bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut Microbial Shifts By Synbiotic Combination of Pediococcus Acidilactici and Lactulose In Weaned Piglets Challenged With Shiga Toxin-Producing Escherichia coli
Authors: Guevarra Robin B. , Cho Jae Hyoung , Cho Jin Ho , Song Minho , Lee Jun Hyung , Kim Hyeri , Kim Sheena , Kim Eun Sol , Keum Gi Beom , Kang Jung Sun , Cho Won Tak , Lee Chan Ho , Watthanaphansak Suphot , Kim In Ho , Kim Hyeun Bum 
Published: June 2021

Abstract
Background: Development of alternatives to in-feed antibiotics in the swine industry have been the focused of many pig gut microbiota studies to improve animal health. In this study, we evaluated the effects of probiotic Pediococcus acidilactici (PRO), prebiotic lactulose (PRE), and their synbiotic combination (SYN) on weaned pig gut microbiota using 16S rRNA gene sequencing in weaned piglets challenged with Shiga-toxin producing Escherichia coli (STEC). Results: Our data showed that prebiotics, probiotics and synbiotics improved the intestinal health in weaned piglets. No significant differences were observed in species richness and species diversity in weaned piglets fed prebiotics, probiotics and their synbiotic combination. However, beta diversity analysis revealed distinct clustering of the microbiota of according to dietary treatment and by oral challenge of STEC. At the phylum level, Firmicutes to Bacteroidetes ratio was lower in the dietary treatment groups than the control group. Oral supplementation of prebiotics, probiotics and synbiotics enriched the abundance of Prevotella and Roseburia. Succinivibrio was elevated in PRO group; however, Phascolarctobacterium was depleted with STEC challenge regardless of dietary treatment. Overall, our data showed that administration of synbiotics in piglets improved intestinal health through gut microbiota modulation. Conclusions: Our data indicated that prebiotics, probiotics and their synbiotic combination could promote intestinal health through gut microbiota modulation in weaned piglets.
M2-Polarized Macrophages Mediate Wound Healing by Regulating Connective Tissue Growth Factor via AKT, ERK 1/2, and STAT 3 Signaling Pathways
Authors: Zhang Si-Min , Wei Chuan-Yuan , Wang Qiang , Wang Lu , Lu Lu , Qi Fa-Zhi 
Published: June 2021

Abstract
Background: Timely and sufficient recruitment of M1 macrophages and M2 polarization are necessary for fibrous repair during cutaneous wound healing. The inherent mechanism of how M2 polarization mediate wound healing is worth exploring and illustrating. Abnormally up-regulated connective tissue growth factor (CTGF) is closely related with multiple organ fibrosis, including cardiac, pulmonary, hepatic, renal, and cutaneous fibrosis. Previous studies have reported that M2-polarized macrophages contribute to hepatic and renal fibrosis by secreting CTGF. It is worth discussing if M2 macrophages regulate fibrosis through secreting CTGF in cutaneous wound healing.Methods: We established the murine full-thickness excisional wound model and inhibited macrophages during proliferation phase (mainly M2 and M1-M2 polarization) with clodronate liposomes to analyze how M2 macrophages mediate wound healing rates, collagen deposition, collagen 1/3 expression, and Ki67 expression in vivo. Furthermore, M2 polarization was induced by IL-4 and in vitro. F4/80+CD206+ M2 macrophages were measured by flow cytometry. The morphological characteristics were observed. Secretion of IL-6, TNF-α, IL-10, TGF-β1, and CTGF was tested by ELISA. CTGF gene of M2 was blocked using siCTGF. Effects of M2 on proliferation and migration of fibroblasts were detected by CCK8 and cellular wound healing assay. Protein level of AKT, ERK1/2, and STAT3 pathway were assessed by western blotting.Results: Depletion of macrophages at proliferation phase (mainly M2 and M1-M2 polarization) resulted in delayed cutaneous wound closure and down-regulation of wound healing rates, collagen deposition, collagen 1/3 expression, and Ki67 expression. M2 polarization was induced, which producing more CTGF, TGF-β1, and IL-6, as well as less TNF-α and IL-10. Blockade of CTGF in M2 macrophages deactivated fibroblast proliferation and migration. Addition of recombinant CTGF restored the promotional effects of M2 macrophages on fibroblast proliferation and migration. Blockade of CTGF in M2 mediate fibroblasts via down-regulating AKT, ERK1/2, and STAT3 signaling pathway.Conclusion: Our research, for the first time, indicated that M2-polarized macrophages promoted cutaneous wound healing by secreting CTGF, which further mediating proliferation and migration of fibroblasts via AKT, ERK1/2, and STAT3 signaling pathway.
Visual analytics of combustion on time-varying turbulent-flow
Authors: An Yifei , Shan Guihua , Liu Jun , Yang Bo 
Published: June 2021

