Miracle-dz/UniFAR-FTUs huggingface dataset:
Porcine zona pellucida vaccine immunocontraception of African elephant (Loxodonta africana) cows: A review of 22 years of research

Background: The native porcine zona pellucida (pZP) vaccine has been successfully used for immunocontraception of wild horses, white-tailed deer and approximately 90 zoo species for more than 25 years.Objectives: To provide proof of concept and test contraceptive efficacy of pZP in African elephants. Once completed, test the population and behavioural effects on cows in the Greater Makalali Private Game Reserve (GMPGR). Following the GMPGR, test efficacy, population effects, safety and reversibility in 25 reserves with populations ranging from 9 to 700 elephants.Method: Histological sections were reacted with anti-pZP antibodies to provide proof of concept. From 1996 to 2000, 21 and 10 cows were treated with pZP vaccine in the Kruger National Park (KNP) and monitored for pregnancy. Population effects of pZP with Freund’s adjuvants (three vaccinations in Year 1 with one annual booster) were studied on 18 cows in the GMPGR. Another six game reserves with a total of 90 cows were added to the project. The project was then expanded to include another 18 reserves.Results: Binding of anti-pZP antibodies to elephant zona proteins was demonstrated in vitro. The KNP provided efficacy results of 56% and 80%, respectively. The contraceptive efficacy in the GMPGR and additional six reserves was 100% following calving of pregnant cows. Safety and lack of impact on social behaviour were demonstrated. In larger populations, efficacy was 95%. Conclusion: Contraceptive efficacy and safety of pZP vaccine could be demonstrated in small to large populations. The methodology is now being implemented in approximately 800 cows on 26 reserves across South Arica.
Disturbed interhemispheric functional connectivity in visual pathway in individuals with unilateral retinal detachment: A resting state fMRI study

Abstract Previous neuroimaging studies demonstrated that retinal detachment (RD) subjects were associated with abnormal spontaneous brain activities; however, whether the altered interhemispheric functional connectivity (FC) occurred in RD patients remains unknown. The current study tried to explore the alternations of interhemispheric FC of the whole brain in unilateral RD patients using the voxel-mirrored homotopic connectivity (VMHC) method and their connections to clinical features. Methods: We recruited 30 patients with RD (16 males and 14 females) and 30 healthy controls (HCs) (16 males and 14 females) whose age and sex were closely matched. All subjects underwent the rs-fMRI scans. The VMHC method was applied to directly assess the hemispheres’ functional interaction. The VMHC in these brain areas, which could be used as biomarkers to differentiate RD from HC, was identified by the receiver operating characteristic (ROC) curve analyses. The relations between these patients’ clinical features and their mean VMHC signal values in multiple brain regions were calculated by Pearson correlation analysis. Results: RD patients had significantly lower VMHC values than HCs in the bilateral occipital lobe (Brodmann areas, BA 18), bilateral superior temporal gyrus (BA 39), and bilateral cuneus (BA 19). Moreover, the mean VMHC signal values of the bilateral cuneus were in positive correlation with the duration of the RD (r = 0.446, P = 0.013). Conclusion: Our results provided an evidence of disturbed interhemispheric FC in the visual area occurred in RD patients, which might provide some useful information to understand the neural mechanism of RD patients with acute vision loss. Furthermore, the VMHC values might indicate the progress of the RD.
Immune cell infiltration and cytokine secretion analysis reveal a non-inflammatory microenvironment of medulloblastoma

Medulloblastoma (MB) is the most common lethal malignant pediatric brain tumor. Adjuvant immunotherapy for medulloblastoma has been proposed in both pre-clinical and clinical practice. To provide a precision strategy of designing immunotherapy for MB, the present study performed a descriptive analysis of immune microenvironment in a cohort and compared the differences between four subgroups of MB. Subtypes (WNT, SHH Group 3 and Group 4) of medulloblastoma were identified using K-means clustering according to the expression of signature genes. Tumor infiltrating immune cell population was assessed by both bio-informative algorithm based on gene expression and immunohistochemistry staining. Cytokines in tumor microenvironment were detected using Luminex. Gene Set Enrichment Analysis demonstrated a raised immune response in the SHH subgroup. Lymphocyte infiltration was low in all four subgroups, while more CD4+ T cells were observed in the Group 4 subtype. Programmed cell death protein 1 (PD1)/ ligand 1 (PD-L1) expression was absent in the cohort. The SHH subtype recruited more activated tumor associated macrophage/microglia compared with the other subgroups. Cytokines within the MB microenvironment were low compared with the glioblastoma samples. In contrast to glioblastoma, the immune microenvironment of pediatric MB is non-inflammatory and does not recruit many immune cells. These observations provide important considerations for the design of immunotherapeutic approaches for MB, such as inducing more lymphocytes into the tumor microenvironment.
A 14 immune-related gene signature predicts clinical outcomes of kidney renal clear cell carcinoma

