Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Dietary Crude Protein Levels on Fecal Crude Protein, Amino Acids Flow Amount, Fecal and Ileal Microbial Amino Acids Composition and Amino Acid Digestibility in Growing Pigs

Simple Summary The purpose of this experiment was to evaluate a low protein corn-soybean meal-based diet with the same Lys, Met + Cys, Thr and Trp level as a high protein diet on fecal crude protein (CP), amino acid (AA) flow amount, AA digestibility and fecal and ileal microbial AA composition in growing pigs. Eighteen pigs with an initial body weight of (30 ± 1.35) kg were randomly divided into three groups, with six replicates in each group, and fed a corn-soybean meal-based diets with 12%, 15% and 18% CP levels, respectively. Our aim was to explain whether the addition of four crystalline essential AAs (EAA) to a low diet affected the digestibility of protein-bound NEAA (non-essential amino acid) and EAA and the composition of microbial AA in ileum and feces. Abstract The purpose of this experiment was to evaluate the effects of low protein corn-soybean meal-based diets on fecal CP, amino acid (AA) flow amount, AA digestibility and fecal and ileal microbial AA composition in growing pigs. Eighteen pigs (initial body weight = 30 ± 1.35) were randomly divided into three groups and fed with basal diets with CP levels of 12%, 15% and 18%, respectively. The Lys, Met + Cys, Thr and Trp level in the 12% CP and 15% CP groups is the same as 18% CP group by the addition of four crystalline Lys, Met + Cys, Thr and Trp to the diet. The results showed that with the decrease of dietary CP level from 18% to 12%, the fecal total nitrogen (N), CP and total AA (TAA) flow amount decreased linearly (p < 0.05). Dry matter (DM) digestibility, CP digestibility, TAA digestibility, essential amino acid (EAA) digestibility and non-essential amino acid (NEAA) digestibility increased linearly with the decrease of dietary CP concentration from 18% to 12%. Compared with 18% CP group, the flow amount of Asp, Ser, Glu, Gly, Tyr, Val, Leu and Phe in feces of pigs in the 15% CP group and 12% CP group decreased significantly, while the flow amount of Arg in the 15% CP group was lower than that in the 18% CP group and 12% CP group. The fecal microbial N and AA of the 15% CP group were higher than those of the 18% CP and 12% CP groups. Fecal TAA flow amount decreased linearly with the decrease of the dietary CP levels from 18% to 12%. Fecal TAA and NEAA flow amount also decreased linearly with the decrease of dietary CP level from 18% to 12%. Except for Glu, Gly, Met, Tyr, Thr and Phe, there were significant differences among the three groups in the composition of 17 kinds of AAs in fecal microorganisms. Among the 17 AA compositions of ileal microorganisms, except Tyr and Lys, the other AAs were significantly different among the three groups (p < 0.05)
Pairing of Parental Noroviruses with Unequal Competitiveness Provides a Clear Advantage for Emergence of Progeny Recombinants

Novel recombinants, generated from inter- and intraspecies recombination of norovirus lineages, often emerge and pose a threat to public health. However, the factors determining emergence of these particular recombinants from all possible combinations of parental lineages remain largely unknown. ABSTRACT Genetic recombination plays a pivotal role in the appearance of human norovirus recombinants that cause global epidemics. However, the factors responsible for the appearance of these recombinants remains largely unknown. In this study, we revealed a selective pressure that restricts parental combinations leading to the emergence of norovirus recombinants. To investigate traces of emerging novel recombinants and their parents in the human population, we isolated mass nucleotide sequence clones of human norovirus genogroups I and II in sewage-affected waters over a 4-year sampling period. Fourteen different phylogenetic combinations of recombinants and their parents were defined from the dozens of phylogenetic lineages circulating in the human population. To evaluate the probability of these combinations, parental lineages of each recombinant were categorized into two groups as HP (relatively higher-competitiveness parents) and LP (relatively lower-competitiveness parents), according to their relative detection frequency. Strong categorization of HP and LP was confirmed by tests with modified data and additional variables. An algorithm that was developed in this study to visualize the chance of mixed infection between parents revealed that HP lineages have a higher chance of mixed infection than LP lineages in the human population. Three parental pairing types in recombinants were defined: HP-HP, HP-LP, and LP-LP. Among these, most recombinants were identified as HP-LP, despite the prediction of dominant emergence of HP-HP-type recombinants. These results suggest that nature favors recombinants of human norovirus that originate from parental pairing of heterogeneous competitiveness. IMPORTANCE Novel recombinants, generated from inter- and intraspecies recombination of norovirus lineages, often emerge and pose a threat to public health. However, the factors determining emergence of these particular recombinants from all possible combinations of parental lineages remain largely unknown. Therefore, current investigations on these recombinants are inevitably limited to postepidemic analyses, which merely identify genetic or phenotypic changes in the newly emerged recombinants compared to their parents. Here, we provide a new theoretical concept that emergence of novel recombinants could be explained by a combination of parental noroviruses thriving in the human population and those circulating at lower levels. This study could provide an additional and important rationale for the proactive environmental monitoring of potential future epidemics due to viral recombinants.
Structure, Intensity and Player Duels in Under-13 Football Training in Switzerland

