bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole Brain 3D MR Fingerprinting in Multiple Sclerosis: A Pilot Investigation
Authors: Mostardeiro Thomaz R. , Panda Ananya , Campeau Norbert G. , Witte Robert J. , Sui Yi , Lu Aiming , McGee Kiaran P. 
Published: January 2021

Abstract
Background: MR fingerprinting (MRF) is a novel imaging method proposed for the diagnosis of Multiple Sclerosis (MS). This study aims to determine if MR Fingerprinting (MRF) relaxometry can differentiate frontal normal appearing white matter (F-NAWM) and splenium in patients diagnosed with MS as compared to controls and to characterize the relaxometry of demyelinating plaques relative to the time of diagnosis.Methods: Three-dimensional (3D) MRF data were acquired on a 3.0T MRI system resulting in isotropic voxels (1x1x1mm3) and a total acquisition time of 4min 38s. Data were collected on 18 subjects paired with 18 controls. Regions of interested were drawn over MRF-derived T1 relaxometry maps encompassing selected MS lesions, F-NAWM and splenium. T1 and T2 relaxometry features from those segmented areas were used to classify MS lesions from F-NAWM and splenium with T-distributed stochastic neighbor embedding algorithms (T-SNE). Partial least squares discriminant analysis (PLS-DA) was performed to discriminate NAWM and Splenium in MS compared with controls. Results: Mean out-of-fold machine learning prediction accuracy for discriminant results between MS patients and controls for F-NAWM was 65% and approached 90% for the splenium. There was significant positive correlation between time since diagnosis and MS lesions mean T2 (p=0.015), minimum T1 (p=0.03) and negative correlation with splenium uniformity (p=0.04). Perfect discrimination (AUC=1) was achieved between selected features from MS lesions and F-NAWM.Conclusions: 3D-MRF has the ability to differentiate between MS and controls based on relaxometry properties from the F-NAWM and splenium. Whole brain coverage allows the assessment of quantitative properties within lesions that provide chronological assessment of the time from MS diagnosis.
Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle
Authors: Cai Wentao , Li Cong , Li Junya , Song Jiuzhou , Zhang Shengli 
Published: January 2021

Abstract
BackgroundMilk protein is one of the most important economic traits in the milk industry. Our previous study has revealed some functional genes responsible for milk protein synthesis in mammals. Yet, the miRNA-mediated gene regulatory network for the synthesis of milk protein in mammary is poorly understood. Results12 samples from Chinese Holstein Cows with three too high and three low phenotypic values for milk protein percentage in lactation and non-lactating were examined through deep small RNA sequencing. By bioinformatics analysis, we characterized 387 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. Using genome-wide association signal (GWAS) enrichment analysis among five milk production traits, we found the differentially expressed targets were significantly related to milk protein traits.ConclusionsThis integrated study on the transcriptional and post-transcriptional regulatory profiles between significantly differential phenotype of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.
Supplementation of a Lacto-fermented Rapeseed-seaweed Blend Promotes Gut Microbial- and Gut Immune-Modulation in Weaner Piglets
Authors: Hui Yan , Tamez-Hidalgo Paulina , Cieplak Tomasz , Satessa Gizaw Dabessa , Kot Witold , Søren Søren Kjærulff , Nielsen Mette Olaf , Nielsen Dennis Sandris , Krych Lukasz 
Published: January 2021

Abstract
BackgroundThe direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders.ResultsThis study assessed whether rapeseed meal added two brown macroalgae species (Saccharina latissima and Ascophylum nodosum) and fermented using lactic acid bacteria (FRS) could improve weaner piglet performance and gut health. From day 28 of life to day 85, the weaned piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. The piglets fed with 2.5% FRS manifested superior phenotype with alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier and numerical increase of final body weight. The colon microbiota composition was determined using the V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina Nextseq and Oxford Nanopore MinION, respectively. The two amplicon sequencing strategies showed high consistence between the detected bacteria. Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaner piglets with increased Shannon diversity. Prevotella stercorea was verified by both technologies to be more abundant in the FRS piglets, and its abundance was positively correlated with colon mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG.ConclusionsFRS supplementation improved the gut health of weaner piglets, and reshaped the gut microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.
Polypharmacology-based Approach for Screening of Traditional Chinese Medicinal extract and Multi-dimensional Targeting Verification
Authors: Wu Zhiyong , Xia Chunli , Wang Ze , Bao Jiaxin , Li Rui , Ishfaq Muhammad , Li Jichang 
Published: January 2021

