Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA-Seq-Based Analysis of the Physiologic Cold Shock-Induced Changes in Moraxella catarrhalis Gene Expression

Background Moraxella catarrhalis, a major nasopharyngeal pathogen of the human respiratory tract, is exposed to rapid downshifts of environmental temperature when humans breathe cold air. The prevalence of pharyngeal colonization and respiratory tract infections caused by M. catarrhalis is greatest in winter. We investigated how M. catarrhalis uses the physiologic exposure to cold air to regulate pivotal survival systems that may contribute to M. catarrhalis virulence. Results In this study we used the RNA-seq techniques to quantitatively catalogue the transcriptome of M. catarrhalis exposed to a 26°C cold shock or to continuous growth at 37°C. Validation of RNA-seq data using quantitative RT-PCR analysis demonstrated the RNA-seq results to be highly reliable. We observed that a 26°C cold shock induces the expression of genes that in other bacteria have been related to virulence a strong induction was observed for genes involved in high affinity phosphate transport and iron acquisition, indicating that M. catarrhalis makes a better use of both phosphate and iron resources after exposure to cold shock. We detected the induction of genes involved in nitrogen metabolism, as well as several outer membrane proteins, including ompA, m35-like porin and multidrug efflux pump (acrAB) indicating that M. catarrhalis remodels its membrane components in response to downshift of temperature. Furthermore, we demonstrate that a 26°C cold shock enhances the induction of genes encoding the type IV pili that are essential for natural transformation, and increases the genetic competence of M. catarrhalis, which may facilitate the rapid spread and acquisition of novel virulence-associated genes. Conclusion Cold shock at a physiologically relevant temperature of 26°C induces in M. catarrhalis a complex of adaptive mechanisms that could convey novel pathogenic functions and may contribute to enhanced colonization and virulence.
Semi-supervised truth discovery

Accessing online information from various data sources has become a necessary part of our everyday life. Unfortunately such information is not always trustworthy, as different sources are of very different qualities and often provide inaccurate and conflicting information. Existing approaches attack this problem using unsupervised learning methods, and try to infer the confidence of the data value and trustworthiness of each source from each other by assuming values provided by more sources are more accurate. However, because false values can be widespread through copying among different sources and out-of-date data often overwhelm up-to-date data, such bootstrapping methods are often ineffective. In this paper we propose a semi-supervised approach that finds true values with the help of ground truth data. Such ground truth data, even in very small amount, can greatly help us identify trustworthy data sources. Unlike existing studies that only provide iterative algorithms, we derive the optimal solution to our problem and provide an iterative algorithm that converges to it. Experiments show our method achieves higher accuracy than existing approaches, and it can be applied on very huge data sets when implemented with MapReduce.
PARTICIPATION OF THE CYTOPLASMIC MEMBRANE IN THE GROWTH AND SPORE FORMATION OF BACILLI

A polyester embedding technique was used to study the early stages of spore formation in members of the genus Bacillus in order to investigate further the origin and nature of the initial spore septum and the resulting forespore envelope. Whereas previously, with a methacrylate procedure, this layer had appeared to be continuous with the cell wall, this study reveals it as a double layer of cytoplasmic membrane. Perisporal, membranous organelles connected both to the developing forspore envelope and to the cytoplasmic membrane were encountered in the four species studied. Similar organelles were prominent during growth at the sites of transverse septa formation. These were connected to, or continuous with, the cytoplasmic membrane and often adherent to the chromatin bodies of the dividing bacilli.
Arabic Dialect Identification Using iVectors and ASR Transcripts

This paper presents the systems submitted by the MAZA team to the Arabic Dialect Identification (ADI) shared task at the VarDial Evaluation Campaign 2017. The goal of the task is to evaluate computational models to identify the dialect of Arabic utterances using both audio and text transcriptions. The ADI shared task dataset included Modern Standard Arabic (MSA) and four Arabic dialects: Egyptian, Gulf, Levantine, and North-African. The three systems submitted by MAZA are based on combinations of multiple machine learning classifiers arranged as (1) voting ensemble; (2) mean probability ensemble; (3) meta-classifier. The best results were obtained by the meta-classifier achieving 71.7% accuracy, ranking second among the six teams which participated in the ADI shared task.
MSCs ameliorates DPN induced cellular pathology via [Ca2+]i homeostasis and scavenging the pro‐inflammatory cytokines

