bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shotgun Proteomics-based distinctive fingerprint of buffalo sperm surface unravels over-representation of proteins driving spermatogenesis, motility, and fertility
Authors: BATRA VIPUL , Dagar Komal , Diwakar Maharana Pratap , Kumaresan Arumugam , Kumar Rakesh , Datta Tirtha Kumar 
Published: October 2022

AbstractThe mammalian sperm surface is radically modified in its biomolecular composition and structure during the transit of sperm through the male and female reproductive tract (MRT, FRT). Numerous distinct secretagogues such as (glyco)proteins and many GPI-anchored proteins (GPI-APs) are applied as peripheral coats on the sperm surface in the MRT, which is critical for the maturation, survival and function of the spermatozoa. This study aimed to characterize the buffalo sperm surface proteins by extracting them either by using elevated salt (NaCl) or Phosphatidylinositol-specific phospholipase-C (for GPI-APs) or by inducing in vitro capacitation. A buffalo sperm surface-specific proteomic fingerprint was subsequently generated using the protein informatics platform, Proteome Discoverer (v2.2) for protein identification. Overall, 1695 unique proteins isoforms (proteoforms) (≥ 1 high-quality PSM/s, minimum 2 peptides, P < 0.05, FDR < 0.01) that exhibited remarkable heterogeneity in their molecular weight, pI, distribution of expression from the genome and their functional roles in the MRT and the FRT were identified. We characterized the identified including 200 orphan proteins by extrapolation of function from their sequence orthologs using BLAST2GO software. The extensive, yet unexplored, reproduction-specific buffalo sperm-surface proteomic repertoire discovered in this study is unparalleled vis-à-vis the depth identification of fertility-related and reproduction-specific cell-surface proteins.
Fission yeast Srr1 and Skb1 promote isochromosome formation at the centromere
Authors: Mongia Piyusha , Toyofuku Naoko , Pan Ziyi , Xu Ran , Oki Keitaro , Takahashi Hiroki , Ogura Yoshitoshi , Hayashi Tetsuya , Nakagawa Takuro 
Published: October 2022

Abstract
Rad51 faithfully repairs DNA damage, whereas Rad52 promotes non-canonical homologous recombination leading to gross chromosomal rearrangements (GCRs). However, the GCR mechanism remains unclear. Here we find that fission yeast Srr1/Ber1 and Skb1/PRMT5 arginine methyltransferase promote isochromosome formation at centromeres. srr1 and skb1 mutations reduce GCR rates. Physical analysis of GCR products reveals that srr1 and skb1 specifically reduce isochromosome formation. Remarkably, srr1 and rad51 additively increase DNA damage sensitivity, suggesting that Srr1 promotes Rad51-independent DNA damage response prone to isochromosome formation. In contrast, loss of Skb1 does not increase damage sensitivity and, intriguingly, reduces chromosome loss in rad51∆ cells, suggesting that Skb1 forms DNA structures that need to be processed by Rad51 or else chromosomes become unstable. Srr1 and Skb1 act in the Rad52-dependent GCR pathway, while Srr1 also has a role in the Rad52-independent pathway. This study has uncovered unprecedented roles for Srr1 and Skb1 in GCRs at centromeres.
Association of Smoking, Alcohol, and Coffee Consumption with the Risk of Ovarian Cancer and Prognosis: A Mendelian Randomization Study
Authors: Liu Sicong , Feng Songwei , Du Furong , Zhang Ke , Shen Yang 
Published: October 2022