Abstract
Visualization is crucial for analyzing the turbulent combustion simulation. Time-varying data allows us to investigate the evolution process of the turbulent flow field. To study the combustion effects, we calculated the enstrophy of the flow field since high enstrophy region can display valuable features, and extract components based on these features. We isolated large components to track their behaviors and characterized them using volume and spatial locations, which helps scientists to explore the dynamics and temporal changes of intense events individually. We analyzed the components' structures and visualized them in contouring and statistical charts.
Identification of Natural Selection in Genomic Data with Deep Convolutional Neural Network
Authors: Fadja Arnaud Nguembang , Riguzzi Fabrizio , Bertorelle Giorgio , Trucchi Emiliano 
Published: June 2021

Abstract
Background: With the increase in the size of genomic datasets describing variability in populations, extracting relevant information becomes increasingly useful as well as complex. Recently, computational methodologies such as Supervised Machine Learning and specifically Convolutional Neural Networks have been proposed to order to make inferences on demographic and adaptive processes using genomic data, Even though it was already shown to be powerful and efficient in different fields of investigation, Supervised Machine Learning has still to be explored as to unfold its enormous potential in evolutionary genomics. Results: The paper proposes a method based on Supervised Machine Learning for classifying genomic data, represented as windows of genomic sequences from a sample of individuals belonging to the same population. A Convolutional Neural Network is used to test whether a genomic window shows the signature of natural selection. Experiments performed on simulated data show that the proposed model can accurately predict neutral and selection processes on genomic data with more than 99% accuracy.
“Making It Okay”: Professionals in High-stress Environments Construct Their Understanding of the Impact of a Yoga-based Retreat Designed to Build Resilience
Authors: Reeves Tegan Jemma , Dyer Natalie L. , Borden Sara , Dusek Jeffery A. , Khalsa Sat Bir Singh 
Published: June 2021

Abstract
Background: While there is growing evidence for resilience building programs, to date research has not explored how professionals construct their understanding of program impact. Methods: Using a qualitative exploration of reflections on a yoga-based retreat at Kripalu Center for Yoga & Health, nested in a larger study, the current inquiry aims to explore long-term perceptions of an occupation-oriented program designed to improve resilience. Called RISE (resilience, integration, self-awareness, engagement), the immersion program was a 5-day professional development for professionals in high-stress jobs. Through a grounded constructivist lens, inductive coding and iterative thematic analysis was employedResults: Semi-structured interviews of 17 adult professionals who attended RISE, conducted 3 months after completion of the program, illustrated two integrated perceptions woven through five themes. Persistent threads of experiential learning and sense of permission provided structure for themes found. Five interrelated themes related to psychological health and workplace dynamics were: (1) use of acquired behavioral skills and practices; (2) lived mindfulness; (3) resilience to stress and emotion regulation (4) self-care and self-compassion, and (5) sharing with others. Conclusion: Findings provide meaningful interpretation of previously reported program efficacy by contextualizing perceived benefits within participants constructed understanding of change. Specifically, environmental, social, and experiential considerations have suggested implications for resilience building programs.
Predation Risk is a Function of Seasonality Rather than Habitat Complexity in a Tropical Semi-arid Forest
Authors: Ferreira Anthony , Faria Renato 
Published: June 2021

Abstract
Predator-prey dynamic is one of the most important species’ interactions in the natural structuring of communities, and is among the more complex ecological processes studied by ecologists. We measure predation risk using artificial lizard replicas to test two competing hypotheses regarding predation pressure in semi-arid environments: (1) predation risk is dependent on the habitat structural complexity; and (2) predation risk is dependent on seasonality. We placed 960 replicas along three sites with different physical structures and in both seasons for seven consecutive days in a caatinga area in northeastern Brazil. Birds were responsible for the majority of attacks and more frequently on artificial lizards placed in trees. Attacks focused on the most vulnerable areas of the body (head and torso), proving that were perceived by predators as true prey items. We found that predation risk is not dependent on the habitat structural complexity, but rather dependent on the caatinga seasonality, with the overall attack being 19% higher in the dry season. Our study suggests that potential predation risk is highly context-dependent and that seasonality consistently drives of trophic interactions strength in the caatinga, an important ecological finding that could contribute to better understanding the complex evolution of predator-prey interactions within communities of animals living in different habitats.
Risk Evaluation of Early-stage Hormone Receptor-positive and Human Epidermal Growth Factor Receptor 2-negative Breast Cancer Patients: a Population-based Study From Taiwan
Authors: Lei Lei , Chan Han-Ching , Lu Tzu-Pin , Cheng Hung-Chun Skye 
Published: June 2021

