bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a sports nutrition knowledge questionnaire for Sri Lankan athletes
Authors: Jayawardena Ranil , Weerasinghe Kalani , Trakman Gina , Madhujith Terrence , Hills Andrew P , Kalupahana Nishan Sudheera 
Published: July 2023

AbstractBackground:Satisfactory nutrition knowledge among athletes is important to encourage proper dietary habits to overcome deficiencies and enhance sports performance. Identifying knowledge gaps in sports nutrition is essential for improving athletes' understanding, ideally through a contemporary tool that evaluates both general nutrition knowledge (GNK) and sports nutrition knowledge (SNK). This study aims to develop the Athletic Sports Nutrition Knowledge Questionnaire (A-SNKQ) specifically for Sri Lankan track and field athletes.Methods:The development of the A-SNKQ followed an extensive step-wise approach. Firstly, a systematic literature review was conducted on existing SNK questionnaires for athletes. Secondly, sports nutrition guidelines were incorporated into the questionnaire. Thirdly, information from local literature was gathered to ensure contextual relevance. Lastly, a qualitative study involving key athletic stakeholders was conducted to gain cultural insights. Additional processes were implemented to format and translate the tool.Results:The final version of the questionnaire consists of 33 questions, categorized into 12 sub-sections under two main sections: GNK (n = 16) and SNK (n = 17). The GNK section covers topics such as macronutrients, micronutrients, energy balance, hydration, and weight management. The SNK section addresses specific areas related to sporting performance, including carbohydrate loading, pre-training meals, meals during training, post-training meals, sports supplements, supplement label reading, alcohol consumption, isotonic drinks, doping, and relative energy deficiency syndrome in sports (RED-S). The questionnaire utilizes two question formats, namely single-best response questions and multiple-choice questions. In addition, three sports supplement labels were included.Conclusions:The GNK section of the A-SNKQ addresses the fundamental nutritional concepts. Conversely, the SNK focuses on the knowledge associated with sporting performance among track and field athletes.
A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing
Authors: Gilfillan Gregor , Bjørnstad Pål , Aaløkken Ragnhild , Åsheim June , Sundaram Arvind , Felde Caroline , Østby Gina , Dalland Marianne , Carrizosa Christian , Vigeland Magnus , Sorte Hanne , Sheng Ying , Ariansen Sarah , Grindedal Eli , Sjursen Wenche 
Published: July 2023

Abstract
Lynch Syndrome (LS) is a hereditary cancer syndrome caused by pathogenic germline variants in one of the four mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. It is characterized by a significantly increased risk of multiple cancer types, particularly colorectal and endometrial cancer, with autosomal dominant inheritance. Access to precise and sensitive methods for genetic testing is important, as early detection and prevention of cancer is possible when the variant is known. We present here two unrelated Norwegian families with family histories strongly suggestive of LS, where immunohistochemical and microsatellite instability analyses indicated presence of a pathogenic variant in MSH2, but targeted exon sequencing and multiplex ligation-dependent probe amplification (MLPA) were negative. Using Bionano optical genome mapping, we detected a 39 kb insertion in the MSH2gene. Precise mapping of the insertion breakpoints and inserted sequence was performed by low-coverage whole-genome sequencing with an Oxford Nanopore MinION. The same variant was present in both families, and later found in other families from the same region of Norway, indicative of a founder event. To our knowledge, this is the first diagnosis of LS caused by a structural variant using these technologies. We suggest that structural variant detection be performed when LS is suspected but not confirmed with first-tier standard genetic testing.
Myocardial performance imaging for the early identification of cardiac dysfunction in neonates with sepsis
Authors: Sumbaraju Sudheshna Lalitha , Nayak Krishnananda , Prabhu Sridevi , Nayak Vidya , Prabhu K Prathiksha , Lewis Leslie Edward 
Published: July 2023

