Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomic Analysis of Streptococcus dysgalactiae subspecies dysgalactiae Isolated From Bovine Mastitis in China

Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) is one of the most prevalent pathogens causing bovine mastitis worldwide. However, there is a lack of comprehensive information regarding genetic diversity, complete profiles of virulence factors (VFs), and antimicrobial resistance (AMR) genes for SDSD associated with bovine mastitis in China. In this study, a total of 674 milk samples, including samples from 509 clinical and 165 subclinical mastitis cases, were collected from 17 herds in 7 provinces in China from November 2016 to June 2019. All SDSD isolates were included in phylogenetic analysis based on 16S rRNA and multi-locus sequence typing (MLST). In addition, whole genome sequencing was performed on 12 representative SDSD isolates to screen for VFs and AMR genes and to define pan-, core and accessory genomes. The prevalence of SDSD from mastitis milk samples was 7.57% (51/674). According to phylogenetic analysis based on 16S rRNA, 51 SDSD isolates were divided into 4 clusters, whereas based on MLST, 51 SDSD isolates were identified as 11 sequence types, including 6 registered STs and 5 novel STs (ST521, ST523, ST526, ST527, ST529) that belonged to 2 distinct clonal complexes (CCs) and 4 singletons. Based on WGS information, 108 VFs genes in 12 isolates were determined in 11 categories. In addition, 23 AMR genes were identified in 11 categories. Pan-, core and accessory genomes were composed of 2,663, 1,633 and 699 genes, respectively. These results provided a comprehensive profiles of SDSD virulence and resistance genes as well as phylogenetic relationships among mastitis associated SDSD in North China.
Hysteresis in PIF4 and ELF3 dynamics dominates warm daytime memory in Arabidopsis

Plants may experience large diurnal temperature fluctuations. Our knowledge of the molecular mechanisms of integration of these fluctuations and the resulting growth patterns is limited. Here we show that hypocotyl growth during the night responded not only to the current temperature but also to preceding daytime temperatures, revealing a memory of previous conditions. Daytime temperature affected the nuclear levels of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and LONG HYPOCOTYL 5 (HY5) during the next night. These jointly accounted for the observed growth kinetics, whereas memory of prior daytime temperature was impaired in the pif4 and hy5 mutants. PIF4 promoter activity largely accounted for the temperature dependent changes in PIF4 protein levels. Noteworthy, the decrease in PIF4 promoter activity triggered by cooling required a stronger temperature shift than the increase caused by warming. This hysteretic pattern required EARLY-FLOWERING 3 (ELF3). Warm temperatures promoted the formation of nuclear condensates of ELF3 in hypocotyl cells during the afternoon but not in the morning. These nuclear speckles showed poor sensitivity to subsequent cooling. We conclude that ELF3 achieves hysteresis and drives the PIF4 promoter into the same behaviour, enabling a memory of daytime temperature conditions.
Machine learning applied to molecular identification of 1 Acinetobacter baumannii Global Clone 1 2 3

20 Since the emergence of clones with epidemic behavior, or "high-risk clones", uninterrupted 21 investigations have been undertaken to understand the genetic and biological basis that led 22 their widespread in nosocomial settings at a global scale. However, its complex genetic and 23 ecological nature only allowed the identification of partial biomarkers with low specificity. 24 The implication of our study is that we successfully applied machine learning algorithms to 25 recognize genetic biomarkers for the identification of Acinetobacter baumannii Global 26 Clone 1, one of the most widespread high-risk clones. Support Vector Machine model 27 predicted U1 sequence with 367 nucleotides length as a specific biomarker for A. 28 baumannii GC1 strains. U1 sequence matched AYE genome in ABAYE1552 locus 29 between 558 and 924 coordinates that corresponds to a fragment of the moaCB gene which 30 encodes a bifunctional protein that includes the molybdenum cofactor biosynthesis protein 31 C and protein B. This region of the gene moaCB allows to differentiate between the A. 32 baumannii GC1 and non-GC1 strains, becoming a suitable biomarker capable of being 33 translated into clinical settings as a molecular typing method such as PCR. Our findings 34 highlight that machine learning can be fruitfully useful even in complex gaps of knowledge 35 of epidemic clones and signify a noteworthy contribution to the literature that could be used 36 to identify challenging nosocomial biomarkers for other multidrug resistant pandemic 37 clones. 38
Novel torin1-sensitive phosphorylation sites on the metabolic regulator AMPK revealed by label-free mass spectrometry

