on the standards of the International Embryo Transfer Society. Data were analysed by ANOVA. No significant difference were observed among breeds in developmental competency of embryos produced in vivo. Development of blastocysts in vivo was significantly higher in Bonsmara and Nguni compared to Boran on day 8. No significant difference was observed between breeds at all development stages for the in vitro environment. There were no significant breed differences in the number of blastocysts and blastocyst quality by either the in vivo or in vitro method. Flushing and Ovum pickup produced a higher number of blastocysts compared to ovary aspiration. The number of Grade I embryos were significantly higher in flushing and OPU compared to ovary aspiration. In conclusion, the study showed that the in vivo method of embryo production is superior to the in vitro method in blastocyst development of Bonsmara, Boran and Nguni breeds.
A TTN-mutation-associated gene signature for prognostic prediction of hepatocellular carcinoma
Authors: Bi Yanqing , Huang rong , Zhang ziying , Tian Zixuan , Liu min , Bao Han , Yan tao , Xia Yuan , Zhang xingguang , zhang nan 
Published: October 2022

Abstract
Mutation in titin (TTN), associated with a worsened prognosis, is among the most common genetic variants in human hepatocellular carcinoma. mRNA expression data and TTN mutation information from TCGA cohort were utilized to characterize a specific TTN-mutation-associated signature according to gene-expression differences between wild type (TTN-WT) and TTN-mutated (TTN-MUT) hepatocellular carcinoma(HCC) patients. Survival analysis was conducted to identify the prognostic gene signature in HCC patients. Depending on this gene signature, patients were grouped into high- and low-risk subgroups and a significant enrichment associated with immunity is detected between the risk groups. Furthermore, the results were further validated in HCC cell lines. In total, 189 differentially expressed genes (DEGs) potentially correlated with TTN mutation status were identified. Five genes (VAX1, MMP3, CXCL5, TKTL1 and KCNA3), identified by survival analyses, constituted an independent OS prognostic gene signature in HCC patients. In addition, the high-risk group was associated with an abundance of macrophages and neutrophils, while the infiltration indices of T follicular helper cells, natural killer cells, and type 2 helper T cells (Th2) were lower compared to low-risk group. MMP3 and CXCL5 expression were further validated in HCC cell lines. We established a novel and unique TTN-mutation-related gene signature for survival outcome prediction for HCC patients.
Metagenomic meta-analysis of the gut microbiome in the different primary locations of colorectal cancer
Authors: DongCheng Luo , Liao Sina , Li Yongqiang , Lai Hao , Lin Youzhi , Liao Xiaoli 
Published: October 2022

Abstract
BACKGROUND
Recent studies have found a relationship between gut microbes and the primary location of colorectal cancer (CRC). However, most of these studies had limitations in sample size or sequencing methods. In this study, we collected metagenomic data from three studies and meta-analyzed the microbiological features according to the grouping of right-side colon cancer (RCC), left-side colon cancer (LCC), and rectal cancer (RC).
METHODS
We first identified confounding factors (except for tumor location) by two-way ANOVA and comparing species diversity. Subsequently, the microbial compositions were compared between different tumor locations. Microbial co-occurrence networks were established based on samples with different tumor locations. A prediction model for primary tumor location was constructed using a random forest algorithm based on microbial abundance features. Finally, tumor location and confounding factors were entered in the MAASLIN2 to identify differential species. Linear discriminant analysis (LDA) also identified the differential species.
RESULTS
Different study sources and BMI influenced gut microbiome and significantly altered α-diversity and β-diversity, bringing the confounding effect when analyzing gut microbial features in different tumor locations. However, α-diversity and β-diversity of gut microbiome had no significant difference in tumor locations. Species belonging to the Phylum of Actinobacteria, Firmicutes, and Proteobacteria played essential linkages in the three microbial networks, while Bacteroidetes were more critical in the microbial network of RCC. There are both the same hub species and different hub species among the three networks. The random forest classification model performed well in predicting RC (class error = 0.217) but poorly classified the RCC and LCC, with an overall classification error of 0.613. In comparing colon cancer (CC) with RC, MAASLIN2 and LDA identified six species significantly enriched in RC and thirteen in CC. In comparing RCC with LCC, MAASLIN2 identified nine species significantly enriched in RCC and six significantly enriched in LCC. Some of the differential species were reported to be associated with CRC location-related Molecular and immune features.
CONCLUSION
This study elucidated the relationship between gut microbiome and CRC location and confirmed that RCC, LCC, and RC had different enrich patterns of microbiota.
Plasma exosome proteomics reveals the pathogenesis mechanism of post stroke cognitive impairment
Authors: Qi Baoyun , Kong Lingbo , Lai Xinxing , Wang Linshuang , Fei Liu , Wei Dongfeng , Ji Weiwei 
Published: October 2022