Abstract
PURPOSE: To assess the prognostic value of the Dutch criteria for patients with early-stage hormone receptor-positive and human epidermal growth factor receptor 2-negative breast cancer from the Taiwan Cancer Database. PATIENTS AND METHODS:We included 8,295 patients with early-stage node-negative breast cancer who underwent surgery during January 2008–December 2012. Patients were stratified into low- and high-risk groups based on the Dutch criteria. The Kaplan–Meier method and log-rank test were used to estimate the difference in breast cancer-specific survival (BCSS) and overall survival (OS) between groups. Multivariable analysis was used to evaluate the prognostic value of the Dutch criteria.RESULTS: Overall, the low-risk and high-risk groups comprised 5,375 and 2,920 patients, respectively. In the low- and high-risk groups, the 5-year BCSS rate was 99.6% and 98.2% (P<0.0001) and the 5-year OS rate was 98.3% and 96.8% (P<0.0001), respectively. The hazard ratio for BCSS was 4.18 (95% confidence interval [CI], 2.63–6.63, P<0.0001), and the hazard ratio for OS was 1.94 (95% CI, 1.48–2.55); both were significantly poorer in the high-risk group than in the low-risk group. In the low-risk group, the 5-year BCSS and OS of patients who did and did not receive adjuvant chemotherapy were similar (99.5% versus 99.6% [P=0.927] and 98.8% and 98.1% [P=0.0683], respectively). CONCLUSIONS: The prognosis of low-risk patients as classified using the Dutch criteria is excellent with or without adjuvant chemotherapy. The benefit of multi-gene testing for chemotherapy decision-making might be minimal in these patients.
Acromegaly Disease Activity According to ACRODAT®, in Spain: ACROVAL Study
Authors: Marazuela Monica , Blanco Concepción , Bernabeu Ignacio , Menendez Edelmiro , Villar Rocío , Paja Miguel , Sampedro-Nuñez Miguel , Samaniego Maria Luz , Díaz-Muñoz Marcos , Sánchez-Cenizo Laura 
Published: June 2021

Abstract
Objectives: To evaluate disease activity status using the Acromegaly Disease Activity Tool (ACRODAT®) in a cohort of Spanish acromegaly patients, to assess the relationship between the level of disease activity according to both ACRODAT® and the physicians’ clinical evaluation, and to study the potential discrepancies in the perception of symptoms between physicians and patients.Design: Multicenter, observational, descriptive and cross-sectional study. Methods: Disease activity was assessed in adult patients with acromegaly under pharmacological treatment during at least 6 months using ACRODAT®.Results: According to ACRODAT®, 48.2%, 31.8% and 20.0% of a total of 111 patients were classified as having a stable disease (S), mild disease activity (M-DA) and significant disease activity (S-DA) respectively. ACRODAT® classification of disease activity significantly correlated with physicians’ opinion, with a moderate inter-rater agreement and a specificity of 92.45% (PPV=86.21%). No correlation was found between IGF-1 levels and severity of symptoms or quality of life (QoL). A decision to take clinical action was significantly more frequent in S-DA and M-DA patients than S patients but no action was taken on 5 (22.7%) and 27 (77.1%) S-DA and M-DA patients, respectivelyConclusions: ACRODAT® detected disease activity in 51.8% of patients. Interestingly, although M-DA and S-DA patients were likely to be in the process of being controlled, action was not always taken on these patients. ACRODAT® is a validated and highly specific tool that may be useful to routinely monitor acromegaly and to identify patients with non-obvious disease activity by incorporating “patient-centered” parameters like symptoms and QoL to the clinical evaluation of acromegaly.
Genetic Diversity of Meat Quality Related Genes in Argentinean Pigs
Authors: Rodriguez Viviana Rita , Maffioly Joaquin Ignacio , Zdanovicz Lara Azul , Fabre Romina , Barrandeguy Maria Eugenia , García Maria Victoria , Lagadari Mariana 
Published: June 2021