Kidney renal clear cell carcinoma (KIRC) is the leading cause of kidney cancer-related deaths. Currently, there are no studies in tumor immunology investigating the use of signatures as a predictor of overall survival in KIRC patients. Our study attempts to establish an immune-related gene risk signature to predict clinical outcomes in KIRC. A total of 528 patients from The Cancer Genome Atlas (TCGA) database were included in our analysis and randomly divided into training (n = 315) and testing sets (n = 213). We collected 1,534 immune-related genes from the Immunology Database and Analysis Portal as candidates to construct our signature. LASSO-COX was used to find gene models with the highest predictive ability. We used survival and Cox analysis to test the model’s independent prognostic ability. Univariate analysis identified 650 immune-related genes with prognostic abilities. After 1,000 iterations, we choose 14 of the most frequent and stable immune-related genes as our signature. We found that the signature was associated with M stage, T stage, and pathological staging. More importantly, the signature can independently predict clinical prognosis in KIRC patients. Gene Set Enrichment Analysis (GSEA) showed an association between our signature and critical metabolism pathways. Our research established a model based upon 14 immune-related genes that predicted the prognosis of KIRC patients based on tumor immune microenvironments.
Reliability of a standing isokinetic shoulder rotators strength test using a functional electromechanical dynamometer: effects of velocity

Background The evaluation of the force in internal rotation (IR) and external rotation (ER) of the shoulder is commonly used to diagnose possible pathologies or disorders in the glenohumeral joint and to assess patient’s status and progression over time. Currently, there is new technology of multiple joint isokinetic dynamometry that allows to evaluate the strength in the human being. The main purpose of this study was to determine the absolute and relative reliability of concentric and eccentric internal and external shoulder rotators with a functional electromechanical dynamometer (FEMD). Methods Thirty-two male individuals (21.46 ± 2.1 years) were examined of concentric and eccentric strength of shoulder internal and external rotation with a FEMD at velocities of 0.3 m s−1 and 0.6 m s−1. Relative reliability was determined by intraclass correlation coefficients (ICC). Absolute reliability was quantified by standard error of measurement (SEM) and coefficient of variation (CV). Systematic differences across velocities testing circumstances, were analyzed with dependent t tests or repeated-measures analysis of variance in case of 2 or more than 2 conditions, respectively. Results Reliability was high to excellent for IR and ER on concentric and eccentric strength measurements, regardless of velocity used (ICC: 0.81–0.98, CV: 5.12–8.27% SEM: 4.06–15.04N). Concentric outcomes were more reliable than eccentric due to the possible familiarization of the population with the different stimuli. Conclusion All procedures examined showed high to excellent reliability for clinical use. However, a velocity of 0.60 m s−1 should be recommended for asymptomatic male patients because it demands less time for evaluation and patients find it more comfortable.
Naringin Attenuates High Fat Diet Induced Non-alcoholic Fatty Liver Disease and Gut Bacterial Dysbiosis in Mice

