Miracle-dz/UniFAR-FTUs huggingface dataset:
Fusarium subtropicale, sp. nov., a novel nivalenol mycotoxin–producing species isolated from barley (Hordeum vulgare) in Brazil and sister to F. praegraminearum

ABSTRACT Surveys were conducted in commercial wheat and barley fields in the south central production regions of state of Paraná, Brazil, from 2011 to 2015. Spikes displaying visible Fusarium head blight symptoms were collected and the pathogen isolated from the tissues. The 754 Fusarium isolates recovered were identified by a high-throughput multilocus genotyping assay (MLGT) designed to identify trichothecene toxin–producing fusaria (i.e., formerly B-clade, but referred to here as F. sambucinum species complex lineage 1 [FSAMSC-1]) together with sequencing a portion of the translation elongation factor 1-α (TEF1) gene. One strain was discovered that appeared to be closely related to but phylogenetically distinct from F. praegraminearum based on the relatively low 97.7% TEF1 identity and positive genotype obtained with one of the two F. praegraminearum species–specific MLGT probes. Molecular phylogenetic analyses of a 10-gene data set resolved this novel FSAMSC-1 species and F. praegraminearum as sisters. Formally described herein as F. subtropicale, it is phenotypically distinct from the 22 other FSAMSC-1 species in that it produces mostly 1–3-septate macroconidia. Whole-genome sequence data were used to predict its potential to produce mycotoxins. Chemical analyses confirmed that F. subtropicale could produce the mycotoxins 4,15-diacetylnivalenol, butenolide, culmorin, and fusarin C in vitro, and the pathogenicity experiment revealed that F. subtropicale could infect but not spread in susceptible hard red spring wheat cultivar “Norm. ”
A comparison of prenatal muscle transcriptome and proteome profiles between pigs with divergent growth phenotypes

The growth of pigs is an important economic trait that involves multiple genes and coordinated regulatory mechanisms. The growth rate and potential of skeletal muscles are largely decided by embryonic myofiber development. Tibetan pig (TP) that is a mini‐type breed has a divergent phenotype in growth rate and adult body weight with Wujin pig (WJ) and large White pig (LW). In the current study, the transcriptome (using RNA‐seq) and proteome (using the isobaric tag for relative and absolute quantification [iTRAQ]) data from the prenatal muscle tissues were analyzed to identify the genes related to postnatal growth rate and growth potential in pigs. In the RNA‐seq experiment, 19 626 genes were detected in the embryonic muscle tissues, and 3626 unique differentially expressed genes (DEGs) were identified in TP in comparison to that in LW and WJ. In the iTRAQ experiment, 2474 proteins were detected, and 735 unique differentially expressed proteins (DEPs) were identified in TP in comparison to that in LW and WJ. Combining the DEGs and DEPs, 209 genes were found to be differentially expressed, consistently at both the messenger RNA and protein levels, between TP and the other two breeds; these are mainly involved in 2‐oxocarboxylic acid metabolism, citrate cycle, and biosynthesis of amino acids. Of these, 20 genes that were related to myoblast differentiation and muscle fiber formation might have important roles in determining the postnatal growth rate and potential body weight in pigs. Our results provide new candidate genes and insights into the molecular mechanisms involved muscle growth traits in pigs.
Adaptation and Inhibition Control Pathological Synchronization in a Model of Focal Epileptic Seizure

Visual Abstract Pharmacoresistant epilepsy is a common neurological disorder in which increased neuronal intrinsic excitability and synaptic excitation lead to pathologically synchronous behavior in the brain. In the majority of experimental and theoretical epilepsy models, epilepsy is associated with reduced inhibition in the pathological neural circuits, yet effects of intrinsic excitability are usually not explicitly analyzed. Here we present a novel neural mass model that includes intrinsic excitability in the form of spike-frequency adaptation in the excitatory population. We validated our model using local field potential (LFP) data recorded from human hippocampal/subicular slices. We found that synaptic conductances and slow adaptation in the excitatory population both play essential roles for generating seizures and pre-ictal oscillations. Using bifurcation analysis, we found that transitions towards seizure and back to the resting state take place via Andronov–Hopf bifurcations. These simulations therefore suggest that single neuron adaptation as well as synaptic inhibition are responsible for orchestrating seizure dynamics and transition towards the epileptic state.
Different Genetic Expression Profiles of Oxidative Stress and Apoptosis-Related Genes in Crohn’s Disease

