Miracle-dz/UniFAR-FTUs huggingface dataset:
Intake, ruminal parameters and plasmatic urea concentration in beef cattle fed diets with different levels of sunflower cake in substitution to the cotton meal.

O objetivo deste trabalho foi avaliar os efeitos da torta de girassol (TG), em cinco niveis de substituicao ao farelo de algodao, sobre o consumo de materia seca (CMS), pH e concentracao de nitrogenio amoniacal (N-NH 3 ) no liquido ruminal e de ureia plasmatica em novilhos de corte. As racoes foram isoproteicas (13,0% PB) e isoenergeticas (72,0% NDT). A silagem de cana-de-acucar in natura , como volumoso, foi utilizada na proporcao de 40% da MS fornecida. Foram utilizados cinco animais fistulados no rumen, machos, castrados, ½ sangue Simental x Nelore, pesando em media 380 kg e 24 meses. Os tratamentos foram: 0% (TG0); 25% (TG25); 50% (TG50); 75% (TG75) e 100% (TG100) de torta de girassol (base na MS) em substituicao ao farelo de algodao. O experimento foi conduzido em quadrado latino 5 x 5, sendo 5 animais e 5 periodos. Cada periodo experimental teve duracao de 15 dias. Os animais alimentados com a racao TG0 ingeriram mais (P 3 do liquido ruminal e ureia plasmatica. Conclui-se que a torta de girassol pode ser usada em substituicao ao farelo de algodao em racoes suplementares visando medias taxas de ganho diario, pois esta em altos niveis de substituicoes do farelo de algodao acarretou menor ingestao de MS.
Genetic study for seed yield and seed quality traits in indian mustard [Brassica juncea L. Czern&coss.]

Combining ability, gene action and heterosis was studied in a set of seven lines, five testers and 35 hybrids of Indian mustard following L x T mating design. The ratio σ2gca/σ2sca was less than one, for the traits, viz., days to flowering, plant height, number of branch per plant, number of siliquae per plant, seed yield per plant, 1000-seed weight, oil content, lenoleic acid content and lenolenic acid content, which suggested greater role of non-additive genetic variance in the inheritance of these traits. The cross CJ 3761 x GM 3 recorded the highest heterosis (22.70%) over check variety GDM 4, followed by ZEM 2 x Kranti (12.06%), while hybrid CJ 3761 x GM 3 exhibited highest heterobeltiosis (75.35%). Parents CJ 3761, DRMR-659-49, ZEM 1, ZEM 2, GM 1 and GM 3 were good combiners for seed yield per plant. ZEM 1 was found to be good combiner for number of branches per plant, number of siliquae per plant, oil content and linolenic acid. Considering mean performance, heterosis and combining ability effects, the parents CJ 3761, DRMR-659-49, ZEM 1, ZEM 2, GM 1 and GM 3 and the hybrids CJ 3761 x GM 3, ZEM 2 x Kranti and DRMR-659-49 x GM 2 were found to be promising for the development of high yielding genotypes.
Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes

Pseudogenes are indicating more and more functional potentials recently, though historically were regarded as relics of evolution. Computational methods for predicting pseudogene functions on Gene Ontology is important for directing experimental discovery. However, no pseudogene-specific computational methods have been proposed to directly predict their Gene Ontology (GO) terms. The biggest challenge for pseudogene function prediction is the lack of enough features and functional annotations, making training a predictive model difficult. Considering the close functional similarity between pseudogenes and their parent coding genes that share great amount of DNA sequence, as well as that coding genes have rich annotations, we aim to predict pseudogene functions by borrowing information from coding genes in a graph-based way. Here we propose Pseudo2GO, a graph-based deep learning semi-supervised model for pseudogene function prediction. A sequence similarity graph is first constructed to connect pseudogenes and coding genes. Multiple features are incorporated into the model as the node attributes to enable the graph an attributed graph, including expression profiles, interactions with microRNAs, protein-protein interactions (PPIs), and genetic interactions. Graph convolutional networks are used to propagate node attributes across the graph to make classifications on pseudogenes. Comparing Pseudo2GO with other frameworks adapted from popular protein function prediction methods, we demonstrated that our method has achieved state-of-the-art performance, significantly outperforming other methods in terms of the M-AUPR metric.
Incidence, Progression, and Patterns of Multimorbidity in Community-Dwelling Middle-Aged Men and Women