We evaluated the structure (i.e., the different training parts), contents (i.e., the various activities used), intensity and occurrence of contact situations and headers during training sessions in under-13 football in Switzerland. A total of 242 players from 20 different teams on average aged 11.4 (SD 0.7) years participated. The participants were filmed during a typical training session while they were equipped with a heart rate sensor. The sessions were systematically recorded to allow for detailed analyses. Furthermore, a preliminary and explorative analysis of the influence of the level of play on these results was conducted. The overall findings indicated that training included 33.4% playing forms, 29.5% training forms, 28.4% inactivity time and 8.7% athletics. The highest heart rates were achieved in the playing forms (166 min−1, 83% HRmax) compared to the other two activities (training forms 154 min−1, 77% HRmax; athletics 150 min−1, 75% HRmax). Each player had 12.8 duels and 0.6 headers per training. Overall, most duels were conducted from the anterior direction. Playing forms induce higher cardio-circulatory load as well as a better learning environment. Potentially dangerous situations like contact with other players or headers occurred in a single player on average every six min during a training session.
Expression Pattern of Connexin Gene Products at the Early Developmental Stages of the Mouse Cardiovascular System

Abstract The synchronized contraction of myocytes in cardiac muscle requires the structural and functional integrity of the gap junctions present between these cells. Gap junctions are clusters of intercellular channels formed by transmembrane proteins of the connexin (Cx) family. Products of several Cx genes have been identified in the mammalian heart (eg, Cx45, Cx43, Cx40, and Cx37), and their expression was shown to be regulated during the development of the myocardium. Cx43, Cx40, and Cx45 are components of myocyte gap junctions, and it has also been demonstrated that Cx40 was expressed in the endothelial cells of the blood vessels. The aim of the present work was to investigate the expression and regulation of Cx40, Cx43, and Cx37 during the early stages of mouse heart maturation, between 8.5 days post coitum (dpc), when the first rhythmic contractions appear, and 14.5 dpc, when the four-chambered heart is almost completed. At 8.5 dpc, only the reverse-transcriptase polymerase chain reaction techniqu.
Therapeutic Approaches to Treat Mitochondrial Diseases: “One-Size-Fits-All” and “Precision Medicine” Strategies

Primary mitochondrial diseases (PMD) refer to a group of severe, often inherited genetic conditions due to mutations in the mitochondrial genome or in the nuclear genes encoding for proteins involved in oxidative phosphorylation (OXPHOS). The mutations hamper the last step of aerobic metabolism, affecting the primary source of cellular ATP synthesis. Mitochondrial diseases are characterized by extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. The limited information of the natural history, the limitations of currently available preclinical models, coupled with the large variability of phenotypical presentations of PMD patients, have strongly penalized the development of effective therapies. However, new therapeutic strategies have been emerging, often with promising preclinical and clinical results. Here we review the state of the art on experimental treatments for mitochondrial diseases, presenting “one-size-fits-all” approaches and precision medicine strategies. Finally, we propose novel perspective therapeutic plans, either based on preclinical studies or currently used for other genetic or metabolic diseases that could be transferred to PMD.
YQFC: a web tool to compare quantitative biological features between two yeast gene lists

