Miracle-dz/UniFAR-FTUs huggingface dataset:
TIM-3 as a therapeutic target in human inflammatory diseases

T-cell immunoglobulin- and mucin-domain-containing molecule-3 (Tim-3) was the first, and is presently the only, surface molecule that can specifically identify TH1 cells in both mice and humans. Engagement of Tim-3 by its ligand galectin-9 negatively regulates IFN-γ secretion and influences the ability to induce T cell tolerance in both mice and man. Numerous studies have demonstrated that Tim-3 influences autoimmune diseases, including diabetes and multiple sclerosis, and its role in other inflammatory diseases including allergies and cancer is beginning to become clear.
Convergence of a Fixed-Point Minimum Error Entropy Algorithm

The minimum error entropy (MEE) criterion is an important learning criterion in information theoretical learning (ITL). However, the MEE solution cannot be obtained in closed form even for a simple linear regression problem, and one has to search it, usually, in an iterative manner. The fixed-point iteration is an efficient way to solve the MEE solution. In this work, we study a fixed-point MEE algorithm for linear regression, and our focus is mainly on the convergence issue. We provide a sufficient condition (although a little loose) that guarantees the convergence of the fixed-point MEE algorithm. An illustrative example is also presented.
THE CONTRIBUTION OF STARBURSTS AND NORMAL GALAXIES TO INFRARED LUMINOSITY FUNCTIONS AT z < 2

We present a parameterless approach to predict the shape of the infrared (IR) luminosity function (LF) at redshifts z ⩽ 2. It requires no tuning and relies on only three observables: (1) the redshift evolution of the stellar mass function for star-forming galaxies, (2) the evolution of the specific star formation rate (sSFR) of main-sequence galaxies, and (3) the double-Gaussian decomposition of the sSFR distribution at fixed stellar mass into a contribution (assumed redshift- and mass-invariant) from main-sequence and starburst activity. This self-consistent and simple framework provides a powerful tool for predicting cosmological observables: observed IR LFs are successfully matched at all z ⩽ 2, suggesting a constant or only weakly redshift-dependent contribution (8%–14%) of starbursts to the SFR density. We separate the contributions of main-sequence and starburst activity to the global IR LF at all redshifts. The luminosity threshold above which the starburst component dominates the IR LF rises from log(LIR/L☉) = 11.4 to 12.8 over 0 < z < 2, reflecting our assumed (1+z)2.8-evolution of sSFR in main-sequence galaxies.
Lightweight Session Programming in Scala

Designing, developing and maintaining concurrent applications is an error-prone and time-consuming task; most difficulties arise because compilers are usually unable to check whether the inputs/outputs performed by a program at runtime will adhere to a given protocol specification. To address this problem, we propose lightweight session programming in Scala: we leverage the native features of the Scala type system and standard library, to introduce (1) a representation of session types as Scala types, and (2) a library, called lchannels, with a convenient API for session-based programming, supporting local and distributed communication. We generalise the idea of Continuation-Passing Style Protocols (CPSPs), studying their formal relationship with session types. We illustrate how session programming can be carried over in Scala: how to formalise a communication protocol, and represent it using Scala classes and lchannels, letting the compiler help spotting protocol violations. We attest the practicality of our approach with a complex use case, and evaluate the performance of lchannels with a series of benchmarks.
Sequential Bayesian prediction in the presence of changepoints

We introduce a new sequential algorithm for making robust predictions in the presence of changepoints. Unlike previous approaches, which focus on the problem of detecting and locating changepoints, our algorithm focuses on the problem of making predictions even when such changes might be present. We introduce nonstationary covariance functions to be used in Gaussian process prediction that model such changes, then proceed to demonstrate how to effectively manage the hyperparameters associated with those covariance functions. By using Bayesian quadrature, we can integrate out the hyperparameters, allowing us to calculate the marginal predictive distribution. Furthermore, if desired, the posterior distribution over putative changepoint locations can be calculated as a natural byproduct of our prediction algorithm.
Goals and plans in decision making