Background: Determining the incidence, progression, and patterns of multimorbidity are important for the prevention, management, and treatment of concurrence of multiple conditions. This study aimed to analyze major multimorbidity patterns and the association of the onset of a primary condition or combinations of a primary and a secondary condition with the progression to subsequent conditions. Methods: We included 53,867 participants aged 45–64 years from the 45 and Up Study who were free of 10 predefined chronic conditions at baseline (2006–2009). The incidence of multimorbidity (coexistence of ≥2, ≥3, and ≥4 conditions) was identified using the claims database until December 31, 2016. The primary, secondary, tertiary, and quaternary condition for each participant was defined according to its temporal order of onset. Results: During a mean 9-years follow-up, the cumulative incidence of primary, secondary, tertiary, and quaternary conditions was 49.6, 23.7, 9.0, and 2.9%, respectively. The time to develop a subsequent condition decreased with the accumulation of conditions (P < 0.0001). Two concurrent cardiometabolic disorders (CMDs, 30.4%) and CMDs clustered with musculoskeletal disorders (15.2%), mental disorders (13.5%), asthma (12.0%), or cancer (8.7%) were the five most common multimorbidity patterns. CMDs tended to occur prior to mental or musculoskeletal disorders but after the onset of cancers or asthma. Compared with all participants who developed cancer as a primary condition, individuals who experienced mental disorders/neurodegenerative disorders and a comorbidity as cardiovascular disease, hypertension, dyslipidemia, diabetes, asthma, or osteoarthritis were 3.36–10.87 times more likely to develop cancer as a tertiary condition. Individuals with neurodegenerative disorders and a comorbidity as hypertension, dyslipidemia, osteoarthritis, or asthma were 5.14–14.15 times more likely to develop mental disorders as a tertiary condition. Conclusions: A high incidence of multimorbidity in middle-aged adults was observed and CMDs were most commonly seen in multimorbidity patterns. There may be accelerated aging after a primary condition occurs. Our findings also reveal a potential preventative window to obviate the development of secondary or tertiary conditions.
Tn Antigen Expression Contributes to an Immune Suppressive Microenvironment and Drives Tumor Growth in Colorectal Cancer

Expression of the tumor-associated glycan Tn antigen (αGalNAc-Ser/Thr) has been correlated to poor prognosis and metastasis in multiple cancer types. However, the exact mechanisms exerted by Tn antigen to support tumor growth are still lacking. One emerging hallmark of cancer is evasion of immune destruction. Although tumor cells often exploit the glycosylation machinery to interact with the immune system, the contribution of Tn antigen to an immunosuppressive tumor microenvironment has scarcely been studied. Here, we explored how Tn antigen influences the tumor immune cell composition in a colorectal cancer (CRC) mouse model. CRISPR/Cas9-mediated knock out of the C1galt1c1 gene resulted in elevated Tn antigen levels on the cell surface of the CRC cell line MC38 (MC38-Tnhigh). RNA sequencing and subsequent GO term enrichment analysis of our Tnhigh glycovariant not only revealed differences in MAPK signaling and cell migration, but also in antigen processing and presentation as well as in cytotoxic T cell responses. Indeed, MC38-Tnhigh tumors displayed increased tumor growth in vivo, which was correlated with an altered tumor immune cell infiltration, characterized by reduced levels of cytotoxic CD8+ T cells and enhanced accumulation of myeloid-derived suppressor cells. Interestingly, no systemic differences in T cell subsets were observed. Together, our data demonstrate for the first time that Tn antigen expression in the CRC tumor microenvironment affects the tumor-associated immune cell repertoire.
The Basic Characteristics of the Pentraxin Family and Their Functions in Tumor Progression