Abstract Nowadays high-throughput omics technologies are routinely used in biological research. From the omics data, researchers can easily get two gene lists (e.g. stress-induced genes vs. stress-repressed genes) related to their biological question. The next step would be to apply enrichment analysis tools to identify distinct functional/regulatory features between these two gene lists for further investigation. Although various enrichment analysis tools are already available, two challenges remain to be addressed. First, most existing tools are designed to analyze only one gene list, so they cannot directly compare two gene lists. Second, almost all existing tools focus on identifying the enriched qualitative features (e.g. gene ontology [GO] terms, pathways, domains, etc.). Many quantitative features (e.g. number of mRNA isoforms of a gene, mRNA half-life, protein half-life, transcriptional plasticity, translational efficiency, etc.) are available in the yeast, but no existing tools provide analyses on these quantitative features. To address these two challenges, here we present Yeast Quantitative Features Comparator (YQFC) that can directly compare various quantitative features between two yeast gene lists. In YQFC, we comprehensively collected and processed 85 quantitative features from the yeast literature and yeast databases. For each quantitative feature, YQFC provides three statistical tests (t-test, U test and KS test) to test whether this quantitative feature is statistically different between the two input yeast gene lists. The distinct quantitative features identified by YQFC may help researchers to study the underlying molecular mechanisms that differentiate the two input yeast gene lists. We believe that YQFC is a useful tool to expedite the biological research that uses high-throughput omics technologies. Database URL: http://cosbi2.ee. ncku.edu. tw/YQFC/
The Effect of Stress on Reproduction and Reproductive Technologies in Beef Cattle—A Review

Simple Summary The economic sustainability of beef herds relies on achieving a reliable percentage of weaned calves. Efforts to lift reproductive efficiency of beef herds have traditionally focused on physical health and nutrition aspects, by extrapolating knowledge from dairy herds. However, animal welfare and stress on beef farms is of outstanding importance. Stress affects the economic sustainability of the farm directly by reducing productive and reproductive performance, as well as indirectly by pushing away customers, who demand farming practices that ensure better animal welfare and lower stress. Despite its relevance and the increasing efforts made by the industry, the detailed ways in which stress influences reproduction of beef herds are still not well understood. Trying to contribute to clarity and reviewing the huge advances made in this topic, we describe the major factors contributing to stress in beef cattle and the effects of that stress on their reproductive performance. We highlight main stressors in beef, such as cattle management, handling stress while passing through the chutes, social hierarchy or weaning effects, besides the nutritional and climate stress and include the acclimatization, acclimation and temperament. We pay attention to the beef bull. And finally, we point out strategies demonstrated to alleviate stressful situations, improving reproductive performance. Abstract Researchers have contributed by increasing our understanding of the factors affecting reproduction in beef, mainly physical health and nutrition aspects, which have been main concerns during decades. Animal welfare is of outmost relevance in all animal production systems and it is strongly associated to stress. Stress responses involve endocrine, paracrine and neural systems and the consequences of this stress on the reproductive efficiency of specifically, beef cattle and bulls, need to be highlighted. We, therefore, describe the fundamentals of stress and its quantification, focusing in beef herds, reviewing the highly valuable pieces of research, already implemented in this field. We examine major factors (stressors) contributing to stress in beef cattle and their effects on the animals, their reproductive performance and the success of reproductive biotechnologies. We include terms such as acclimatization, acclimation or temperament, very relevant in beef systems. We examine specifically the management stress due to handling, social environment and hierarchy or weaning effects; nutritional stress; and thermal stress (not only heat stress) and also review the influence of these stressors on reproductive performance and effectiveness of reproductive biotechnologies in beef herds. A final message on the attention that should be devoted to these factors is highlighted.
Quantitative Microbial Risk Assessment Based on Whole Genome Sequencing Data: Case of Listeria monocytogenes