We propose a constructed-choice model for general decision making. The model departs from utility theory and prospect theory in its treatment of multiple goals and it suggests several different ways in which context can affect choice.It is particularly instructive to apply this model to protective decisions, which are often puzzling. Among other anomalies, people insure against non-catastrophic events, underinsure against catastrophic risks, and allow extraneous factors to influence insurance purchases and other protective decisions. Neither expected-utility theory nor prospect theory can explain these anomalies satisfactorily. To apply this model to the above anomalies, we consider many different insurance-related goals, organized in a taxonomy, and we consider the effects of context on goals, resources, plans and decision rules.The paper concludes by suggesting some prescriptions for improving individual decision making with respect to protective measures.
Uncovering Spatiotemporal Characteristics of Human Online Behaviors during Extreme Events

In response to an extreme event, individuals on social media demonstrate interesting behaviors depending on their backgrounds. By making use of the large-scale datasets of posts and search queries collected from Twitter and GoogleTrends, we first identify the distinct categories of human collective online concerns and durations based on the distributions of solo tweets and new incremental tweets about events. Such a characterization enables us to gain a better understanding of dynamic changes in human behaviors corresponding to different types of events. Next, we observe the heterogeneity of individual responses to events through measuring the fraction of event-related tweets relative to the tweets released by an individual, and thus empirically confirm the heterogeneity assumption as adopted in the meta-population models for characterizing collective responses to events. Finally, based on the correlations of information entropy in different regions, we show that the observed distinct responses may be caused by their different speeds in information propagation. In addition, based on the detrended fluctuation analysis, we find that there exists a self-similar evolution process for the collective responses within a region. These findings have provided a detailed account for the nature of distinct human behaviors on social media in presence of extreme events.
Statin prevents chondrocyte aging and degeneration of articular cartilage in osteoarthritis (OA)

Recent reports have shown that statin (HMG-CoA reductase inhibitors) may have the potential to inhibit inflammatory arthritis. More recently, the idea that chondrocyte aging is closely associated with the progression of cartilage degeneration has been promulgated. Here, we demonstrate the potential of statin as protective agents against chondrocyte aging and degeneration of articular cartilage during the progression of osteoarthritis (OA), both in vitro and in vivo. The OA-related catabolic factor, IL-1β induced marked downregulation of cellular activity, expression of a senescent biomarker, specific senescence-associated β-galactosidase activity and shortening of the cellular lifespan in chondrocytes. In contrast, treatment with statin inhibited the IL-1β-induced production of cartilage matrix degrading enzymes (metalloprotease-1 and -13) and cellular senescence in of chondrocytes in vitro. In addition, this statin accelerated the production of cartilage matrix proteoglycan in chondrocytes. The in vivo study was performed on the STR/OrtCrlj mouse, an experimental model which spontaneously develops an osteoarthritic process. In this mouse model, treatment with statin significantly reduced the degeneration of articular cartilage, while the control knee joints showed progressive cartilage degeneration over time. These findings suggest that statin may have the potential to prevent the catabolic stress-induced chondrocyte disability and aging observed in articular cartilage. Our results indicate that statin are potential therapeutic agents for protection of articular cartilage against the progression of OA.
Cytotoxicity of the Ascidian Cystodytes dellechiajei Against Tumor Cells and Study of the Involvement of Associated Microbiota in the Production of Cytotoxic Compounds