The incidence of non-alcoholic fatty liver disease (NAFLD) is rising annually, and emerging evidence suggests that the gut bacteria plays a causal role in NAFLD. Naringin, a natural flavanone enriched in citrus fruits, is reported to reduce hepatic lipid accumulation, but to date, no investigations have examined whether the benefits of naringin are associated with the gut bacteria. Thus, we investigated whether the antilipidemic effects of naringin are related to modulating the gut bacteria and metabolic functions. In this study, C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks, then fed an HFD with or without naringin administration for another 8 weeks. Naringin intervention reduced the body weight gain, liver lipid accumulation, and lipogenesis and attenuated plasma biochemical parameters in HFD-fed mice. Gut bacteria analysis showed that naringin altered the community compositional structure of the gut bacteria characterized by increased benefits and fewer harmful bacteria. Additionally, Spearman’s correlation analysis showed that at the genus level, Allobaculum, Alloprevotella, Butyricicoccus, Lachnospiraceae_NK4A136_group, Parasutterella and uncultured_bacterium_f_Muribaculaceae were negatively correlated and Campylobacter, Coriobacteriaceae_UCG-002, Faecalibaculum and Fusobacterium were positively correlated with serum lipid levels. These results strongly suggest that naringin may be used as a potential agent to prevent gut dysbiosis and alleviate NAFLD.
COVID-19 Pandemic: Adaptation in Antenatal Care for Better Pregnancy Outcomes

Department of Preventive & Community Dentistry, School of Dentistry, University of Rwanda College of Medicine and Health Sciences, Kigali, Rwanda, Department of Nursing, School of Nursing and Midwifery, University of Rwanda College of Medicine and Health Sciences, Kigali, Rwanda, Department of Midwifery, School of Nursing and Midwifery, University of Rwanda College of Medicine and Health Sciences, Kigali, Rwanda, Department of Pathology, Lake Erie College of Osteopathic Medicine, Erie, PA, United States, Department of Obstetrics & Gynecology, Chittagong Medical College
The mRNA and lncRNA landscape of the non-pregnant endometrium during the oestrus cycle in dairy goat

Cyclic changes in the endometrium are essential for embryo implantation in mammals; many studies report that such changes constitute a complex process involving numerous molecular mediators. In the present study, goat endometria at oestrus Day 5 and oestrus Day 15 were selected to systematically analyse the transcriptome using strand-specific Ribo-Zero RNA sequencing. Over 120 million high-quality paired-end reads were generated and 440400 transcripts were identified in the endometrial tissue of dairy goats. In total, 489 differentially expressed mRNAs and 854 differentially expressed long non-coding RNAs were identified when comparing the endometrium at goat endometria at oestrus Day 5 and oestrus Day 15. Neurotensin was found to play a potentially important role in the non-pregnant goat endometrium during the oestrus cycle. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses of the cis-target genes of the differentially expressed long non-coding RNAs showed that GO:0005198 (structural molecule activity) and ko04510 (focal adhesion) might be involved in cyclic endometrial changes. Taken together, the resulting transcriptomic profiles elucidate global trends in mRNA and lncRNA expression in non-pregnant endometria during the oestrus cycle in dairy goats.
SARS-CoV-2 antibody signatures for predicting the outcome of COVID-19

The COIVD-19 global pandemic is far from ending. There is an urgent need to identify applicable biomarkers for predicting the outcome of COVID-19. Growing evidences have revealed that SARS-CoV-2 specific antibodies remain elevated with disease progression and severity in COIVD-19 patients. We assumed that antibodies may serve as biomarkers for predicting disease outcome. By taking advantage of a newly developed SARS-CoV-2 proteome microarray, we surveyed IgM/ IgG responses against 20 SARS-CoV-2 proteins in 1,034 hospitalized COVID-19 patients on admission, who were followed till 66 days. The microarray results were correlated with clinical information, laboratory test results and patient outcomes. Cox proportional hazards model was used to explore the association between SARS-CoV-2 specific antibodies and COVID-19 mortality. We found that high level of IgM against ORF7b at the time of hospitalization is an independent predictor of patient survival (p trend = 0.002), while levels of IgG responses to 6 non-structural proteins and 1 accessory protein, i. e. , NSP4, NSP7, NSP9, NSP10, RdRp (NSP12), NSP14, and ORF3b, possess significant predictive power for patient death, even after further adjustments for demographics, comorbidities, and common laboratory markers for disease severity (all with p trend < 0.05). Spline regression analysis indicated that the correlation between ORF7b IgM, NSP9 IgG, and NSP10 IgG and risk of COVID-19 mortality is linear (p = 0.0013, 0.0073 and 0.0003, respectively). Their AUCs for predictions, determined by computational cross-validations (validation1), were 0.74 (cut-off = 7.59), 0.66 (cut-off = 9.13), and 0.68 (cut-off = 6.29), respectively. Further validations were conducted in the second and third serial samples of these cases (validation2A, n = 633, validation2B, n = 382), with high accuracy of prediction for outcome. These findings have important implications for improving clinical management, and especially for developing medical interventions and vaccines.
Estimation and Uncertainty of the Mixing Effects on Scots Pine—European Beech Productivity from National Forest Inventories Data