The pentraxin is a superfamily of proteins with the same domain known as the pentraxin domain at C-terminal. This family has two subgroups, namely; short pentraxins (C-reactive protein and serum amyloid P component) and long pentraxins (neuronal pentraxin 1, neuronal pentraxin 2, neuronal pentraxin receptor, pentraxin 3 and pentraxin 4). Each group shares a similar structure with the pentameric complexes arranged in a discoid shape. Previous studies revealed the functions of different pentraxin family members. Most of them are associated with human innate immunity. Inflammation has commonly been associated with tumor progression, implying that the pentraxin family might also participate in tumor progression. Therefore, we reviewed the basic characteristics and functions of the pentraxin family and their role in tumor progression.
NLRC5 Inhibits Inflammation of Secretory Phase Ectopic Endometrial Stromal Cells by Up-Regulating Autophagy in Ovarian Endometriosis

Nod-like receptor (NLR) family caspase activation and recruitment domain containing 5 (NLRC5) is a newly identified sub-class of the NLR family. It regulates inflammation and has a key function in innate and adaptive immunologic reactions. Autophagy has been reported to be crucially linked to the pathogenesis of endometriosis. Our recent study identify there is a negative correlation between NLRC5 and autophagy in endometriosis, indicating that NLRC5 and autophagy together act as promising predictors in endometriosis patients. However, the mechanism associating NLRC5 and autophagy in endometriosis is still not completely understood. We hypothesize that autophagy could be involved in NLRC5-mediated inflammation in endometriosis. In order to validate the assumption, we evaluate the effects of NLRC5 and autophagy in the inflammation of ectopic endometrial stromal cells (EESCs) of ovarian endometriosis patients, to specifically determine whether autophagy is involved in NLRC5-mediated inflammation in EESCs. Our results show that over-expression of NLRC5 results in the up-regulation of autophagy in EESCs and inhibition of NLRC5 restricts the level of autophagy in EESCs. Furthermore, over-expression of NLRC5 and promotion of autophagy inhibit interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) expressions, whereas inhibition of NLRC5 and autophagy up-regulate IL-6 and TNF-α expressions in EESCs. Additionally, promotion of autophagy contributes to the NLRC5-mediated inhibition of IL-6 and TNF-α expressions in EESCs; inhibition of autophagy restricts NLRC5-mediated inhibition of IL-6 and TNF-α expressions in EESCs. Our results suggest that over-expression of NLRC5 promotes autophagy, thereby inhibiting inflammation in ovarian endometriosis.
Investigation of Plasma Metabolic and Lipidomic Characteristics of a Chinese Cohort and a Pilot Study of Renal Cell Carcinoma Biomarker

Plasma metabolomics and lipidomics have been commonly used for biomarker discovery. Studies in white and Japanese populations suggested that gender and age can affect circulating plasma metabolite profiles; however, the metabolomics characteristics in Chinese population has not been surveyed. In our study, we applied liquid chromatography-mass spectrometry-based approach to analyze Chinese plasma metabolome and lipidome in a cohort of 534 healthy adults (aging from 15 to 79). Fatty-acid metabolism was found to be gender- and age-dependent in Chinese, similar with metabolomics characteristics in Japanese and white populations. Differently, lipids, such as TGs and DGs, were found to be gender-independent in Chinese population. Moreover, nicotinate and nicotinamide metabolism was found to be specifically age-related in Chinese. The application of plasma metabolome and lipidome for renal cell carcinoma diagnosis (143 RCC patients and 34 benign kidney tumor patients) showed good accuracy, with an area under the curve (AUC) of 0.971 for distinction from healthy control, and 0.839 for distinction from the benign. Bile acid metabolism was found to be related to RCC probably combination with intestinal microflora. Definition of the variation and characteristics of Chinese normal plasma metabolome and lipidome might provide a basis for disease biomarker analysis.
Is the Deliberate Practice View Defensible? A Review of Evidence and Discussion of Issues