Many cytotoxic compounds of therapeutic interest have been isolated from marine invertebrates, and some of them have been reported to be of microbial origin. Pyridoacridine alkaloids are the main compounds extracted from the ascidian Cystodytes dellechiajei. Here we describe the in vitro antiproliferative activity against different tumor cell lines of the ascidian extracts and provide some insights on the role of the microbial community associated with the tunicate in the production of these compounds. C. dellechiajei extracts showed remarkably high antiproliferative activity (IC50 ≤5 μg/mL) in human lung carcinoma A-549, colon adenocarcinoma H-116, pancreatic adenocarcinoma PSN-1 and breast carcinoma SKBR3 cell lines. Moreover, we found that the maximum activity was located in the tunic tissue of the colony, which harbours a microbial community. In order to ascertain the involvement of this community in the synthesis of the bioactive compounds different approachs that included culture and culture independent methods were carried out. We undertook a screening for antiproliferative activities of the bacterial isolates from the ascidian, as well as a comprative analysis of the cytotoxic activities and the microbial communities from two color morphs of the ascidian, green and blue. In addition, the changes of the antiproliferative activities and the composition of the microbial communities were studied from ascidians kept in aquaria and treated with antibiotics for one month. Our data obtained from the different experiments did not point out to bacteria as the source of the cytotoxic compounds, suggesting thus an ascidian origin.
Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725

Caldicellulosiruptor bescii DSM 6725 utilizes various polysaccharides and grows efficiently on untreated high-lignin grasses and hardwood at an optimum temperature of ∼80°C. It is a promising anaerobic bacterium for studying high-temperature biomass conversion. Its genome contains 2666 protein-coding sequences organized into 1209 operons. Expression of 2196 genes (83%) was confirmed experimentally. At least 322 genes appear to have been obtained by lateral gene transfer (LGT). Putative functions were assigned to 364 conserved/hypothetical protein (C/HP) genes. The genome contains 171 and 88 genes related to carbohydrate transport and utilization, respectively. Growth on cellulose led to the up-regulation of 32 carbohydrate-active (CAZy), 61 sugar transport, 25 transcription factor and 234 C/HP genes. Some C/HPs were overproduced on cellulose or xylan, suggesting their involvement in polysaccharide conversion. A unique feature of the genome is enrichment with genes encoding multi-modular, multi-functional CAZy proteins organized into one large cluster, the products of which are proposed to act synergistically on different components of plant cell walls and to aid the ability of C. bescii to convert plant biomass. The high duplication of CAZy domains coupled with the ability to acquire foreign genes by LGT may have allowed the bacterium to rapidly adapt to changing plant biomass-rich environments.
Evaluation of an Immunofluorescent-Antibody Test Using Monoclonal Antibodies Directed against Enterocytozoon bieneusi and Encephalitozoon intestinalis for Diagnosis of Intestinal Microsporidiosis in Bamako (Mali)

ABSTRACT A 2-month study was carried out in Mali to evaluate an immunofluorescent-antibody test (IFAT) using monoclonal probes specific for Enterocytozoon bieneusi or Encephalitozoon intestinalis. Sixty-one human immunodeficiency virus (HIV)-seropositive adult patients and 71 immunocompetent children were enrolled. Microsporidia were detected in stools from 8 of 61 patients (13.1%) seropositive for HIV. A single species, E. bieneusi, was identified. All the children were negative for microsporidia. The sensitivity and specificity of IFAT were 100% compared with those of PCR, which was used as the “gold standard. ” Moreover, species identification by IFAT was more rapid and less expensive than that by PCR. These results show the suitability of IFAT for detection of microsporidia in developing countries.
The Genetic Basis for Inflorescence Variation Between Foxtail and Green Millet (Poaceae)

Grass species differ in many aspects of inflorescence architecture, but in most cases the genetic basis of the morphological difference is unknown. To investigate the genes underlying the morphology in one such instance, we undertook a developmental and QTL analysis of inflorescence differences between the cereal grain foxtail millet and its presumed progenitor green millet. Inflorescence differences between these two species are the result of changes in primary branch number and density, spikelet number, and bristle (sterile branchlet) number; these differences also account for inflorescence variation within the clade of 300+ species that share the presence of bristles in the inflorescence. Fourteen replicated QTL were detected for the four inflorescence traits, and these are suggested to represent genes that control differences between the species. Comparative mapping using common markers from rice and maize allowed a number of candidate genes from maize to be localized to QTL regions in the millet genome. Searches of regions of the sequenced rice genome orthologous to QTL regions on foxtail millet identified a number of transcription factors and hormone pathway genes that may be involved in control of inflorescence branching.
Survey and distribution of rodent inhabiting eight districts at Gharbia governorate, Egypt