The MSCs of various origins are known to ameliorate or modulate cell survival strategies. We investigated, whether UCB MSCs could improve the survival of the human neuronal cells and/or fibroblast assaulted with DPN sera. The results showed, the co‐culture of UCB MSCs with human neuronal cells and/or fibroblasts could effectively scavenge the pro‐inflammatory cytokines TNF‐α, IL‐1β, IFN‐ɤ and IL − 12 and control the pro‐apoptotic expression of p53/Bax. Further co‐culture of UCB MSCs have shown to induce anti‐inflammatory cytokines like IL‐4, IL‐10 and TGF‐β and anti‐apoptotic Bclxl/Bcl2 expression in the DPN sera stressed cells. Amelioration of elevated [Ca2+]i and cROS, the portent behind the NFκB/Caspase‐3 mediated inflammation in DPN rescued the cells from apoptosis. The results of systemic administration of BM MSCs improved DPN pathology in rat as extrapolated from human cell model. The BM MSCs ameliorated prolonged distal motor latency (control: 0.70 ± 0.06, DPN: 1.29 ± 0.13 m/s DPN + BM MSCs: 0.89 ± 0.02 m/s, p < 0.05) and lowered high amplitude of compound muscle action potentials (CMAPs) (control: 12.36 ± 0.41, DPN: 7.52 ± 0.61 mV, DPN + MSCs: 8.79 ± 0.53 mV, p < 0.05), while slowly restoring the plasma glucose levels. Together, all these results showed that administration of BM or UCB MSCs improved the DPN via ameliorating pro‐inflammatory cytokine signaling and [Ca2+]i homeostasis.
The Novel CXCL12γ Isoform Encodes an Unstructured Cationic Domain Which Regulates Bioactivity and Interaction with Both Glycosaminoglycans and CXCR4

Background CXCL12α, a chemokine that importantly promotes the oriented cell migration and tissue homing of many cell types, regulates key homeostatic functions and pathological processes through interactions with its cognate receptor (CXCR4) and heparan sulfate (HS). The alternative splicing of the cxcl12 gene generates a recently identified isoform, CXCL12γ, which structure/function relationships remain unexplored. The high occurrence of basic residues that characterize this isoform suggests however that it could feature specific regulation by HS. Methodology/Principal Findings Using surface plasmon resonance and NMR spectroscopy, as well as chemically and recombinantly produced chemokines, we show here that CXCL12γ first 68 amino acids adopt a structure closely related to the well described α isoform, followed by an unfolded C-terminal extension of 30 amino acids. Remarkably, 60 % of these residues are either lysine or arginine, and most of them are clustered in typical HS binding sites. This provides the chemokine with the highest affinity for HP ever observed (Kd = 0.9 nM), and ensures a strong retention of the chemokine at the cell surface. This was due to the unique combination of two cooperative binding sites, one strictly required, found in the structured domain of the protein, the other one being the C-terminus which essentially functions by enhancing the half life of the complexes. Importantly, this peculiar C-terminus also regulates the balance between HS and CXCR4 binding, and consequently the biological activity of the chemokine. Conclusions/Significance Together these data describe an unusual binding process that gives rise to an unprecedented high affinity between a chemokine and HS. This shows that the γ isoform of CXCL12, which features unique structural and functional properties, is optimized to ensure its strong retention at the cell surface. Thus, depending on the chemokine isoform to which it binds, HS could differentially orchestrate the CXCL12 mediated directional cell kinesis.
A Comparison of Computation Span and Reading Span Working Memory Measures’ Relations With Problem-Solving Criteria

Researchers have operationalized working memory in different ways and although working memory–performance relationships are well documented, there has been relatively less attention devoted to determining whether seemingly similar measures yield comparable relations with performance outcomes. Our objective is to assess whether two working memory measures deploying the same processes but different item content yield different relations with two problem-solving criteria. Participants completed a computation-based working memory measure and a reading-based measure prior to performing a computerized simulation. Results reveal differential relations with one of the two criteria and support the notion that the two working memory measures tap working memory capacity and other cognitive abilities. One implication for theory development is that researchers should consider incorporating other cognitive abilities in their working memory models and that the selection of those abilities should correspond to the criterion of interest. One practical implication is that researchers and practitioners shouldn’t automatically assume that different phonological loop-based working memory scales are interchangeable.
The Potential for Xanthine Oxidase Inhibition in the Prevention and Treatment of Cardiovascular and Cerebrovascular Disease

