Miracle-dz/UniFAR-FTUs huggingface dataset:
Gastrointestinal manifestations associated with systemic sclerosis: results from the nationwide inpatient sample

Background Systemic sclerosis (SSc) is a multisystem disease associated with significant morbidity and increased mortality. The prevalence of different gastrointestinal (GI) manifestations has been investigated in multiple, but mainly small, retrospective studies. In this study, we investigated the prevalence and risk for a broad spectrum of GI disorders and malignancies in a large sample of inpatients with SSc in the United States. Methods We conducted a retrospective analysis using the 2010-2011 Healthcare Cost and Utilization Project – Nationwide Inpatient Sample (HCUP-NIS). SSc patients were identified by ICD-9-CM code 710.1. Non-SSc patients (“controls”) were matched to cases 4:1 by age and sex. We examined demographics, clinical characteristics, and a range of GI conditions. Results From 15,824,031 total patients, 13,633 cases of SSc were matched to 54,532 controls. The prevalence of GI manifestations among SSc patients was 59.24% compared to 29.96% for controls (P<0.0001). Significantly elevated GI manifestations in SSc patients included dysphagia (4.3% vs. 1.9%, P<0.0001), esophageal reflux (34.8% vs. 15.4%, P<0.0001), Barrett’s esophagus (1.7% vs. 0.3%, P<0.0001), constipation (6% vs. 4.6%, P<0.0001), diarrhea (4.5% vs. 2.4%, P<0.0001), fecal incontinence (0.4% vs. 0.2%, P<0.0001), and celiac disease (0.2% vs. 0%, P<0.0001). Some GI disorders were significantly lower in SSc patients, including cholelithiasis (1.6% vs. 2.1%, P<0.0001) and GI malignancies (1% vs. 2.2%, P<0.0001). Conclusions Our results emphasize the established association between SSc and esophageal disorders, such as dysphagia and reflux disease. Our analysis indicated a significant positive association between SSc and celiac disease, and a negative association between SSC and cholelithiasis.
Referee consensus: a platform technology for nonlinear optimization

Electrical current flow within populations of neurons is a fundamental constituent of brain function. The resulting fluctuating magnetic fields may be sampled noninvasively with an array of magnetic field detectors positioned outside the head. This is magnetoencephalography (MEG). Each source may be characterized by 5-6 parameters, the xyz location and the xyz direction. The magnetic field measurements are nonlinear in the location parameters; hence the source location is identifiable only via search of the brain volume. When there is one or a very few sources, this may be practical; solutions for the general problem have poor resolution and are readily defeated. Referee consensus is a novel cost function which enables identification of a source at one location at a time regardless of the number and location of other sources. This "independence" enables solution of the general problem and insures suitability to grid computing. The computation scales linearly with the number of nonlinear parameters. Since the method is not readily disrupted by noise or the presence of multiple unknown source, it is applicable to single trial data. MEG recordings were obtained from 26 volunteers while they performed a cognitive task The single trial recordings were processed on the Open Science Grid (≈300 CPU hours/sec of data) On average 500+ active sources were found throughout. Statistical analyses demonstrated 1-2 mm resolving power and high confidence findings (p < 0.0001) when testing for task specific information in the extracted virtual recordings. Referee consensus is applicable to a variety of systems in addition to MEG, e.g. the connectivity problem, the blurred image, both passive and active SONAR, and seismic tomography. Applicability requires (1) that the measurements be linear in at least one of the source parameters and (2) that a sequence of measurements in time be obtained.
Developing Real-Time Emergency Management Applications: Methodology for a Novel Programming Model Approach

The last years have been characterized by the arising of highly distributed computing platforms composed of a heterogeneity of computing and communication resources including centralized high-performance computing architectures (e.g. clusters or large shared-memory machines), as well as multi-/many-core components also integrated into mobile nodes and network facilities. The emerging of computational paradigms such as Grid and Cloud Computing, provides potential solutions to integrate such platforms with data systems, natural phenomena simulations, knowledge discovery and decision support systems responding to a dynamic demand of remote computing and communication resources and services.
PAC-C 3 D : A New Software Architectural Model for Designing 3 D Collaborative Virtual Environments

