Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased synaptic facilitation and exploratory behavior in mice lacking the presynaptic protein Mover

In vertebrates and invertebrates, neurotransmitter release relies on a highly conserved molecular machinery. A surprisingly small number of presynaptic proteins evolved specifically in vertebrates. How they expand the power or versatility of the conserved core machinery is unclear. One of these vertebrate-specific proteins, called Mover / TPRGL / SVAP30, is heterogeneously expressed throughout the brain, suggesting that it adds special functions to subtypes of presynaptic terminals. In this study we generated Mover knockout mice to investigate the role of Mover from synaptic transmission to behavior. Deletion of Mover did not affect synaptic transmission at CA3 to CA1 synapses. In contrast, Mover deficient mice had strongly increased short-term facilitation at mossy fiber to CA3 synapses. This increase included frequency facilitation, a hallmark of mossy fiber terminal function. The effect was age- and Ca2+-dependent, and relied on the Kainate receptor/cAMP pathway in the mossy fiber terminals. Despite this change in presynaptic plasticity, the absence of Mover did not affect long-term spatial reference memory or working memory, but led to reduced anxiety. These discoveries suggest that Mover has distinct roles at different synapses. At mossy-fiber terminals, it acts to constrain the extent of presynaptic facilitation. Its role in activity-dependent neurotransmission could be necessary for normal anxiety responses. Significance Statement The enormous increase in the complexity of brains during evolution is accompanied by a remarkably small number of new, vertebrate-specific presynaptic proteins. These proteins are unlikely to be essential for transmitter release, because invertebrate synapses do not need them. But what functions do they fulfill? We show that the vertebrate-specific protein Mover is involved in constraining the release of neurotransmitters in some synapses in the hippocampus, while not affecting others. We further demonstrate that the absence of this protein leads to decreased anxiety levels. Understanding the function of such a protein can help us further understand synaptic transmission, the specializations that are brought about in vertebrate synapses, and how this can help or hinder neurological or psychiatric disorders.
Detection of OXA Beta Lactamases Among Clinical Isolates of Acinetobacter baumannii Isolated from Tehran Hospitals, Iran

Acinetobacter baumanniiis a non-motile Gram-negative bacterial pathogen with the history of vast resistant to antibiotics. The aim of this study was to determine the possibility of existence of OXAs genes among clinical isolates ofA. baumanniiobtained from Tehran hospitals.A total of 101 isolates were identified asA. baumanniiby common biochemical and molecular tests. The susceptibility to different antibiotics was assessed with Kirby-Bauer disk diffusion method. Phenotypic Detection of MBLs was performed with CDT test and PCR assay was also performed for detection ofblaOXA-23-like,blaOXA-24-like,blaOXA-40-like,blaOXA-51-like,blaOXA-58-likeandblaOXA-143-likegenesAll isolates ofA. baumanniishowed high-level of resistance to all antibiotics except for Polymyxin B. TheblaOXA-51 likegenes was found in all of the isolates and the prevalence ofblaOXA-143like,blaOXA-23like,blaOXA-40likeandblaOXA-24likewere 56%, 45.45%, 33% and 11.8%, respectively.TheblaOXA-51-likewas the predominant mechanism of resistance to imipenem inA. baumanniiand therefore, early recognition of carbapenem-resistantA. baumanniiisolates is a useful tools to prevent their spreading within the hospital environment.
Hierarchical Bayesian optimization of targeted motor outputs with spatiotemporal neurostimulation

