Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-linear dynamics in patients with stable angina pectoris

Dynamic analysis techniques may quantify abnormalities in heart rate behaviour based on nonlinear and fractal analysis. To investigate the clinical and prognostic significance of the fractal dimension and de-trended fluctuation analysis, a group of patients with stable angina pectoris without previous myocardial infarction and an age-matched healthy control group were studied. The fractal dimension of the R-R series was determined by the range-rescaled analysis technique. To quantify the fractal long-range correlation properties of heart rate variability, the de-trended fluctuation analysis technique was used The short-term fractal scaling exponent (/spl alpha//sub 1/) was significantly lower in patients with stable angina pectoris (0.95/spl plusmn/0.05 vs. 1.08/spl plusmn/0.06; p<0.05). The patients with stable angina pectoris had a higher fractal dimension than the healthy control group (p<0.01).
Investigation of Structural and Electronic Properties of CH3NH3PbI3 Stabilized by Varying Concentrations of Poly(Methyl Methacrylate) (PMMA)

Studies have shown that perovskites have a high potential of outdoing silicon based solar cells in terms of solar energy conversion, but their rate of degradation is also high. This study reports on improvement on the stability of CH3NH3PbI3 by passivating it with polymethylmethacrylate (PMMA). Structural and electronic properties of CH3NH3PbI3 stabilized by polymethylmethacrylate (PMMA) were investigated by varying concentrations of PMMA in the polymer solutions. Stability tests were performed over a period of time using modulated surface photovoltage (SPV) spectroscopy, X-ray diffraction (XRD), and photoluminescence (PL) measurements. The XRD patterns confirm the tetragonal structure of the deposited CH3NH3PbI3 for every concentration of PMMA. Furthermore, CH3NH3PbI3 coated with 40 mg/mL of PMMA did not show any impurity phase even after storage in air for 43 days. The Tauc gap (ETauc) determined on the basis of the in-phase SPV spectra was found in the range from 1.585 to 1.62 eV for the samples stored during initial days, but shifted towards lower energies as the storage time increased. This can be proposed to be due to different chemical reactions between CH3NH3PbI3/PMMA interfaces and air. PL intensity increased with increasing concentration of PMMA except for the perovskite coated with 40 mg/mL of PMMA. PL quenching in the perovskite coated with 40 mg/mL of PMMA can be interpreted as fast electron transfer towards the substrate in the sample. This study shows that, with an optimum concentration of PMMA coating on CH3NH3PbI3, the lifetime and hence stability on electrical and structural behavior of CH3NH3PbI3 is improved.
Interleukin 3, granulocyte-macrophage colony-stimulating factor, and interleukin 5 in eosinophilic gastroenteritis.

BACKGROUND & AIMS Eosinophilic gastroenteritis (EG) is characterized by an eosinophilic infiltration of the gastrointestinal tract. The mechanism for the intestinal recruitment of eosinophils in EG remains unknown. Eosinophil recruitment and activation is induced by three main cytokines: interleukin (IL) 3, granulocyte-macrophage colony-stimulating factor (GM-CSF), and IL-5. The aim of this study was to examine the immunoreactivity for IL-3, GM-CSF, and IL-5 within the duodenal and colonic mucosa of 10 patients with EG. METHODS Endoscopic biopsy specimens were obtained from 10 patients with EG and 10 controls. IL-3, GM-CSF, and IL-5 was evaluated by immunohistochemistry. Electron microscopy combined with immunogold staining was used to identify the labeled cells and to localize these growth factors ultrastructurally. RESULTS A significant increase in the number of eosinophils was found in both duodenal and colonic mucosa from all 10 patients with EG compared with controls. In the same tissue, immunohistochemistry detected IL-3, GM-CSF, and IL-5 in 9 of 10 patients with EG. The one exception had received treatment with steroids. These cytokines were not detected in the control group. Ultrastructurally, IL-3, GM-CSF, and IL-5 were localized in the granule matrix of eosinophils. CONCLUSIONS The release of these cytokines with autocrine and/or paracrine activities by eosinophils may be involved in the persistence of intestinal eosinophil infiltration.
Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K. W. , et al. (2010) Biochemistry 49, 2987–2998]. The overwhelming positive response to this publication we received motivates us to here share the next iteration of these tutorials that feature de novo folding, comparative modeling, loop construction, protein docking, small molecule docking, and protein design. This updated and expanded set of tutorials is needed, as since 2010 Rosetta has been fully redesigned into an object-oriented protein modeling program Rosetta3. Notable improvements include a substantially improved energy function, an XML-like language termed “RosettaScripts” for flexibly specifying modeling task, new analysis tools, the addition of the TopologyBroker to control conformational sampling, and support for multiple templates in comparative modeling. Rosetta’s ability to model systems with symmetric proteins, membrane proteins, noncanonical amino acids, and RNA has also been greatly expanded and improved.
Multi-gene biomarker panel for reference free prostate cancer diagnosis: determination and independent validation