We propose PAC-C3D as a new software model for 3D Collaborative Virtual Environments (CVE). This model merges the results from two research fields: distribution models for CVE and HCI design for computer-supported cooperative work. PAC-C3D proposes to describe each part of a shared virtual object through explicit interfaces to ensure a strong separation between the core functions of a virtual environment, its (visual) representations, and its collaborative features such as synchronization and consistency maintenance between remote users. PAC-C3D makes it possible to design a CVE with low dependency between the core functions, the distribution mode and the 3D graphics API used. It explicitly deals with the main distribution modes encountered in CVE. It makes it easy to use different 3D graphics API for different nodes involved in the same collaborative session, providing interoperability between these 3D graphics API. It also makes it possible to integrate other kinds of 3D representations such as physics engines into the CVE.
Hypersensitivity drug reactions.

In this new issue of Current Opinion in Allergy and Clinical Immunology, five major areas of research in the field of hypersensitivity reactions to drugs in the past year are reviewed. The manuscript of Blanca-Lopez et al.[1] is devoted to hypersensitivity reactions to NSAIDs. NSAIDs are the drugs most frequently involved in hypersensitivity drug reactions [2,3]. In a study published recently, it has been shown that almost 50% of the cases had confirmed NSAIDs hypersensitivity followed by 20% with beta-lactam hypersensitivity. Both groups of drugs together contributed to more than the 70% of drug hypersensitivity reactions [2]. These results are consistent with data published by other groups [3]. There has been increasing interest in the nonpulmonary manifestations of NSAID hypersensitivity, which have not been studied in detail. An expert group from the European Academy of Allergy Asthma and Clinical Immunology has provided a consensus document, carefully defining these reactions [4]. Five major clinical entities are now recognized, and it is expected that in the future major subgroups will be identified making genome-wide association studies more specific to each clinical entity [5–7].
High-sensitivity phase noise measurement of RF sources by photonic-delay line and digital phase demodulation

A high-sensitivity phase noise measurement scheme using photonic-delay line and digital phase demodulation is proposed, which is free of complicate calibration and amplitude noise by using digital phase demodulation. In the experiment, a phase noise measurement sensitivity as high as −134 dBc/Hz@10 kHz@10 GHz is achieved applying a 2-km single mode fiber as the delay line. Besides, accurate phase noise measurement in a large frequency bandwidth from 2 to 35 GHz is achieved.
Individualizing Risk of Multidrug-Resistant Pathogens in Community-Onset Pneumonia

Introduction The diffusion of multidrug-resistant (MDR) bacteria has created the need to identify risk factors for acquiring resistant pathogens in patients living in the community. Objective To analyze clinical features of patients with community-onset pneumonia due to MDR pathogens, to evaluate performance of existing scoring tools and to develop a bedside risk score for an early identification of these patients in the Emergency Department. Patients and Methods This was an open, observational, prospective study of consecutive patients with pneumonia, coming from the community, from January 2011 to January 2013. The new score was validated on an external cohort of 929 patients with pneumonia admitted in internal medicine departments participating at a multicenter prospective study in Spain. Results A total of 900 patients were included in the study. The final logistic regression model consisted of four variables: 1) one risk factor for HCAP, 2) bilateral pulmonary infiltration, 3) the presence of pleural effusion, and 4) the severity of respiratory impairment calculated by use of PaO2/FiO2 ratio. A new risk score, the ARUC score, was developed; compared to Aliberti, Shorr, and Shindo scores, this point score system has a good discrimination performance (AUC 0.76, 95% CI 0.71-0.82) and calibration (Hosmer-Lemeshow, χ2 = 7.64; p = 0.469). The new score outperformed HCAP definition in predicting etiology due to MDR organism. The performance of this bedside score was confirmed in the validation cohort (AUC 0.68, 95% CI 0.60-0.77). Conclusion Physicians working in ED should adopt simple risk scores, like ARUC score, to select the most appropriate antibiotic regimens. This individualized approach may help clinicians to identify those patients who need an empirical broad-spectrum antibiotic therapy.
Pupation Site Selection of Cat Fleas (Siphonaptera: Pulicidae) in Various Carpet Types and Its Influence on Insecticide Efficacy