The development of neurostimulation techniques to evoke motor patterns is an active area of research. It serves as a crucial experimental tool to probe computation in neural circuits, and has applications in neuroprostheses used to aid recovery of motor function after stroke or injury to the nervous system. There are two important challenges when designing algorithms to unveil and control neurostimulation-to-motor correspondences, thereby linking spatiotemporal patterns of neural stimulation to muscle activation: (1) the exploration of motor maps needs to be fast and efficient (exhaustive search is to be avoided for clinical and experimental reasons) (2) online learning needs to be flexible enough to deal with occasional spurious responses. We propose a stimulation search algorithm to address these issues, and demonstrate its efficacy with experiments in the motor cortex (M1) of a non-human primate model. Our solution is a novel iterative process using Bayesian Optimization via Gaussian Processes on increasingly complex signal spaces. We show that our algorithm can successfully and rapidly learn correspondences between complex stimulation patterns and evoked muscle activation patterns, where standard approaches fail. Importantly, we uncover nonlinear circuit-level computations in M1 that would not have been possible to identify using conventional mapping techniques.
Identification of potential therapeutic targets in hepatocellular carcinoma using an integrated bioinformatics approach

Background: Hepatocellular carcinoma (HCC) frequently recurs and has poor prognosis, and thus it is essential to investigate the molecular mechanisms associated with HCC development using integrated bioinformatics approaches to identify potential therapeutic targets. Methods: Gene expression data from three microarray datasets, namely, GSE36376, GSE45267, and GSE51401 and 318 HCC tissues and 266 adjacent non-tumorous tissues from HCC patients were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were selected with the limma package in R language, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional enrichment analysis. A protein-protein interaction (PPI) network and a sub-network were established using Search Tool for the Retrieval of Interacting Genes (STRING) and visualized with Cytoscape. Results: A total of 2,249 DEGs were identified in the three datasets, which included 1,735 upregulated and 514 downregulated DEGs. Functional annotation of the DEGs using GO analysis identified categories that were mainly associated with mitotic nuclear division, chromosome segregation, and sister chromatid segregation. KEGG pathway analysis showed that the categories of cell cycle and the p53 signaling pathway, which contributes to the development of HCC, were mainly enriched with DEGs. PPI network and sub-network analyses identified cyclin dependent kinase 2 (CDK2), cyclin B1 (CCNB1), and cell division cycle 20 (CDC20) as hub genes. Furthermore, the categories of cell cycle and p53 signaling pathway were enriched with the hub genes CCNB1 and CDK2. Conclusions: DEGs such as CCNB1, CDC20, and CDK2 as well as classified under the categories of the p53 signaling pathway and the cell cycle were associated with HCC and thus may be potentially utilized as therapeutic targets for the treatment of HCC.
Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

Cellular microscopy images contain rich insights about biology. To extract this information, researchers use features, or measurements of the patterns of interest in the images. Here, we introduce a convolutional neural network (CNN) to automatically design features for fluorescence microscopy. We use a selfsupervised method to learn feature representations of single cells in microscopy images without labelled training data. We train CNNs on a simple task that leverages the inherent structure of microscopy images and controls for variation in cell morphology and imaging: given one cell from an image, the CNN is asked to predict the fluorescence pattern in a second different cell from the same image. We show that our method learns high-quality features that describe protein expression patterns in single cells both yeast and human microscopy datasets. Moreover, we demonstrate that our features are useful for exploratory biological analysis, by capturing high-resolution cellular components in a proteome-wide cluster analysis of human proteins, and by quantifying multi-localized proteins and single-cell variability. We believe paired-cell inpainting is a generalizable method to obtain feature representations of single cells in multichannel microscopy images.
LABOR MARKET AND WAGE DEVELOPMENTS IN THE EU AND BULGARIA

Labor plays an important role in the functioning of the economy. From an enterprise perspective, it represents a cost (labor cost) that includes not only wages and salaries paid to employees, but also indirect labor costs - mainly social security contributions paid by the employer. Therefore, labor is a key factor in the competitiveness of enterprises, although it is also influenced by the cost of capital (for example, interest on loans and dividends on equity) and from non-price elements such as entrepreneurship, skills and productivity, innovation and positioning. brand / products on the market. Labor costs are formed by wage and salary costs plus indirect labor costs, such as employers' social security contributions. Over the last 10 years, improvements in the EU labor market have continued at a steady pace. Employment plays a fundamental role in every society. People are often determined and define themselves by what they do. Employment is called "the glue that holds our society together. " The number of employees in the Eurozone and across the Union already exceeds pre-crisis levels, Eurostat data show. The statistics show a sharp decline in employment at the end of 2008, which then continues with varying intensity for 4 years, and at the end of 2013 begins a rapid recovery - then the peak of post-crisis unemployment in Bulgaria. While the EU has reached pre-crisis levels already in 2016, this process has been slower in the Eurozone, whose labor market has been outperforming since 2008. A number of sociological and economic surveys highlight the fact that employment is not only the main source of social status in any country, but it is also important in securing the purpose, income, social security, structure and instruments for participation in society. Market incentives to increase investment in education and professional development may play a specific role in mitigating the increasing inequality between working capacity and pay and the resulting potential poverty. If people are hired, they are less likely to be poor.
Classification and general differential diagnostic approach to dystonic syndromes