The question of what explains individual differences in expertise within complex domains such as music, games, sports, science, and medicine is currently a major topic of interest in a diverse range of fields, including psychology, education, and sports science, to name just a few. Ericsson and colleagues’ deliberate practice view is a highly influential perspective in the literature on expertise and expert performance—but is it viable as a testable scientific theory? Here, reviewing more than 25 years of Ericsson and colleagues’ writings, we document critical inconsistencies in the definition of deliberate practice, along with apparent shifts in the standard for evidence concerning deliberate practice. We also consider the impact of these issues on progress in the field of expertise, focusing on the empirical testability and falsifiability of the deliberate practice view. We then discuss a multifactorial perspective on expertise, and how open science practices can accelerate progress in research guided by this perspective.
Case Report: Challenging Otologic Surgery in Patients With 22q11.2 Deletion Syndrome

Patients with 22q11.2 deletion syndrome frequently have conductive hearing loss and/or chronic otitis media. Otologic surgery is often opted for. We present two patients undergoing otologic surgery. This case report outlines the typical otologic surgical challenges in patients with 22q11.2 deletion syndrome. Case one is a 52 year old male patient with chronic otitis media who underwent a mastoidectomy. The pre-operative CT scan showed a fused lateral semicircular canal and vestibule. Peroperatively, the lateral semicircular canal could not be used as a landmark to identify the facial nerve. Case two is a 10 year old female patient with conductive hearing loss. A middle ear inspection was performed where a bony epitympanic fixation of the malleus was encountered. In addition, the manubrium of the malleus was atrophic and also fixated. The bony fixation was removed, as was the manubrium of the malleus. Otologists should be aware of these typical anatomical variations in patients with 22q11.2 deletion syndrome. We recommend to use CT scanning of the middle and inner ear when preparing for otologic surgery in 22q11.2 deletion syndrome.
The Relationship Between Dog-Related Factors and Owners' Attitudes Toward Pets: An Exploratory Cross-Sectional Study in Korea

In Korea, there is a need for research on human–animal relationships because of an increase in the number of companion animals and the positive changes in public perception toward them. Few studies have examined these changes. This epidemiological study investigates the characteristics of Korean dog owners and their pet dogs and identifies the owner- and dog-dependent factors that influence the owners' attitudes toward pets. We conducted a cross-sectional study of dog owners by asking them to complete a Pet Attitude Scale-based questionnaire about their dogs and themselves. The participants included 654 young adults between 19 and 39 years of age who lived in Seoul and owned dogs. We found that most dogs were owned by single, educated, high-income men who preferred small purebred dogs. Most were also likely to underestimate their dog's body condition score (BCS). The multivariable logistic regression (odds ratio, OR) and the multiple linear regression (unstandardized coefficients, B) models suggested that positive pet attitudes were associated with nine factors: overweight (OR = 2.68, B = 5.28) or a normal BCS (OR = 2.09, B = 5.58), having a medical history of related diseases (OR = 2.36, B = 6.38) and vaccination (OR = 2.10, B = 6.22), buying the pet dog (OR = 0.60, B = −3.85), having a small dog (≤10 kg) (OR = 1.66), visiting the veterinarian frequently (OR = 1.08, B = 0.39), spending more time with the dog (OR = 1.23, B =1.32), and keeping other species in the house (B = −4.27). This study is the first to identify the relationships between owner- and dog-dependent factors and pet owner attitude toward pets, all within a Korean cultural context. This study highlights the factors associated with the development of relationships between pet dogs and their owners. The exploratory study is novel because it examines pet ownership in the context of the Korean culture; previous pet ownership studies were set in the West and are analyzed with Western cultural values in mind.
Cognitive-Locomotor Dual-Task Interference in Stroke Survivors and the Influence of the Tasks: A Systematic Review

