Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome‐wide profiling of normal gastric mucosa identifies Helicobacter pylori‐ and cancer‐associated DNA methylome changes

The large geographic variations in the incidence of gastric cancer (GC) are likely due to differential environmental exposures, in particular to Helicobacter pylori (H. pylori) infection. We aimed to investigate the impact of H. pylori on the epigenome in normal gastric mucosa and methylation changes associated with cancer risk independent of H. pylori. A discovery set of normal gastric mucosa from GC cases (n = 42) and controls (n = 42), nested in a large case–control study and stratified by H. pylori status, were subjected to genome‐wide methylation profiling. Single‐nucleotide polymorphism arrays from peripheral blood leukocytes were used to conduct methylation quantitative trait loci (mQTL) analysis. A validation set of gastric mucosa samples (n = 180) was used in the replication phase. We found 1,924 differentially methylated positions (DMPs) and 438 differentially methylated regions (DMRs) associated with H. pylori infection, most of which were hypermethylated. Significant methylation alterations identified in the initial set were successfully replicated. Furthermore, the H. pylori‐associated DMP/Rs showed marked stability (‘epigenetic memory’) after H. pylori clearance. Interestingly, we found 152 DMRs associated with cancer risk independent of the H. pylori status in normal gastric mucosa. The methylation score derived from three biomarkers was a strong predictor of GC. Finally, the mQTL analysis indicated that the H. pylori‐ and cancer‐specific methylation signatures were minimally affected by genetic variation. The comprehensively characterized methylome changes associated with H. pylori infection and GC risk in our study might serve as potential biomarkers for early cancer progression in tumour‐free gastric mucosa.
Image based Arabic Sign Language Recognition System

Through history, humans have used many ways of communication such as gesturing, sounds, drawing, writing, and speaking. However, deaf and speaking impaired people cannot use speaking to communicate with others, which may give them a sense of isolation within their societies. For those individuals, sign language is their principal way to communicate. However, most people (who can hear) do not know the sign language. In this paper, we aim to automatically recognize Arabic Sign Language (ArSL) alphabets using an image-based methodology. More specifically, various visual descriptors are investigated to build an accurate ArSL alphabet recognizer. The extracted visual descriptors are conveyed to One-Versus-All Support Vector Machine (SVM). The analysis of the results shows that Histograms of Oriented Gradients (HOG) descriptor outperforms the other considered descriptors. Thus, the ArSL gesture models that are learned by One-Versus-All SVM using HOG descriptors are deployed in the proposed system.
Influence of Natural Convection in an Insulated Cavity on the Thermal Performance of a Wall

The influence of the airtightness of the insulation layer in a partially filled cavity construction is discussed. In theory it is assumed that the insulation forms a continuous layer that is perfectly fixed against the inner wall of the cavity, leaving an air space between the outer wall and the insulation. However, in practice we frequently notice the presence of air gaps in the insulation layer, and of a second small cavity between the insulation and the inner wall. The influence of these inaccuracies on the heat transfer is studied by means of experimental research and computer simulations. This paper presents the results of extensive measurements on a partially filled cavity wall (temperature profiles, heat loss), using a calibrated Hot Box-Cold Box. These results are compared with calculations of the temperature profiles and the overall heat transfer. A second series of measurements deals with the influence of the slope of the cavity.
Patient involvement in diabetes care: experiences in nine diabetes care groups