The application of high-throughput DNA sequencing technologies (WGS) data remain an increasingly discussed but vastly unexplored resource in the public health domain of quantitative microbial risk assessment (QMRA). This is due to challenges including high dimensionality of WGS data and heterogeneity of microbial growth phenotype data. This study provides an innovative approach for modeling the impact of population heterogeneity in microbial phenotypic stress response and integrates this into predictive models inputting a high-dimensional WGS data for increased precision exposure assessment using an example of Listeria monocytogenes. Finite mixture models were used to distinguish the number of sub-populations for each of the stress phenotypes, acid, cold, salt and desiccation. Machine learning predictive models were selected from six algorithms by inputting WGS data to predict the sub-population membership of new strains with unknown stress response data. An example QMRA was conducted for cultured milk products using the strains of unknown stress phenotype to illustrate the significance of the findings of this study. Increased resistance to stress conditions leads to increased growth, the likelihood of higher exposure and probability of illness. Neglecting within-species genetic and phenotypic heterogeneity in microbial stress response may over or underestimate microbial exposure and eventual risk during QMRA.
Prevalence of depression in Latin America and the Caribbean: a systematic review and meta-analysis protocol.

OBJECTIVE To evaluate the best available evidence to determine the prevalence of depression in the general population of Latin America and the Caribbean countries. INTRODUCTION Depression is a common mental disorder that affects quality of life and has been ranked as the largest contributor to non-fatal health loss. Knowledge of this disorder serves as a relevant instrument for policy makers and for the reassignment of public health resources. Although prevalence of depression is well documented in high-income countries, little is known about the prevalence in Latin America and the Caribbean. INCLUSION CRITERIA This review will include studies that report the prevalence of depression in the general adult (14 and older) population of countries in Latin America and the Caribbean. Non-representative subsets of the population will be excluded. METHODS The search strategy will be designed to obtain both published and unpublished studies. Information sources include PubMed, PsycINFO, Cochrane CENTRAL, and SciELO. Sources of unpublished studies include literature from government departments, international agencies, and academic institution repositories or websites. Eligible studies will be critically appraised for methodological quality. Prevalence estimates will be statistically pooled into a meta-analysis after heterogeneity interpretation; data not appropriate for pooling will be reported in a narrative review. Finally, risk of publication bias will be studied via funnel plot analysis and the Egger test. SYSTEMATIC REVIEW REGISTRATION NUMBER PROSPERO CRD42019143054.
RNF11 at the Crossroads of Protein Ubiquitination

RNF11 (Ring Finger Protein 11) is a 154 amino-acid long protein that contains a RING-H2 domain, whose sequence has remained substantially unchanged throughout vertebrate evolution. RNF11 has drawn attention as a modulator of protein degradation by HECT E3 ligases. Indeed, the large number of substrates that are regulated by HECT ligases, such as ITCH, SMURF1/2, WWP1/2, and NEDD4, and their role in turning off the signaling by ubiquitin-mediated degradation, candidates RNF11 as the master regulator of a plethora of signaling pathways. Starting from the analysis of the primary sequence motifs and from the list of RNF11 protein partners, we summarize the evidence implicating RNF11 as an important player in modulating ubiquitin-regulated processes that are involved in transforming growth factor beta (TGF-β), nuclear factor-κB (NF-κB), and Epidermal Growth Factor (EGF) signaling pathways. This connection appears to be particularly significant, since RNF11 is overexpressed in several tumors, even though its role as tumor growth inhibitor or promoter is still controversial. The review highlights the different facets and peculiarities of this unconventional small RING-E3 ligase and its implication in tumorigenesis, invasion, neuroinflammation, and cancer metastasis.
Charakterisierung und Einsatz eines tragbaren FTIR-Spektrometers

Die Arbeit beschaftigt sich mit der Charakterisierung des tragbaren FTIR-Spektrometers Designs & Prototypes Model 102. Daruber hinaus wurden verschiedene Methoden verwendet, um die Oberflachentemperatur und Emissivitat von Wasser und Calcit im thermalen Infrarotbereich von 625 - 3000 cm^-1 gleichzeitig zu bestimmen.
Clinical and laboratory signs of haemophagocytic lymphohistiocytosis associated with pandemic influenza A(H1N1) infection in patients needing extracorporeal membrane oxygenation: A retrospective observational study.

