Miracle-dz/UniFAR-FTUs huggingface dataset:
Ferrets Infected with Bundibugyo Virus or Ebola Virus Recapitulate Important Aspects of Human Filovirus Disease

ABSTRACT Bundibugyo virus (BDBV) is the etiological agent of a severe hemorrhagic fever in humans with a case-fatality rate ranging from 25 to 36%. Despite having been known to the scientific and medical communities for almost 1 decade, there is a dearth of studies on this pathogen due to the lack of a small animal model. Domestic ferrets are commonly used to study other RNA viruses, including members of the order Mononegavirales. To investigate whether ferrets were susceptible to filovirus infections, ferrets were challenged with a clinical isolate of BDBV. Animals became viremic within 4 days and succumbed to infection between 8 and 9 days, and a petechial rash was observed with moribund ferrets. Furthermore, several hallmarks of human filoviral disease were recapitulated in the ferret model, including substantial decreases in lymphocyte and platelet counts and dysregulation of key biochemical markers related to hepatic/renal function, as well as coagulation abnormalities. Virological, histopathological, and immunohistochemical analyses confirmed uncontrolled BDBV replication in the major organs. Ferrets were also infected with Ebola virus (EBOV) to confirm their susceptibility to another filovirus species and to potentially establish a virus transmission model. Similar to what was seen with BDBV, important hallmarks of human filoviral disease were observed in EBOV-infected ferrets. This study demonstrates the potential of this small animal model for studying BDBV and EBOV using wild-type isolates and will accelerate efforts to understand filovirus pathogenesis and transmission as well as the development of specific vaccines and antivirals. IMPORTANCE The 2013-2016 outbreak of Ebola virus in West Africa has highlighted the threat posed by filoviruses to global public health. Bundibugyo virus (BDBV) is a member of the genus Ebolavirus and has caused outbreaks in the past but is relatively understudied, likely due to the lack of a suitable small animal model. Such a model for BDBV is crucial to evaluating vaccines and therapies and potentially understanding transmission. To address this, we demonstrated that ferrets are susceptible models to BDBV infection as well as to Ebola virus infection and that no virus adaptation is required. Moreover, these animals develop a disease that is similar to that seen in humans and nonhuman primates. We believe that this will improve the ability to study BDBV and provide a platform to test vaccines and therapeutics.
Clinical Characteristics and Microorganisms Isolated in Community-Acquired Pneumonia in the COVID-19 Period

Introduction Community-acquired pneumonia is a leading cause of mortality and hospital admissions. The aetiology remains unknown in 30–65% of the cases. Molecular tests are available for multiple pathogen detection and are under research to improve the causal diagnosis. Methods We carried out a prospective study to describe the clinical characteristics and aetiology of community-acquired pneumonia during the COVID-19 pandemic and to assess the diagnostic effectivity of the microbiological tests, including a molecular test of respiratory pathogens (FilmArray™ bioMérieux). Results From the 1st of February 2021 until the 31st of March 2022, 225 patients were included. Failure in microorganism identification occurred in approximately 70% of patients. Streptococcus pneumoniae was the most common isolate. There were 5 cases of viral pneumonia. The tested FilmArray exhibited a low positivity rate of 7% and mainly aided in the diagnosis of viral coinfections. Conclusions Despite our extensive diagnostic protocol, there is still a low rate of microorganism identification. We have observed a reduction in influenza and other viral pneumoniae during the COVID-19 pandemic. Having a high NEWS2 score on arrival at the emergency department, an active oncohematological disease or chronic neurological conditions and a positive microbiological test result were related to worse outcomes. Further research is needed to determine the role of molecular tests in the microbiological diagnosis of pneumonia.
Gender difference in symptoms related to temporomandibular disorders in a population of 50-year-old subjects.