Abstract
Background: The genetic influence on pork quality exists between breeds and within a breed. The variation is caused by a large set of genes and pork quality traits have a multi factorial background. Research into the genetics of meat quality found causative mutations associated with marked effects on pig meat value. The main objective of this study was to investigate the diversity of single nucleotide polymorphisms (SNPs) of meat quality-related genes in pigs from commercial and family farms in the North-West of Argentina. A screen for SNPs in RYR1, RN, CAST, and SOX6 candidate genes and the differentiation of their genotypes by PCR–RFLP was conducted. Results: All genes were characterized by a high level of polymorphism and heterozygosity. Additionally, both populations, commercial and Creole pigs, showed genetic closeness for the analyzed SNPs and a moderate selection for RYR1 and RN loci consistent with their allele´s adverse effects. Conclusions: The results obtained here highlighted the role of pig genotypes as a source of basic variability potentially affecting processed meat products as well as fresh meat.
In-Silico Design of Peptides for Inhibition of HLA-A*03-KLIETYFSK Complex as a New Drug Design for Treatment of Multiples Sclerosis Disease
Authors: Ghobadi Zahra , mahnam karim , Shakhsi-Niaei Mostafa 
Published: June 2021

Abstract
Multiple sclerosis is recognized as a chronic inflammatory disease. Human leukocyte antigen (HLA) plays an important role in initiating adaptive immune responses. HLA class I is present in almost all nucleated cells and presents the cleaved endogenous peptide antigens to cytotoxic T cells. HLA-A*03 is one of the HLA class I alleles, which is reported as substantially related HLA to MS disease. In 2011, structure of the HLA-A*03 in complex was identified with an immunodominant proteolipid protein (PLP) epitope (KLIETYFSK). This complex has been reported as an important autoantigen-presenting complex in MS pathogenesis. In this study, new peptides were designed to bind to this complex that may prevent specific pathogenic cytotoxic T cell binding to this autoantigen-presenting complex and CNS demyelination. Herein, 14 new helical peptides containing 19 amino acids were designed and their structures were predicted using the PEP-FOLD server. Binding of each designed peptide to the mentioned complex was then performed. A mutation approach was used by the BeAtMuSiC server to improve binding affinity of the designed peptide. In each position, amino acid substitutions leading to an increase in binding affinity of the peptide to the mentioned complex were determined. Finally, the resulting complexes were simulated for 40 ns using AMBER18 software. The results revealed that out of 14 designed peptides, “WRYWWKDWAKQFRQFYRWF” peptide exhibited the highest affinity for binding to the mentioned complex. This peptide can be considered as a potential drug to control multiple sclerosis disease in patients carrying the HLA-A*03 allele.
Tree diversity and natural regeneration in Tropical Dry Deciduous Forest of Panna Tiger Reserve, India
Authors: Parveen Talat , Ilyas Orus 
Published: June 2021

Abstract
The disturbance is a major factor driving the decline of tropical forests and their associated fauna. Henceforth, basic information on species diversity would be useful for assessing the success of management in the fragmented and human-disturbed landscape. We accounted for tree species diversity and their regeneration pattern from the tropical dry deciduous forest of Panna Tiger Reserve (PTR), India. Considering this, random vegetation sampling along with transects was carried out in different ranges of PTR. It is spread over in an area of 2998.98 km2 that situated in the northern part of Madhya Pradesh and distributed in Panna and Chhatarpur district. The tropical dry deciduous forest inventory in the 10.6132-ha area yielded a total of 46 woody species of > 10 cm GBH, belonged to 23 Families and 40 genera. The regeneration represented 27 species of < 30 cm height (seedling) under 16 families and 24 genera while sapling, which ranges from > 30cm to 1.3m, showed 24 species of 13 families and 32 genera. The Shannon diversity of Trees, seedlings, and saplings was 2.684, 2.525, and 2.401 respectively. A total stand density and basal area of 2391 stems of trees were estimated as 225.285 stand ha− 1 and 90.016 m2ha− 1 respectively. Tectona grandis scored the highest IVI value of 59.44 (19.81% of total IVI for all species) among the dominated tree species, followed by Acacia catechu (24.94), Abrus precatorius (23.25), Zizyphus xylopyra (22.94), Anogeissus latifolia (22.16) and Lagerstroemia parviflora (22.18). Nearly 23.913% of the total number of species was recorded as rare species. The highest seedling density was obtained for Diospyros melanoxylon followed by Zizyphus xylopyra, Aegle marmelos, Wrightia tintoria, and Tectona grandis, which declined in the subsequent sapling stage and showed a reverse pattern. Hence, the highest sapling density was recorded for Tectona grandis then Aegle marmelos, Wrightia tintoria, Diospyros melanoxylon, and Zizyphus xylopyra. A total of 36.956% of tree species were found to fail to establish in the community because species were represented by only adult or tree stage that listed as Not-regenerating. In terms of the most diverse family among the plant categories; viz. Tree, Seedling, Sapling, Fabaceae had the highest species richness. The highest tree stand density (127.576 stand ha− 1) was recorded in the girth class of 31-60cm (48.687% of the total tree stand density) followed by 10-30cm and 61-90cm. Likewise, a total basal area of 20.824 m2ha− 1 was occupied by 31-60cm that contributed 23.051% of the total basal area, so our data on the population structure of forest shows a similar trend wherein the distribution curve exponentially decreases with increasing girth classes that indicates not only a mid-successional forest but also a human-disturbed.
The Anti-Inflammatory Activity of Palmitoylethanolamide Ameliorates Osteoarthritis Induced by Monosodium Iodoacetate in Sprague Dawley Rats
Authors: Jung Jae In , Lee Hyun Sook , Jeon Young Eun , Kim So Mi , Hong Su Hee , Moon Joo Myung , Lim Cho Young , Kim Yoon Hee , Kim Eun Ji 
Published: June 2021