An increasing amount of research is focusing on comparing productivity in monospecific versus mixed stands, although it is difficult to reach a general consensus as mixing effects differ both in sign (over-yielding or under-yielding) and magnitude depending on species composition as well as on site and stand conditions. While long-term experimental plots provide the best option for disentangling the mixing effects, these datasets are not available for all the existing mixtures nor do they cover large gradients of site factors. The objective of this study was to evaluate the effects and uncertainties of tree species mixing on the productivity of Scots pine–European beech stands along the gradient of site conditions in Europe, using models developed from National and Regional Forest Inventory data. We found a positive effect of pine on beech basal area growth, which was slightly greater for the more humid sites. In contrast, beech negatively affected pine basal area growth, although the effects switched to positive in the more humid sites. However, the uncertainty analysis revealed that the effect on pine at mid- and more humid sites was not-significant. Our results agree with studies developed from a European transect of temporal triplets in the same pine–beech mixtures, confirming the suitability of these datasets and methodology for evaluating mixing effects at large scale.
Statistical Machine Translation between Myanmar (Burmese) and Dawei (Tavoyan)

This paper contributes the first evaluation of the quality of statistical machine translation (SMT) between Myanmar (Burmese) and Dawei (Tavoyan). We also developed a Myanmar-Dawei parallel corpus (around 9K sentences) based on the Myanmar language of ASEAN MT corpus. The 10 folds cross-validation experiments were carried out using three different statistical machine translation approaches: phrase-based, hierarchical phrase-based, and the operation sequence model (OSM). In addition, two types of segmentation were studied: word and syllable segmentation. The results show that all three statistical machine translation approaches give comparable BLEU and RIBES scores for both Myanmar to Dawei and Dawei to Myanmar machine translations. OSM approach achieved the highest BLEU and RIBES scores among three SMT approaches for both word and syllable segmentation.
Penalized longitudinal mixed models with latent group structure, with an application in neurodegenerative diseases

Large-scale longitudinal data are often heterogeneous, spanning latent subgroups such as disease subtypes. In this paper, we present an approach called {it longitudinal joint cluster regression} (LJCR) for penalized mixed modelling in the latent group setting. LJCR captures latent group structure via a mixture model that includes both the multivariate distribution of the covariates and a regression model for the response. The longitudinal dynamics of each individual are modeled using a random effect intercept and slope model. Inference is done via a profile likelihood approach that can handle high-dimensional covariates via ridge penalization. LJCR is motivated by questions in neurodegenerative disease research, where latent subgroups may reflect heterogeneity with respect to disease presentation, progression and diverse subject-specific factors. We study the performance of LJCR in the context of two longitudinal datasets: a simulation study and a study of amyotrophic lateral sclerosis (ALS). LJCR allows prediction of progression as well as identification of subgroups and subgroup-specific model parameters.
Molecular Basis Underlying Common Cutworm Resistance of the Primitive Soybean Landrace Peking

The common cutworm (CCW; Spodoptera litura) is one of the major insect pests of soybean in Asia and Oceania. Although quantitative trail loci related to CCW resistance have been introduced into leading soybean cultivars, these do not exhibit sufficient resistance against CCW. Thus, understanding the genetic and metabolic resistance mechanisms of CCW as well as integrating other new resistance genes are required. In this study, we focused on a primitive soybean landrace, Peking, which has retained resistances to various pests. We found a resistance to CCW in Peking by the detached-leaf feeding assay, and subsequently determined the genetic and metabolic basis of the resistance mechanism using chromosome segment substitution lines (CSSLs) of Peking. Several characteristic metabolites for Peking were identified by the metabolomic approach using liquid chromatography/mass spectrometry combined with a principle component analysis. The structure of seven metabolites were determined by nuclear magnetic resonance (NMR) analysis. The genomic segments of Peking on chromosome 06 (Chr06) and Chr20 had a clear association with these metabolites. Moreover, a line possessing a Peking genomic segment on Chr20 inhibited growth of the CCW. The genetic factors and the metabolites on Chr20 in Peking will be useful for understanding mechanisms underlying CCW resistance and breeding resistant soybean cultivars.
Metabolomic/lipidomic profiling of COVID-19 and individual response to tocilizumab