Abstract

Purpose:
The assessment of cardiac performance in septic new-borns is crucial for detecting hemodynamic instability and predicting outcome. The aim of the study is to assess myocardial performance in neonates with sepsis for the early identification of cardiac dysfunction
Material and methods:
A case control study was carried out from September 2022 to May 2023 at the NICU, KMC, Manipal. A total of 68 neonates were included in the study, with 33 female and 35 males. The study population was further subdivided into 3 groups namely preterm septic neonates (n=21), term septic neonates (n=10) and non-septic healthy controls (n=37). The cardiac structure and function were assessed using conventional method, Tissue Doppler imaging (Sm) and speckle tracking echocardiography (GLS)
The study was approved by the Institutional Ethics Committee, Kasturba Medical College, Manipal (approval number IEC: 90/2022). The CTRI registration number for the study is CTRI/2022/09/045437 and was approved on September 12, 2022. Prior to the neonate’s enrolment, informed consent was obtained from their mothers or legal guardians.
Results:
Out of the total 68 neonates, 31 were cases and 37 were controls which included 33 females and 35 males. LV systolic function was not statistically significant between cases and controls. E/A ratio of the mitral valve was significantly lower in septic newborns than in healthy neonates. preterm neonates showed significantly lower Lateral E’ and RV E’ velocities than term neonates. TAPSE was significantly lower in septic preterm neonates. No significant difference was noted in MPI between septic neonates and healthy neonates.LV GLS was slightly lower in preterm septic neonates than in term neonates with sepsis
Conclusion:
Septic newborns are associated with LV diastolic dysfunction, RV systolic dysfunction and substantially higher pulmonary systolic pressures.
DrugRep-HeSiaGraph: When heterogenous siamese neural network meets knowledge graphs for drug repurposing
Authors: Ghorbanali Zahra , Zare-Mirakabad Fatemeh , Salehi Najmeh , Akbari Mohammad , Masoudi-Nejad Ali 
Published: July 2023

Abstract
Background: The Drug repurposing is an approach that holds promise in identifying new therapeutic uses for existing drugs. Recently, knowledge graphs have emerged as significant tools for addressing the challenges of drug repurposing. However, there are still major issues in constructing and embedding knowledge graphs.
Results: This study proposes a two-step method called DrugRep-HeSiaGraph to address these challenges. The method integrates the drug-diseases knowledge graph with the application of a heterogeneous siamese neural network. In the first step, a drug-diseases knowledge graph named DDKG-V1 is constructed by defining new relationship types, and then numerical vector representations for the nodes are created using distributional learning method. In the second step, a heterogeneous siamese neural network called HeSiaNet is applied to enrich the embedding of drugs and diseases by bringing them closer in a new unified latent space. Then, it predicts potential drug candidates for diseases. DrugRep-HeSiaGraph achieves impressive performance metrics, including an AUC-ROC of 91.16%, an AUC-PR of 90.32%, an accuracy of 84.52%, a BS of 0.119, and an MCC of 69.12%.
Conclusion: We demonstrate the effectiveness of the proposed method in identifying potential drugs for COVID-19 as a case study. In addition, this study shows the role of dipeptidyl peptidase 4 (DPP-4) as a potential receptor for SARS-CoV-2 and the effectiveness of DPP-4 inhibitors in facing COVID-19. This highlights the practical application of the model in addressing real-world challenges in the field of drug repurposing.
Actionability and Familial Uptake Following Opportunistic Genomic Screening in a Pediatric Cancer Cohort
Authors: Birgitte Diness , Hammer-Hansen Sophia , Stoltze Ulrik , Bartels Emil , Hansen Thomas , Byrjalsen Anna , Tybjaerg-Hansen Anne , Juul Klaus , Schmiegelow Kjeld , Tfelt-Hansen Jacob , Bundgaard Henning , Wadt Karin 
Published: July 2023