BACKGROUND Severe pandemic influenza has been associated with the hyperinflammatory condition secondary haemophagocytic lymphohistiocytosis (HLH). OBJECTIVES To determine the frequency, degree, character and possible cause of influenza-associated HLH in critically ill patients with severe acute respiratory distress syndrome due to influenza A(H1N1) infection requiring extracorporeal membrane oxygenation (ECMO) support at our hospital. DESIGN A retrospective observational study. PATIENTS AND SETTING Medical data were retrieved retrospectively from 11 consenting patients of thirteen adults infected with pandemic influenza A(H1N1) 2009 requiring ECMO between July 2009 and January 2010 at the ECMO Centre of Karolinska University Hospital, Stockholm, Sweden. All patients were evaluated for HLH using HLH-2004 criteria and HScore. RESULTS Eleven patients (median age 31 years) were included in the study and all survived. All patients showed signs of multiple organ dysfunction and pronounced inflammation, more severe in the four patients with HLH who had significantly higher peak serum concentrations of ferritin (P = 0.024), alkaline phosphatase (P = 0.012) and gamma-glutamyl transferase (P = 0.024), lower concentration of albumin (P = 0.0086) and more frequently hepatomegaly (P = 0.048). Abnormal lymphocyte cytotoxicity (lytic units <10) and a low proportion of natural killer (NK) cells were observed in three of four patients with HLH. Notably, we found a significant inverse correlation between serum ferritin concentration and NK cell and cytotoxic T lymphocyte percentages (rs = -0.74, P = 0.0013 and rs = -0.79, P = 0.0025, respectively). One HLH patient received HLH-directed cytotoxic therapy, another intravenous immunoglobulin and the other two no specific HLH-directed therapy. CONCLUSION Critically ill patients, including healthy young adults, with pandemic influenza may develop HLH and should be monitored for signs of hyperinflammation and increasing organ dysfunction, and evaluated promptly for HLH because HLH-directed therapy may then be beneficial. The association of low NK percentages with hyperferritinaemia may suggest a role for reduced NK cell numbers, possibly also cytotoxic T lymphocytes, and subsequently reduced lymphocyte cytotoxicity, in the pathogenesis of hyperinflammation and secondary HLH.
Trop2: Jack of All Trades, Master of None

Simple Summary Metastatic progression represents a major clinical challenge and remains the leading cause of death in cancer patients. Identification of suitable therapeutic targets, followed by a rational design of effective drug agents and their long-term, extensive pre-clinical and clinical testing is one of the key goals in cancer research. Trophoblast cell surface antigen 2 (Trop2) was first described as a protein highly expressed on the surface of trophoblast cells in 1981. Just recently, nearly 40 years after this discovery, sacituzumab govitecan, a Trop2-targeting antibody drug conjugate, has been granted an accelerated approval for therapy of metastatic triple-negative breast cancer, opening a new chapter of such successful story. The aim of this review is to summarize the current knowledge about Trop2 function in healthy tissue and pathology, with a special focus on its still controversial role in plasticity and heterogeneity during cancer progression. We further discuss the development and potential of Trop2-targeted therapy. Abstract Trophoblast cell surface antigen 2 (Trop2) is a widely expressed glycoprotein and an epithelial cell adhesion molecule (EpCAM) family member. Although initially identified as a transmembrane protein, other subcellular localizations and processed forms were described. Its congenital mutations cause a gelatinous drop-like corneal dystrophy, a disease characterized by loss of barrier function in corneal epithelial cells. Trop2 is considered a stem cell marker and its expression associates with regenerative capacity in various tissues. Trop2 overexpression was described in tumors of different origins; however, functional studies revealed both oncogenic and tumor suppressor roles. Nevertheless, therapeutic potential of Trop2 was recognized and clinical studies with drug–antibody conjugates have been initiated in various cancer types. One of these agents, sacituzumab govitecan, has been recently granted an accelerated approval for therapy of metastatic triple-negative breast cancer. In this article, we review the current knowledge about the yet controversial function of Trop2 in homeostasis and pathology.