Dystónia a dystonické syndrómy predstavujú heterogénnu skupinu ochorení, ktoré môžu v rámci bežnej klinickej praxe predstavovať zásadnejší diferenciálne-diagnostický problém. V tomto článku je bližšie prediskutovaný základný pragmatický prístup k dystonickým syndrómom z hľadiska ich klasifikácie ako aj diferenciálnej diagnostiky. Kľúčové slová: dystónia, klasifikácia, diferenciálna diagnostika, diagnostický algoritmus.
Inbreeding depression and performance of partially self-fertilized maize progenies in a top cross

Information on the effect of endogamy and combining ability of inbred families is essential in hybrid maize (Zea mays L.) breeding programs. The objective of this study was to evaluate the effect of inbreeding in a maize population and the performance of top-cross hybrids from this population, with a broad genetic base tester. First, 110 S1 families were generated and established in the field along with families from the original population. The experiment was arranged in a randomized block design with three replicates, in 3.0 m plots with 15 plants. Traits of agronomic importance, inbreeding depression, and the general effect of dominance deviations were estimated the first stage. In the second stage, 69 inbred families (S2) with low inbreeding depression were evaluated by top-cross tests using the F2 generation of the commercial hybrid AG 6040 as tester. The same traits from the first stage were evaluated. Inbreeding depression in the first stage was higher for traits related to production, which indicates that the heterozygous loci contribute more to these traits, with the additive effects being less important. In the second stage, the best estimates of the general combining ability (GCA) for grain weight were found in progenies 51, 33, 17, 9, 3, and 67, showing good performance and good potential for use in breeding programs.
Detection of virulence factors of Pseudomonas aeruginosa in different animals by using bacteriological and molecular methods

The aim of this study was to detect the presence of virulence factors of Pseudomonas aeruginosa in different animals. For this purpose 120 samples were collected and examined to detect fourteen virulence factors by using biochemical and molecular methods. The results showed that the highest isolation rate was recorded in doges (29.6%) among studied animals, and highest isolation rate was recorded in milk samples (26.8%) among the studied samples. The virulence factors were detected in different ratio, and highest of them were capsule detected in 50% from skin isolates, amylase enzyme detected in 28.5% from milk isolates, hemolysin enzyme detected in 75% from wound isolates, protease detected in 100% from skin isolates, phospholipase enzyme detected in 56.1% from milk isolates, urease enzyme detected in 50% from skin isolates, gelatin liquefaction detected in 100% from skin and ear isolates, β -lactamase production detected in 100% from skin and wound isolates, pigments production detected in 100% from skin and ear isolates, oprI, oprL and exoT detected in 100% from skin and wound isolates, exoS detected in 100% and 85.7% from skin and milk isolates respectively. We conclude from his study that the dogs are more sensitive in compare with studied animal, while the milk sample is more susceptible to contamination by Pseudomonas aeruginosa. Regarding the virulence factors we noticed that the appearance of it basis on infection state.
Identification of cancer drivers, conserved alteration patterns and evolutionary trajectories in tumors