Abstract

The care for patients with serious conditions is increasingly guided by genomic medicine, and genomic medicine may equally transform care for healthy individual if genomic population screening is implemented. This study examines the medical impact of opportunistic genomic screening (OGS) in a cohort of patients undergoing comprehensive genomic germline DNA testing for childhood cancer, including the impact on their relatives. Medical actionability and uptake after cascade testing in the period following disclosure of OGS results was quantified.
A secondary finding was reported to 19/595 (3,2%) probands primarily in genes related to cardiovascular and lipid disorders. After a mean follow up time of 1.6 years (IQR: 0.57-1.92 yrs) only 12 (63%) of these variants were found to be medically actionable. Thirty-eight relatives underwent additional genetic or clinical testing due to the return of the secondary finding. Clinical follow up or treatment was planned in 16 relatives, and as in the probands, the prescribed treatment was primarily betablockers or cholesterol lowering therapy. No invasive procedures or implantation of medical devices were performed in probands or relatives, and no reproductive counseling was requested. After an average of 1.6 years of follow-up 2.25 relatives per family with an actionable finding had been tested. This real-world experience of OGS grants new insight into the potentials, pitfalls and derived health care demands of genotype-first screening. If OGS is undertaken, the resulting health care effect and impact on demand for genetic counseling and workup in relatives extends beyond the effect in the probands.
Comparative Study of Encoded and Alignment-Based Methods for Virus Taxonomy Classification
Authors: Shaukat Muhammad Arslan , Nguyen Thanh Thi , Hsu Edbert B. , Yang Samuel , Bhatti Asim 
Published: July 2023

Abstract
The emergence of viruses and their variants has made virus taxonomy more important than ever before in controlling the spread of diseases. The creation of efficient treatments and cures that target particular virus properties can be aided by understanding virus taxonomy. Alignment-based methods are commonly used for this task, but are computationally expensive and time-consuming, especially when dealing with large datasets or when detecting new virus variants is time sensitive. An alternative approach, the encoded method, has been developed that does not require prior sequence alignment and provides faster results. However, each encoded method has its own claimed accuracy. Therefore, careful evaluation and comparison of the performance of different encoded methods are essential to identify the most accurate and reliable approach for virus taxonomy classification. This study aims to address this issue by providing a comprehensive and comparative analysis of the potential of encoded methods for virus classification and phylogenetics. We compared the vectors generated for each encoded method using distance metrics to determine their similarity to alignment-based methods. The results and their validation show that K-Mer followed by CgrDft encoded methods, perform similarly to state-of-the-art multi-sequence alignment methods. This is the first study to incorporate and compare encoded methods that will facilitate future research in making more informed decisions regarding selection of a suitable method for virus taxonomy.
From network analysis to experimental validation: identification of regulators of non-muscle myosin II contractility using the folded-gastrulation signaling pathway
Authors: Zhao Andy , Varady Sophia , O’Kelley-Bangsberg Madelyn , Deng Vicki , Platenkamp Amy , Wijngaard Petra , Bern Miriam , Gormerly Wyatt , Kushkowski Elaine , Thompson Kat , Tibbets Logan , Conner A. Tamar , Noeckel David , Teran Aidan , Ritz Anna , Applewhite Derek A. 
Published: July 2023

Abstract
The morphogenetic process of apical constriction, which relies on non-muscle myosin II (NMII) generated constriction of apical domains of epithelial cells, is key to the development of complex cellular patterns. Apical constriction occurs in almost all multicellular organisms, but one of the most well-characterized systems is the Folded-gastrulation (Fog)-induced apical constriction that occurs in Drosophila. The binding of Fog to its cognizant receptors Mist/Smog results in a signaling cascade that leads to the activation of NMII-generated contractility. Despite our knowledge of key molecular players involved in Fog signaling, we sought to explore whether other proteins have an undiscovered role in its regulation. We developed a computational method to predict unidentified candidate NMII regulators using a network of pairwise protein-protein interactions called an interactome. We first constructed a Drosophilainteractome of over 500,000 protein-protein interactions from several databases that curate high-throughput experiments. Next, we implemented several graph-based algorithms that predicted 14 proteins potentially involved in Fog signaling. To test these candidates, we used RNAi depletion in combination with a cellular contractility assay in DrosophilaS2R+ cells, which respond to Fog by contracting in a stereotypical manner. Of the candidates we screened using this assay, two proteins, the serine/threonine phosphatase Flapwing and the putative guanylate kinase CG11811 were demonstrated to inhibit cellular contractility when depleted, suggestive of their roles as novel regulators of the Fog pathway.
On a certain retarded Volterra-Fredholm type integral inequalities in several variables and applications
Authors: Ammar Boudeliou 
Published: July 2023