AIMS To investigate, by means of a mail questionnaire, the prevalence of symptoms related to temporomandibular disorders (TMD) in 50-year-old subjects living in the counties of Orebro and Ostergötland, Sweden. METHODS The total population comprised 8,888 individuals, and the overall response rate was 71%. A clinical evaluation of the masticatory system was performed in subgroups to validate the responses to the questionnaire. There was satisfactory correspondence between self-reports and well-defined clinical conditions. RESULTS Women reported, more often than men, pain from the temporomandibular joints (TMJs), TMJ sounds, bruxism, sensitive teeth, and burning mouth symptoms. The prevalences of difficulties in jaw opening, loss of anterior teeth due to trauma, and masticatory problems were greater in men than in women. No gender difference was found in the number of remaining teeth. Logistic regression analysis with pain from the TMJ as the dependent variable identified bruxism, impaired chewing efficiency, and gender (women) as the most significant risk factors. With reduced chewing ability as the dependent variable, several missing teeth constituted the highest risk, followed by pain from the TMJ, bruxism, gender (men), and loss of anterior teeth due to trauma. CONCLUSION There were significant gender differences in reported TMD-related symptoms in 50-year-old Swedes. Bruxism was a significant risk factor for pain from the TMJ. Reduced number of teeth and pain from the TMJ were significant risk factors for impaired chewing ability.
Effects of Statins on Endothelium and Signaling Mechanisms

Endothelium dysfunction may result from increased production of reactive oxygen species and decreased availability of nitric oxide. Inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (ie, statins) exert cholesterol-independent vasoprotective effects that are mediated, in part, through the inhibition of small G-proteins Rho and Rac. Rho negatively regulates endothelial nitric oxide synthase and Rac contributes to NAD(P)H-oxidase activation and superoxide production. Statins inhibit both Rho and Rac GTPase activity via inhibition of geranylgeranylation, which confers endothelial nitric oxide synthase upregulation and decreases superoxide production, respectively. Sudden discontinuation of statin therapy may have negative effects. Withdrawal of statin treatment leads to an overshoot activation of Rho and Rac with dramatic effects on nitric oxide bioavailability, NAD(P)H-oxidase activity, and superoxide production.
Heat-Shock Induction of Tumor-Derived Danger Signals Mediates Rapid Monocyte Differentiation into Clinically Effective Dendritic Cells

Purpose: This study characterizes, biologically and clinically, a novel type of dendritic cells (DC) produced in the short term and called tumor antigen–presenting cells (TAPCells). In particular, we identified factors present in a lysate derived from heat-shocked allogeneic melanoma cells (TRIMEL) that are associated with TAPCells' enhanced capability to induce CD8+ T-cell responses in vitro and in vaccinated melanoma patients. Experimental Design: First, extensive phenotypic and functional characterization of TAPCells was performed, followed by vaccination of 45 melanoma patients with four doses of TAPCells over a period of 2 months. Specific delayed-type hypersensitivity (DTH) reaction was analyzed posttreatment and correlated with overall survival rates. Furthermore, heat-shock (HS)-induced factors present in TRIMEL and their effects on DC activation were identified and studied. Results: TRIMEL induced a committed, mature, DC-like phenotype in TAPCells and effectively activated melanoma-specific CD4+ and CD8+ T cells. Clinically, 64% of vaccinated patients showed positive DTH reaction against TRIMEL, and this was associated with improved overall survival. HS treatment of tumor cells increased calreticulin (CRT) plasma membrane translocation and induced the release of high-mobility group box 1 proteins (HMGB1). Both CRT and HMGB1 mobilization were associated with enhanced TAPCells' maturation and antigen (Ag) cross-presentation, respectively. DTH infiltration analysis revealed the presence of CD8+/CD45RO+ T cells, thus confirming TAPCells' ability to cross-present Ags in vivo. Conclusions: Our results indicate that lysates derived from heat-shocked tumor cells are an optimal source of tumor-associated Ags, which are crucial for the generation of DCs with improved Ag cross-presentation capacity and clinically effective immunogenicity. Clin Cancer Res; 17(8); 2474–83. ©2011 AACR.
Effect of Posaconazole on Cyclosporine Blood Levels and Dose Adjustment in Allogeneic Blood and Marrow Transplant Recipients