There is a now a wealth of epidemiological, animal, and clinical data to suggest the benefits of uric acid reduction and hxanthine oxidase inhibition in prevention of vascular disease. This review discusses the available epidemiological, preclinical, and clinical data and considers arguments for and against a role for serum uric acid in common cardiovascular disorders. It concludes that large scale trials with clinical endpoints are justified to address this important question and to define whether use of drugs such as allopurinol should be a routine part of preventative strategies.
Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Lengthy developmental programs generate cell diversity within an organotypic framework, enabling the later physiological actions of each organ system. Cell identity, cell diversity and cell function are determined by cell type-specific transcriptional programs; consequently, transcriptional regulatory factors are useful markers of emerging cellular complexity, and their expression patterns provide insights into the regulatory mechanisms at play. We performed a comprehensive genome-scale in situ expression screen of 921 transcriptional regulators in the developing mammalian urogenital system. Focusing on the kidney, analysis of regional-specific expression patterns identified novel markers and cell types associated with development and patterning of the urinary system. Furthermore, promoter analysis of synexpressed genes predicts transcriptional control mechanisms that regulate cell differentiation. The annotated informational resource (www.gudmap.org) will facilitate functional analysis of the mammalian kidney and provides useful information for the generation of novel genetic tools to manipulate emerging cell populations.
Perceptual Averaging in Individuals with Autism Spectrum Disorder

There is mounting evidence that observers rely on statistical summaries of visual information to maintain stable and coherent perception. Sensitivity to the mean (or other prototypical value) of a visual feature (e.g., mean size) appears to be a pervasive process in human visual perception. Previous studies in individuals diagnosed with Autism Spectrum Disorder (ASD) have uncovered characteristic patterns of visual processing that suggest they may rely more on enhanced local representations of individual objects instead of computing such perceptual averages. To further explore the fundamental nature of abstract statistical representation in visual perception, we investigated perceptual averaging of mean size in a group of 12 high-functioning individuals diagnosed with ASD using simplified versions of two identification and adaptation tasks that elicited characteristic perceptual averaging effects in a control group of neurotypical participants. In Experiment 1, participants performed with above chance accuracy in recalling the mean size of a set of circles (mean task) despite poor accuracy in recalling individual circle sizes (member task). In Experiment 2, their judgments of single circle size were biased by mean size adaptation. Overall, these results suggest that individuals with ASD perceptually average information about sets of objects in the surrounding environment. Our results underscore the fundamental nature of perceptual averaging in vision, and further our understanding of how autistic individuals make sense of the external environment.
A Search for Energy Minimized Sequences of Proteins

In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10-7. In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.
The coding of odour‐intensity in the honeybee antennal lobe: local computation optimizes odour representation

We investigated strategies involved in odour intensity coding by the primary olfactory centre of insects, the antennal lobe (AL), the structural and functional analogue of the olfactory bulb. Using calcium imaging in the honeybee, we simultaneously measured the projection neuron output responses and a compound signal dominated by receptor neuron input in identified olfactory glomeruli to odours spanning seven log units of concentration. A comparison of the two processing levels indicates that the intercellular computation within the AL modulates and contrast‐enhances the primary olfactory signals. As a result the AL network optimizes the olfactory code: odour representation is improved at lower concentrations, the relative activity of olfactory glomeruli allows encoding odour quality over up to four log‐unit concentrations, and odour‐intensity is reliably represented in the overall excitation across AL.
Improved survival in rheumatoid arthritis: a general population-based cohort study

Objective Mortality trends of rheumatoid arthritis (RA) are largely unknown over the past decade when new drugs and management strategies have been adopted to effectively treat RA. Methods Using The Health Improvement Network, an electronic medical record database representative of the UK general population, we identified patients with incident RA and up to five individuals without RA matched for age, sex and year of diagnosis between 1999 and 2014. The RA cohort was divided in two sub-cohorts based on the year of RA diagnosis: the early cohort (1999–2006) and the late cohort (2007–2014). We compared mortality rates, HRs (using a Cox proportional hazard model) and rate differences (using an additive hazard model) between RA and non-RA cohorts adjusting for potential confounders. Results Patients with RA diagnosed between 1999 and 2006 had a considerably higher mortality rate than their comparison cohort (ie, 29.1 vs 18.0 deaths/1000 person-years), as compared with a moderate difference in patients with RA diagnosed between 2007 and 2014 and their comparison cohort (17.0 vs 12.9 deaths/1000 years). The corresponding absolute mortality rate differences were 9.5 deaths/1000 person-years (95% CIs 7.5 to 11.6) and 3.1 deaths/1000 person-years (95% CI 1.5 to 4.6) and the mortality HRs were 1.56 (95% CI 1.44 to 1.69) and 1.29 (95% CI 1.17 to 1.42), respectively (both p values for interaction <0.01). Conclusion This general population-based cohort study indicates that the survival of patients with RA has improved over the past decade to a greater degree than in the general population. Improved management of RA and its associated comorbidities over recent years may be providing a survival benefit.
Net Surface Shortwave Radiation from GOES Imagery - Product Evaluation Using Ground-Based Measurements from SURFRAD