Abstract
Objective: Currently, the association between smoking, alcohol, and coffee intake and the risk of ovarian cancer (OC) remains conflicting. In this study, we used a two-sample mendelian randomization (MR) method to evaluate the association of smoking, drinking and coffee consumption with the risk of OC and prognosis.
Methods: Five risk factors related to lifestyles (cigarettes per day, smoking initiation, smoking cessation, alcohol consumption and coffee consumption) were chosen from the Genome-Wide Association Study, and 28, 105, 10, 36 and 36 single-nucleotide polymorphisms (SNPs) were obtained as instrumental variables (IVs). Outcome variables were achieved from the Ovarian Cancer Association Consortium. Inverse-variance-weighted method was mainly used to compute odds ratios (OR) and 95% confidence intervals (Cl).
Results: The two-sample MR analysis supported the causal association of genetically predicted smoking initiation (OR: 1.15 per SD, 95%CI: 1.02-1.29, P=0.027) and coffee consumption (OR: 1.40 per 50% increase, 95%CI: 1.02-1.93, P=0.040) with the risk of OC, but not cigarettes per day, smoking cessation, and alcohol consumption. Subgroup analysis based on histological subtypes revealed a positive genetical predictive association between coffee consumption and endometrioid OC (OR: 3.01, 95%CI: 1.50-6.04, P=0.002). Several smoking initiation-related SNPs (rs7585579, rs7929518, rs2378662, rs10001365, rs11078713, rs7929518, and rs62098013), and coffee consumption-related SNPs (rs4410790, and rs1057868) were all associated with overall survival and cancer-specific survival in OC.
Conclusion: Our findings provide the evidence for a favorable causal association of genetically predicted smoking initiation and coffee consumption with OC risk, and coffee consumption is linked to a greater risk of endometrioid OC.
Effect of management practices on the age of puberty in Murrah buffalo male calves
Authors: C Kotresh Prasad , Singh Pawan , Panchbhai Girish , Bhatt Ninad , Barman Deepandita , Lathwal Surender Singh , Mukesh Manishi , Tyagi Amrish Kumar , Singh Sohan Vir , Uddin Jashim 
Published: October 2022

Abstract
This study was conducted to assess the effect of management practices along with different feed supplementation in the age of puberty of Murrah buffalo male calves. Thirty calves were divided into 5 groups, having 6 in each Group. Groups 1 to 3 were reared under routine management, while 4 to 5 were under better management practices. A basal diet was provided in Group 1. Group 2 had access to a 10% higher energy supplement (molasses) along with basal diet, Group 3 had access to a basal diet plus 10% higher energy till 12 months of age and thereafter roasted flax seed till the age of first semen ejaculation; Group 4 fed similar to Group 2, and Group 5 fed similar to Group 3. Growth performance, scrotal circumference, semen quality and quantity, testosterone concentration, and fatty acid profile of blood serum were measured fortnightly. In One-way Analysis of Variance, it was found that the provision of better management practices and a high-energy diet reduced the age of puberty (P < 0.05). The concentration of serum testosterone increased linearly with the increase in body weight. The semen quality and quantity (volume, concentration, motility, live %) were higher in Group 5 than that in Groups 1 to 4 (P < 0.01). This study concluded that the Murrah buffalo male calves have the potential to attain the age of puberty earlier with the provision of better management practices and an energy-rich diet than that of conventional.
Acute Malnutrition Recovery Rates Improve with COVID-19 Adapted Nutrition Treatment Protocols in South Sudan: A Mixed Methods Study
Authors: Lyles Emily , Banks Sandra , Ramaswamy Maya , Ismail Sule , Leidman Eva , Doocy Shannon 
Published: October 2022

Abstract
Background.
Globally, emergency nutrition program adaptations were implemented as part of COVID-19 mitigation strategies, but the implications of the adoption of all protocol changes at scale in the context of deteriorating food security are not yet well characterized. With ongoing conflict, widespread floods, and declining food security, the secondary impacts of COVID-19 on child survival in South Sudan is of great concern.
Methods.
A mixed methods approach including a desk review and secondary analysis of facility-level program data was used to analyze trends in program indicators over time and compare two 15-month periods prior to the onset of COVID-19 (January 2019 – March 2020; “pre-COVID period”) and after the start of the pandemic (April 2020 – June 2021; “COVID” period) in South Sudan.
Results.
The median number of reporting CMAM sites increased from 1,167 pre-COVID to 1,189 during COVID. Admission trends followed historic seasonal patterns in South Sudan; however, compared to pre-COVID, declines were seen during COVID in total admissions (-8.2%) and median monthly admissions (-21.8%) for SAM. For MAM, total admissions increased slightly during COVID (1.1%) while median monthly admissions declined (-6.7%). States with the largest admission declines also saw reductions in the number of treatment facilities during COVID. Median monthly recovery rates improved for SAM (92.0% pre-COVID to 95.7% during COVID) and MAM (91.5–94.3%); all states saw improvements in median monthly recovery rates for both SAM and MAM. At the national level, rates also decreased for default (-2.4% for SAM, -1.7% for MAM) and non-recovery (-0.9% for SAM, -1.1% for MAM), with mortality rates remaining constant at 0.05–0.15%. While median monthly mortality rates were stable for both SAM and MAM, the total number of SAM deaths fell by 35.2% and the total number of MAM deaths decreased by 42.1%.
Conclusions.
Within the context of the ongoing COVID-19 pandemic in South Sudan, improved recovery, default, and non-responder rates were observed following adoption of changes to nutrition protocols. Policymakers in South Sudan and other resource-constrained settings should consider if simplified nutrition treatment protocols adopted during COVID-19 improved performance and should be maintained in lieu of reverting to standard treatment protocols.
Frequency of Cardiometabolic Diseases and Medications in Children with Cerebral Palsy
Authors: Dum Rachel , Walter Vonn , Thomas Neal J. , Krawiec Conrad 
Published: October 2022

