Miracle-dz/UniFAR-FTUs huggingface dataset:
Herpes Simplex Virus and Interferon Signaling Induce Novel Autophagic Clusters in Sensory Neurons

ABSTRACT Herpes simplex virus 1 (HSV-1) establishes lifelong infection in the neurons of trigeminal ganglia (TG), cycling between productive infection and latency. Neuronal antiviral responses are driven by type I interferon (IFN) and are crucial to controlling HSV-1 virulence. Autophagy also plays a role in this neuronal antiviral response, but the mechanism remains obscure. In this study, HSV-1 infection of murine TG neurons triggered unusual clusters of autophagosomes, predominantly in neurons lacking detectable HSV-1 antigen. Treatment of neurons with IFN-β induced a similar response, and cluster formation by infection or IFN treatment was dependent upon an intact IFN-signaling pathway. The autophagic clusters were decorated with both ISG15, an essential effecter of the antiviral response, and p62, a selective autophagy receptor. The autophagic clusters were not induced by rapamycin or starvation, consistent with a process of selective autophagy. While clusters were triggered by other neurotropic herpesviruses, infection with unrelated viruses failed to induce this response. Following ocular infection in vivo, clusters formed exclusively in the infected ophthalmic branch of the TG. Taken together, our results show that infection with HSV and antiviral signaling in TG neurons produce an unorthodox autophagic response. This autophagic clustering is associated with antiviral signaling, the presence of viral genome, and the absence of HSV protein expression and may therefore represent an important neuronal response to HSV infection and the establishment of latency. IMPORTANCE Herpes simplex virus type 1 (HSV-1) is a ubiquitous virus and a significant cause of morbidity and some mortality. It is the causative agent of benign cold sores, but it can also cause blindness and life-threatening encephalitis. The success of HSV-1 is largely due to its ability to establish lifelong latent infections in neurons and to occasionally reactivate. The exact mechanisms by which neurons defend against virus infection is poorly understood, but such defense is at least partially mediated by autophagy, an intracellular pathway by which pathogens and other unwanted cargoes are degraded. The study demonstrates and investigates a new autophagic structure that appears to be specific to the interaction between neurotropic herpesviruses and murine primary sensory neurons. This work may therefore have important implications for our understanding of latency and reactivation.
Improving Thai Optical Character Recognition Using Circular-Scan Histogram

While most previous works focus on invariant features that capture salient for higher recognition accuracy, they face an issue of misclassification among similar characters. This paper proposes a feature called circular-scan histogram that enables us to capture small salient parts of the Thai characters. With scanning distances, the distance from the edge to the first pixel on the character's boundary, a circular-scan histogram is constructed by rotating the characters during scanning, and counting frequency of each distance bin. By experiments, using approximately 60,000 single-character images of forty four Thai consonant characters with balance distribution, our proposed method can classify similar characters with accuracy of 95.72%. As baselines, we compare our method with Shape Context and Histogram of Oriented Gradient.
miR-155 Modifies Inflammation, Endothelial Activation and Blood-Brain Barrier Dysfunction in Cerebral Malaria

AbstractmiR-155 has been shown to participate in host response to infection and neuroinflammation via negative regulation of blood-brain barrier (BBB) integrity and T cell function. We hypothesized that miR-155 may contribute to the pathogenesis of cerebral malaria (CM). To test this hypothesis, we used a genetic approach to modulate miR-155 expression in an experimental model of cerebral malaria (ECM). In addition, an engineered endothelialized microvessel system and serum samples from Ugandan children with CM were used to examine anti-miR-155 as a potential adjunctive therapeutic for severe malaria. Despite higher parasitemia, survival was significantly improved in miR-155−/− mice versus wild-type littermate mice in ECM. Improved survival was associated with preservation of BBB integrity and reduced endothelial activation, despite increased levels of proinflammatory cytokines. Pretreatment with antagomir-155 reduced vascular leak induced by human CM sera in an ex vivo endothelial microvessel model. These data provide evidence supporting a mechanistic role for miR-155 in host response to malaria via regulation of endothelial activation, microvascular leak and BBB dysfunction in CM.
Improving Collaborative Filtering's Rating Prediction Quality by Considering Shifts in Rating Practices