Rodent individuals were noticed in buildings from eight districts viz., Samannoud, El-Mahala, Tanta, Elsanta, Zifta, Bassuon, Kotor and Kafr-El-Zayat districts during two years at Gharbia Governorate, Egypt. The residents noticed 193, 146, 112, 109, 102, 82, 77 and 34 rodent individuals in Samannoud, El-Mahala, Tanta, Elsanta, Zifta, Bassuon, Kotor and Kafr-El-Zayat districts respectively during from January 2014 to December 2016 at Gharbia Governorate. There was no significant difference between number of rodent during study period (years), but there was significant difference among places and months. Rodents recorded in Elsanta and Tanta distracts were Rattus rattus (Linn.), Rattus rattus frugivorous (Rafinesque) and Rattus rattus alexandrines (Geoffray) and Rattus norvegicus Berk. , and Mus musculus Linn. , belonging to two genera ( Rattus and Mus ) from family Muridae. There was no significant difference between number of rodent during (cities, years and species) but there was significant difference between number of rodent during months and locations. These results could be used in the Integrated Pest Management program to control the rodents. This work proved the presence of R. rattus (Linn.);( R.rattus frugivorous (Rafinesque) and R. rattus alexandrines (Geoffray)] followed by R. norvegicus Berk. , and Mus musculus Linn. , belonging to two genera ( Rattus and Mus ) from family Muridae, were recorded in Elsanta and Tanta distracts at Gharbia Governorate. R. norvegicus Berk. ; R. rattus frugivorous (Rafinesque) followed by. R. rattus alexandrines (Geoffray); were recorded in Elsanta and Tanta districts. The highest number of R. norvegicus Berk. , were recorded 6 individuals during Summer and Winter seasons in 1 st year while 8 individuals were recorded during Autumn in 2 nd year from AL-Santa district. The highest number of R. norvegicus Berk. , (8 individuals) were recorded during Spring season in 1 st year while 5 individuals were recorded during Winter and Spring seasons in 2 nd year from Tanta distract. The highest number of R.rattus frogivorus (Rafinesque) were recorded 5 individuals during Spring season in1 st year while 6 individuals were recorded during Winter season in 2 nd year from Al-Santa district. The highest number of R. rattus frogivorus (Rafinesque),(4 individuals) were recorded during Summer seasonin1 st year while 4 individuals were recorded during Summer, Autumm and Winter seasons in 2 nd year from Tanta district. The highest numbers of R. rattus alexandrines (Geoffray) were recorded 5 individuals during Spring season in1 st year while 6 individuals were recorded during Spring in 2 nd year from Al-Santa district. The highest number of R. rattus alexandrines (Geoffray). ,(4 individuals) were recorded during Summer season in 1 st year while 4 individuals were recorded during Summer, Autumm and Winter seasons in 2 nd year from Tanta district. There were no significant difference between number of rodent during (Cities, Years and Species) but there were significant difference between number of rodent during months and locations.
Loss of PINK1 Increases the Heart's Vulnerability to Ischemia-Reperfusion Injury