AMPK and mTORC1 are nutrient-sensitive protein kinases that form a fundamental negative feedback loop that governs cell growth and proliferation. AMPK is an αβγ heterotrimer that is directly phosphorylated by mTORC1 on α2S345 to suppress AMPK activity and promote cell proliferation under nutrient stress conditions. Using mass spectrometry, we generated precise phosphorylation profiles of all 12 AMPK complexes expressed in proliferating human cells. Of the 18 phosphorylation sites detected, seven were sensitive to pharmacological mTORC1 inhibition, including four in the AMPK γ2 isoform NH2-terminal domain and α2S377 which is located in the nucleotide-sensing motif. In particular, β1S182 and β2S184 were found to be mTORC1 substrates in vitro and near-maximally or substantially phosphorylated under cellular growth conditions. βS182 phosphorylation was elevated in α1-containing complexes, relative to α2, an effect partly attributable to the non-conserved α-subunit serine/threonine-rich loop. While mutation of β1S182 to a non-phosphorylatable Ala had no effect on basal and ligand-stimulated AMPK activity, β2-S184A mutation increased nuclear AMPK activity and enhanced cell proliferation under nutrient stress. We conclude that mTORC1 governs the nuclear activity of AMPK to regulate transcription factors involved in metabolism and cell survival during nutrient shortage.
KIMGENS: A novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure

Motivation Kinship estimation is necessary for evaluating violations of assumptions or testing certain hypotheses in many population genomic studies. However, kinship estimators are usually designed for diploid systems and cannot be used in populations with mixed haploid diploid genetic systems. The only estimators for different ploidies require datasets free of population structure, limiting their usage. Results We present KIMGENS, an estimator for kinship estimation among individuals of various ploidies, that is robust to population structure. This estimator is based on the popular KING-robust estimator but uses diploid relatives of the individuals of interest as references of heterozygosity and extends its use to haploid-diploid and haploid pairs of individuals. We demonstrate that KIMGENS estimates kinship more accurately than previously developed estimators in simulated panmictic, structured and admixed populations, but has lower accuracy when the individual of interest is inbred. KIMGENS also outperforms other estimators in a honeybee dataset. Therefore, KIMGENS is a valuable addition to a population geneticist’s toolbox. Availability and Implementation KIMGENS and its association simulation tool are implemented and available open-source at https://github.com/YenWenWang/HapDipKinship. Contact Yen-Wen Wang Email: ywang883@wisc.edu
Uncovering the Genetic Architecture of Broad Antisocial Behavior through a Genome-Wide Association Study Meta-analysis

Despite the substantial heritability of antisocial behavior (ASB), specific genetic variants robustly associated with the trait have not been identified. The present study by the Broad Antisocial Behavior Consortium (BroadABC) meta-analyzed data from 28 discovery samples (N = 85,359) and five independent replication samples (N = 8,058) with genotypic data and broad measures of ASB. We identified the first significant genetic associations with broad ASB, involving common intronic variants in the forkhead box protein P2 (FOXP2) gene (lead SNP rs12536335, P = 6.32 x 10-10). Furthermore, we observed intronic variation in Foxp2 and one of its targets (Cntnap2) distinguishing a mouse model of pathological aggression (BALB/cJ strain) from controls (BALB/cByJ strain). The SNP-based heritability of ASB was 8.4% (s.e.= 1.2%). Polygenic-risk-score (PRS) analyses in independent samples revealed that the genetic risk for ASB was associated with several antisocial outcomes across the lifespan, including diagnosis of conduct disorder, official criminal convictions, and trajectories of antisocial development. We found substantial genetic correlations of ASB with mental health (depression rg□=□0.63, insomnia rg = 0.47), physical health (overweight rg = 0.19, waist-to-hip ratio rg = 0.32), smoking (rg□=□0.54), cognitive ability (intelligence rg= −0.40), educational attainment (years of schooling rg = −0.46) and reproductive traits (age at first birth rg=□- 0.58, father’s age at death rg= −0.54). Our findings provide a starting point towards identifying critical biosocial risk mechanisms for the development of ASB.
Aldh2 is a lineage-specific metabolic gatekeeper in melanocyte stem cells