Abstract Pupation sites of cat flea, Ctenocephalides felis (Bouché), larvae were determined in three styles of nylon and one style of wool carpet. Nylon saxony carpet had 59.3% of pupae at the top of the pile and 40% at the base of the pile. In nylon contract carpet, 55.2% of pupae were found at the top, 42.6% in the middle, and only 2.2% at the base of the pile. Nylon loop carpet contained 59.2% of pupae at the base, 25.5% in the middle, and 15.3% in the top of the pile. Wool loop carpet had 92.4% at the base and 3.8% both in the middle and top of the pile. Bioassays comparing the control of pupae manually placed at the base of carpets to that in carpets with natural pupation showed that control of pupae in the latter was 39–68% higher. Pupal control after natural pupation was greatest in nylon saxony and nylon contract carpets and lowest in nylon loop and wool loop carpets. Additional studies demonstrated that vacuuming provided the same level of pupal control on nylon saxony carpet as a spray application of permethrin to the carpet surface. Therefore, pupae that survived chemical and mechanical control treatments in nylon saxony carpet probably pupated away from the surface of the pile. Application of permethrin to the base of nylon saxony carpet did not significantly increase control. Future bioassays with cat flea pupae in carpet should be performed after natural pupation and consider carpet make and style.
FDSOI versus BULK CMOS at 28 nm node which technology for ultra-low power design?

Compared to BULK CMOS, FDSOI (Fully-Depleted Silicon-On-Insulator) introduces an ultra-thin buried oxide (BOX) layer and a dopant-free channel, which provides better performance and enhances ultra-low power (ULP) operation. To investigate benefits of utilizing FDSOI for ULP design, FDSOI and BULK CMOS 28 nm nodes are compared by simulating a test circuit. Threshold voltage tuning by back-plane biasing (BPB) for FDSOI and bulk biasing (BB) for BULK is analyzed. Contours of constant energy with minimum energy points (MEPs) are shown as well as energy delay products (EDPs). Simulation results show that FDSOI forward BPB can be used effectively to control operating frequency, EDP and MEP operation. Implications of the results are discussed last to give an overview how FDSOI performance gain over BULK CMOS can support in ULP design.
Mus81-Mms4 Functions as a Single Heterodimer To Cleave Nicked Intermediates in Recombinational DNA Repair

ABSTRACT The formation of crossovers is a fundamental genetic process. The XPF-family endonuclease Mus81-Mms4 (Eme1) contributes significantly to crossing over in eukaryotes. A key question is whether Mus81-Mms4 can process Holliday junctions that contain four uninterrupted strands. Holliday junction cleavage requires the coordination of two active sites, necessitating the assembly of two Mus81-Mms4 heterodimers. Contrary to this expectation, we show that Saccharomyces cerevisiae Mus81-Mms4 exists as a single heterodimer both in solution and when bound to DNA substrates in vitro. Consistently, immunoprecipitation experiments demonstrate that Mus81-Mms4 does not multimerize in vivo. Moreover, chromatin-bound Mus81-Mms4 does not detectably form higher-order multimers. We show that Cdc5 kinase activates Mus81-Mms4 nuclease activity on 3′ flaps and Holliday junctions in vitro but that activation does not induce a preference for Holliday junctions and does not induce multimerization of the Mus81-Mms4 heterodimer. These data support a model in which Mus81-Mms4 cleaves nicked recombination intermediates such as displacement loops (D-loops), nicked Holliday junctions, or 3′ flaps but not intact Holliday junctions with four uninterrupted strands. We infer that Mus81-dependent crossing over occurs in a noncanonical manner that does not involve the coordinated cleavage of classic Holliday junctions.
Aqueous Cytokine Changes Associated with Posner-Schlossman Syndrome with and without Human Cytomegalovirus