Abstract
Background
Recently, the plasma exosome biomarkers of post-stroke cognitive impairment (PSCI) have been brought into focus. Exploration and utilization of exosome biomarkers and their related functions provided the possibility for the diagnosis and treatment of PSCI. Aims To identify for new diagnostic and prognostic biomarkers of plasma exosome using label-free quantitative proteomics and biological information analysis in PSCI patients.
Methods
A series of behavioral assessments were performed, including the Mini-Mental Status Examination (MMSE), the Montreal Cognitive Assessment (MoCA), the Barthel index, the Morse Fall Seale (MFS) beteen control group (n = 10) and PSCI group (n = 10). The blood samples were collected to analyse the biomarker and differentially expressed proteins of plasma exosome using label-free quantitative proteomics and biological information. The exosomes marker proteins were determined by Western blot. The exosome morphology was observed by transmission electron microscopy.
Results
The scores of MMSE and MoCA were significantly decreasd in the PSCI group. The PT% and high-density lipoprotein decreasd and the INR ratio increasd in PSCI group. The mean size of exosome was approximately 71.6 nm and the concentration was approximately 6.8E + 7 particles/mL. Exosome proteomics identificated 259 differentially expressed proteins, including 131 up-regulated proteins and 128 down-regulated proteins. The mechanisms of cognitive impairment are related to up-regulation of degradation of ubiquitinated proteins, calcium dependent protein binding, cytoskeleton reorganization, platelet aggregation and down-regulation of cell adhesive protein binding, formation of fibrin clot, complement activation, lipid metabolism and ATP-dependent degradation of ubiquitinated proteins in plasma exosome of PSCI patients. Plasma levels of YWHAZ and BAIAP2 were significantly increased while that of IGHD, ABCB6 and HSPD1 were significantly decreased in PSCI patients.
Conclusion
These proteins might be target-related proteins and provide global insights into pathogenesis mechanisms of PSCI at plasma exosome proteins level.
Delta (B1.617.2) variant of SARS-CoV-2 induces severe neurotropic patterns in K18-hACE2 mice
Authors: Yang Ju-Hee , Yang Myeon-Sik , Kim Dae-Min , Kim Bumseok , Tark Dongseob , Kang Sangmin , Lee Gun-Hee 
Published: October 2022

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a highly contagious virus, emerged and quickly spread globally, resulting in the coronavirus disease 19 (COVID-19) pandemic. Genetic variants of SARS-CoV-2 have been reported to circulate throughout the COVID-19 pandemic. The major symptoms of COVID-19 are respiratory symptoms, fever, muscle pain, and breathing difficulty. In addition, up to 30% of patients with COVID-19 complain of neurological complications such as headache, nausea, stroke, and anosmia. However, the neurotropism of SARS-CoV-2 infection remains largely unknown. This study investigated neurotropic patterns between the B1.617.2 (Delta) and Hu-1 variants (Wuhan, early strain) in K18-hACE2 mice. B1.617.2-infected K18-hACE2 mice displayed massive weight loss, greater lethality, and severe conjunctivitis compared to the findings Hu-1–infected mice despite their similar pathogenic patterns in various organs. Additionally, we demonstrated through histopathological analysis that B1.617.2 more readily infects the brain than the lungs and infects the brain earlier after inoculation. Finally, we found that the upregulation of various signature genes involved in type I interferon- and cytokine-mediated signaling was most pronounced after B1.617.2 infection, and a small population of cells exhibited necrosis-related responses. This study has provided helpful information for potential treatment strategies.
Effect of economic growth, FDI inflows, trade openness, environment related technologies, and environment related revenues taxes on CO2 emission with pooled mean group (PMG) panel ARDL
Authors: Fatima Nudrat , Yanting Zheng , Guohua Ni 
Published: October 2022