Objectives Mutations in PTEN inducible kinase-1 (PINK1) induce mitochondrial dysfunction in dopaminergic neurons resulting in an inherited form of Parkinson’s disease. Although PINK1 is present in the heart its exact role there is unclear. We hypothesized that PINK1 protects the heart against acute ischemia reperfusion injury (IRI) by preventing mitochondrial dysfunction. Methods and Results Over-expressing PINK1 in HL-1 cardiac cells reduced cell death following simulated IRI (29.2±5.2% PINK1 versus 49.0±2.4% control; N = 320 cells/group P<0.05), and delayed the onset of mitochondrial permeability transition pore (MPTP) opening (by 1.3 fold; P<0.05). Hearts excised from PINK1+/+, PINK1+/− and PINK1−/− mice were subjected to 35 minutes regional ischemia followed by 30 minutes reperfusion. Interestingly, myocardial infarct size was increased in PINK1−/− hearts compared to PINK1+/+ hearts with an intermediate infarct size in PINK1+/− hearts (25.1±2.0% PINK1+/+, 38.9±3.4% PINK1+/− versus 51.5±4.3% PINK1−/− hearts; N>5 animals/group; P<0.05). Cardiomyocytes isolated from PINK1−/− hearts had a lower resting mitochondrial membrane potential, had inhibited mitochondrial respiration, generated more oxidative stress during simulated IRI, and underwent rigor contracture more rapidly in response to an uncoupler when compared to PINK1+/+ cells suggesting mitochondrial dysfunction in hearts deficient in PINK1. Conclusions We show that the loss of PINK1 increases the heart's vulnerability to ischemia-reperfusion injury. This may be due, in part, to increased mitochondrial dysfunction. These findings implicate PINK1 as a novel target for cardioprotection.
Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy

HIV infection profoundly affects many parameters of the immune system and ultimately leads to AIDS, yet which factors are most important for determining resistance, pathology, and response to antiretroviral treatment – and how best to monitor them – remain unclear. We develop a quantitative high-throughput sequencing pipeline to characterize the TCR repertoires of HIV-infected individuals before and after antiretroviral therapy, working from small, unfractionated samples of peripheral blood. This reveals the TCR repertoires of HIV+ individuals to be highly perturbed, with considerably reduced diversity as a small proportion of sequences are highly overrepresented. HIV also causes specific qualitative changes to the repertoire including an altered distribution of V gene usage, depletion of public TCR sequences, and disruption of TCR networks. Short-term antiretroviral therapy has little impact on most of the global damage to repertoire structure, but is accompanied by rapid changes in the abundance of many individual TCR sequences, decreases in abundance of the most common sequences, and decreases in the majority of HIV-associated CDR3 sequences. Thus, high-throughput repertoire sequencing of small blood samples that are easy to take, store, and process can shed light on various aspects of the T-cell immune compartment and stands to offer insights into patient stratification and immune reconstitution.
Plasmodium falciparum var genes expressed in children with severe malaria encode CIDRα1 domains

Most severe Plasmodium falciparum infections are experienced by young children. Severe symptoms are precipitated by vascular sequestration of parasites expressing a particular subset of the polymorphic P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion molecules. Parasites binding human endothelial protein C receptor (EPCR) through the CIDRα1 domain of certain PfEMP1 were recently associated with severe malaria in children. However, it has remained unclear to which extend the EPCR‐binding CIDRα1 domains epitomize PfEMP1 expressed in severe malaria. Here, we characterized the near full‐length transcripts dominating the var transcriptome in children with severe malaria and found that the only common feature of the encoded PfEMP1 was CIDRα1 domains. Such genes were highly and dominantly expressed in both children with severe malarial anaemia and cerebral malaria. These observations support the hypothesis that the CIDRα1‐EPCR interaction is key to the pathogenesis of severe malaria and strengthen the rationale for pursuing a vaccine or adjunctive treatment aiming at inhibiting or reducing the damaging effects of this interaction.
Probabilistic Seismic Hazard Analysis for Offshore Bangladesh Including Fault Sources

This paper presents the methodology and results of a probabilistic seismic hazard analysis (PSHA) for a site offshore Maheshkhali Island, Bangladesh. The tectonic setting of the area is complex, and the PSHA includes active crustal faults, megathrust and intraplate subduction faults, as well as a background gridded seismicity areal source zone based on historical and recorded seismicity. Previous studies only included areal source zones based on recorded seismicity, whereas this study takes advantage of recent publications to include faults sources in the PSHA. The peak ground acceleration values for return periods of 475 years and 2475 years are 0.33 g and 0.63 g, respectively. The deaggregation plots show that the main contributors to the hazard are a magnitude 6.5-7.1 earthquake 15-20 km from the site on the Maheshkhali fault and a magnitude 8.0-8.8 earthquake 120-250 km from the site on the Ramree megathrust.