Over the past decade, high-throughput sequencing efforts have provided an unprecedented opportunity to identify genomic alterations that can lead to changes in gene regulation, protein structure, and function. During tumor progression, cancer cells accumulate a multitude of genomic alterations, a small fraction of which provide tumor cells with selective advantage – known as “driver” alterations. However, most of them are inconsequential “passenger” alterations that are effectively neutral and greatly outnumber driver alterations. Moreover, due to a high amount of heterogeneity, alteration landscapes of tumors differ between different patients and different sites. This thesis first presents HIT’nDRIVE, a method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered potential driver genes, with sufficient collective influence over dysregulated transcripts through interactome. Applied to 2200 tumors, HIT’nDRIVE revealed many potentially clinically actionable driver genes and demonstrated its robustness in selecting cancer-implicated drivers. The results also show that small network modules seeded by HIT’nDRIVE-selected drivers significantly improve classification of cancer phenotypes and drug efficacy in pan-cancer cell lines compared to alternative methods and approaches. Next, a method for detection of functionally meaningful and recurrent alteration patterns within gene interaction networks, cd-CAP, is presented. In a number of TCGA data sets, cd-CAP identified large subnetworks with identically conserved alteration patterns (across many tumor samples), that were significantly associated with patients’ clinical outcome. As multi-region, time-series and single cell sequencing data become more widely available, computational methods have been developed with the goal of inferring the subclonal composition and evolutionary history of tumors from tumor biopsy sequencing data. Unfortunately, the phylogenetic trees reported for many tumor samples differ significantly from other tumors with similar characteristics. This thesis presents CONETT, the first computational method for detection of conserved trajectories of alteration events in tumor evolution. Applied to two multi-region sequencing data sets of 100 tumors each, CONETT confirms all findings of the original studies and identifies additional repeated trajectories.
Correlation between body condition score and hormone level of Bali cattle with postpartum anestrus

Body Condition Score (BCS) is a simpler and more practical method to evaluate the body’s energy and fat reserves in cows. Nutrition play a direct role both in the hypothalamus by synthesizing and releasing GnRH, as well as on the anterior pituitary by controlling the synthesis and release of Leptin, FSH, LH and Estrogen. The purpose of this study was to determine the relationship between the body condition score with the activation of hormones in the hypothalamic–pituitary–gonadal axis on Bali cattle that experienced postpartum anestrus. This research was an observational analytic study with Cross-Sectional Study design. The samples used were Bali cattle that have given birth and have not shown estrus for more than three months. BCS assessment method is qualitatively conducted through visual and tactile techniques. Measurements of Leptin, FSH, LH and estrogen hormone levels were performed using the ELISA Double Antibody Sandwich method. The results showed a correlation between body condition score to hormone level i.e. Leptin level of 0.861; LH level of 0.960; FSH level of 0.799; and Estrogen level of 0.761. These data demonstrated that BCS significantly affects Leptin hormone concentrations. It takes Leptin with a certain concentration to trigger the release of LH in follicle maturation and ovulation, thus achieving a threshold that causes the activation of the hypothalamic–pituitary–gonadal axis.
Analysis of P97 and P102 paralogs of Mycoplasma hyopneumoniae

~ LITERATURE REVIEW 1 General Information 1 Molecular Characteristics 2 Genome 2 Alternate codon usage 3 Disease Pathology 3 Host Interactions 5 Virulence factors and cell cytotoxicity 5 General adherence 5 Mycoplasma hyopneumoniae adherence 6 Paralogous families 8 Immune interactions 10 DNA Vaccines 11 MATERIALS AND METHODS 14 Bacterial Strains and Plasmids 14 Reagents and Buffers 15 Plasmid Constructions 16 Polymerase Chain Reaction 17 Site-Directed Mutagenesis 18 Primer Synthesis and DNA Sequencing 18 Transformation 19 Plasmid Preparations 19 Rabbits 20 Vaccinations and Blood Collection 20 Recombinant Protein Purification 21 Antibody Purification 23 Immunoblot Analysis 23 Reverse Transcriptase-Polymerase Chain Reaction 24 RESULTS 29 Plasmid Constructions 29 Analysis and cloning of unique gene sequences from P97 and Pl02 paralogs 29 Site-directed mutagenesis 34 Antibody Production 34 Recombinant Protein Purification 38 Immunoblot Analysis 38 Open reading frame mhp 107 40 Open reading frame mhp684 Open reading frame mhp493 Open reading frame mhp385 Open reading frame mhp272 Open reading frame mhp275 Open reading frame mhp 108 Open reading frame mhp683 Open reading frame mhp384 IV Reverse Transcriptase-Polymerase Chain Reaction DISCUSSION General Discussion Cloning Site-Directed Mutagenesis DNA Vaccination and Antibody Production Recombinant Protein Purification Immunoblot Analysis Reverse Transcriptase-Polymerase Chain Reaction
Time and space dimensions of gene dosage imbalance of aneuploidies revealed by single cell transcriptomes