Abstract
Background: Natural products and their unique polypharmacology offer significant advantages for finding novel therapeutics particularly for the treatment of complex diseases. Meanwhile, natural products in traditional Chinese medicine possess drug-like properties. In this study, we used the previously established co-infection model of Mycoplasma gallisepticum and Escherichia coli as a representative of complex diseases. The multi-omics joint analysis was used to reverse screen TCMs from the Chinese medicinal database and then targeted verification was conducted from multiple dimensions. Results: The results showed that the Chinese herbal compound screened by the target network played a good therapeutic effect in the case of co-infection. Furthermore, the four methods were performed at gene, protein, and metabolite levels, as well as molecular docking in vitro respectively, which were used to verify the multi-target therapeutic effect. Conclusions: These data suggest that we may provide a new method to validate target combinations of natural products that can be used to optimize their multiple structure-activity relationships to obtain drug-like natural product derivatives. Furthermore, the study could establish a new methodology for the research of Chinese herbal medicinal extract and provide a new multi-target treatment method for the occurrence of co-infection.
Health Anxiety, Perceived Stress, and Coping Styles in the Shadow of the COVID-19
Authors: Garbóczy Szabolcs , Szemán-Nagy Anita , Ahmad Mohamed S. , Harsányi Szilvia , Ocsenás Dorottya , Rekenyi Viktor , Al-Tammemi Ala'a B. , Kolozsvári László Robert 
Published: January 2021

Abstract
Background In the case of people who carry an increased number of anxiety traits due to their maladaptive coping strategies, psychosocial stressors may further increase the level of perceived stress they experience. In our research study, we aimed to examine perceived stress and health anxiety levels as well as coping styles among students at one of the higher education institutions in Hungary, in the midst of the COVID-19 pandemic.Methods A cross-sectional study was conducted using an online-based survey at the University of Debrecen, during the official lockdown in Hungary when dormitories were closed, and teaching was conducted using online platforms. Our questionnaire solicited information using three international scales, namely, the Perceived Stress Scale (PSS), the Ways of Coping Questionnaire (WCQ), and the Short Health Anxiety Inventory (SHAI).Results A total of 1320 students have participated in our study, of whom 6 responses were excluded due to incompleteness. Among the remaining 1314 participants, 948 (72.1%) and 366 (27.9%) were Hungarian and international students, respectively. Female students predominated the overall sample with 939 participants (71.5%). In general, there was a statistically significant positive relationship between perceived stress and health anxiety. Health anxiety and perceived stress levels were significantly higher among international students compared to the Hungarian ones. Also, the elevation in perceived stress was significantly greater among students who mostly used emotion-focused coping strategies, both in the Hungarian and in the international student samples. Besides, a higher proportion of international students used emotion-focused coping methods compared to Hungarian students. Concerning health anxiety, female students (Hungarian and international) had significantly higher levels of health anxiety compared to males. Moreover, female students had significantly higher levels of perceived stress compared to males in the international group, however, there was no significant difference in perceived stress between males and females in the Hungarian group. Conclusion People’s elevated perceived stress levels during major life events can be further deepened by disengagement from home by using inadequate coping methods. By following and adhering to international recommendations that primarily convey problem-focused strategies, people’s emotional-focus strategies and the associated higher levels of perceived stress may be mitigated.
PEAK Predicts Gene Regulatory Network Linkages during Sea Urchin Development with High Sensitivity from Gene Expression Data Alone
Authors: Zhang Jingyi , Ibrahim Farhan , Altarawy Doaa , Heath Lenwood S , Tulin Sarah 
Published: January 2021