ABSTRACT The posaconazole prescribing information recommends an upfront cyclosporine dose reduction upon initiation of posaconazole prophylaxis. We examined this recommendation in the early phase of allogeneic transplantation, where cyclosporine levels potentially becoming subtherapeutic following upfront dose reduction would be deleterious to transplant outcome. Our data show that while posaconazole leads to an increase in cyclosporine levels, subsequent cyclosporine dose reduction can be safely guided by therapeutic drug monitoring and is not required upfront. Therefore, the current recommendation may be modified.
Unified graph matching in Euclidean spaces

Graph matching is a classical problem in pattern recognition with many applications, particularly when the graphs are embedded in Euclidean spaces, as is often the case for computer vision. There are several variants of the matching problem, concerned with isometries, isomorphisms, homeo-morphisms, and node attributes; different approaches exist for each variant. We show how structured estimation methods from machine learning can be used to combine such variants into a single version of graph matching. In this paradigm, the extent to which our datasets reveal isometries, isomorphisms, homeomorphisms, and other properties is automatically accounted for in the learning process so that any such specific qualification of graph matching loses meaning. We present experiments with real computer vision data showing the leverage of this unified formulation.
A Review of Window Query Processing for Data Streams

In recent years, progress in hardware technology has resulted in the possibility of monitoring many events in real time. The volume of incoming data may be so large, that monitoring all individual data might be intractable. Revisiting any particular record can also be impossible in this environment. Therefore, many database schemes, such as aggregation, join, frequent pattern mining, and indexing, become more challenging in this context. This paper surveys the previous efforts to resolve these issues in processing data streams. The emphasis is on specifying and processing sliding window queries, which are supported in many stream processing engines. We also review the related work on stream query processing, including synopsis structures, plan sharing, operator scheduling, load shedding, and disorder control.
Inhibition of NMDA receptor function with an anti-GluN1-S2 antibody impairs human platelet function and thrombosis

Abstract GluN1 is a mandatory component of N-methyl-D-aspartate receptors (NMDARs) best known for their roles in the brain, but with increasing evidence for relevance in peripheral tissues, including platelets. Certain anti-GluN1 antibodies reduce brain infarcts in rodent models of ischaemic stroke. There is also evidence that human anti-GluN1 autoantibodies reduce neuronal damage in stroke patients, but the underlying mechanism is unclear. This study investigated whether anti-GluN1-mediated neuroprotection involves inhibition of platelet function. Four commercial anti-GluN1 antibodies were screened for their abilities to inhibit human platelet aggregation. Haematological parameters were examined in rats vaccinated with GluN1. Platelet effects of a mouse monoclonal antibody targeting the glycine-binding region of GluN1 (GluN1-S2) were tested in assays of platelet activation, aggregation and thrombus formation. The epitope of anti-GluN1-S2 was mapped and the mechanism of antibody action modelled using crystal structures of GluN1. Our work found that rats vaccinated with GluN1 had a mildly prolonged bleeding time and carried antibodies targeting mostly GluN1-S2. The monoclonal anti-GluN1-S2 antibody (from BD Biosciences) inhibited activation and aggregation of human platelets in the presence of adrenaline, adenosine diphosphate, collagen, thrombin and a protease-activated receptor 1-activating peptide. When human blood was flowed over collagen-coated surfaces, anti-GluN1-S2 impaired thrombus growth and stability. The epitope of anti-GluN1-S2 was mapped to α-helix H located within the glycine-binding clamshell of GluN1, where the antibody binding was computationally predicted to impair opening of the NMDAR channel. Our results indicate that anti-GluN1-S2 inhibits function of human platelets, including dense granule release and thrombus growth. Findings add to the evidence that platelet NMDARs regulate thrombus formation and suggest a novel mechanism by which anti-GluN1 autoantibodies limit stroke-induced neuronal damage.
Sizing and energy management of a stand-alone PV/hydrogen/battery-based hybrid system

This paper presents a sizing method and supervisory control for the suitable energy management of a stand-alone hybrid system with photovoltaic (PV) solar panels, hydrogen subsystem and battery. The battery and hydrogen subsystem, composed of fuel cell (FC), electrolyzer and hydrogen storage tank, act as energy storage and support system. A sizing method based on Simulink Design Optimization (SDO) of MATLAB is used to perform a technical optimization of the components of the hybrid system. The dynamic model of the designed hybrid system is detailed in this paper. The models, implemented in MATLAB-Simulink environment, are designed from commercially available components. It is designed, primarily, to satisfy the load power demand and, secondly, to maintain certain level at the hydrogen tank (hydrogen energy reserve), and at the state of charge (SOC) of the battery bank to extend its life.
SSRI use during pregnancy and risk of stillbirth and neonatal mortality.