Users that populate ratings databases, such as IMDB, follow different marking practices, in the sense that some are stricter, while others are more lenient. This aspect has been captured by the most widely used similarity metrics in collaborative filtering, namely the Pearson Correlation and the Adjusted Cosine Similarity, which adjust each individual rating by the mean of the ratings entered by the specific user, when computing similarities. However, relying on the mean value presumes that the users' marking practices remain constant over time; in practice though, it is possible that a user's marking practices change over time, i.e. a user could start as strict and subsequently become lenient, or vice versa. In this work, we propose an approach to take into account marking practices shifts by (1) introducing the concept of dynamic user rating averages which follow the users' marking practices shifts, (2) presenting two alternative algorithms for computing a user's dynamic averages and (3) performing a comparative evaluation among these two algorithms and the classic static average (unique mean value) that the Pearson Correlation uses.
Text Independent Writer Identification for Telugu Script Using Directional Filter Based Features

In this paper, a novel approach for writer identification from handwritten Telugu script is introduced. A new dataset of Telugu handwritten documents of 150 writers called the IIITS-THDB is created under this work for doing the experimental analysis and this dataset is made available publicly. Descriptive convolution based features are extracted from given handwritten text using directional filters. Feature reduction is performed to find the optimal linear subspace for the extracted features and identification is done using these reduced features. Smaller blocks of text with uniform textures are created using the available data that show an improved identification accuracy during experimentation. We also study the effects of noise and compare the results of our features with various other features over our dataset.
On Automating Decentralized Multi-Step Service Combination

Information on the Web is heterogeneous and available in constantly increasing quantities. Consequently, there are numerous, partly redundant data analytics services, each optimized for data with certain characteristics. Often, analytics tasks require multiple services to be pipelined to find a solution, where combinations of exchangeable services for single steps might outperform one-service-predictions. This work proposes a Multi-Agent System (MAS) perception of prior setting, where decentralized agents are considered to manage services, having to coordinate their decisions to find a consensus. We, first, propose a supervised method for service accuracy estimation and, therefore, exploit locality-sensitive features of training data. Given a committee of services managed by agents, we develop coordination strategies to handle conflicting confidences and reduce erroneous predictions due to service correlation. We evaluate our approach with Named Entity Recognition (NER)- and Named Entity Disambiguation (NED) services on text corpora with heterogeneous characteristics (i.e. news articles and tweets). Our empirical results improve the out-of-the-box performance of the original services.
Konsensus der Deutschen Gesellschaft der Plastischen, Rekonstruktiven und Ästhetischen Chirurgen (DGPRÄC) zur Eigenfett-Transplantation

Zusammenfassung Der Vorstand der Deutschen Gesellschaft der Plastischen, Rekonstruktiven und Ästhetischen Chirurgen (DGPRÄC) hat gemeinsam mit einer Expertengruppe, die auch an der Erstellung der kürzlich erschienen S2k Leitlinie „Eigenfett-Transplantation“ beteiligt waren ein Konsensus-Statement aus plastisch-chirurgischer Sicht zur Bewertung der gegenwärtigen Situation unter Berücksichtigung des aktuellen Rechtsrahmens verfasst: 1. Die Eigenfett-Transplantation ist ein seit langem bewährtes Therapieverfahren und unterscheidet sich nicht von anderen Gewebetransplantationen. 2. Die mechanische Bearbeitung des Eigen-Fettgewebes stellt dabei keine substanzielle Veränderung dar. 3. Falls bei anderen Aufbereitungsverfahren mit dem Ziel Vorläuferzellen aus dem Eigen-Fettgewebe anzureichern z. B. durch enzymatische Vorgänge kein Nachweis vorliegt, dass Eigen-Fettgewebe oder Zellen nicht substanziell verändert wurden, könnte nach der derzeitigen Rechtslage eine Einstufung als Arzneimittel in Frage kommen (Anwendung des AMG/ATMP).
Prevalence of past‐year dental visit among US adults, 1999–2010: comparison of trends and estimates between the Behavioral Risk Factor Surveillance System and three national surveys