ABSTRACT Melanocyte stem cells (McSCs) in zebrafish serve as an on-demand source of melanocytes during growth and regeneration, but metabolic programs associated with their activation and regenerative processes are not well known. Here, using live imaging coupled with scRNA-sequencing, we discovered that, during regeneration, quiescent McSCs activate a dormant embryonic neural crest transcriptional program followed by an aldehyde dehydrogenase (Aldh) 2 metabolic switch to generate progeny. Unexpectedly, although ALDH2 is well known for its aldehyde-clearing mechanisms, we find that, in regenerating McSCs, Aldh2 activity is required to generate formate – the one-carbon (1C) building block for nucleotide biosynthesis – through formaldehyde metabolism. Consequently, we find that disrupting the 1C cycle with low doses of methotrexate causes melanocyte regeneration defects. In the absence of Aldh2, we find that purines are the metabolic end product sufficient for activated McSCs to generate progeny. Together, our work reveals McSCs undergo a two-step cell state transition during regeneration, and that the reaction products of Aldh2 enzymes have tissue-specific stem cell functions that meet metabolic demands in regeneration.
MPIN: a macro-pixel integration network for light field super-resolution

Most existing light field (LF) super-resolution (SR) methods either fail to fully use angular information or have an unbalanced performance distribution because they use parts of views. To address these issues, we propose a novel integration network based on macro-pixel representation for the LF SR task, named MPIN. Restoring the entire LF image simultaneously, we couple the spatial and angular information by rearranging the four-dimensional LF image into a two-dimensional macro-pixel image. Then, two special convolutions are deployed to extract spatial and angular information, separately. To fully exploit spatial-angular correlations, the integration resblock is designed to merge the two kinds of information for mutual guidance, allowing our method to be angular-coherent. Under the macro-pixel representation, an angular shuffle layer is tailored to improve the spatial resolution of the macro-pixel image, which can effectively avoid aliasing. Extensive experiments on both synthetic and real-world LF datasets demonstrate that our method can achieve better performance than the state-of-the-art methods qualitatively and quantitatively. Moreover, the proposed method has an advantage in preserving the inherent epipolar structures of LF images with a balanced distribution of performance.
k-experts - Online Policies and Fundamental Limits

We introduce the $\texttt{$k$-experts}$ problem - a generalization of the classic Prediction with Expert's Advice framework. Unlike the classic version, where the learner selects exactly one expert from a pool of $N$ experts at each round, in this problem, the learner can select a subset of $k$ experts at each round $(1\leq k\leq N)$. The reward obtained by the learner at each round is assumed to be a function of the $k$ selected experts. The primary objective is to design an online learning policy with a small regret. In this pursuit, we propose $\texttt{SAGE}$ ($\textbf{Sa}$mpled Hed$\textbf{ge}$) - a framework for designing efficient online learning policies by leveraging statistical sampling techniques. For a wide class of reward functions, we show that $\texttt{SAGE}$ either achieves the first sublinear regret guarantee or improves upon the existing ones. Furthermore, going beyond the notion of regret, we fully characterize the mistake bounds achievable by online learning policies for stable loss functions. We conclude the paper by establishing a tight regret lower bound for a variant of the $\texttt{$k$-experts}$ problem and carrying out experiments with standard datasets.
Anaerobic Digestion of Wheat Straw Pretreated with Soaking in Water and Alkali Medium