The current pandemic emergence of novel coronavirus disease (COVID-19) poses a relevant threat to global health. SARS-CoV-2 infection is characterized by a wide range of clinical manifestations, ranging from absence of symptoms to severe forms that need intensive care treatment. Here, plasma-EDTA samples of 30 patients compared with age- and sex-matched controls were analyzed via untargeted nuclear magnetic resonance (NMR)-based metabolomics and lipidomics. With the same approach, the effect of tocilizumab administration was evaluated in a subset of patients. Despite the heterogeneity of the clinical symptoms, COVID-19 patients are characterized by common plasma metabolomic and lipidomic signatures (91.7% and 87.5% accuracy, respectively, when compared to controls). Tocilizumab treatment resulted in at least partial reversion of the metabolic alterations due to SARS-CoV-2 infection. In conclusion, NMR-based metabolomic and lipidomic profiling provides novel insights into the pathophysiological mechanism of human response to SARS-CoV-2 infection and to monitor treatment outcomes.
Leave No Trace Communication: Effectiveness Based on Assessments of Resource Conditions

The efficacy of different Leave No Trace (LNT) communication interventions designed to persuade forest visitors to practice low-impact camping behaviors were evaluated. Three depreciative campsite behaviors—littering, tree damage, and surface disposal of human waste—were evaluated by before-and-after resource condition assessments. Three LNT communication interventions were evaluated against a control: (1) an LNT brochure and poster display (non-personal), (2) personal LNT communication by a forest naturalist, and (3) a combination of both non-personal and personal methods. The study population was overnight campers using dispersed road-accessed campsites in Western Maryland’s Green Ridge State Forest. LNT communication successfully improved resource conditions for the targeted depreciative behaviors. For litter and human waste, personal communication by a forest naturalist was effective, but the non-personal method was ineffective. In contrast, tree damage was significantly reduced by both non-personal and personal communication methods. Combining personal and non-personal communication efforts did not result in an increased benefit. The core implication of this study is that several camping resource impacts can be measurably reduced when uniformed staff personally communicate the desired low impact practices.
Nutrient Enrichment Improves Growth and Food Quality of Two Strains of the Economic Seaweed Pyropia haitanensis

Chinese coastal waters are subject to eutrophication because of rapid economic development and population growth. To study the effects of nutrient enrichment on the growth and quality of Pyropia haitanensis, the thalli of a red-brown (Z-61) strain and a green (Z-26) strain of P. haitanensis were cultured semi-continuously for 15 days in four media with different nitrogen and phosphorus concentrations. High-nutrient conditions had no significant effect on the growth rate of Z-26 and Z-61. Higher concentrations of nutrients increased the chlorophyll a content of Z-61 and Z-26 by 116.7 and 34.2%, respectively. High concentrations of nutrients also significantly increased the average phycoerythrin and phycocyanin contents by 57.4 and 56.0%, respectively (strain Z-61); and by 37.7 and 44.7%, respectively (strain Z-26). As the nitrogen and phosphorus concentrations increased, the mean contents of total protein, essential amino acids, and flavor amino acids increased by 130.0, 102.5, and 341%, respectively, for strain Z-61, and by 25.1, 23.9, and 497%, respectively, for strain Z-26. Under high-nutrient conditions, the mean total amino acids content was 40.7% higher in Z-26 than in Z-61; the total flavor amino acids content was 117% higher in Z-61 than in Z-26; but there was no significant difference in the total essential amino acids content between the two strains. Interestingly, under low-nutrient conditions, Z-26 had a higher nutritional value than Z-61, but Z-61 tasted better than Z-26. Based on the results of these laboratory experiments, nutrient enrichment might enhance the market value of P. haitanensis by significantly improving its food quality.