Abstract
The current research study employed PMG (Pooled Mean Group) estimator to examine the impact of foreign direct investment inflows (FDI Inflows), Trade Openness (TO), environmental-related technologies (ERTs), environmental-related tax revenues (ERTRs), and Economic growth (EG) on carbon dioxide (CO2) emission with a dataset of 36 OECD countries spanning from 1990 to 2020. Kao and Pedroni cointegration test results show that study variables are stationary at I(0) and I(I) that conform pooled mean group (PMG) panel ARDL method can be employed. Empirical results of PMG demonstrate that environmental-related tax revenues (ERTRs) help reduce CO2 emission while foreign direct investment inflows (FDI Inflows), Trade Openness (TO), environmental-related technologies (ERTs) and Economic growth (EG) are significantly and positively related to environmental degradation. In context of study findings several relevant financial globalization policies are suggested.
Nasal anti-CD3 mAb (Foralumab) dampens CD3+ T effector function and decreases NKG7 in COVID-19 through a mechanism involving GIMAP-7 and TGFb1
Authors: Moreira Thais , Gauthier Christian , Murphy Liam , Lanser Toby , Paul Anu , Matos Kimble , Mangani Davide , Izzy Saef , Rezende Rafael , Healy Brian , Baecher-Allan Clare , Chitnis Tanuja , Kuchroo Vijay , Weiner Howard 
Published: October 2022

Abstract
T cells are present in early stages of the SARS-CoV-2 infection and play a major role in disease outcome and long-lasting immunity. Nasal administration of a fully humanized anti-CD3 monoclonal antibody (Foralumab) reduced lung inflammation as well as serum IL-6 and C-reactive protein in moderate cases of COVID-19. Using RNA-sequencing and serum proteomics, we investigated the immune changes in patients treated with nasal Foralumab. In a randomized trial, mild to moderate COVID-19 outpatients received nasal Foralumab (100ug/day) given for 10 consecutive days and were compared to patients that did not receive Foralumab. We found that naïve-like T cells were increased in Foralumab treated subjects and NGK7+ effector T cells were reduced. CCL5, IL32, CST7, GZMH, GZMB, GZMA, PRF1, and CCL4 gene expression were downregulated in T cells and CASP1 was downregulated in T cells, monocytes and B cells in subjects treated with Foralumab. In addition to the downregulation of effector function, an increase in TGFb1 gene expression in cell types with known effector function was observed in Foralumab treated subjects. We also found increased expression of GTP-binding gene GIMAP7 in subjects treated with Foralumab. Rho/ROCK1, a downstream pathway of GTPases and TGF-b1 signaling, was downregulated in Foralumab treated individuals. TGFb1, GIMAP7 and NKG7 transcriptomic changes observed in Foralumab treated COVID-19 subjects was also observed in healthy volunteers, MS subjects and mice treated with nasal anti-CD3. Our findings demonstrate that nasal Foralumab modulates the inflammatory response in COVID-19 and provides a novel avenue to treat the disease.
Numerical Analysis of the Influence of Size Upgrading on Oxygen and Carbon Impurities in Casting Silicon
Authors: Su Wenjia , Zhang Zhen , Li Jiulong , Guan Zhicheng , Li Jiaqi 
Published: October 2022

Abstract
Size upgrading is the main method to increase production capacity and reduce production costs during the directional solidification of silicon ingots. The performance of solar cells depends directly on the quality of the wafer and impurities distributions in silicon ingots. The distributions of oxygen and carbon impurities in G6 and G7 directional solidification furnaces are studied. The transient global simulation method is used to calculate the coupled thermal and flow fields in the furnaces, considering the convection of gas and melt, chemical reactions, and segregations of the impurities at the crystal-melt interface. The simulation results show that the distributions of oxygen and carbon impurities change significantly in the silicon ingot at different growth stages, especially the position of the highest concentration of carbon impurities has shifted. Compared with the G6 furnace, the average concentrations of oxygen and carbon in silicon crystal in the G7 furnace are reduced by 6.7%, and 7.3% respectively. With the growth of silicon crystal, the average concentration of oxygen gradually decreases, while the average concentration of carbon gradually increases.
A Pangenome Reference of 36 Chinese populations
Authors: Xu Shuhua , Gao Yang , Yang Xiaofei , Chen Hao , Tan Xinjiang , Yang Zhaoqing , Deng Lian , Wang Yimin , Wang Baonan , Li Songyang , Cui Yuhang , Pan Yuwen , Ma Sen , Sun Hao , Kong Shuang , Zhao Xiaohan , Wu Dongdong , Wu Shaoyuan , Shi Bingyin , Jin Li , Lu Yan , Chu Jiayou , Ye Kai 
Published: October 2022

