Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinctive Roles for Type I and Type II Interferons and Interferon Regulatory Factors in the Host Cell Defense against Varicella-Zoster Virus

While both type I and type II IFNs are involved in the control of herpesvirus infections in the human host, to our knowledge, their relative contributions to the restriction of viral replication and spread have not been assessed. We report that IFN-γ has more potent activity than IFN-α against VZV. Findings from this comparative analysis show that the IFN-α–IRF9 axis functions as a first line of defense to delay the onset of viral replication and spread, whereas the IFN-γ–IRF1 axis has the capacity to block the infectious process. Our findings underscore the importance of IRFs in IFN regulation of herpesvirus infection and account for the clinical experience of the initial control of VZV skin infection attributable to IFN-α production, together with the requirement for induction of adaptive IFN-γ-producing VZV-specific T cells to resolve the infection. ABSTRACT Both type I and type II interferons (IFNs) have been implicated in the host defense against varicella-zoster virus (VZV), a common human herpesvirus that causes varicella and zoster. The purpose of this study was to compare their contributions to the control of VZV replication, to identify the signaling pathways that are critical for mediating their antiviral activity, and to define the mechanisms by which the virus counteracts their effects. Gamma interferon (IFN-γ) was much more potent than IFN-α in blocking VZV infection, which was associated with a differential induction of the interferon regulatory factor (IRF) proteins IRF1 and IRF9, respectively. These observations account for the clinical experience that while the formation of VZV skin lesions is initially controlled by local immunity, adaptive virus-specific T cell responses are required to prevent life-threatening VZV infections. IMPORTANCE While both type I and type II IFNs are involved in the control of herpesvirus infections in the human host, to our knowledge, their relative contributions to the restriction of viral replication and spread have not been assessed. We report that IFN-γ has more potent activity than IFN-α against VZV. Findings from this comparative analysis show that the IFN-α–IRF9 axis functions as a first line of defense to delay the onset of viral replication and spread, whereas the IFN-γ–IRF1 axis has the capacity to block the infectious process. Our findings underscore the importance of IRFs in IFN regulation of herpesvirus infection and account for the clinical experience of the initial control of VZV skin infection attributable to IFN-α production, together with the requirement for induction of adaptive IFN-γ-producing VZV-specific T cells to resolve the infection.
LIMSI@CLEF eHealth 2018 Task 2: Technology Assisted Reviews by Stacking Active and Static Learning

This paper describes the participation of the LIMSI-MIROR team at CLEF eHealth 2018, task 2. The task addresses the automatic ranking of articles in order to assist with the screening process of Diagnostic Test Accuracy (DTA) Systematic Reviews. We ranked articles by stacking two models, one linear regressor trained on untargeted training data, and one model using active learning. The workload reduction to retrieve 95% of the relevant articles was estimated at 82.4%, and we observe a workload reduction less than 70% in only two topics. The results suggest that automatic assistance is promising for ranking the DTA literature.
PASA: Identifying More Credible Structural Variants of Hedou12

Although plenty of structural variant detecting approaches for human genomes can be looked up in the literatures, little has been acknowledged on the effectiveness of those structural variant softwares for plant genomes. Moreover, it has been demonstrated frequent occurrences for those structural variant detecting softwares to find too many false structural variants. In this paper, we devote to detect deletions, insertions, and inversions, in total of three kinds of structural variants occurring in Hedou12 genome in contrast to Williams82 genome. To find more potential structural variants, we try to develop new principles to detect discordant and split read map sets supporting structural variants. Aiming to enhance the precision of structural variant detections, we propose two new sequencing characteristic based probability models, which use the sequencing parameters of Hedou12 genome as well as the parameters for Hedou12 paired-end reads to be aligned onto Williams82, to evaluate the probability for a potential structural variant to occur in. To remove the false members from those potential structural variants, we propose a set cover problem model to describe formally on which potential structural variants it should accept to achieve as high as possible a probability summation. This will achieve a solution with more credible structural variants, which can be verified by comparing with DELLY version 0.5. 8 and LUMPY version 0.2. 2.3. Our algorithm has been verified to be able to find deletions, insertions, and inversions in Hedou12 in contrast to Williams82 DELLY as well as LUMPY fails to find.
Detection of HCV genome in peripheral blood mononuclear cells of Iranian seropositive and HCV RNA negative in plasma of patients with beta‐thalassemia major: Occult HCV infection