Abstract
Introduction/Objectives: Cerebral palsy (CP) patients may be at risk of obesity, but outcomes and risk factors are understudied. The objectives of this study are to evaluate the body mass index (BMI) types of CP patients and to evaluate the presence of cardiometabolic specific diseases and medications. We hypothesize CP subjects with an increased BMI have a higher frequency of cardiometabolic specific diseases and medications.
Methods: This is a retrospective observational cohort study utilizing TriNetX ®, an electronic health record (EHR) database, in CP subjects aged 2 to 18 years who had a BMI value available. The study population was divided into 4 BMI percentile groups, underweight (<5th BMI percentile), healthy weight (≥5th to <85th percentile), overweight (≥85th to <95th percentile), and obese (≥95th percentile), and the following variables were evaluated: demographics, diagnostic codes, and medication codes.
Results: A total of 5993 subjects were included [underweight (251, 4.2%), healthy weight (2390, 39.9%), overweight (943, 15.7%), and obese (2409, 40.2%)]. Obese subjects had a higher frequency of the following: asthma [811 (33.7%), p=0.0001], diabetes mellitus [102 (4.2%), p=0.0001], hypertension [213 (8.8%), p=0.0001], and sleep apnea [686 (28.5%), p=0.0001]. Overweight subjects had a higher frequency of spastic diplegic cerebral palsy [574 (60.9%), p=0.0001).
Conclusions: This study found CP patients classified as obese had a higher frequency of cardiometabolic comorbidity and medication codes that influence weight. BMI measurements are limited in this population but may be used cautiously to evaluate the body type of CP children, and monitor the occurrence of cardiometabolic associated comorbidities.
The Outcome of Kidney Transplantation in Lupus Patients
Authors: Lin Ting-Chih , Tsai Meng-Kun , Lee Jyh-Hong , Yang Yao-Hsu , Lin Yu-Tsan , Yu Hsin-Hui , Chiang Bor-Luen , Wang Li-Chieh 
Published: October 2022

Abstract
Kidney transplantation is one of the treatments for end-stage renal disease in lupus patients. The impact of lupus activity on graft survival is a concern. In this study, we aimed to analyze graft survival and factors affecting outcome of kidney transplantation in 45 lupus patients. The graft survival rate was 98, 98, 88, 85 and 78% at 1, 5, 10, 15 and 20 years, respectively. Hypertension, positive penal reactive antibodies against HLA class 2 antigens, retransplant, younger age of lupus nephritis onset, lower postoperative C4 level and the presence of HBsAg and/or anti-HBe antibody showed significantly negative correlation on graft survival by univariate logistic regression. The only factor that is significantly associated with graft failure after adjusting above factors by multiple regression is the presence of HBsAg and/or anti-HBe antibody (p = .0161). Serological markers for activity including C3, C4 and anti-dsDNA antibody before kidney transplantation and recurrent lupus nephritis were not significantly associated with graft failure. In conclusion, in lupus patients underwent kidney transplantation, preoperative serological markers for lupus activity and recurrent lupus nephritis did not affect the graft outcome. However, hepatitis B virus serology might be a single predictor for graft failure in lupus patients.
Toxoplasma gondii GRA25 alters the morphology of the parasitophorous vacuole membrane communicating with host mitochondria
Authors: Nishigori Mitsuhiro , Shimoda Naomi , Nishi Shohei , Chen Yu , Masatani Tatsunori , Ban Tadato , Nishikawa Yoshifumi , Koshiba Takumi 
Published: October 2022