Background/Aims: Increased oxidative stress and decreased immune cell apoptosis have been reported to be important factors in the pathogenesis of Crohn’s disease (CD). Our aim was to characterize the genetic expression of molecules implicated in the regulation of oxidative stress and apoptosis in peripheral white mononuclear cells of 18 healthy volunteers (controls) and 20 patients at the onset of CD (active CD [aCD]): 10 who achieved remission (inactive CD [iCD]) and 10 who did not present a complete and deep response to treatment (aCD-T). Methods: mRNA expression was measured by the Agena MassARRAY quantitative gene expression analysis application. The genes analyzed were Fas-receptor (FASR), Fas-ligand (FASL), signal transducer and activator of transcription 1 (STAT1), nuclear factor kappa-light-chain-enhancer of activated B cells (NFKB1), apoptosis signal-regulating kinase 1 (ASK1), serine/threonine-protein kinase H1 (PSKH1), ATP-binding cassette sub-family B1 (ABCB1) and peptidylprolyl isomerase D (PPID). Results: During a CD flare, we found specific upregulated expression of the genes STAT1 and PSKH1, whereas ABCB1 and FASL were downregulated. In the patients with iCD, FASR and NFKB1 were upregulated. The expression levels of NFKB1, STAT1 and ABCB1 did not show any difference in patients with aCD at the onset of the disease and after treatment (aCD-T). The expression levels of PPID and ASK1 did not show any differences in the patients with aCD, iCD and the controls. We have also reviewed the cellular function and role of these genes in CD. Conclusions: These findings contribute to improving the understanding of the pathogenesis of CD and highlight potential genes involved.
Use of High Density Single Nucleotide Polymorphism (SNP) Arrays to Assess Genetic Diversity and Population Structure of Dairy Cattle in Smallholder Dairy Systems: The Case of Girinka Programme in Rwanda

In most smallholder dairy programmes, farmers are not fully benefitting from the genetic potential of their dairy cows. This is in part due to the mismatch between the available genotypes and the environment, including management, in which the animals perform. With sparse performance and pedigree records in smallholder dairy farms, the true degree of baseline genetic variability and breed composition is not known and hence rendering any genetic improvement initiative difficult to implement. Using the Girinka programme of Rwanda as an exemplar, the current study was aimed at better understanding the genetic diversity and population structure of dairy cattle in the smallholder dairy farm set up. Further, the association between farmer self-reported cow genotypes and genetically determined genotypes was investigated. The average heterozygosity estimates were highest (0.38 ± 0.13) for Rwandan dairy cattle and lowest for Gir and N’Dama (0.18 ± 0.19 and 0.25 ± 0.20, respectively). Systematic characterization of the genetic variation and diversity available may inform the formulation of sustainable improvement strategies such as targeting and matching the genotype of cows to productivity goals and farmer profile and hence reducing the negative impact of genotype by environment interaction.
From Simulation to Real-World Robotic Mobile Fulfillment Systems

In a new type of automated parts-to-picker warehouse system - a Robotic Mobile Fulfillment System (RMFS) - robots are sent to transport pods (movable shelves) to human operators at stations to pick/put items from/to pods. There are many operational decision problems in such a system, and some of them are interdependent and influence each other. In order to analyze the decision problems and the relationships between them, there are two open-source simulation frameworks in the literature, Alphabet Soup and RAWSim-O. However, the steps between simulation and real-world RMFS are not clear in the literature. Therefore, this paper aims to bridge this gap. The simulator is firstly transferred as core software. The core software is connected with an open-source ERP system, called Odoo, while it is also connected with real robots and stations through an XOR-bench. The XOR-bench enables the RMFS to be integrated with several mini-robots and mobile industrial robots in (removed) experiments for the purpose of research and education.
PI3Kδ Is a Therapeutic Target in Hepatocellular Carcinoma