Abstract
BackgroundGene regulatory network (GRN) inference can now take advantage of powerful machine learning algorithms to predict the entire landscape of gene-to-gene interactions with the potential to complement traditional experimental methods in building gene networks. However, the dynamical nature of embryonic development -- representing the time-dependent interactions between thousands of transcription factors, signaling molecules, and effector genes -- is one of the most challenging arenas for GRN prediction. ResultsIn this work, we show that successful GRN predictions for developmental systems from gene expression data alone can be obtained with the Priors Enriched Absent Knowledge (PEAK) network inference algorithm. PEAK is a noise-robust method that models gene expression dynamics via ordinary differential equations and selects the best network based on information-theoretic criteria coupled with the machine learning algorithm Elastic net. We test our GRN prediction methodology using two gene expression data sets for the purple sea urchin (S. purpuratus) and cross-check our results against existing GRN models that have been constructed and validated by over 30 years of experimental results. Our results found a remarkably high degree of sensitivity in identifying known gene interactions in the network (maximum 76.32%). We also generated 838 novel predictions for interactions that have not yet been described, which provide a resource for researchers to use to further complete the sea urchin GRN. ConclusionsGRN predictions that match known gene interactions can be produced using gene expression data alone from developmental time series experiments.
Coupling the structure evolution and the oxygen redox electrochemistry in layered transition metal oxides
Authors: Eum Donggun , Kim Byunghoon , Song Jun-Hyuk , Park Hyeokjun , Kim Sung Joo , Cho Sung-Pyo , Jang Ho-Young , Lee Myeong Hwan , Heo Jae Hoon , Ko Youngmin , Park Sung Kwan , Oh Kyungbae , Kim Do-Hoon , Kang Kisuk 
Published: January 2021

Abstract
Lattice oxygen redox activity offers an unexplored way to access the latent superior electrochemical property of transition metal oxides for rechargeable batteries. However, the redox reaction of the lattice oxygen is often accompanied by unfavorable structural transformations and the corresponding degradation of electrochemical performances, precluding its practical application. Herein, we explore the close interplay between the local structural change during the dynamic intercalation process and the solid-state oxygen electrochemistry in the short- or long-term battery operation for layered transition metal oxides. By employing two model systems of the layered Na0.6(Li0.2TixMn0.8−x)O2 with the oxygen redox capability, it is demonstrated that the substantially distinct evolutions in the oxygen redox activity and reversibility are caused by different cation migration mechanisms available in the system during the de/intercalation (i.e. out-of-plane and in-plane migrations of transition metals (TMs)). We show that the π stabilization upon the oxygen oxidation initially aids in the reversibility of the oxygen redox and is predominant in the absence of TM migrations, however, the π-interacting oxygens are gradually replaced by the σ-interacting oxygens that trigger the formation of O–O dimers and the structural destabilization over cycles. More importantly, it is revealed that the distinct TM migration paths available in the respective layered materials govern the conversion from π to σ interactions and its kinetics. It infers that regulating the dynamics of TMs in the layered materials can play a key role in delaying or inhibiting the deterioration of the oxygen redox reversibility. These findings constitute a step forward in unraveling the correlation between the local structural evolution and the reversibility of solid-state oxygen electrochemistry, and provide a guidance for developing oxygen-redox layered electrode materials.
What Motivates Smoking Cessation? A Cross-Sectional Study in a Lower-Middle-Income Country
Authors: Martins Russell , Junaid Muhammad Umer , Khan Muhammad Sharjeel , Aziz Namrah , Fazal Zoha Zahid , Umoodi Mariam , Shah Fatima , Khan Javaid 
Published: January 2021

Abstract
IntroductionOnly one-quarter of smokers in Pakistan attempt to quit smoking, and less than 3% are successful. In the absence of any literature from the country, this study aimed to explore factors motivating and strategies employed in successful smoking cessation attempts in Pakistan, a lower-middle-income country.MethodsA survey was carried out in Karachi, Pakistan, amongst adult (≥ 18 years) former smokers (individuals who had smoked ≥ 100 cigarettes in their lifetime but who had successfully quit smoking for > 1 month at the time of survey). Multivariable logistic regression, adjusted for age, gender and monthly family income, was performed with number of quit attempts (single vs. multiple) as the dependent variable.ResultsOut of 330 former smokers, 50.3% quit successfully on their first attempt (50.3%) with 62.1% quitting “cold turkey”. Only 10.9% used a cessation aid (most commonly nicotine replacement therapy; 8.2%). Motivations for quitting included self-health (74.5%), promptings by one’s family (43%), and family’s health (14.8%). Other social pressures included peer-pressure to quit smoking (31.2%) and social avoidance by non-smokers (22.7%). Successful smoking cessation on one’s first attempt was associated with being married (OR: 3.239 [95% CI:1.593-6.585]), employing an abrupt cessation mode of quitting (4.144 [2.512-6.836]), and telling oneself that one has the willpower to quit (1.635 [1.027-2.604]).ConclusionIn Pakistan, smoking cessation is motivated by concern for self-health and family’s health, family’s support, and social pressures. Our results lay a comprehensive foundation for the development of smoking-cessation interventions tailored to the population of the country.
A Novel Nomogram Based on Lipid Metabolism-Related Risk Gene Expression Can Better Predict Overall Survival for Hepatocellular Carcinoma
Authors: Lu Qiliang , hu linjun , zeng zhi , xiao zunqiang , wang yuyang , liu yang , zhao junjun , shi zhan , tu yifeng , zhu ning , xu qiuran , huang dongsheng 
Published: January 2021