Abstract
In the present paper some new explicit bounds on solutions to a class of new nonlinear retarded integral inequalities of Volterra-Fredholm type of several variables are established. The results obtained extend some known results in the literature and can be used as useful tools in the analysis of the qualitative properties of solutions of certain integral and differential equations. An application is given to illustrate the usefulness of our results to the boundedness and the uniqueness of the solutions of Volterra-Fredholm type integral equation with delay in n variables.
MSC 2010: 26D15; 45B05; 45D05.
Characterization and transcriptome analysis of triadimefon-degrading strain Enterobacter hormaechei TY18
Authors: Wang Yan , Guan Qi , Zhao Rui , Li Jiangbo , Zhang Xiqian , Fan Weixin , Wang Chunwei 
Published: July 2023

Abstract

Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, extensive application of triadimefon contributes to austere environmental pollution, and even threatens human health. In our study, Enterobacter hormaechei strain TY18 could grew well in carbon salt medium (CSM) with triadimefon as sole nitrogen source, and could significantlydegrade triadimefon. Under triadimefon stress, a total of 430 differentially expressed genes (DEGs), including 197 up-regulated and 233 down-regulated DEGs, were found in strain TY18 from transcriptome sequencing (RNA-Seq). Functional classification and enrichment analysis revealed that these DEGs were mainly related to amino acid transport and metabolism, carbohydrate transport and metabolism, small molecule and pyrimidine metabolism. Interestingly, the DEGs encoding monooxygenase and hydrolase activity acting on carbon-nitrogen were highly up-regulated, might be mainly responsible for the metabolism in triadimefon. The finding in this work suggested that the novel strain E. hormaechei TY18 could degrade efficiently triadimefon for the first time, and contribute to further understanding of the degradation mechanism related to triadimefon in strain TY18.
Investigation on Reliability of Intelligent Transmission based Large Intelligent Meta-surface Assisted Downlink OMA systems
Authors: Shalini R. Baby , Priyadharsini Naveena A , Kumar J. Arun 
Published: July 2023

Abstract
Data transmission through large intelligent meta-surfaces (LIMs) is one of the trending and key enabling technologies for 6G and beyond mobile and wireless communication networks. While the wireless communication emerges, the channel characteristics are highly unpredictable and uncontrollable. But, LIMs can control the phase shift of individual user signals from base station, and thus improves the performance of the wireless communication link. This paper proposes a passive beamforming technique and provides phase optimization which helps to improve the communication quality, and thus improves the reliability of the wireless link. Also, spreading is used to improve the end user’s receiver performance. The error rate and capacity of the proposed system are calculated, and compared with decode and forward (DF) relaying scheme. The performance of LIMs is analysed with two different channel estimation approaches, and for different number of reflecting elements. The simulation is performed under the existing orthogonal multiple access (OMA) scheme, and it evidently shows the superiority of the proposed intelligent signal estimation method.
Transcriptional reprogramming during human osteoclast differentiation identifies regulators of osteoclast activity
Authors: Rauch Alexander , Hansen Morten , Madsen Kaja , Price Maria , Søe Kent , Omata Yasunori , Zaiss Mario , Gorvin Caroline , Frost Morten 
Published: July 2023

Abstract
Enhanced osteoclastogenesis and osteoclast activity contribute to the development of osteoporosis, which is characterized by increased bone resorption and inadequate bone formation. As novel anti-osteoporotic therapeutics are needed, understanding the genetic regulation of human osteoclastogenesis could help identify potential treatment targets. This study aimed to provide an overview of the transcriptional reprogramming during human osteoclast differentiation. Osteoclasts were differentiated from CD14+-monocytes from eight female donors. RNA-sequencing during differentiation demonstrated 8446 differentially expressed genes grouped into eight temporal patterns conserved across donors. These patterns showed distinct molecular functions, associated with postmenopausal osteoporosis susceptibility genes based on RNA from iliac crest biopsies, and bone mineral density SNPs. Network analyses showed mutual dependencies between the expression patterns and detected subspecific transcriptional networks. Differentially expressed G-protein coupled receptors showed strong expression during osteoclast differentiation and associated with bone mineral density SNPs, implying a pivotal role in osteoclast differentiation and activity. The regulatory effects of three differentially expressed G-protein coupled receptors were exemplified by in vitro pharmacological modulation of complement 5A receptor 1 (C5AR1), somatostatin receptor 2 (SSTR2), and free fatty acid receptor 4 (FFAR4/GPR120). Activating C5AR1 enhanced osteoclast formation, while activating SSTR2 decreased resorptive activity of mature osteoclasts, and activating FFAR4 decreased both number and resorptive activity of mature osteoclasts. In conclusion, we report the transcriptional reprogramming during human osteoclast differentiation and identified SSTR2 and FFAR4 as anti-resorptive G-protein coupled receptors. These data can help future investigations to identify molecular regulators of osteoclast differentiation and activity and provide the basis for novel anti-osteoporotic targets.
Nonlinear Modeling of Magnetic Materials for Circuit Simulations
Authors: Kutorasiński Kamil , Pawłowski Jarosław , Szewczyk Marcin , Leszczyński Paweł 
Published: July 2023