The Earth’s surface net radiation controls the energy and water exchanges between the Earth’s surface and the atmosphere, and can be derived from satellite observations. The ability to monitor the net surface radiation over large areas at high spatial and temporal resolution is essential for many applications, such as weather forecasting, short-term climate prediction or water resources management. The objective of this paper is to derive the net surface radiation in the shortwave domain at high temporal (half-hourly) and spatial resolution (~1 km) using visible imagery from Geostationary Operational Environmental Satellite (GOES). The retrieval algorithm represents an adaptation to GOES data of a standard algorithm initially developed for the NASA-operated Clouds and Earth’s Radiant Energy System (CERES) scanner. The methodology relies on: (1) the estimation of top of atmosphere shortwave radiation from GOES spectral measurements; and (2) the calculation of net surface shortwave (SW) radiation accounting for atmospheric effects. Comparison of GOES-retrieved net surface shortwave radiation with ground-measurements at the National Oceanic and Atmospheric Administration’s (NOAA) Surface Radiation (SURFRAD) stations yields very good agreement with average bias lower than 5 W·m−2 and root mean square difference around 70 W·m−2. The algorithm performance is usually higher over areas characterized by low spatial variability in term of land cover type and surface biophysical properties. The technique does not involve retrieval and assessment of cloud properties and can be easily adapted to other meteorological satellites around the globe.
ISSLS Prize Winner: Collagen Fibril Sliding Governs Cell Mechanics in the Anulus Fibrosus: An In Situ Confocal Microscopy Study of Bovine Discs

Study Design. In situ investigation of collagen and cell mechanics in bovine caudal discs using novel techniques of confocal microscopy. Objective. To measure simultaneously the in situ intercellular and collagen matrix mechanics in the inner and outer anulus fibrosus of the intervertebral disc subjected to flexion. Summary of Background Data. Mechanobiology studies, both in vivo and in vitro, clearly demonstrate that mechanical factors can influence the metabolic activity of disc cells, altering the expression of key extracellular matrix molecules. Essential to elucidating the mechanotransduction mechanisms is a detailed understanding of the in situ mechanical environment of disc cells in response to whole-body mechanical loads. Methods. Confocal microscopy was used to simultaneously track and capture in situ images of fluorescently labeled cells and matrix during an applied flexion. The position of the nuclear centroids was calculated before and after applied flexion to quantify the in situ intercellular mechanics of both lamellar and interlamellar cells. The deflection patterns of lines photobleached into the extracellular matrix were used to quantify collagen fibril sliding and collagen fibril strains in situ. Results. The extracellular matrix was observed to deflect nonuniformly due to the relative sliding of the collagen fibrils. Intercellular displacements within the lamellar layers were also nonuniform, both along a cell row andbetween adjacent rows. Within a cell row, the intercellular displacements were small (<1%). Conclusions. The in situ cell mechanics of anular cells was found to be strongly influenced by collagen fibril sliding in the extracellular matrix and could not be inferred directly from applied tissue loads.
Orai1 and Orai3 in Combination with Stim1 Mediate the Majority of Store-operated Calcium Entry in Astrocytes

Astrocytes are non-excitable cells in the brain and their activity largely depends on the intracellular calcium (Ca2+) level. Therefore, maintaining the intracellular Ca2+ homeostasis is critical for proper functioning of astrocytes. One of the key regulatory mechanisms of Ca2+ homeostasis in astrocytes is the store-operated Ca2+ entry (SOCE). This process is mediated by a combination of the Ca2+-store-depletion-sensor, Stim, and the store-operated Ca2+-channels, Orai and TrpC families. Despite the existence of all those families in astrocytes, previous studies have provided conflicting results on the molecular identification of astrocytic SOCE. Here, using the shRNA-based gene-silencing approach and Ca2+-imaging from cultured mouse astrocytes, we report that Stim1 in combination with Orai1 and Orai3 contribute to the major portion of astrocytic SOCE. Gene-silencing of Stim1 showed a 79.2% reduction of SOCE, indicating that Stim1 is the major Ca2+-store-depletion-sensor. Further gene-silencing showed that Orai1, Orai2, Orai3, and TrpC1 contribute to SOCE by 35.7%, 20.3%, 26.8% and 12.2%, respectively. Simultaneous gene-silencing of all three Orai subtypes exhibited a 67.6% reduction of SOCE. Based on the detailed population analysis, we predict that Orai1 and Orai3 are expressed in astrocytes with a large SOCE, whereas TrpC1 is exclusively expressed in astrocytes with a small SOCE. This analytical approach allows us to identify the store operated channel (SOC) subtype in each cell by the degree of SOCE. Our results propose that Stim1 in combination with Orai1 and Orai3 are the major molecular components of astrocytic SOCE under various physiological and pathological conditions.