Abstract
Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form but populations of Asian ancestry are underrepresented. Here, we present the first effort (Phase I) of the Chinese Pangenome Consortium (CPC) with a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With > 30.65× High-Fidelity long-reads sequence coverage, an average contiguity N50 > 35.63 Mb, and an average total size of 3.01 Gb, the CPC core assemblies cover ~96.54% and ~93.59% of the latest reference sequence GRCh38 and a Telomere-to-Telomere haploid assembly T2T-CHM13, respectively. Moreover, the CPC Phase I data add 189 million base pairs of euchromatic polymorphic sequence and 1,367 protein-coding gene duplications to GRCh38. We also identify from the CPC pangenome ~15.9 million small variants and ~78 thousand structural variants (SVs), of which ~6.1 million (38.0%) small variants and ~25 thousand (32.4%) SVs are not reported in a recently released pangenome reference by the Human Pangenome Reference Consortium (HPRC)1. The CPC data demonstrate a remarkable increase in discovering novel or missing sequences when individuals are included from underrepresented minority ethnic groups, suggesting the necessity of a more comprehensive sampling effort for both CPC and HPRC.
Autophagy mediates cementoblast mineralization through periostin/β-catenin signaling axis under compression
Authors: Li Weiran , Yang Yuhui , Liu Hao , Wang Ruoxi , Zhao Yi , Zheng Yunfei , Huang Yiping 
Published: October 2022

Abstract
Repair of orthodontic external root resorption and periodontal tissue dysfunction induced by mechanical force remains a clinical challenge. Cementoblasts are vital in cementum mineralization, a process important for restoring damaged cementum and regaining healthy periodontal function. Autophagy is a vital self-renewal process for cellular homeostasis under various environmental stimuli. However, how autophagy mediated cementoblast mineralization remains unclear. Here we verified that murine cementoblasts exhibit compromised mineralization under compressive force. Autophagy was indispensable for cementoblast mineralization, and autophagic activation markedly reversed the capacity for cementoblast mineralization and cementum damage in mice. Subsequently, mRNA sequencing analyses identified periostin (Postn) as a regulator of autophagy and cementoblast mineralization. Cementoblast mineralization was significantly inhibited following knockdown of Postn. Furthermore, Postn silencing downregulated Wnt transcriptional activity by promoting ubiquitination of β-catenin. Together our results highlight autophagy as a mediator of cementoblast mineralization via Postn/β-catenin signaling under compressive force and may provide a new strategy for the remineralization of cementum and regeneration of periodontal tissue.
Text Mining: Identification of Similarity of Text documents using Hybrid Similarity model
Authors: KM Shiva Prasad 
Published: October 2022

Abstract
The volume of data that is accessible on the internet has increased dramatically. This growth of data will only increase exponentially in the future as more data exhaust devices are connected to the network. A part of this data consists of documents from various sources. As the data from various digital sources increases, it becomes tough to perform the process of identification of relevant information which is most essentially needed for their further usage. Our paper aims at providing a hybrid similarity algorithm that identifies similar documents both in terms of semantic similarity and contextual similarity using text summarization techniques. Some of these techniques use deep learning with multiple layers and prebuilt models of NLP to provide similarity between documents and attempt to provide a quantitative number to the polysemy quotient of the corpus. The experimental results of our model provided an accuracy of 76.25% compared with other traditional algorithms
Microkinetics of Lidocaine and Bupivacaine Transfer across Myelinated Nerve Fibre
Authors: Smrkolj Vladimir , Pregeljc Domen , Kavcic Hana , Umek Nejc , Mavri Janez 
Published: October 2022