Class I phosphoinositide 3‐kinase (PI3K) signaling is a major pathway in human cancer development and progression. Among the four PI3K isoforms, PI3Kα and PI3Kβ are ubiquitously expressed, whereas PI3Kγ and PI3Kδ are found primarily in leukocytes. Until now, PI3K targeting in solid tumors has focused on inhibiting PI3Kα‐mediated and PI3Kβ‐mediated cancer cell–intrinsic PI3K activity. The role of PI3Kδ in solid tumors is unknown. Here, we evaluated the effects of PI3Kδ using established hepatocellular carcinoma (HCC) cells, malignant hepatocytes derived from patients with advanced HCC, murine models, and HCC tissues using RNA sequencing, quantitative PCR, immunoblotting, immunofluorescence, microarray, liquid chromatography–tandem mass spectrometry, and kinase assay. We established a chemical carcinogenesis model of liver malignancy that reflects the malignant phenotype and the in vivo environment of advanced HCC. In this in vivo advanced HCC‐mimic system using HCC cells treated with hydrogen peroxide (H2O2), we showed that H2O2 selectively increases PI3Kδ activity while decreasing that of other class I PI3Ks. Blocking PI3Kδ activity with a PI3Kδ inhibitor or small interfering RNA–mediated PI3Kδ gene silencing inhibited HCC‐cell proliferation and dampened key features of malignant HCC, including the up‐regulation of telomerase reverse transcriptase (TERT). Mechanistically, H2O2 induced oxidative modification of the serpin peptidase inhibitor, serpin peptidase inhibitor (SERPINA3), blocking its ubiquitin‐dependent degradation and enhancing its activity as a transcriptional activator of PI3Kδ and TERT. High PI3Kδ levels in HCC were found to correlate with poor survival rates, with human advanced HCC showing positive correlations between the protein levels of oxidized SERPINA3, PI3Kδ, and TERT. Thus, PI3Kδ plays significant roles in malignant liver tumors. Conclusion: Our data identify PI3Kδ inhibition, recently approved for the treatment of human B‐cell malignancies, as a potential treatment for HCC.
PENERAPAN METODE PEMBELAJARAN PROBLEM SOLVING UNTUK MENINGKATKAN HASIL BELAJAR SISWA PADA MATERI KONSEP MOL DI KELAS X MIPA DI SMA NEGERI 6 KOTA BEKASI

ABSTRAK Penelitian Tindakan Kelas ini dilakukan oleh karena rendahnya hasil belajar siswa pada materi konsep mol dan masih belum terlaksana dengan baik penerapan metode pembelajaran terutama pada proses pembelajaran Kimia di kelas X MIPA Sma Negeri 6 Kota Bekasi. Hasil penelitian ini menunjukkan bahwa metode pembelajaran Problem Solving memiliki dampak positif dalam meningkatkan hasil belajar siswa. Berdasarkan analisis data, aktivitas guru dalam proses pembelajaran Problem Solving dalam setiap siklus juga mengalami peningkatan serta berdampak positif terhadap prestasi belajar siswa. Hal ini dapat ditunjukkan dengan nilai rata â€“ rata siswa pada setiap siklus yang terus mengalami peningkatan. Dengan demikian hipotesis tindakan dalam penelitian ini terbukti bahwa penerapan metode pembelajaran problem Solving dalam proses belajar mengajar dapat meningkatkan hasil belajar siswa pada materi konsep mol. Kata kunci: Hasil Belajar , Kimia, Konsep Mol, Metode Pembelajaran Problem Solving ABSTRACT The Classroom Action Research was conducted because of the low learning achievements of MOL concept and still has not done well the use of learning methods, especially in the learning process in Chemistry class of X MIPA SMAN 6 Bekasi . This research outputs indicated that Problem Solving has a positive impact in improving learning achievements of students. Based on data analysis the activity of the teacher in the learning process using Problem Solving method in each cycle also increased as well as the positive impact on the student achievement. This can be shown by the average value of student in each cycle which is constantly increasing. Thus the hypothesis of action in the study proved that the application of the problem solving method in the teaching and learning can enhance learning achievement student to learn Chemistry with the material theory of Mol concept. Keywords: achievement, Chemistry, Concept Mol, Problem Solving Method
No Association Between Active Commuting to School, Adiposity, Fitness, and Cognition in Spanish Children: The MOVI-KIDS Study.