Introduction Despite the expected beneficial effects on quality of care, patient involvement in diabetes care groups, which deliver a bundled paid integrated care programme for diabetes type 2, seems to be limited. The aim of this study was to gain insight into levels and methods of patient involvement, into facilitators and barriers, and into the future preferences of care groups and patient representatives. Theory and methods Semi-structured interviews were held with 10 representatives of care groups and 11 representatives of patient advocacy groups. An adapted version of Arnstein's ladder of citizen participation was used to define five levels of patient involvement. Results Patient involvement in care groups was mostly limited to informing and consulting patients. Higher levels, i.e., advising, co-producing and decision-making, were less frequently observed. Care groups and patient representatives perceived largely the same barriers and facilitators and had similar preferences regarding future themes and design of patient involvement. Conclusion Constructive collaboration between diabetes care groups and patient representatives to enhance patient involvement in the future seems viable. Several issues such as the lack of evidence for effectiveness of patient involvement, differences in viewpoints on the role and responsibilities of care groups and perceived barriers need to be addressed.
Physician Assimilation in Medical Schools: Dualisms of Biomedical and Biopsychosocial Ideologies in the Discourse of Physician Educators

ABSTRACT Although health communication research and popular literature on physicians have heightened awareness of the dualisms physicians face, research is yet to focus on the discourse of physician educators who assimilate students into medicine for dualisms of the biomedical (BMD) and biopsychosocial (BPS) ideologies. The study drew on a dualism-centered model to analyze the discourse of 19 behavioral science course directors at 10 medical schools for the emergence of dualisms in instantiations of BPS ideologies and for the management of dualism in discourse that instantiated both BMD and BPS ideologies as part of the curriculum. Dualism emerged in the BPS ideologies of “patient-centeredness” and “cultural competence. ” While a dualism between “patients’ data” and “patients’ stories” emerged in the patient-centeredness ideology, a dualism between enhancing “interaction skill” and “understanding” emerged in the cultural competence ideology. Moreover, the study found educator discourse managing dualism between BMD and BPS ideologies through the strategies of “connection” and “separation. ” The study concludes with a discussion and the implications for theory and research.
Lightweight Word-Level Confidence Estimation for Neural Interactive Translation Prediction

In neural interactive translation prediction, a system provides translation suggestions (“auto-complete” functionality) for human translators. These translation suggestions may be rejected by the translator in predictable ways; being able to estimate con-ﬁdence in the quality of translation suggestions could be useful in providing additional information for users of the system. We show that a very small set of features (which are already generated as byproducts of the process of translation prediction) can be used in a simple model to estimate conﬁdence for interactive translation prediction.
Evaluation of in vitro antiprotozoal activity of Ajuga laxmannii and its secondary metabolites

Abstract Context Some Ajuga L. (Lamiaceae) species are traditionally used for the treatment of malaria, as well as fever, which is a common symptom of many parasitic diseases. Objective In the continuation of our studies on the identification of antiprotozoal secondary metabolites of Turkish Lamiaceae species, we have investigated the aerial parts of Ajuga laxmannii. Materials and methods The aerial parts of A. laxmannii were extracted with MeOH. The H2O subextract was subjected to polyamide, C18-MPLC and SiO2 CCs to yield eight metabolites. The structures of the isolates were elucidated by NMR spectroscopy and MS analyses. The extract, subextracts as well as the isolates were tested for their in vitro antiprotozoal activities against Plasmodium falciparum, Trypanasoma brucei rhodesiense, T. cruzi and Leishmania donovani at concentrations of 90–0.123 μg/mL. Results Two iridoid glycosides harpagide (1) and 8-O-acetylharpagide (2), three o-coumaric acid derivatives cis-melilotoside (3), trans-melilotoside (4) and dihydromelilotoside (5), two phenylethanoid glycosides verbascoside (6) and galactosylmartynoside (7) and a flavone-C-glycoside, isoorientin (8) were isolated. Many compounds showed moderate to good antiparasitic activity, with isoorientin (8) displaying the most significant antimalarial potential (an IC50 value of 9.7 μg/mL). Discussion and conclusion This is the first report on the antiprotozoal evaluation of A. laxmannii extracts and isolates. Furthermore, isoorientin and dihydromelilotoside are being reported for the first time from the genus Ajuga.
Who Gained Insurance Coverage in 2014, the First Year of Full ACA Implementation?