Aim To study the differences in aqueous cytokines in Posner-Schlossman Syndrome (PSS) patients with and without human cytomegalovirus (CMV) DNA in the aqueous humor. Methods This is a prospective study. Fifty-three uveitis patients with clinical signs of PSS were enrolled and aqueous humor samples were collected. Fourteen PSS patients were positive of CMV DNA in the aqueous by polymerase chain reaction (PCR) analysis. These eyes were negative of common ocular pathogens such as herpes simplex virus, varicella-zoster virus, rubella virus and toxoplasma. Twenty-five otherwise healthy cataract patients were enrolled as controls. Cytokine concentration was measured by a magnetic color-bead-based multiplex assay and analyzed using statistical and classification approaches. Results The average age of 53 PSS patients was 48.74±13.43 years (yrs) (mean ± standard deviation) and 66.3±15.0 yrs for the controls. The median CMV viral DNA copy number was 26000/mL aqueous (range 1400 to 85000 copies/mL) in 14 CMV positive patients as determined by quantitative PCR. PSS aqueous had significantly higher Interleukin (IL)-8 (CXCL8), monocyte chemotactic protein-1 (CCL2), macrophage inhibitory protein 1-β (CCL4), granulocyte colony-stimulating factor (GCSF) and transforming growth factor-β (TGF-β) levels than controls after adjusted by age and gender. IL-2, IL-12, tumor necrosis factor-α (TNF-α) and interferon-α (IFN-α) levels were significantly lower in PSS aqueous than controls. No difference between CMV positive PSS and CMV negative PSS aqueous was observed. Over 97% of PSS samples were distinguished from controls by elevated CXCL10 (>500 ng/mL), CXCL8 (>30 ng/mL) and CCL2 (>60 ng/mL) levels. Conclusion PSS eyes were characterized by elevated aqueous chemokine concentration. The presence of CMV viral DNA was not associated with significant change of the type of cytokine expression in PSS patients.
Post-Partum Factor VIII Inhibitors

Summary In a retrospective study 51 published cases of post-partum factor VIII inhibitors were analyzed with regard to the outcome according to treatment. The overall outcome was favorable with 97% survival at two years. The probability of complete remission (CR, absence of the inhibitor and normalization of factor VIII activity) was almost 100% at 30 months. Steroid treatment appears to be not superior to no treatment, but patients treated with immunosuppressive drugs (cyclophosphamide, azathioprine, 6-mercaptopurine) had a significantly shorter time to CR. In the absence of a randomized trial this analysis may be helpful for decision-making in women with factor VIII post-partum inhibitors. Because of the retrospective study design, conclusions have to be regarded with caution.
Automatic Generation of Semantic Fields for Annotating Web Images

The overwhelming amounts of multimedia contents have triggered the need for automatically detecting the semantic concepts within the media contents. With the development of photo sharing websites such as Flickr, we are able to obtain millions of images with user-supplied tags. However, user tags tend to be noisy, ambiguous and incomplete. In order to improve the quality of tags to annotate web images, we propose an approach to build Semantic Fields for annotating the web images. The main idea is that the images are more likely to be relevant to a given concept, if several tags to the image belong to the same Semantic Field as the target concept. Semantic Fields are determined by a set of highly semantically associated terms with high tag co-occurrences in the image corpus and in different corpora and lexica such as WordNet and Wikipedia. We conduct experiments on the NUS-WIDE web image corpus and demonstrate superior performance on image annotation as compared to the state-of-the-art approaches.
Apparent size correlation: A simple method to determine vertical positions of particles using conventional microscopy

This paper reports a simple and widely applicable particle tracking technique using conventional fluorescence microscopy to determine vertical positions of particles suspended in a fluid. Previous experimental work in this area has been restricted to two-dimensional intensity profiles or confocal and stereoscopic setups for three-dimensional tracking. Using a calibration-based defocusing method, our technique has been experimentally verified and compared with previously observed trends in inertial flow focusing. The technique has proven to be a simple and valuable tool for determining locations of micron-sized particles in microscale flows.
What Teacher Candidates Need to Know about Academic Learning Time.