The mechanisms underlying cellular and organismal phenotypes due to copy number alterations (CNA) are not fully understood. Aneuploidy is a major source of gene dosage imbalance due to CNA and viable human trisomies are model disorders of altered gene expression. To understand the cellular impact of gene dosage imbalance, we studied gene and allele specific expression (ASE) of 9668 single-cell fibroblasts in trisomies T21, T18, T13 and T8. To limit the bias of interindividual noise, all comparisons between euploid and trisomic single-cells were performed on an isogenic setting for all trisomies studied. Initially we examined 928 single cells with deep RNA-Seq. For T21 we used fibroblasts from one pair of monozygotic twins discordant for T21 and from mosaic T21. For T18, T13 and T8 we analyzed single cells from mosaic individuals. Single-cell analyses revealed inconsistencies concerning the overexpression of some genes observed in differential trisomic vs euploid bulk RNAseq while this imbalance was not detectable in trisomic vs. euploid single cells. Moreover, ASE profiling of all single cells uncovered a substantial monoallelic pattern of expression in the trisomic fraction of the genome. By classifying genes according to the level of mono and bi-allelic transcription, we have observed that, for genes with monoallelic and low-to-average expression, the altered gene dosage is mainly due to the higher fraction of cells simultaneously expressing these genes in the trisomic samples. These results were confirmed in a further experiment of 8740 single fibroblasts from the monozygotic twins discordant for T21 samples. We conclude that gene dosage imbalance is of bidimensional nature: over time (simultaneous expression of all alleles resulting in increased accumulation of RNA of copy altered genes in each single cell) as previously stated, and over space (increased fraction of cells simultaneously expressing copy altered genes). These results strongly suggest that each class of genes contributes to the phenotypic variability of trisomies according to its temporal and spatial behavior and propose an improved model to understand the effects of copy number alterations.
Increasing compound warm spells and droughts during the growing season in the Mediterranean Basin

The Mediterranean Basin is known as a hot spot of climate change and therefore especially prone to increasing frequencies of warm spells and droughts. Investigating these events in isolation neglects their interactions, which illustrates the need to account for such compound events in a holistic manner. We analysed during which months the frequency of compound warm spells and droughts increased most over the 40-year period from 1979 – 2018. Warm spells and droughts were detected using daily maximum air temperature, precipitation and potential evaporation data from ERA 5. The two drought indices Standardised Precipitation Index (SPI) and Standardised Precipitation-Evapotranspiration Index (SPEI) were calculated.
The Comparative Analysis of Conventional and Sharia Mutual Funds Performance From January 2017 to December 2018

- This study aims to compare the performance of mutual funds based on returns and risk, and also classify the efficiency of mutual funds based on the Capital Asset Pricing Model (CAPM) method. The research sample was 44 conventional equity mutual funds, 9 sharia equity mutual funds, 44 sharia fixed income mutual funds, and 9 sharia fixed income mutual funds. The research period is from 2017 to 2018. The results show that the rate of return and risk between conventional mutual funds and sharia mutual funds are the same or have no difference. While the calculation of the rate of return and risk between equity funds and fixed income mutual funds also shows that there are no differences between the two types of mutual funds. The classification of efficient mutual funds found that there were 15 equityfunds and 40 fixed income mutual funds,which were included inefficient mutual funds.