Abstract The most significant pieces of the Affordable Care Act (exchanges, subsidies, Medicaid expansion, and individual mandate), implemented in 2014, were associated with sizable gains in coverage nationally that were divided equally between gains in Medicaid and private coverage. These national trends mask heterogeneity in gains by state Medicaid expansion status, age, income level, and source of coverage. © 2016 The Authors. Health Economics published by John Wiley & Sons Ltd.
Predicting multicellular function through multi-layer tissue networks

Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue‐specific cellular function remains a critical challenge for biomedicine. Results: Here, we present OhmNet, a hierarchy‐aware unsupervised node feature learning approach for multi‐layer networks. We build a multi‐layer network, where each layer represents molecular interactions in a different human tissue. OhmNet then automatically learns a mapping of proteins, represented as nodes, to a neural embedding‐based low‐dimensional space of features. OhmNet encourages sharing of similar features among proteins with similar network neighborhoods and among proteins activated in similar tissues. The algorithm generalizes prior work, which generally ignores relationships between tissues, by modeling tissue organization with a rich multiscale tissue hierarchy. We use OhmNet to study multicellular function in a multi‐layer protein interaction network of 107 human tissues. In 48 tissues with known tissue‐specific cellular functions, OhmNet provides more accurate predictions of cellular function than alternative approaches, and also generates more accurate hypotheses about tissue‐specific protein actions. We show that taking into account the tissue hierarchy leads to improved predictive power. Remarkably, we also demonstrate that it is possible to leverage the tissue hierarchy in order to effectively transfer cellular functions to a functionally uncharacterized tissue. Overall, OhmNet moves from flat networks to multiscale models able to predict a range of phenotypes spanning cellular subsystems. Availability and implementation: Source code and datasets are available at http://snap.stanford. edu/ohmnet. Contact: jure@cs.stanford. edu
A Survey and Taxonomy of Self-Aware and Self-Adaptive Cloud Autoscaling Systems

Autoscaling system can reconfigure cloud-based services and applications, through various configurations of cloud software and provisions of hardware resources, to adapt to the changing environment at runtime. Such a behavior offers the foundation for achieving elasticity in a modern cloud computing paradigm. Given the dynamic and uncertain nature of the shared cloud infrastructure, the cloud autoscaling system has been engineered as one of the most complex, sophisticated, and intelligent artifacts created by humans, aiming to achieve self-aware, self-adaptive, and dependable runtime scaling. Yet the existing Self-aware and Self-adaptive Cloud Autoscaling System (SSCAS) is not at a state where it can be reliably exploited in the cloud. In this article, we survey the state-of-the-art research studies on SSCAS and provide a comprehensive taxonomy for this field. We present detailed analysis of the results and provide insights on open challenges, as well as the promising directions that are worth investigated in the future work of this area of research. Our survey and taxonomy contribute to the fundamentals of engineering more intelligent autoscaling systems in the cloud.
Phosphate Concentration and Arbuscular Mycorrhizal Colonisation Influence the Growth, Yield and Expression of Twelve PHT1 Family Phosphate Transporters in Foxtail Millet (Setaria italica)

Phosphorus (P) is an essential element which plays several key roles in all living organisms. Setaria italica (foxtail millet) is a model species for panacoid grasses including several millet species widely grown in arid regions of Asia and Africa, and for the bioenergy crop switchgrass. The growth responses of S. italica to different levels of inorganic phosphate (Pi) and to colonisation with the arbuscular mycorrhizal fungus Funneliformis mosseae (syn. Glomus mosseae) were studied. Phosphate is taken up from the environment by the PHT1 family of plant phosphate transporters, which have been well characterized in several plant species. Bioinformatic analysis identified 12 members of the PHT1 gene family (SiPHT1;1-1;12) in S. italica, and RT and qPCR analysis showed that most of these transporters displayed specific expression patterns with respect to tissue, phosphate status and arbuscular mycorrhizal colonisation. SiPHT1;2 was found to be expressed in all tissues and in all growth conditions tested. In contrast, expression of SiPHT1;4 was induced in roots after 15 days growth in hydroponic medium of low Pi concentration. Expression of SiPHT1;8 and SiPHT1;9 in roots was selectively induced by colonisation with F. mosseae. SiPHT1;3 and SiPHT1;4 were found to be predominantly expressed in leaf and root tissues respectively. Several other transporters were expressed in shoots and leaves during growth in low Pi concentrations. This study will form the basis for the further characterization of these transporters, with the long term goal of improving the phosphate use efficiency of foxtail millet.
Flow Cytometric Detection of PrPSc in Neurons and Glial Cells from Prion-Infected Mouse Brains