OBJECTIVES To compare estimated prevalence of past-year dental visit (PPYDV) among US adults aged ≥18 years from the Behavioral Risk Factor Surveillance System (BRFSS) to estimates from the Medical Expenditure Panel Survey (MEPS), National Health Interview Survey (NHIS), and National Health and Nutrition Examination Survey (NHANES). METHODS We estimated PPYDV adjusted for covariates (age, race/ethnicity, education level, poverty status, edentulism) using BRFSS, MEPS, and NHIS 1999-2010, and NHANES 1999-2004. We tested trend in overall PPYDV for BRFSS, MEPS, and NHIS from 1999-2010. For 2002 and 2010, we calculated absolute differences (AD) and 95% confidence intervals (CI) in PPYDV between BRFSS and each of the other surveys overall and among subpopulations defined by covariates. We pooled NHANES 1999-2004 data for comparison with BRFSS 2002. RESULTS From 1999 to 2010, BRFSS (68.5% vs. 67.5%), MEPS (43.5% vs. 39.7%), and NHIS (63.3% vs. 59.7%) showed small but significant decreases in overall PPYDV. In 2002, estimates for overall PPYDV were highest for BRFSS (70.0%) and lowest for MEPS (43.9%) with estimates for NHIS (61.5%) and NHANES (1999-2004: 58.1%) in between; the largest AD (26.2%, 95% CI: 25.0%-27.3%) was between BRFSS and MEPS. ADs were consistent in 2002 and 2010, overall and by covariates, except among edentate persons, where PPYDV estimates from BRFSS and NHIS were similar. CONCLUSIONS Estimates of PPYDV from BRFSS were notably higher than estimates from MEPS, NHIS, or NHANES except among the edentate. Trends in PPYDV over time, however, were consistent across all surveys.
What Paper Types Are Accepted at the International Conference on Software Engineering?

With the aim of identifying good structures and examples for papers in the software engineering field, we conducted a study of the type of papers accepted along four decades in the Research Track of the International Conference on Software Engineering (ICSE). We used for this purpose a categorization scheme for Software Engineering papers that was obtained by merging, extending and revising a few existing paper scheme proposals. This paper summarizes some outcomes relative to what topics and problems are addressed, what types of contribution are presented and how they are validated. Insights from the study could help ICSE authors, reviewers and conference organizers in focusing and improving future efforts.
Chronological Profiling for Paleography

This paper approaches manuscript dating from a Bayesian perspective. Prior work on paleographic date recovery has generally sought to predict a single date for a manuscript. Bayesian analysis makes it possible to estimate a probability distribution that varies with respect to time. This in turn enables a number of alternative analyses that may be of more use to practitioners. For example, it may be useful to identify a range of years that will include a document's creation date with a particular confidence level. The methods are demonstrated on a selection of Syriac documents created prior to 1300 CE.
Comparative Effects of mEOC on the Structures and Properties of PP/SGF and PP/EOC/SGF Composite Foams

Abstract To improve the impact toughness of short glass fiber (SGF) reinforced polypropylene (PP) composite foams, maleic anhydride grafted ethylene-α-octene copolymer (mEOC) was employed as impact modifier and interfacial compatibilizer. And for comparison, mEOC was also introduced into PP/EOC/SGF composite foams. Then, the foaming qualities, interfacial structures and mechanical properties of samples against varying mEOC contents were examined and compared in detail. Results showed that adequate mEOC significantly improved the foamabilities of the composites, while the optimized mass fraction was 8% for PP/SGF composite foams and 3% for PP/EOC/SGF system. Increased mEOC facilitated the higher impact toughness, which was increased by 77% for PP/SGF composite foams, whereas only 5% for PP/EOC/SGF foams. However, the flexural strengths were just improved slightly, while compressive strengths decreased monotonically with mEOC for the investigated composite foams.
Measurement of Complex Permittivity of Biological Tissues