A model assignment was designed and tested to enhance special education teacher candidates’ skills and understandingin order to improve student learning. The model includes university and school-site activities that develop teacher candidates’ awareness of the relationship between on-task learning time and student achievement. Teacher candidates (N=90) systematically gathered data on their own teaching behaviors and the learning behaviors of their students to measure the level of engaged teaching and learning. The process of guiding teacher candidates through the gathering, graphing, and analysis of student data is presented. Findings, as documented by candidates’ responses to the data, indicate the proposed assignment was successful in developing candidates’ understanding of the relationship between student achievement and on-task learning.
Transcriptome Analysis of Differentially Expressed Genes Induced by Low and High Potassium Levels Provides Insight into Fruit Sugar Metabolism of Pear

Potassium (K) deficiency is a common abiotic stress that can inhibit the growth of fruit and thus reduce crop yields. Little research has been conducted on pear transcriptional changes under low and high K conditions. Here, we performed an experiment with 7-year-old pot-grown “Huangguan” pear trees treated with low, Control or high K levels (0, 0.4, or 0.8 g·K2O/kg soil, respectively) during fruit enlargement and mature stages. We identified 36,444 transcripts from leaves and fruit using transcriptome sequencing technology. From 105 days after full blooming (DAB) to 129 DAB, the number of differentially expressed genes (DEGs) in leaves and fruit in response to low K increased, while in response to high K, the number of DEGs in leaves and fruit decreased. We selected 17 of these DEGs for qRT-PCR analysis to confirm the RNA sequencing results. Based on GO enrichment and KEGG pathway analysis, we found that low-K treatment significantly reduced K nutrient and carbohydrate metabolism of the leaves and fruit compared with the Control treatment. During the fruit development stages, AKT1 (gene39320) played an important role on K+ transport of the leaves and fruit response to K stress. At maturity, sucrose and acid metabolic pathways were inhibited by low K. The up-regulation of the expression of three SDH and two S6PDH genes involved in sorbitol metabolism was induced by low K, promoting the fructose accumulation. Simultaneously, higher expression was found for genes encoding amylase under low K, promoting the decomposition of the starch and leading the glucose accumulation. High K could enhance leaf photosynthesis, and improve the distribution of the nutrient and carbohydrate from leaf to fruit. Sugar components of the leaves and fruit under low K were regulated by the expression of genes encoding 8 types of hormone signals and reactive oxygen species (ROS). Our data revealed the gene expression patterns of leaves and fruit in response to different K levels during the middle and late stages of fruit development as well as the molecular mechanism of improvement of fruit sugar levels by K and provided a scientific basis for improving fruit quality with supplemental K fertilizers.
Bronchial responsiveness to distilled water and methacholine and its relationship to inflammation and remodeling of the airways in asthma.

Although bronchial hyperresponsiveness in asthma is associated with inflammation within the airways, it is not known whether the degree and type of inflammation influence the response to different stimuli and whether pathologic changes of airway structure influence the bronchoconstrictive responses. Therefore, number of inflammatory cells in the epithelium and the lamina propria and the basement membrane thickness were estimated from bronchial biopsies taken in 27 asthmatic subjects (range percent predicted FEV1: 75.6 to 132.1, range of daily PEF variability: 1.9% to 20%) and related to the degree of bronchial responsiveness to ultrasonically nebulized distilled water (UNDW) and methacholine (M). PD20UNDW (provocative dose) was measurable in 15 of 27 patients and ranged between 1.01 and 20.4 ml. PC20M (provocative concentration) ranged between 0.15 and 31.7 mg/ml. In the 15 responders to UNDW, total inflammatory cells (p<0.04) and eosinophils (p<0.015) within the epithelium were higher than in 12 nonresponders to UNDW (PD20 > 34.8 ml). There was no correlation between PD20UNDW and any cell counts whereas negative correlations were found between PC20M and both total inflammatory cells (rs = -0.57; p<0.005) and eosinophils (rs = -0.63; p< 0.0015) within the epithelium. The degree of thickening of subepithelial layer ranged between 7 and 16 micrometers+ (n=26). Thickness correlates both with total inflammatory cells (rs = 0.49; p<0.025) and eosinophils (rs = 0.61; p< 0.003) within the epithelium. Moreover, it was correlated with baseline FEV1 (rs = -0.57; p<0.003) and daily peak expiratory flow (PEF) variability (rs = 0.51; p<0.01). A weak but significant correlation was also found between subepithelial layer thickness and PC20M (rs = -0.42; p<0.04). The results of this study demonstrate that eosinophilic inflammation of bronchial epithelium plays a role in determining UNDW and M responsiveness in asthma. Moreover, they suggest that remodeling of the airways such as thickening of subepithelial layer correlates with indices of asthma severity and could contribute to the degree of M but not to UNDW responsiveness.