ABSTRACT In prion diseases, an abnormal isoform of prion protein (PrPSc) accumulates in neurons, astrocytes, and microglia in the brains of animals affected by prions. Detailed analyses of PrPSc-positive neurons and glial cells are required to clarify their pathophysiological roles in the disease. Here, we report a novel method for the detection of PrPSc in neurons and glial cells from the brains of prion-infected mice by flow cytometry using PrPSc-specific staining with monoclonal antibody (MAb) 132. The combination of PrPSc staining and immunolabeling of neural cell markers clearly distinguished neurons, astrocytes, and microglia that were positive for PrPSc from those that were PrPSc negative. The flow cytometric analysis of PrPSc revealed the appearance of PrPSc-positive neurons, astrocytes, and microglia at 60 days after intracerebral prion inoculation, suggesting the presence of PrPSc in the glial cells, as well as in neurons, from an early stage of infection. Moreover, the kinetic analysis of PrPSc revealed a continuous increase in the proportion of PrPSc-positive cells for all cell types with disease progression. Finally, we applied this method to isolate neurons, astrocytes, and microglia positive for PrPSc from a prion-infected mouse brain by florescence-activated cell sorting. The method described here enables comprehensive analyses specific to PrPSc-positive neurons, astrocytes, and microglia that will contribute to the understanding of the pathophysiological roles of neurons and glial cells in PrPSc-associated pathogenesis. IMPORTANCE Although formation of PrPSc in neurons is associated closely with neurodegeneration in prion diseases, the mechanism of neurodegeneration is not understood completely. On the other hand, recent studies proposed the important roles of glial cells in PrPSc-associated pathogenesis, such as the intracerebral spread of PrPSc and clearance of PrPSc from the brain. Despite the great need for detailed analyses of PrPSc-positive neurons and glial cells, methods available for cell type-specific analysis of PrPSc have been limited thus far to microscopic observations. Here, we have established a novel high-throughput method for flow cytometric detection of PrPSc in cells with more accurate quantitative performance. By applying this method, we succeeded in isolating PrPSc-positive cells from the prion-infected mouse brains via fluorescence-activated cell sorting. This allows us to perform further detailed analysis specific to PrPSc-positive neurons and glial cells for the clarification of pathological changes in neurons and pathophysiological roles of glial cells.
Leflunomide/teriflunomide inhibit Epstein-Barr virus (EBV)-induced lymphoproliferative disease and lytic viral replication

EBV infection causes mononucleosis and is associated with specific subsets of B cell lymphomas. Immunosuppressed patients such as organ transplant recipients are particularly susceptible to EBV-induced lymphoproliferative disease (LPD), which can be fatal. Leflunomide (a drug used to treat rheumatoid arthritis) and its active metabolite teriflunomide (used to treat multiple sclerosis) inhibit de novo pyrimidine synthesis by targeting the cellular dihydroorotate dehydrogenase, thereby decreasing T cell proliferation. Leflunomide also inhibits the replication of cytomegalovirus and BK virus via both “on target” and “off target” mechanisms and is increasingly used to treat these viruses in organ transplant recipients. However, whether leflunomide/teriflunomide block EBV replication or inhibit EBV-mediated B cell transformation is currently unknown. We show that teriflunomide inhibits cellular proliferation, and promotes apoptosis, in EBV-transformed B cells in vitro at a clinically relevant dose. In addition, teriflunomide prevents the development of EBV-induced lymphomas in both a humanized mouse model and a xenograft model. Furthermore, teriflunomide inhibits lytic EBV infection in vitro both by preventing the initial steps of lytic viral reactivation, and by blocking lytic viral DNA replication. Leflunomide/teriflunomide might therefore be clinically useful for preventing EBV-induced LPD in patients who have high EBV loads yet require continued immunosuppression.
Frontiers of Complex Disease Mechanisms: Membrane Surface Tension May Link Genotype to Phenotype in Glaucoma