Beta (β) thalassemia major is a genetic blood disorder with a deficiency in the hemoglobin beta chain, requiring blood transfusion therapy. Multiple blood transfusions increase the risk of transmitting blood‐borne infections. The aim of this study is to determine the frequency of hepatitis C virus (HCV) infection in Iranian individuals with β‐thalassemia major. A total of 164 patients with β‐thalassemia major were recruited for this study. HCV RNA testing was done on plasma and peripheral blood mononuclear cells (PBMCs) from the HCV seropositive samples (with reverse transcriptase–nested polymerase chain reaction [PCR] method using primers from the 5′‐untranslated region [UTR]), and all HCV RNA positive samples were genotyped by the restriction fragment length polymorphism assay. For confirmation of the HCV genotyping in PBMCs of occult HCV infection [OCI]‐positive patients, the PCR products of two different regions of HCV (5′‐UTR and nonstructural protein 5B [NS5B]) were sequenced. Of 164 patients, 29.3% were positive for anti‐HCV antibodies, and HCV RNA was detected in the plasma specimens of 13.4% patients and in the PBMC samples of 15.2% participants. The genomic HCV‐RNA was detected in PBMC samples in 3 (6.3%) of the total 48 individuals who were HCV seropositive, and plasma HCV‐RNA negative (occult HCV infection). The subtypes of HCV in the plasma and PBMC samples of three participants were not identical. This study shows that among this group of Iranian patients with β‐thalassemia major, 13.4% had active HCV infection and 6.3% had occult HCV infection as evidenced by HCV RNA detected in PBMC specimens. Therefore, the design of a prospective study that focuses on the diagnosis of OCI can be very valuable and provide more information.
Thy-1 (CD90) promotes bone formation and protects against obesity

Thy-1 on mesenchymal stem cells promotes osteogenesis while inhibiting adipogenesis and obesity. Stem cells’ balancing act Mesenchymal stem cells (MSCs) differentiate into multiple cell types. Picke et al. investigated how MSC differentiation is regulated to maintain homeostasis between the bone and fat lineages. Genetic deletion of Thy-1, a protein expressed on multiple cell types including MSCs, prevented MSC differentiation into osteoblasts but promoted differentiation into adipocytes. Thy-1–deficient mice had increased body fat and decreased bone mass. High-fat diet induced obesity in wild-type mice and concurrent reduction in bone formation, which was associated with decreased Thy-1 expression on MSCs. Obese human subjects and subjects with osteoporosis showed reductions in serum soluble Thy-1. This study suggests that Thy-1 regulates the balance between bone and fat lineages, with possible implications for bone and metabolic disorders. Osteoporosis and obesity result from disturbed osteogenic and adipogenic differentiation and present emerging challenges for our aging society. Because of the regulatory role of Thy-1 in mesenchyme-derived fibroblasts, we investigated the impact of Thy-1 expression on mesenchymal stem cell (MSC) fate between osteogenic and adipogenic differentiation and consequences for bone formation and adipose tissue development in vivo. MSCs from Thy-1–deficient mice have decreased osteoblast differentiation and increased adipogenic differentiation compared to MSCs from wild-type mice. Consistently, Thy-1–deficient mice exhibited decreased bone volume and bone formation rate with elevated cortical porosity, resulting in lower bone strength. In parallel, body weight, subcutaneous/epigonadal fat mass, and bone fat volume were increased. Thy-1 deficiency was accompanied by reduced expression of specific Wnt ligands with simultaneous increase of the Wnt inhibitors sclerostin and dickkopf-1 and an altered responsiveness to Wnt. We demonstrated that disturbed bone remodeling in osteoporosis and dysregulated adipose tissue accumulation in patients with obesity were mirrored by reduced serum Thy-1 concentrations. Our findings provide new insights into the mutual regulation of bone formation and obesity and open new perspectives to monitor and to interfere with the dysregulated balance of adipogenesis and osteogenesis in obesity and osteoporosis.
Can Network Analysis Techniques Help to Predict Design Dependencies? An Initial Study