Identification of biomarkers that can accurately and reliably diagnose prostate cancer is clinically highly desirable. A novel classification method, K-closest resemblance was applied to several high-quality transcriptomic datasets of prostate cancer leading to the discovery of a panel of eight gene biomarkers that can detect prostate cancer with over 96% specificity and sensitivity in leave-one-out cross-validation. Independent validation on clinical samples confirmed the discriminatory power of this gene panel, yielding over 95% accuracy of diagnosis based on receiver-operating characteristic curve analyses. Different levels of validation of the proposed biomarker panel have shown that it allows extremely accurate diagnosis of prostate cancer. Application of this panel can possibly add a fast and objective tool to the pathologist’s arsenal following further clinical testing.
Comparison of system penalties from first- and multiorder polarization-mode dispersion

We experimentally investigate the polarization-mode dispersion (PMD)-induced system penalty arising from first-order and all-order PMD. We use a measurable quantity, "string" length, to parameterize the penalty, find a deterministic correction to the accepted first-order PMD-induced system penalty approximation, and discuss the implications for system outages. Further, we show that higher orders of PMD introduce an additional penalty scatter that is nearly independent of "string" length, and correlated to the magnitude of the second-order PMD vector.
Evidence Against Evidence Theory (?!)

This paper is concerned with the apparent greatest weakness of the Mathematical Theory of Evidence (MTE) of Shafer \cite{Shafer:76}, which has been strongly criticized by Wasserman \cite{Wasserman:92ijar} - the relationship to frequencies. Weaknesses of various proposals of probabilistic interpretation of MTE belief functions are demonstrated. A new frequency-based interpretation is presented overcoming various drawbacks of earlier interpretations.
Achieving quasi constant machining strip width in five-axis frontal grinding with toroidal tools

Five-axis frontal grinding has an advantage in finish machining of freeform surface due to high surface accuracy and material removal rate. This article focuses on achieving nearly constant machining strip width with toroidal cutter. To begin with, the initial tool path is generated to realize the maximum machining strip width with fixed yaw angle at each cut contact point and then the verges of machined area convergent to the effective machined area after modifying tool posture. The experimental test shows that the proposed method can obtain quasi constant machining strip width.
Hyaluronan-binding protein in endothelial cell morphogenesis

Previous studies from several laboratories have provided evidence that interaction of hyaluronan (HA) with the surface of endothelial cells may be involved in endothelial cell behavior. We have recently characterized a mAb, mAb IVd4, that recognizes and neutralizes HA- binding protein (HABP) from a wide variety of cell types from several different species (Banerjee, S. D., and B. P. Toole. 1991. Dev. Biol. 146:186-197). In this study we have found that mAb IVd4 inhibits migration of endothelial cells from a confluent monolayer after "wounding" of the monolayer. HA hexasaccharide, a fragment of HA with the same disaccharide composition as polymeric HA, also inhibits migration. In addition, both reagents inhibit morphogenesis of capillary-like tubules formed in gels consisting of type I collagen and basement membrane components. Immunocytology revealed that the antigen recognized by mAb IVd4 becomes localized to the cell membrane of migrating cells, including many of their lamellipodia. Treatment with high concentrations of HA hexamer causes loss of immunoreactivity from these structures. We conclude that HABP recognized by mAb IVd4 is involved in endothelial cell migration and tubule formation.
Software Platforms for Smart Cities