This paper describes and evaluates a method for determining complex permittiv- ity, and presents results of permittivity measurement of agar phantom of biological tissue. A nondestructive and non-invasive method based on re∞ection coe-cient measurement of an open- ended coaxial line attaching the material under test is used. Vector measurement of the re∞ection coe-cient on the interface between probes and measured samples is performed with the aid of network analyzer in the frequency range from 300kHz to 3GHz. The results indicate that using the coaxial probe with dimensions of N connector is suitable in the frequency range approximately from 30MHz to 1GHz. 1. INTRODUCTION Relative permittivity, loss factor and conductivity are basic parameters for electromagnetic fleld modeling and simulations. Although for many materials these parameters could be found in the tables, very often their experimental determination is necessary. Dielectric properties of biological tissues are determining factors for the dissipation of electromagnetic energy in the human body and therefore they are useful in hyperthermia cancer treatment. Measurement of the dielectric parameters of biological tissues is also a promising method in the medical diagnostics and imag- ing. Knowledge of the complex permittivity in an treated area, i.e., knowledge of the complex permittivity of healthy and tumor tissue, is very important for example in the diagnosing of tumor regions in the human body or in the design of thermo-therapeutic applicators which transform electromagnetic energy into thermal energy in the tissue. Permittivity is known as " = "0"c (1) where "0 is free space permittivity and "c is complex relative permittivity. Complex relative per- mittivity can be written as "c = "r i j"r tan-
Evaluation of Multiple Methods for Detection of Gastrointestinal Colonization of Carbapenem-Resistant Organisms from Rectal Swabs

ABSTRACT Rectal swabs from high-risk patients were screened for carbapenem-resistant organisms (CROs) using several methods. The direct MacConkey plate method was the most sensitive for CROs (95%), while chromID CARBA and the Check-Direct CPE screen assay were the most sensitive for the detection of carbapenemase-producing organisms (CPOs) (100%; all bla KPC). All methods had a specificity of >90% for CROs, and for CPOs, the specificity ranged from 85 to 98%. Broth enrichment methods performed poorly compared to direct inoculation methods, negating the need for the broth enrichment step.
Identification and characterization of the proteins in broth of stewed traditional Chinese yellow‐feathered chickens

&NA; Soups and broths are popular in the world due to their nutrition and flavor, and flavor compounds tend to be bound by the proteins in the soups and broth, influencing the flavor perception. Thus, identification of the major proteins in meat‐based broth may present a basis for understanding protein adsorption of flavor compounds. The present study aimed to identify the major proteins in traditional Chinese chicken broth and to describe the structural changes of proteins during stewing (1, 2, or 3 h). As stewing time increased, protein content in the broth significantly increased. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE) indicated that the macro‐molecule proteins (>10 kDa) in the broth were mainly gelatin and actin and that the micro‐molecule proteins fractions (<10 kDa) increased substantially. The gelatin had an ordered structure even after 3 h of stewing, as seen by circular dichroism (CD) spectroscopy. The presence of reactive sulfhydryl groups increased remarkably with stewing time. The surface hydrophobicity of the proteins significantly increased within 2 h then deceased slightly after 3 h. The intermolecular crosslinks, as indicated by dispersion index, increased remarkably, consistent with the result of atomic force microscopy (AFM), which together suggested that protein aggregation increased during stewing. These findings suggested that gelatin was the structural protein in the broth system and that intermolecular crosslinks functioned to maintain the broth system.
Structure, Regulation, and Inhibition of the Quorum-Sensing Signal Integrator LuxO

In a process called quorum sensing, bacteria communicate with chemical signal molecules called autoinducers to control collective behaviors. In pathogenic vibrios, including Vibrio cholerae, the accumulation of autoinducers triggers repression of genes responsible for virulence factor production and biofilm formation. The vibrio autoinducer molecules bind to transmembrane receptors of the two-component histidine sensor kinase family. Autoinducer binding inactivates the receptors’ kinase activities, leading to dephosphorylation and inhibition of the downstream response regulator LuxO. Here, we report the X-ray structure of LuxO in its unphosphorylated, autoinhibited state. Our structure reveals that LuxO, a bacterial enhancer-binding protein of the AAA+ ATPase superfamily, is inhibited by an unprecedented mechanism in which a linker that connects the catalytic and regulatory receiver domains occupies the ATPase active site. The conformational change that accompanies receiver domain phosphorylation likely disrupts this interaction, providing a mechanistic rationale for LuxO activation. We also determined the crystal structure of the LuxO catalytic domain bound to a broad-spectrum inhibitor. The inhibitor binds in the ATPase active site and recapitulates elements of the natural regulatory mechanism. Remarkably, a single inhibitor molecule may be capable of inhibiting an entire LuxO oligomer.
Comparison of Hepatic 2D Sandwich Cultures and 3D Spheroids for Long-term Toxicity Applications: A Multicenter Study