OBJECTIVE The authors investigated whether in utero exposure to selective serotonin reuptake inhibitors (SSRIs) increases the risk of stillbirth or neonatal mortality. METHOD The authors conducted a population-based cohort study using the Danish Fertility Database to identify every birth in Denmark between 1995 and 2008. Time of exposure to SSRIs was calculated on the basis of standard treatment dosages and dispensed pack sizes according to the prescription register. Exposure was divided into first-, second-, and third-trimester exposure. Multivariate logistic regression models were used. RESULTS The authors identified 920,620 births; the incidence of stillbirths was 0.45%, and the incidence of neonatal mortality was 0.34%. A total of 12,425 offspring were exposed to an SSRI during pregnancy. Stillbirth was not associated with first-trimester SSRI use (adjusted odds ratio=0.77, 95% CI=0.43-1.36), first- and second-trimester use (odds ratio=0.84, 95% CI=0.40-1.77), or first-, second-, and third-trimester use (odds ratio=1.06, 95% CI=0.71-1.58). Neonatal mortality was not associated with SSRI first-trimester use (odds ratio=0.56, 95% CI=0.25-1.24), first- and second-trimester use (odds ratio=0.90, 95% CI=0.37-2.17), or first-, second-, and third-trimester use (odds ratio=1.27, 95% CI=0.82-1.99). CONCLUSIONS This study found no association between exposure to SSRIs during pregnancy and stillbirth or neonatal mortality.
Comparative Cooling Efficiency of Brick Walls for Poultry House in Hot Climatic Conditions

The attainment of thermo-neutral condition in a poultry house is determined, to some extent, by the choice of wall materials. The extent to which bricks produce desired cooling in relation to other materials as walls for poultry houses is uncertain. This study was aimed at determining the relative cooling efficiency of brick walls over sand-crete block walls on one hand, and a combination of thatch insulation and iron-roofing sheets on the other. The quasi-experimental research design employed thermo-anemometer to determine temperatures inside five poultry houses: three made up of brick-walls; one of sand-crete block-walls; and one of insulated iron roofing sheet-walls. Analysis of variance (ANOVA) was employed to establish any significant difference in temperature in the houses (at 0.05 level of significance). The result showed that brick walls have higher cooling efficiency than the other materials, but not at a significant level. Also, thermo-neutral condition was not attained in any of the five poultry houses. It was recommended that architectural strategies that may further reduce temperature to thermo-neutral condition in poultry houses be investigated.
Use of Sindbis virus-mediated RNA interference to demonstrate a conserved role of Broad-Complex in insect metamorphosis

The transcription factor Broad-Complex (BR-C) is required for differentiation of adult structures as well as for the programmed death of obsolete larval organs during metamorphosis of the fruit fly Drosophila melanogaster. Whether BR-C has a similar role in other holometabolous insects could not be proven without a loss-of-function genetic test, performed in a non-drosophilid species. Here we use a recombinant Sindbis virus as a tool to silence BR-C expression in the silkmoth Bombyx mori. The virus expressing a BR-C antisense RNA fragment reduced endogenous BR-C mRNA levels in infected tissues (adult wing and leg primordia) via RNA interference (RNAi). The RNAi knock-down of BR-C resulted in the failure of animals to complete the larval–pupal transition or in later morphogenetic defects, including differentiation of adult compound eyes, legs, and wings from their larval progenitors. BR-C RNAi also perturbed the programmed cell death of larval silk glands. These developmental defects correspond to loss-of-function phenotypes of BR-C Drosophila mutants in both the morphogenetic and degenerative aspects, suggesting that the critical role of BR-C in metamorphosis is evolutionarily conserved. We also demonstrate that the Sindbis virus is a useful vehicle for silencing of developmental genes in new insect models.
SupWSD: A Flexible Toolkit for Supervised Word Sense Disambiguation