Abstract
Mitochondria participate in a wide range of cellular processes, from energy metabolism to host defense. Some infectious microbes alter their host environments by accessing/altering mitochondrial functions. The intracellular parasite Toxoplasma gondii sequestrates host mitochondria, in part by nutrient uptake. Here we show that the T. gondii dense granule protein 25 (TgGRA25) interconnects parasite and host mitochondria in infected cells. Using a combination of biochemical and cell biologic approaches, we reveal that TgGRA25 contributes to mitochondrial-tethering by its association with the phosphatidic acid-producing mitochondrial phospholipase MitoPLD. TgGRA25/MitoPLD interactions suppress the efficiency of parasite egress from host cells. Moreover, targeted deletion of TgGRA25 in type II parasites caused dramatic deformation of the parasitophorous vacuole membrane and severe defects in the lytic cycle of T. gondii, indicating an essential role of TgGRA25 in parasite morphogenesis. Our results suggest the existence of multiple routes by which communication is maintained between the parasite and host mitochondria, and this translocation event could be a potential therapeutic target.
Off-label Use of an External Hand Fixator for Craniomaxillofacial Fractures – an Anatomical Feasibility Study
Authors: Wichlas Florian , Necchi Marco , Gruber Teresa , Hofmann Valeska , Deininger Susanne , Deininger Markus Sebastian Hubertus , Steidle-Kloc Eva , Pruszak Jan , Deininger Christian 
Published: October 2022

AbstractBackgroundThe lack of resources limits the treatment of craniomaxillofacial fractures in low-income countries (LIC). Therefore, Barton bandage and/or interdental wiring are considered being gold standard in these regions. The fracture reduction is maintained by permanent occlusion for 6 weeks, which often leads to limited compliance and dissatisfying results. Furthermore, in these conditions the healing of nasopharyngeal fistula is difficult. During humanitarian missions CMF need to be treated by trauma surgeons. The aim of this cadaver-based study is to evaluate the feasibility of the use of an external face fixator (EFF) for the treatment of CMF, its biomechanical values and to define the optimal pin insertion points and angles.Material and methodsA commercially available AO hand fixator was used. Craniomaxillofacial fractures type Le Fort 1-3 with split fracture of the hard palate were treated with EFF on 13 anatomical specimens. The fractures were created using a chisel. The pins were placed in specific anatomical regions. The maximal pull-out force [N] of the pins was analysed by a tensile force gauge. As a reference, Fmax of the mandibular pins was evaluated. Computer tomography (CT) scans were performed on the healthy, fractured and EFF-treated skulls. After reduction and EFF placement an adequate reposition was shown in the CT scans.ResultsThe pull-out forces for the single pins were as follows: mandibular pins (n=15, median 488N), supraorbital pins (n=15, median 455.0N), zygomatic pins (n=14, median 269.1N), medial hard palate pins (n=12, median 208.4N) and lateral hard palate pins (n=8, median 49.6N).ConclusionsThe results of the presented study on the cadaver show, that the operation technique is feasible, and the stability of the EFF is sufficient for maintaining the reduction. In addition, the required pins can be safely inserted into the described areas and a good reduction result can be achieved. The technique of the EFF offers a feasible alternative to the non-surgical treatment of CMF in LIC. Thus, the gap between the open reduction and internal fixation techniques (mini-plates) used in High-income countries and the Barton bandage used in LIC can be closed.Trial registration:A vote of the local ethics committee was obtained (13.01.2022, Ethikkommission Land Salzburg, Austria). EK Nr: 1198/2021Level of evidence:Level 2
Calculation of component activities for Se-based binary systems by NRTL equation
Authors: Yang Hongwei. , Wang Weiyi , He Bei , Xu Baoqiang , Jiang Wenlong 
Published: October 2022