Background: Walking in the community can be challenging for stroke survivors. The fact that community walking often requires performing another task while walking further adds to this challenge and can lead to a deterioration of performance in one or both tasks. Objective: To review the existing literature about cognitive-locomotor dual-task interference (DTI) magnitude and pattern while walking in patients with stroke and to explore the influence of tasks' nature on DTI. Moreover, this review investigated the differences in DTI between stroke survivors and age-matched healthy adults. Methods: The literature search was conducted in 4 databases (MEDLINE, CINAHL, EMBASE and PEDro). Two authors independently identified relevant studies based on predetermined selection criteria. Among these criteria, studies had to include both locomotor and cognitive DTI. Methodological quality of the studies was independently assessed by two raters using a standardized checklist. Studies were categorized according to the nature of the locomotor and the cognitive tasks. Results: A total of twenty studies, with good to high methodological quality, were selected. Task combinations, outcome measures and participants characteristics varied widely from one study to another. Despite heterogeneous results across studies, mutual DTI (decrements in both locomotor and cognitive performance) was the most frequently observed pattern in participants with stroke. Interestingly, this DTI pattern was systematically obtained when participants had to avoid obstacles while walking. DTI seemed also to be influenced by the nature of the cognitive task. Compared to age-matched healthy participants, stroke survivors had greater DTI. Mutual interferences were also more frequently observed in stroke survivors than in age-matched healthy adults. Conclusions: DTI magnitude and pattern in persons with stroke varied considerably across studies. Multiple factors, including nature of the tasks, may influence dual-task abilities when assessing individuals with stroke. Consequently, dual-task assessments should be performed in similar contexts of individuals' daily lives to ensure ecological validity.
Image-Based Methods to Investigate Synchronization between Time Series Relevant for Plasma Fusion Diagnostics

Advanced time series analysis and causality detection techniques have been successfully applied to the assessment of synchronization experiments in tokamaks, such as Edge Localized Modes (ELMs) and sawtooth pacing. Lag synchronization is a typical strategy for fusion plasma instability control by pace-making techniques. The major difficulty, in evaluating the efficiency of the pacing methods, is the coexistence of the causal effects with the periodic or quasi-periodic nature of the plasma instabilities. In the present work, a set of methods based on the image representation of time series, are investigated as tools for evaluating the efficiency of the pace-making techniques. The main options rely on the Gramian Angular Field (GAF), the Markov Transition Field (MTF), previously used for time series classification, and the Chaos Game Representation (CGR), employed for the visualization of large collections of long time series. The paper proposes an original variation of the Markov Transition Matrix, defined for a couple of time series. Additionally, a recently proposed method, based on the mapping of time series as cross-visibility networks and their representation as images, is included in this study. The performances of the method are evaluated on synthetic data and applied to JET measurements.
Proteome-scale Analysis of Vertebrate Protein Thermoadaptation Modulated by Dynamic Allostery and Protein Solvation

Despite large differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins often with subtle differences in amino acid sequence. By comparing a set of substantially homologous proteins between model vertebrate organisms at a sub-proteome level, we discover a pattern of amino acid conservation and a shift in amino acid use, noticeably with an apparent distinction between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, we establish a connection between the thermoadaptation of protein sequences manifest in the evolved proteins and two of their physical features: a change in their proteins dynamics and in their solvation. For poikilotherms such as frog and fish, the lower body temperature is expected to increase the association of proteins due to a decrease in protein dynamics and correspondingly lower entropy penalty on binding. In order to prevent overly-sticky protein association at low temperatures, we find that poikilotherms enhance the solvation of their proteins by favoring polar amino acids on their protein’s surface. This study unveils a general mechanism behind amino acid choices that constitute part of the thermoadaptation of vertebrate organisms at the molecular level.