Abstract Primary human hepatocytes (PHHs) are commonly used for in vitro studies of drug-induced liver injury. However, when cultured as 2D monolayers, PHH lose crucial hepatic functions within hours. This dedifferentiation can be ameliorated when PHHs are cultured in sandwich configuration (2Dsw), particularly when cultures are regularly re-overlaid with extracellular matrix, or as 3D spheroids. In this study, the 6 participating laboratories evaluated the robustness of these 2 model systems made from cryopreserved PHH from the same donors considering both inter-donor and inter-laboratory variability and compared their suitability for use in repeated-dose toxicity studies using 5 different hepatotoxins with different toxicity mechanisms. We found that expression levels of proteins involved in drug absorption, distribution, metabolism, and excretion, as well as catalytic activities of 5 different CYPs, were significantly higher in 3D spheroid cultures, potentially affecting the exposure of the cells to drugs and their metabolites. Furthermore, global proteomic analyses revealed that PHH in 3D spheroid configuration were temporally stable whereas proteomes from the same donors in 2Dsw cultures showed substantial alterations in protein expression patterns over the 14 days in culture. Overall, spheroid cultures were more sensitive to the hepatotoxic compounds investigated, particularly upon long-term exposures, across testing sites with little inter-laboratory or inter-donor variability. The data presented here suggest that repeated-dosing regimens improve the predictivity of in vitro toxicity assays, and that PHH spheroids provide a sensitive and robust system for long-term mechanistic studies of drug-induced hepatotoxicity, whereas the 2Dsw system has a more dedifferentiated phenotype and lower sensitivity to detect hepatotoxicity.
Cytomegaloviruses in a Community of Wild Nonhuman Primates in Taï National Park, Côte D’Ivoire

Cytomegaloviruses (CMVs) are known to infect many mammals, including a number of nonhuman primates (NHPs). However, most data available arose from studies led on captive individuals and little is known about CMV diversity in wild NHPs. Here, we analyzed a community of wild nonhuman primates (seven species) in Taï National Park (TNP), Côte d’Ivoire, with two PCR systems targeting betaherpesviruses. CMV DNA was detected in 17/87 primates (4/7 species). Six novel CMVs were identified in sooty mangabeys, Campbell’s monkeys and Diana monkeys, respectively. In 3/17 positive individuals (from three NHP species), different CMVs were co-detected. A major part of the glycoprotein B coding sequences of the novel viruses was amplified and sequenced, and phylogenetic analyses were performed that included three previously discovered CMVs of western red colobus from TNP and published CMVs from other NHP species and geographic locations. We find that, despite this locally intensified sampling, NHP CMVs from TNP are completely host-specific, pinpointing the absence or rarity of cross-species transmission. We also show that on longer timescales the evolution of CMVs is characterized by frequent co-divergence with their hosts, although other processes, including lineage duplication and host switching, also have to be invoked to fully explain their evolutionary relationships.
Tritordeum: a novel cereal for food processing with good acceptability and significant reduction in gluten immunogenic peptides in comparison with wheat.

BACKGROUND Tritordeum is a novel cereal obtained from the hybridization between durum wheat and a wild barley. This study evaluates acceptance, digestibility and immunotoxic properties of tritordeum, a novel cereal for food processing. Nineteen healthy volunteers participated in a study with different diets to compare tritordeum bread with wheat and gluten-free breads. RESULTS Tritordeum breads had a similar acceptance to the wheat bread usually consumed, and the acceptance was significantly higher than the gluten-free bread and standardized wheat bread supplied in the study. There was no evidence for gastrointestinal symptoms among volunteers during the study. The reductions in the numbers of immunogenic epitopes in tritordeum in comparison with wheat were 78% for α-gliadins, 57% for γ-gliadins and 93% for ω-gliadins. The analysis of gluten immunogenic peptides (GIP) in stool samples showed a significantly lower excretion in the tritordeum ingestion phase than in the wheat ingestion phase. CONCLUSIONS These results suggest that tritordeum may be an option of interest for general food processing, and especially for those who want to reduce their intake of gluten. However, it is not suitable for celiac disease sufferers as it contains gluten. © 2017 Society of Chemical Industry.