BACKGROUND Walking and bicycling (active commuting) to school may be a useful strategy to increase the daily amount of physical activity, and, potentially, improve children's health. However, it is unclear whether active commuting to school (ACS) has the potential to improve physical health and cognitive performance in children. Our aim was to examine the relationship between ACS with adiposity indicators, physical fitness, and cognitive performance in 4- to 7-year-old children. METHODS We conducted a cross-sectional study with 1159 children from the provinces of Cuenca and Ciudad Real, Spain. ACS was self-reported by parents. Adiposity (body mass index, waist circumference, body fat mass, and triceps skinfold thickness) and physical fitness (cardiorespiratory and muscular fitness) were measured by standard procedures. Cognitive performance was assessed using the Battery of General and Differential Aptitudes. Data analysis included analysis of covariance. RESULTS We found no differences in adiposity, physical fitness, and cognitive performance between active commuters and nonactive commuters. CONCLUSIONS Walking to school had no positive impact on adiposity, physical fitness, and cognition in 4- to 7-year-old children. Future studies should examine the intensity and duration of walking to school needed to provide benefits in health and cognitive performance.
A Comparison of Methamphetamine-Induced Psychosis and Schizophrenia: A Review of Positive, Negative, and Cognitive Symptomatology

Methamphetamine is a potent psychostimulant that can induce psychosis among recreational and chronic users, with some users developing a persistent psychotic syndrome that shows similarities to schizophrenia. This review provides a comprehensive critique of research that has directly compared schizophrenia with acute and chronic METH psychosis, with particular focus on psychiatric and neurocognitive symptomatology. We conclude that while there is considerable overlap in the behavioral and cognitive symptoms between METH psychosis and schizophrenia, there appears to be some evidence that suggests there are divergent aspects to each condition, particularly with acute METH psychosis. Schizophrenia appears to be associated with pronounced thought disorder, negative symptoms more generally and cognitive deficits mediated by the parietal cortex, such as difficulties with selective visual attention, while visual and tactile hallucinations appear to be more prevalent in acute METH-induced psychosis. As such, acute METH psychosis may represent a distinct psychotic disorder to schizophrenia and could be clinically distinguished from a primary psychotic disorder based on the aforementioned behavioral and cognitive sequelae. Preliminary evidence, on the other hand, suggests that chronic METH psychosis may be clinically similar to that of primary psychotic disorders, particularly with respect to positive and cognitive symptomatology, although negative symptoms appear to be more pronounced in schizophrenia. Limitations of the literature and avenues for future research are also discussed.
Deep residual networks for automatic sleep stage classification of raw polysomnographic waveforms

We have developed an automatic sleep stage classification algorithm based on deep residual neural networks and raw polysomnogram signals. Briefly, the raw data is passed through 50 convolutional layers before subsequent classification into one of five sleep stages. Three model configurations were trained on 1850 polysomnogram recordings and subsequently tested on 230 independent recordings. Our best performing model yielded an accuracy of 84.1% and a Cohen’s kappa of 0.746, improving on previous reported results by other groups also using only raw polysomnogram data. Most errors were made on non-REM stage 1 and 3 decisions, errors likely resulting from the definition of these stages. Further testing on independent cohorts is needed to verify performance for clinical use.
Joint Unsupervised Learning of Optical Flow and Depth by Watching Stereo Videos

Learning depth and optical flow via deep neural networks by watching videos has made significant progress recently. In this paper, we jointly solve the two tasks by exploiting the underlying geometric rules within stereo videos. Specifically, given two consecutive stereo image pairs from a video, we first estimate depth, camera ego-motion and optical flow from three neural networks. Then the whole scene is decomposed into moving foreground and static background by compar- ing the estimated optical flow and rigid flow derived from the depth and ego-motion. We propose a novel consistency loss to let the optical flow learn from the more accurate rigid flow in static regions. We also design a rigid alignment module which helps refine ego-motion estimation by using the estimated depth and optical flow. Experiments on the KITTI dataset show that our results significantly outperform other state-of- the-art algorithms. Source codes can be found at https: //github.com/baidu-research/UnDepthflow
The Impact of Autonomy-Framed and Control-Framed Implementation Intentions on Snacking Behaviour: The Moderating Effect of Eating Self-Efficacy.