The influence of the alkaline pretreatment of wheat straw with use 0.05M solution of NaOH by 22 hours at 25 °C temperature on the effectiveness of anaerobic digestion under mesophilic condition was the subject of this study. The water soaked straw was used as a control. The results showed that alkaline pretreatment improved the solubility of the straw biomass, increasing dissolved COD and concentration of VFA in the feedstock of 10% and 21%, respectively, compared to the water soaked samples. Consequently, the cumulative biogas yield was enhanced by 21.5%, reaching 412.1 mL gVS -1 for the pretreated biomass. The digestates were similar in terms of TS and VS, but it significantly differed in terms of phenols concentration, the content of which was considerably higher both in the feedstock as also as in digestate containing alkaline pretreated straw. Initial concentration of phenols in the feedstock of 27 mg L-1 did not block the anaerobic digestion, although its inhibiting effect is forecasted. It was concluded that soaking the straw at low loading of NaOH (4% of raw mass (w/w)) under ambient conditions can efficiently improve its usability for biogas production.
ExMrec2vec: Explainable Movie Recommender System based on Word2vec

According to the user profile, a recommender system intends to offer items to the user that may interest him. The recommendations have been applied successfully in various fields. Recommended items include movies, books, travel and tourism services, friends, research articles, research queries, and much more. Hence the presence of recommender systems in many areas, in particular, movies recommendations. Most current Machine Learning recommender systems serve as black boxes that do not provide the user with any insight into or justification for the system's logic. What puts users at risk of losing their confidence. Recommender systems suffer from an overload of information, which poses numerous problems, including high cost, slow data processing, and low time complexity. That is why researchers in have been using graph embeddings algorithms in the recommendation field to reduce the quantity of data, as these algorithms have been successful in the last few years. This work aims to improve the quality of recommendation and the simplicity of recommendation explanation based on the word2vec graph embeddings model. Keywords—Recommender system; explainable artificial intelligence machine learning; Word2vec
Effect of Open Lung Ventilation on Respiratory Mechanic, Postoperative Organ Function and Inflammatory Mediators in Coronary Artery Bypass Surgery

1. Dept. of Anesthesiology, Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran 2. Dept. of Anesthesiology, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran 3. Exceptional Talent Development Center (EDTC), Tehran University of Medical Sciences, Tehran, Iran 4. Dept. of Anesthesiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran. 5. Hasheminejad Kidney Center (HKC), Iran University of Medical Sciences, Tehran, Iran.
Stacking Tetraurea Macrocycles as Self-Assembled Chloride Receptors in Aqueous Solutions

Artificial receptors that recognise anionic species via noncovalent interactions have a wide range of biomedical, industrial and environmental applications. A major challenge in this area of research is to achieve high affinity and selective anion binding in aqueous media. So far, only a few rare examples of receptors capable of strong (>105 M-1) anion binding in solutions containing > 50% water are available and none show selectivity for the highly biologically relevant anion chloride. We report here the discovery of a D4-symmetric fluorinated tetraurea macrocycle that fulfils this function owing to its unique self-assembly properties. The macrocycle has a strong tendency to self-associate into columnar aggregates via intermolecular hydrogen bonds and aromatic stacking interactions. In aqueous solutions, macrocycle aggregation generates size-selective and hydrophobic binding pockets favourable for interactions with chloride via urea hydrogen bond donors. As a result, micromolar affinity and highly selective chloride binding has been achieved with this simple small molecule (MV < 700) in 60 vol% water/acetonitrile.
Detection of Hepatoma based on Gene Expression using Unitary Matrix of Singular Vector Decomposition