The degree of dependencies among the modules of a software system is a key attribute to characterize its design structure and its ability to evolve over time. Several design problems are often correlated with undesired dependencies among modules. Being able to anticipate those problems is important for developers, so they can plan early for maintenance and refactoring efforts. However, existing tools are limited to detecting undesired dependencies once they appeared in the system. In this work, we investigate whether module dependencies can be predicted (before they actually appear). Since the module structure can be regarded as a network, i.e, a dependency graph, we leverage on network features to analyze the dynamics of such a structure. In particular, we apply link prediction techniques for this task. We conducted an evaluation on two Java projects across several versions, using link prediction and machine learning techniques, and assessed their performance for identifying new dependencies from a project version to the next one. The results, although preliminary, show that the link prediction approach is feasible for package dependencies. Also, this work opens opportunities for further development of software-specific strategies for dependency prediction.
The Padua Inventory–Washington State University Revision of Obsessions and Compulsions: A Reliability Generalization Meta-Analysis

Abstract The Padua Inventory–Washington State University Revision (PI–WSUR) is a frequently used test to assess obsessive–compulsive symptoms in screening and clinical contexts. A reliability generalization meta-analysis was carried out to estimate the average reliability of the PI–WSUR scores and its subscales and to search for characteristics of the studies that can explain the heterogeneity among reliability coefficients. A total of 124 independent samples reported some coefficient alpha or test–retest correlation with the data at hand for the PI–WSUR scores. The average internal consistency reliability of the PI–WSUR total scores was . 929 (95% CI [.922, .936]), and for the subscales, the means ranged from . 792 to . 900. The test–retest reliability for PI–WSUR total scores was . 767 (95% CI [.700, .820]), with the subscales ranging from . 540 to . 790. Moderator analyses revealed a positive relationship between the standard deviation of PI–WSUR total scores and alpha coefficients, as well as higher reliability estimates for the original version of the test and for studies from North America. The reliability induction rate for the PI–WSUR was 53.7%. Regarding reliability, the PI–WSUR ranks among the best scales for assessing obsessive–compulsive symptoms. Internal consistency reliability was excellent for the PI–WSUR total score and good for the subscales.
The cone of flow matrices: Approximation hierarchies and applications

Let G be a directed acyclic graph with n arcs, a source s and a sink t . We introduce the cone K of flow matrices, which is a polyhedral cone generated by the matrices 1P1PT∈ℝn×n , where 1P∈ℝn is the incidence vector of the (s,t)− path P . We show that several hard flow (or path) optimization problems, that cannot be solved by using the standard arc‐representation of a flow, reduce to a linear optimization problem over K . This cone is intractable: we prove that the membership problem associated to K is NP‐complete. However, the affine hull of this cone admits a nice description, and we give an algorithm which computes in polynomial‐time the decomposition of a matrix X∈span K as a linear combination of some 1P1PT 's. Then, we provide two convergent approximation hierarchies, one of them based on a completely positive representation of K . We illustrate this approach by computing bounds for the quadratic shortest path problem, as well as a maximum flow problem with pairwise arc‐capacities.
The link between self-compassion and psychotic-like experiences: A matter of distress?