BACKGROUND Autonomy-supportive implementation intention exercises have been shown to facilitate goal-directed behaviour (Koestner et al., ). The current study explored whether eating self-efficacy moderated the impact of autonomy-framed versus control-framed implementation intentions to reduce high-calorie snack intake. METHODS The study employed a randomised prospective design, involving two waves of data collection conducted in 2016. At Time 1, UK participants (N = 300) completed an online questionnaire which asked them to report their snacking behaviour over the previous 7 days. Participants were subsequently asked to form either an autonomy-framed implementation intention or a control-framed implementation intention. Seven days later, participants reported their consumption of high-calorie snacks and completed a measure of eating self-efficacy. RESULTS Hierarchical multiple regression analysis revealed that eating self-efficacy moderated the effects of implementation intention framing. Autonomy-framed implementation intentions had a greater impact on the avoidance of snacking for high eating self-efficacy participants than did control-framed implementation intentions. In contrast, for low eating self-efficacy participants, control-framed implementation intentions had more impact than did autonomy-framed implementation intentions. CONCLUSIONS The results suggest that if implementation intentions to promote healthy diet are to be effective, the role of eating self-efficacy should be considered, and the design of interventions adapted accordingly.
Predicting 3-Year Survival in Patients Receiving Maintenance Dialysis: An External Validation of iChoose Kidney in Ontario, Canada

Background: Many patients with end-stage kidney disease (ESKD) do not appreciate how their survival may differ if treated with a kidney transplant compared with dialysis. A risk calculator (iChoose Kidney) developed and validated in the United States provides individualized mortality estimates for different treatment options (dialysis vs living or deceased donor kidney transplantation). The calculator can be used with patients and families to help patients make more educated treatment decisions. Objective: To validate the iChoose Kidney risk calculator in Ontario, Canada. Design: External validation study. Setting: We used several linked administrative health care databases from Ontario, Canada. Patients: We included 22 520 maintenance dialysis patients and 4505 kidney transplant recipients. Patients entered the cohort between 2004 and 2014. Measurements: Three-year all-cause mortality. Methods: We assessed model discrimination using the C-statistic. We assessed model calibration by comparing the observed versus predicted mortality risk and by using smoothed calibration plots. We used multivariable logistic regression modeling to recalibrate model intercepts using a correction factor, when appropriate. Results: In our final version of the iChoose Kidney model, we included the following variables: age (18-80 years), sex (male, female), race (white, black, other), time on dialysis (<6 months, 6-12 months, >12 months), and patient comorbidities (hypertension, diabetes, and/or cardiovascular disease). Over the 3-year follow-up period, 33.3% of dialysis patients and 6.2% of kidney transplant recipients died. The discriminatory ability was moderate (C-statistic for dialysis: 0.70, 95% confidence interval [CI]: 0.69-0.70, and C-statistic for transplant: 0.72, 95% CI: 0.69-0.75). The 3-year observed and predicted mortality estimates were comparable and even more so after we recalibrated the intercepts in 2 of our models (dialysis and deceased donor kidney transplantation). As done in the United States, we developed a Canadian Web site and an iOS application called Dialysis vs. Kidney Transplant- Estimated Survival in Ontario. Limitations: Missing data in our databases precluded the inclusion of all variables that were in the original iChoose Kidney (ie, patient ethnicity and low albumin). We were unable to perform all preplanned analyses due to the limited sample size. Conclusions: The original iChoose Kidney risk calculator was able to adequately predict mortality in this Canadian (Ontario) cohort of ESKD patients. After minor modifications, the predictive accuracy improved. The Dialysis vs. Kidney Transplant- Estimated Survival in Ontario risk calculator may be a valuable resource to help ESKD patients make an informed decision on pursuing kidney transplantation.