Hepatoma is a long-term disease with a high risk of mortality. However, the disease is late detected, at the fourth level stadium due to silent symptoms. The infected hepatitis B virus gene HBx is a genome virus to trigger liver disease. This virus inserts material genetic into the host and disturbs the cell cycle. The regulation of gene expression is blocked to make work abnormal, especially for repairing and degrading. A microarray is a tool to quantify the RNA gene expression in huge volumes without any information for the related potential gene. Therefore, this study is proposed a feature extraction method using a unitary singular matrix for simplifying the classification model of hepatoma detection. Principally, the feature is decomposed using a singular vector to get the k-rank value of pattern. This matrix is applied to the representative machine learning algorithm, including KNN, Naïve Bayes, C5.0 Decision Tree, and SVM. The experimental result achieved high performance with Area under the Curve (AUC) of above 90% on average. Keywords—Hepatoma; gene expression; feature extraction; unitary matrix
Basic taste sensitivity, eating behaviour, and propensity of dairy foods of preadolescent children: How are they related?

Background: Taste sensitivity has been reported to influence children’s eating behaviour and contribute to their food preferences and intake. This study aimed to investigate the associations between taste sensitivity and eating behaviour in preadolescents. Methods: Children’s taste sensitivity was measured by detection threshold with five different concentration levels of sweetness (sucrose), sourness (citric acid), saltiness (sodium chloride), bitterness (caffeine, quinine), and umami (monosodium glutamate). In addition, the Child Eating Behaviour Questionnaire (CEBQ), the Food Propensity Questionnaire (FPQ), and the children’s body weight and height were completed by the parents. Children conducted the sensory evaluation test at schools while parents completed the questionnaires online. Results: A total of 69 child-parent dyads participated. Taste sensitivity was significantly associated with eating behaviour in food responsiveness, emotional overeating, and desire to drink. Children who were less sensitive to caffeine bitterness (higher detection threshold) had higher food responsiveness scores, while those who were less sensitive to sweetness and caffeine bitterness had higher emotional overeating scores. In addition, children who were less sensitive to sourness and bitterness of both caffeine and quinine demonstrated to have higher scores in desire to drink. There was no association between taste sensitivity and FPQ, but significant differences were observed across children’s body mass index (BMI) regarding their FPQ of dairy food items, indicating higher consumption of low-fat milk in the overweight/obese compared to the normal-weight subjects. There was no significant difference in taste sensitivity according to BMI. Children’s eating behaviour differed across BMI, demonstrating a positive association between BMI and food approach, and a negative association between BMI and food avoidance. Conclusions: This study contributes to the preliminary understanding of the relationships between taste sensitivity and eating behaviour in preadolescents which could be used to develop effective strategies to promote healthy eating practices in children by considering their taste sensitivity.
A robust control design approach for altitude control and trajectory tracking of a quadrotor

Introduction. Unmanned aerial vehicles as quadcopters, twin rotors, fixed-wing crafts, and helicopters are being used in many applications these days. Control approaches applied on the quadrotor after decoupling the model or separate altitude control and trajectory tracking have been reported in the literature. A robust linear H∞ controller has been designed for both altitude control and circular trajectory tracking at the desired altitude. Problem. The ability of the quadrotor system to hover at a certain height and track any desired trajectory makes their use in many industrial applications in both military and civil applications. Once a controller has been designed, it may not be able to maintain the desired performance in practical scenarios, i.e. in presence of wind gusts. Originality. This work presents the control strategy to ensure both altitude control and trajectory tracking using a single controller. Purpose. However, there is a need for a single controller that ensures both altitude control and trajectory tracking. Novelty. This paper presents a robust H∞ control for altitude control and trajectory tracking for a six degree of freedom of unmanned aerial vehicles quadrotor. Methodology. Multi input multi output robust H∞ controller has been proposed for the quadrotor for altitude control and tracking the desired reference. For the controller validation, a simulation environment is developed in which a 3D trajectory is tracked by the proposed control methodology. Results. Simulation results depict that the controller is efficient enough to achieve the desired objective at minimal control efforts. Practical value. To verify that the proposed approach is able to ensure stability, altitude control, and trajectory tracking under practical situations, the performance of the proposed control is tested in presence of wind gusts. The ability of the controller to cater to the disturbances within fractions of seconds and maintaining both transient and steady-state performance proves the effectiveness of the controller.