Although many monogenic diseases are understood based upon structural changes of gene products, less progress has been made concerning polygenic disease mechanisms. This article presents a new interdisciplinary approach to understand complex diseases, especially their genetic polymorphisms. I focus upon primary open angle glaucoma (POAG). Although elevated intraocular pressure (IOP) and oxidative stress are glaucoma hallmarks, the linkages between these factors and cell death are obscure. Reactive oxygen species (ROS) promote the formation of oxidatively truncated phosphoglycerides (OTP), free fatty acids, lysophosphoglycerides, oxysterols, and other chemical species that promote membrane disruption and decrease membrane surface tension. Several POAG-linked gene polymorphisms identify proteins that manage damaged lipids and/or influence membrane surface tension. POAG-related genes expected to participate in these processes include: ELOVL5, ABCA1, APOE4, GST, CYP46A1, MYOC, and CAV. POAG-related gene products are expected to influence membrane surface tension, strength, and repair. I propose that heightened IOP overcomes retinal ganglion cell (RGC) membrane compressive strength, weakened by damaged lipid accumulation, to form pores. The ensuing structural failure promotes apoptosis and blindness. The linkage between glaucoma genotype and phenotype is mediated by physical events. Force balancing between the IOP and compressive strength regulates pore nucleation; force balancing between pore line tension and membrane surface tension regulates pore growth. Similar events may contribute to traumatic brain injury, Alzheimer's disease, and macular degeneration.
MiRNA Analysis by Quantitative PCR in Preterm Human Breast Milk Reveals Daily Fluctuations of hsa-miR-16-5p

Background and Aims Human breast milk is an extremely dynamic fluid containing many biologically-active components which change throughout the feeding period and throughout the day. We designed a miRNA assay on minimized amounts of raw milk obtained from mothers of preterm infants. We investigated changes in miRNA expression within month 2 of lactation and then over the course of 24 hours. Materials and Methods Analyses were performed on pooled breast milk, made by combining samples collected at different clock times from the same mother donor, along with time series collected over 24 hours from four unsynchronized mothers. Whole milk, lipids or skim milk fractions were processed and analyzed by qPCR. We measured hsa-miR-16-5p, hsa-miR-21-5p, hsa-miR-146-5p, and hsa-let-7a, d and g (all -5p). Stability of miRNA endogenous controls was evaluated using RefFinder, a web tool integrating geNorm, Normfinder, BestKeeper and the comparative ΔΔCt method. Results MiR-21 and miR-16 were stably expressed in whole milk collected within month 2 of lactation from four mothers. Analysis of lipids and skim milk revealed that miR-146b and let-7d were better references in both fractions. Time series (5H-23H) allowed the identification of a set of three endogenous reference genes (hsa-let-7d, hsa-let-7g and miR-146b) to normalize raw quantification cycle (Cq) data. We identified a daily oscillation of miR-16-5p. Perspectives Our assay allows exploring miRNA levels of breast milk from mother with preterm baby collected in time series over 48–72 hours.
Comparison of the safety of electrotome, Harmonic scalpel, and LigaSure for management of thyroid surgery

Energy‐based surgical devices, including electrotome, the Harmonic scalpel, and LigaSure, have been widely applied in thyroid surgery, although a comparison of their safety and efficacy has not been reported yet. In this study, we investigated the feasibility of using hemostatic energy‐based surgical devices during thyroid surgery in a canine model.