Abstract
The activity of components is the fundamental thermodynamic property of vapor-liquid equilibrium in vacuum distillation of crude selenium. The activities of components for the Pb-Se, Bi-Se, Sb-Se, and Tl-Se binary systems were calculated and discussed using the Nonrandom two-liquid (NRTL) equation and Wilson equation. The interaction energy parameters of the NRTL equation for Se-based binary systems were employed to predict the activities of components at corresponding temperatures. The mixing enthalpies and Gibbs free energies of these systems were obtained based on the predicted activities and NRTL equation parameters. Compared to the experimental data from literature, the present calculations for the four binary systems using the NRTL equation are better than the Wilson equation. It shows that the NRTL equation is reasonable and accurate based on the concept of local composition and two-fluid theory, especially for binary systems containing liquid-liquid immiscibility. The method proposed in this work is reliable for predicting thermodynamic properties for Se-based binary systems.
Development and validation of a prognostic nomogram for incidental gallbladder adenocarcinoma patients without distant metastasis after surgery: a SEER population-based study
Authors: Chen Jie , Huang Shifei , Han Yehong 
Published: October 2022

Abstract
Background
Gallbladder cancer is the most common malignant tumor of the biliary system, most of which is adenocarcinoma. Our study explored developing and validating a nomogram to predict overall and cancer-specific survival probabilities internally and externally for incidental gallbladder adenocarcinoma patients without distant metastasis after surgery.
Methods
Patients screened and filtered in the Surveillance, Epidemiology, and End Results (SEER) database, whose years of diagnosis between 2010 and 2015 were collected as a derivation cohort, while those between 2016 and 2019 were a temporal validation cohort. Overall survival (OS) and cancer-specific survival (CSS) were chosen as our retrospective cohort study's primary and secondary endpoints. Potential clinical variables were selected for a cox regression model analysis by performing both-direction stepwise selection to confirm the final variables. The performance of final nomograms was evaluated by Harrell's C statistic and Brier score, with a graphical receptor operating characteristic (ROC) curve and calibration curve.
Results
6 variables of age, race, tumor size, histologic grade, T stage, and positive regional lymph nodes were finally determined for the OS nomogram; sex had also been added to the CSS nomogram equally. Novel dynamic nomograms were established to predict the prognosis of incidental gallbladder adenocarcinoma patients without distant metastasis after surgery. The ROC curve demonstrated good accuracy in predicting 1-, 3-, and 5-year OS and CSS in both derivation and validation cohorts. Correspondingly, the calibration curve presented perfect reliability between the death or cancer-specific death probability and observed death or cancer-specific death proportion in both derivation and validation cohorts.
Conclusions
Our study established novel dynamic nomograms based on 6 and 7 clinical variables separately to predict OS and CSS of incidental gallbladder adenocarcinoma patients without distant metastasis after surgery, which might assist doctors in advising and guiding therapeutic strategies for intraoperative or postoperative gallbladder adenocarcinoma patients in the future.
LEMON: LanguagE MOdel for Negative Sampling of Knowledge Graph Embeddings
Authors: Rony Md Rashad Al Hasan , Alam Mirza Mohtashim , Ali Semab , Saleem Qasid , Lehmann Jens , Vahdati Sahar 
Published: October 2022

Abstract
Knowledge Graph Embedding models have become an important area of machine learning. Those models provide a latent representation of entities and relations of a knowledge graph which can then be used in downstream machine learning tasks such as link prediction.The learning process of such models can be performed by contrasting positive and negative triples.While the triples of the underlying knowledge graph are considered positive, the generation of the negative samples has its own process. Therefore, the sampling procedures for obtaining the negative triples play a crucial role in the performance and effectiveness of Knowledge Graph Embedding models. Most of the existing techniques draw negative samples from a random distribution of entities of the underlying Knowledge Graph which often includes uninformative negative triples. Different works employ adversarial techniques or generative neural networks for negative sampling, which improve the performance of models with the cost of additional sophisticated mechanisms. In this paper, we propose an approach for generating informative negative samples by utilizing complementary knowledge about entities. Particularly, pre-trained language models are used to form neighborhood clusters by computing the distances between entities to obtain representations of symbolic entities via their complementary textual information. Our proposed approach achieved the biggest leaps in performance over the baseline models KBGAN, NSCaching, Uni-SANS with an absolute difference of +22.38, +6.45 and +7.16, respectively on WN18RR dataset.