Abstract
Metabolic reprogramming has been proven to be a hallmark of cancer. The pathogenic factors involved in Hepatocellular carcinoma (HCC) lead to an abnormal lipid metabolism that facilitates the malignant transformation of liver cells . However, the association between lipid metabolism and the prognosis of HCC has not been systematically delineated. In this study, the training set comprised 221 patients from The Cancer Genome Atlas (TCGA) based on the gene expression details, whereas 230 patients within the International Cancer Genome Consortium (ICGC) comprised the validation set. Ten lipid metabolism-related risk genes were screened; they were found to be significantly related to the prognosis of HCC. The risk score was calculated based on ten screened lipid metabolism-related risk genes and was confirmed to be an independent prognostic factor for HCC even when excluding clinical features. Therefore, a novel nomogram integrating the risk score and other proven clinical attributes was constructed. The results of the area under the receiver operating characteristics curve (AUC), C index, and calibration plot supported the better predictive capacity of the nomogram over others. Treatment with metformin significantly positively affected the expression of four out of ten genes; this was beneficial to longer overall survival. The results provide a new insight into accurate prognostic prediction, as well as understanding the carcinogenesis and process of HCC .
2009-2019: A comparative study on CMS of plateau migrants around ten years
Authors: Gao Zhiqi , Xie Shenwei , Gao Wenxiang , Yin Jun , Ni Bing , Gao Yuqi , He Wenjuan , Chen Dewei 
Published: January 2021

Abstract
BackgroundChronic mountain sickness (CMS), is a common disease occurred to people who migrate to plateau. Current CMS studies in different periods or areas have poor comparability due to the inconsistent diagnosis methods. Here we carried out a comparative study of the CMS prevalence in the year 2019 and 2009, to provide evidence for the prevention and diagnosis of CMS. Methods The Qinghai CMS Scoring System (Qinghai standard) was used to investigate the subjects who lived for at least months in the 3300-5400 m altitude area in 2019 and 2009, respectively. Their prevalence and symptom scores were also analyzed and statistically compared.ResultsThe prevalence of CMS in 2019 survey subjects (15.60%) was significantly lower than that in 2009 (31.18%). The prevalence of dyspnea, venous dilatation, paresthesia, headache, tinnitus, and hemoglobin concentration reached 21g/dL or above decreased significantly among the survey subjects in 2019. The scores of cyanosis, venous dilatation, paresthesia, and headache significantly decreased in the 2019 survey subjects. But among the CMS patients, the sleep disturbance scores of the 2019 survey subjects increased significantly. ConclusionCompared to 2009, the health level of high altitude living population in 2019 has been significantly improved, indicating that the sleep research on high-altitude living population and the application of high altitude oxygen therapy has been effective in the past ten years. Among the CMS associated symptoms, sleep disturbance is an important indicator for the prevention and diagnosis of CMS, which deserves special attention.
Application of Extended Finite Element Method in Fracture Propagation Simulation of Plastic Formation
Authors: Hu Yafei , Li Junshi , WU Zhiying , Hou Jianfeng 
Published: January 2021

Abstract
Current hydraulic fracture models are mainly based on elastic theories, which fail to give accurate prediction of fracture parameters in plasticity formation. This paper proposed a fluid–solid coupling model for fracture propagation in elastoplastic formations. The rock plastic deformation in the model satisfied the Mohr-Coulomb yield criterion and plastic strain increment theory. The coupled model is solved by using extended finite-element method(XFEM) and the cohesive zone method (CZM). The accuracy of the model is verified by comparing the calculated results with existing models. The influences of stress difference, friction angle and dilation angle on fracture shape (length, width), injection pressure, plastic deformation, induced stress and pore pressure are investigated. The results indicate that compared with elastic formation, fracture shape in elastoplastic formation is wider and shorter and fracture propagation is more difficult with greater breakdown pressure and extending pressure. Plastic deformation also cause blunt fracture tip. High stress difference or low friction angle formations tend to occur large plastic deformation area and form wide and short fracture. Compared with friction angle, dilation angle is less sensitive to plastic deformation and fracture parameters and geometry. For the formation with high stress difference and friction angle, plasticity effects on fracture propagation should not be ignored.