In this demonstration we present SupWSD, a Java API for supervised Word Sense Disambiguation (WSD). This toolkit includes the implementation of a state-of-the-art supervised WSD system, together with a Natural Language Processing pipeline for preprocessing and feature extraction. Our aim is to provide an easy-to-use tool for the research community, designed to be modular, fast and scalable for training and testing on large datasets. The source code of SupWSD is available at http://github.com/SI3P/SupWSD.
Progress and perspectives on the role of RPE cell inflammatory responses in the development of age-related macular degeneration

Age-related macular degeneration (AMD) is the leading cause of blindness in developed countries. The etiology of AMD remains poorly understood and no treatment is currently available for the atrophic form of AMD. Atrophic AMD has been proposed to involve abnormalities of the retinal pigment epithelium (RPE), which lies beneath the photoreceptor cells and normally provides critical metabolic support to these light-sensing cells. Cumulative oxidative stress and local inflammation are thought to represent pathological processes involved in the etiology of atrophic AMD. Studies of tissue culture and animal models reveal that oxidative stress-induced injury to the RPE results in a chronic inflammatory response, drusen formation, and RPE atrophy. RPE degeneration in turn causes a progressive degeneration of photoreceptors, leading to the irreversible loss of vision. This review describes some of the potential major molecular and cellular events contributing to RPE death and inflammatory responses. In addition, potential target areas for therapeutic intervention will be discussed and new experimental therapeutic strategies for atrophic AMD will be presented.
Embryoscopic and cytogenetic analysis of 233 missed abortions: factors involved in the pathogenesis of developmental defects of early failed pregnancies.

BACKGROUND While chromosomal abnormalities are often the cause of missed abortions, other defects could be involved, which might be screened for by transcervical embryoscopy. METHODS A total of 272 patients with missed abortion underwent transcervical embryoscopy prior to dilatation and curettage, together with cytogenetic analysis of chorionic villi, using either standard G-banding cytogenetic techniques or comparative genomic hybridization in combination with flow cytometry analysis. RESULTS Visualization of the embryo or early fetus (12 cases) was successful in 233 patients, and karyotyping in 221. Among 233 examined cases, 33 had normal external features, 71 were classified as growth-disorganized and 129 had either isolated or multiple defects, including holoprosencephaly, anencephaly, encephalocele, spina bifida, microcephaly, facial dysplasia, limb reduction defect, cleft hand, syndactyly, pseudosyndactly, polydactyly, various forms of cleft lip and an amniotic adhesion. Of the 165 cases with an abnormal karyotype, there were 46 grossly disorganized embryos, 98 multiple defects, six single defects and 15 morphologically normal cases. Of the 56 cases with a normal karyotype, there were 20 grossly disorganized embryos, 16 multiple defects, four single defects and 16 morphologically normal cases. CONCLUSIONS A total of 75% of the cases with missed abortion had an abnormal karyotype, 18% had a morphological defect with a normal karyotype, while no embryonic or chromosomal abnormality could be diagnosed in 7% of the cases. Correlation of morphological and cytogenetic findings in spontaneous abortion specimens could provide valuable information for genetic counselling and prenatal care in future pregnancies in couples with a history of repeated pregnancy loss.
ParsCit: an Open-source CRF Reference String Parsing Package

We describe ParsCit, a freely available, open-source implementation of a reference string parsing package. At the core of ParsCit is a trained conditional random field (CRF) model used to label the token sequences in the reference string. A heuristic model wraps this core with added functionality to identify reference strings from a plain text file, and to retrieve the citation contexts. The package comes with utilities to run it as a web service or as a standalone utility. We compare ParsCit on three distinct reference string datasets and show that it compares well with other previously published work.