OBJECTIVES Self-shaming and self-criticism have been shown to contribute to the emergence of distressing psychotic symptoms and psychotic-like experiences (PLEs). In contrast, a self-compassionate mindset may protect against negative evaluations in response to PLEs leading to less distress. This study explores the association between self-compassion, the frequency of PLEs, and their associated distress. DESIGN The study used a correlational, cross-sectional design on a German community sample. METHODS A total of 234 participants completed the self-compassion scale (SCS), the Peters' Delusions Inventory, and a modified version of the Launay-Slade Hallucination Scale that measures frequency and distress of hallucinatory experiences. Pearson correlations between SCS and frequency of PLEs as well as between SCS and PLE-distress were compared. Additionally, network analyses of SCS and PLE-measures were calculated. RESULTS Self-compassion was associated with less-frequent PLEs and with less PLE-distress, with stronger correlations between self-compassion and PLE-distress. The network analysis showed the self-compassion facets isolation and overidentification to be the closest links to PLE-distress. CONCLUSIONS Self-compassion is associated with less PLE related distress. Prevention programmes and interventions that target the negative facets associated with lack of self-compassion may be promising. However, future studies need to explore the causal role of self-compassion facets in the formation of PLE-distress. PRACTITIONER POINTS Low levels of self-compassion are associated with being more distressed by psychotic experiences. As the self-compassion facets isolation and overidentification are most strongly related to distress, prevention and intervention programmes may benefit from focusing on these negative facets.
Cells in the adult human spinal cord ependymal region do not proliferate after injury

In vertebrates that regenerate the injured spinal cord, cells at the ependymal region proliferate and coordinate the formation of bridges between the lesion stumps. In mammals, these cells also proliferate profusely around the central canal after spinal cord injury, although their actual contribution to repair is controversial. In humans, however, the central canal disappears from early childhood in the majority of individuals, being replaced by astrocyte gliosis, ependymocyte clusters, and perivascular pseudo‐rosettes. In this human ependymal remnant, cells do not proliferate under normal conditions, but it is not known if they do after a lesion. Here, we studied the human ependymal remnant after traumatic spinal cord injury using samples from 21 individuals with survival times ranging from days to months post‐injury. With three different monoclonal antibodies raised against two different proliferation markers (Ki67 and MCM2), we found that the ependymal remnant in adult humans does not proliferate after injury at any time or distance from the lesion. Our results seriously challenge the view of the spinal cord ependymal region as a neurogenic niche in adult humans and suggest that it would not be involved in cell replacement after a lesion. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Cryptogenic and non-cryptogenic liver abscess: A retrospective analysis of 178 cases revealed distinct characteristics

Objective To enhance theoretical support of pyogenic liver abscess (PLA) treatment by comparing characteristics of patients with either PLA with an identified infectious origin (non-cryptogenic) or PLA with no obvious underlying cause (cryptogenic). Methods This retrospective study included all first episodes of PLA in adults admitted to a tertiary hospital between 2009 and 2016. Relevant clinical data were collected for patients with cryptogenic or non-cryptogenic PLA and compared across a number of characteristics. Results In all, 178 patients were included: 111 cases (62.4%) of cryptogenic PLA, and 67 cases (37.6%) of non-cryptogenic PLA. Diabetes mellitus was significantly more prevalent in patients with cryptogenic PLA than those with non-cryptogenic PLA. The proportion of multidrug resistance/poly-microbial infection was significantly lower and Klebsiella pneumoniae infection was significantly higher in the cryptogenic versus non-cryptogenic PLA group. Metastatic infection occurred in four patients with cryptogenic PLA only, and all had diabetes and K. pneumoniae infection. Multivariate logistic regression analysis revealed that male sex, diabetes and K. pneumoniae were independent predictors for cryptogenic PLA. Conclusions Cryptogenic and non-cryptogenic PLA have distinctly different characteristics, suggesting a potential need for different treatment approaches.
Regulation of endothelial inflammation by TAM receptors

The TAM (Tyro3, Axl, Mer) receptors tyrosine kinases together with their ligands Gas6 and protein S play an important role in many cellular processes such as resolution of inflammation and phagocytosis. Notably, they were found to have an important function in vasculature, acting as a pro-survival factors and regulators of angiogenesis. Nevertheless, their role in endothelial inflammation is still poorly understood. Conflicting conclusions have been published, indicating both pro and anti-inflammatory properties of TAM-mediated signaling in endothelium. In this study we sought to elucidate the role of these receptors in endothelial inflammation by measuring the levels of pro-inflammatory markers, such as cytokines and adhesion molecules, in response to inflammatory stimuli in TAM and TAM ligand-deficient human umbilical vein endothelial cells (HUVEC). We found that Axl/Gas6 signaling acts as a pro-inflammatory agent by promoting an increased expression of adhesion molecules and cytokine secretion. Conversely, we suggest anti inflammatory tendencies of the Mer/protein S axis. Moreover, we demonstrate that starvation strongly upregulates Mer expression in HUVEC cells. Finally, we propose that TAM receptors expression is differently regulated depending on cell type, as inflammatory regulators known to induce TAM-expression in immune cells fail to upregulate TAMs in HUVECs. Taken together, we present diversification and complexity of Axl and Mer receptor functions in endothelial inflammation, thus suggesting the need for further investigations.
Biology of the wasp Polistes (Epicnemius) cinerascens Saussure (Hymenoptera: Vespidae)