Abstract
Novel treatment strategies are urgently required for osteoarthritis (OA), a degenerative joint disease. Palmitoylethanolamide (PEA) is a naturally occurring fatty acid amide with analgesic and anti-inflammatory effects. We aimed to examine its effect on OA and molecular mechanism of actions in monosodium iodoacetate (MIA)-induced OA Sprague Dawley rats. The experimental animals were divided into five groups: normal control group (injected with saline + treated with phosphate-buffered saline (PBS), NOR), control group (injected with MIA + treated with PBS, CON), 50 or 100 mg/kg body weight (BW)/day PEA-treated group (injected with MIA + treated with 50 or 100 mg of PEA/kg BW/day, PEA50 or PEA 100), and positive control group (injected with MIA + treated with 6 mg of diclofenac/kg BW/day, DiC). Changes in blood and body parameters, gene expression of inflammatory mediators and cytokines, knee thickness, and joint tissue were observed. We found no adverse effects of oral administration of PEA on BW, liver, or kidneys. PEA reduced knee joint swelling and cartilage degradation in MIA-induced OA rats. The serum levels of leukotriene B4, nitric oxide, tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and prostaglandin E2 considerably reduced in the PEA100 group compared to those in the CON group. In the synovia of knee joints, mRNA expression of iNOS, 5-Lox, Cox-2, Il-1β, Tnf-α, Mmp-2, -3, -9, and − 13 noticeably reduced with MIA administration. Meanwhile, Timp-1 mRNA expression noticeably decreased in the CON group but increased to the normal level with PEA treatment. Thus, we demonstrated that PEA can be used as an effective therapeutic agent for OA.
A Novel Nomogram for Predicting Cancer-specific Survival in Women With Uterine Sarcoma: a Large Population-based Study
Authors: Li Yuan-jie , Lyu Jun , Li Chen , He Hai-rong , Wang Jin-feng , Wang Yue-ling , Fang Jing , Ji Jing 
Published: June 2021

Abstract
Background: To perform a comprehensive nomogram to predict the cancer-specific survival (CSS) for uterine sarcoma (US) based on the Surveillance, Epidemiology, and End Results (SEER) database.Methods: A total of 3861 patients with US between 2010 and 2015 were identified in this study. They were randomly divided into a training cohort (n = 2702) and a validation cohort (n = 1159) in a 7-to-3 ratio by R software. We performed multivariate Cox analysis to select predictive variables and identify independent prognostic factors. Then, the discrimination and calibration of the nomogram were evaluated by concordance index (C-index) and the area under the curve (AUC). Finally, the net reclassification improvement (NRI), the integrated discrimination improvement (IDI), calibration plotting, and decision-curve analysis (DCA) were used to evaluate the benefits of the new prediction model.Results: We have established a nomogram to predict 1-, 3-, and 5-year CSS for US patients. In this nomogram, pathology grade has the highest risk on CSS in US, followed by age at diagnosis, then surgery status. Comparing to the AJCC staging system, the nomogram showed better predictive discrimination with higher C-index in both training and validation cohort (0.796 and 0.767 vs0.706 and 0.713, respectively) . Furthermore, AUC value, calibration plotting, NRI, IDI, and DCA also demonstrated better performance than the traditional system.Conclusion: Our study validated the first comprehensive nomogram for US which could provide more accurately and individualized survival predictions for US patients in clinical practice.