Abstract
Magnetic materials in the form of magnetic rings are widely used in power engineering products. In many cases, they operate in high frequency and in nonlinear conditions, e.g., as damping elements in electrical power substations equipped with Gas-Insulated Switchgear (GIS) where they provide suppression of Very Fast Transient Overvoltages (VFTOs). To model phenomena in GIS with magnetic rings it is required to have realistic time-dependent models of magnetic materials operating in a wide frequency range and nonlinear conditions. Nowadays, this has become even more relevant due to the actual trend in the industry to create digital twins of physical devices. Models composed of high-precise discrete lumped nonlinear elements are in demand in circuit simulators like SPICE. This work introduces a method based on classical algorithms that find equivalent lumped models of magnetic cores based on frequency-dependent measurements of impedance under DC-bias current. The model is specifically designed to achieve numerically stable simulations.
Association of Pulmonary Pathogenic Microbial Load and Cytokine Levels with Sepsis Mortality: A Cross- Sectional Study
Authors: Zhao Jian , Wang Xian-wen , Huang Dan , Xia Hui , Chen Yuan-zhuo , Zhuang Yu-gang 
Published: July 2023

Abstract
Background
Sepsis, a severe systemic inflammatory response resulting from an infection, often culminates in high mortality rates. Cytokines, specifically IL-10, and pathogenic microbial load, play a pivotal role in its pathogenesis. IL-10's integral role in immune regulation potentially impacts the clearance of pathogenic microorganisms and the disease's severity. However, the correlation between IL-10 levels, pulmonary pathogenic microbial load in sepsis, and their subsequent impact on patient prognosis remain unclear. Therefore, this study aims to elucidate the association between IL-10 levels, lung pathogenic microbial load, and their impact on the prognosis of sepsis.
Methods
We gathered clinical data from 79 patients with sepsis, including age, gender, BMI, history of chronic diseases, laboratory test results, cytokine levels, and mNGS analysis results. Univariate analysis and multivariate linear regression were utilized to examine the relationship between each variable and the pathogenicic microbial load in bronchoalveolar lavage fluid, as determined by mNGS. To further study the prognosis, patients were categorized based on the quantity of pathogenic microbes, and survival analysis was conducted using the Kaplan-Meier method.
Results
The study identified a significant positive correlation between cytokine IL-10 levels and the quantity of pathogenic microbes (β: 0.018,95%CI: 0.014 ~ 0.021,P value < 0.001). Multivariate linear regression analysis further confirmed this positive correlation (β:0.01,95%CI: 0.01 ~ 0.02,P value < 0.001), which held stable after adjusting for all potential confounders. Furthermore, Kaplan-Meier survival analysis revealed a significant increase in the 28-day mortality rate for sepsis patients when the count of pathogenic microbes reached or exceeded three.
Conclusion
Our study discloses the correlation between IL-10 levels and pathogenic microbial load, and their substantial predictive value for the short-term survival of sepsis patients. These findings highlight the critical importance of meticulous monitoring and managing of IL-10 levels and pathogenic microbial load in clinical practice. Timely intervention measures are particularly imperative for sepsis patients exhibiting both high IL-10 levels and pathogenic microbial load. These results provide fresh insights and understanding that can potentially enhance the clinical treatment and prognosis of sepsis.