Abstract
Background
The present study aimed to predict the time to onset and duration of action of two local anesthetics (lidocaine and bupivacaine) based on the experimental dimensions of a typical nerve and experimental octanol/water partition coefficients.
Methods
We started our compilation of experimental data with a numerical solution of the diffusion equation of transfer of lidocaine and bupivacaine across the axon membrane at the region of the node of Ranvier (axolemma) and across the Schwann cell. By including the coordinate-dependent chemical potential, the difference between the aqueous and lipid environments of the neuron was simulated. In the second step, permeation rates calculated using the diffusion equation were applied to solve a system of four ordinary differential equations. This approach allowed us to simulate the cell environment for longer, enabling us to compare our model to the pharmacokinetic properties (time to onset and duration of action) of local anaesthetics found in the literature. The behaviour of local anaesthetics under physiological conditions and in the case of local acidosis was also simulated.
Results
We demonstrated that local anaesthetics cross the axolemma on a sub-microsecond time scale. Time to onset, controlled by diffusion from epineurium to an axon with a typical distance of 500 µm, was 167 s and 186 s for lidocaine and bupivacaine, respectively. Calculated half-time, which is a measure of the duration of action, was 41min and 328 min for lidocaine and bupivacaine, respectively.
Conclusions
Duration of action is controlled by the storage capacity of lipophilic compartments around the axon that are higher for bupivacaine and lower in the case of local acidosis. For the latter case, the literature, including textbooks, provides an incorrect interpretation that protonated species cannot penetrate the membrane.
Strongly sexually dimorphic forelegs are not more condition-dependent than less dimorphic traits in Drosophila prolongata
Authors: Ferreira Jhoniel Perdigon , Rohner Patrick T. , Lüpold Stefan 
Published: October 2022

Abstract
Directional sexual selection drives the evolution of traits that are most closely linked to reproductive success, giving rise to trait exaggeration and sexual dimorphism. Exaggerated structures are often costly and, therefore, thought to be expressed in a condition-dependent manner. Sexual selection theory thus predicts a direct link between directional sexual selection, sexual dimorphism, and sex-specific condition dependence. However, only a handful of studies investigate the relationship between sexual dimorphism and condition dependence. Using 21 genetic lines of Drosophila prolongata, we here compared the degree of sexual dimorphism and sex-specific condition dependence in sexually selected and non-sexual traits. Our data revealed male-biased sexual dimorphism in all traits examined, most prominently in the sexually selected forelegs. However, there was no relationship between the degree of sex-specific condition dependence and sexual dimorphism across traits and genetic lines. Our results contradict theoretical predictions and highlight the importance of understanding the role of exaggerated traits in the context of both sexual and natural selection.
Feasibility of in vivo swine models using guide wire-assisted intraductal radiofrequency ablation for benign biliary stricture
Authors: Park Jae Keun , Yang Ju-Il , Park Joo Kyung , Lee Kwang Hyuck , Lee Jong Kyun , Lee Kyu Taek 
Published: October 2022

Abstract
Background/Aims: Several in vivoswine models of benign biliary stenosis (BBS) have been recently reported for preclinical studies of novel endoscopic techniques and devices. The aim of this study was to evaluate the efficacy and feasibility of large animal models of BBS by using intraductal radiofrequency ablation (RFA) assisted by guide wire.
Methods: Six in vivoswine models were made by using an intraductal RFA for cauterization at 10 W, 80 °C, 90 sec in the common bile duct. Endoscopic retrograde cholangiopancreatography (ERCP) was performed with cholangiography and histologic evaluation was done for the common bile duct. Blood tests were examined before, after, and at the final follow-up.
Results: Guide wire assisted RFA electrode produced BBS in all (6/6, 100%) animal models without severe complications. Fluoroscopy findings at 2 weeks after intraductal RFA in every model revealed BBS in the common bile duct. In histologic evaluations, fibrosis and chronic inflammatory changes were noted. After the procedure, ALP, GGT, and CRP were elevated and decreased after an appropriate drain.
Conclusions: A swine model of BBS is developed by inducing intraductal thermal injury using intraductal RFA assisted by guide wire. This novel technique for inducing BBS in swine is effective and feasible.