Saussure apresentaram correlacao entre o tamanho do favo e a largurado pedunculo, bem como com a altura das celulas e numero de geracoes pro-duzidas. Foi verificado o tempo de duracao do ciclo biologico das colonias (199,3dias), numero de celulas construidas (102,9) e de adultos produzidos (94,2), alemdas taxas: 0,5 celulas/dia, 0,3 adultos/dia e 0,8 adultos/celula, da percentagem decelulas produtivas/ninho (55,2 %) e do numero de geracoes/colonia (ate 4). Onumero de instares larvais foi 5, a taxa de crescimento 1,3, o tempo de duracaodos estagios imaturos foi: ovos = 13,0 dias, larvas = 23,7, pupas - 22,2 e a duracaototal = 58,6 dias. A longevidade dos adultos foi 38,3 dias.PALAVRAS-CHAVE: Insecta, ciclo colonial, estagios imaturos, longevidade, tabela de vida.ABSTRACT - Studies on nests of the social wasp
Factors Affecting the Health-Related Quality of Life of Community-Dwelling Elderly in Japan: A Focus on Spirituality

This study aimed to explain factors affecting health-related quality of life among community-dwelling elderly individuals living in Japan. We conducted a questionnaire survey of 898 individuals at senior citizens clubs in a rural area near the Tokyo metropolitan area in 2015, and analyzed the responses of 715 who provided valid responses. The survey questions included basic attributes (e.g., age, economic affluence), state of health (e.g., whether s/he has heart disease or not), the Spirituality Rating Scale Related to Health in the Elderly (SP Health Scale, composed of, e.g., meaning and purpose of living, self-transcendence), the Abbreviated Lubben Social Network Scale, and the MOS 8-Item Short Form Health Survey (SF-8). Multiple regression analyses were performed using the physical component summary (PCS) and mental component summary (MCS) of the SF-8 as dependent variables and all others as independent variables. Factors associated with improved PCS were economic affluence and SP Health Scale (meaning and purpose of living), while the factors associated with reduced PCS were age and state of health (heart disease, gastrointestinal disease, osteoarthritis, lower back pain, knee pain, and eligible for long-term care). Meanwhile, factors associated with improved MCS were economic affluence, while those that were associated with reduced MCS were state of health (cancer and headache) and SP Health Scale (self-transcendence). These results suggest the need to understand spirituality in addition to the subjective economic situation, age, and medical condition of elderly individuals in order to improve their physical and mental health.
A Study of Whole Classroom Mathematical Discourse and Teacher Change

This article presents a comparison of the first 2 years of an experienced middle school mathematics teacher's efforts to change her classroom practice as a result of an intervening professional development program. The teacher's intention was for her teaching to better reflect her vision of reform-based mathematics instruction. We compared events from the 1st and 2nd year's whole class discussions within a multilevel framework that considered the flow of information and the nature of peer- and teacher-directed scaffolding. Discourse analyses of classroom videos served both as an analytic tool for our study of whole classroom interactions, as well as a resource for promoting discussion and reflection during professional development meetings. The results show that there was little change in the teacher's specific goals and beliefs in light of a self-evaluation of her Year 1 practices, but substantial changes in how she set out to enact those goals. In Year 2, the teacher maintained a central, social scaffolding role, but removed herself as the analytic center to invite greater student participation. Consequently, student-led discussion increased manifold, but lacked the mathematical precision offered previously by the teacher. The analyses lead to insights about how classroom interactions can be shaped by a teacher's beliefs and interpretations of educational reform recommendations.