Information and communication technologies (ICT) can be instrumental in progressing towards smarter city environments, which improve city services, sustainability, and citizens’ quality of life. Smart City software platforms can support the development and integration of Smart City applications. However, the ICT community must overcome current technological and scientific challenges before these platforms can be widely adopted. This article surveys the state of the art in software platforms for Smart Cities. We analyzed 23 projects concerning the most used enabling technologies, as well as functional and non-functional requirements, classifying them into four categories: Cyber-Physical Systems, Internet of Things, Big Data, and Cloud Computing. Based on these results, we derived a reference architecture to guide the development of next-generation software platforms for Smart Cities. Finally, we enumerated the most frequently cited open research challenges and discussed future opportunities. This survey provides important references to help application developers, city managers, system operators, end-users, and Smart City researchers make project, investment, and research decisions.
Script-Aware Monitoring Model : Using Teachers ’ Pedagogical Intentions to Guide Learning Analytics

In computer-supported collaborative learning, teachers do not usually get the information they need for regulating a learning situation during its enactment. To address this need, we propose to provide teachers with monitoring feedback guided by their pedagogical intentions. In particular, those pedagogical intentions captured in the scripts where teachers reflect their learning designs. In order to configure monitoring in alignment with such pedagogical intentions, a model that gathers all the necessary data elements is required. This paper presents this “script-aware monitoring model”, and the teachers’ positive opinions about its usefulness and efficiency from three pilot studies where the model was tested.
Their Conversion into Th17-Like T Cells IDO Activates Regulatory T Cells and Blocks

TLR ligands are effective vaccine adjuvants because they stimulate robust proinﬂammatory and immune effector responses and they abrogate suppression mediated by regulatory T cells (Tregs). Paradoxically, systemic administration of high doses of CpGs that bind to TLR9 ligands stimulated Tregs in mouse spleen to acquire potent suppressor activity dependent on interactions between programmed death-1 and its ligands. This response to CpG treatment manifested 8–12 h and was mediated by a rare population of plasmacytoid dendritic cells (CD19 (cid:1) pDC) induced to express the immunosuppressive enzyme IDO after TLR9 ligation. When IDO was blocked, CpG treatment did not activate Tregs, but instead stimulated pDCs to uniformly express the proinﬂammatory cytokine IL-6, which in turn reprogrammed Foxp3-lineage Tregs to express IL-17. Thus, CpG-induced IDO activity in pDCs acted as a pivotal molecular switch that induced Tregs to acquire a stable suppressor phenotype, while simultaneously blocking CpG-induced IL-6 expression required to reprogram Tregs to become Th17-like effector T cells. These ﬁndings support the hypothesis that IDO dominantly controls the functional status of Tregs in response to inﬂammatory stimuli in physiological settings. The Journal of Immunology, 2009, 183: 2475–2483.
Extracting structure from human-readable semistructured text

The explosion of Web data over the past fifteen years has fostered a rich body of research in extracting structure from semistructured HTML and XML documents. Today, we are also in the middle of an explosion of semistructured documents that originate from outside the Web domain. This latter kind of semistructured data is everywhere: in electronic medical records (EMRs), government reports, digital humanities archives, and datasets from many other domains. In contrast to HTML or XML, semistructured text that has not been marked up is typically human-readable (HR), and its structure implicitly reflects a schema. Our high-level goals are to (1) explicitly recover meaningful structure in semistructured text corpora, and (2) demonstrate that this effort enables more accurate analytics and facilitates or enriches other applications. To motivate our approach and work, we highlight the differences between HR and marked-up semistructured text and illustrate concrete use cases of HR semistructured text. We identify specific instances of implicit structure along a spectrum of “structuredness” commonly found in HR semistructured text and describe a corresponding array of methods for extracting structured features. It has not been our goal to develop “the best” such methods, but to instead present a principled framework for evaluating and combining multiple extraction methods in the context of specific data analytic tasks. We also present example applications that can be quickly built on top of a substrate of features extracted from semistructured text. For concreteness, we focus this report around semistructured text found in EMRs and evaluate our framework using a large corpus of text reports from real EMRs exhibiting highly heterogeneous schema.
In-memory file system for non-volatile memory

Current memory system hierarchy consists of cache memory, main memory, and secondary storage. Each level in this hierarchy has a different access speed to tolerate the long latency of the lower level but supports a large capacity as a whole memory system. As new technologies introduce non-volatile memories powerful enough to close the performance gap of the previous generation non-volatile memories, we can devise a new memory system that replaces DRAM with non-volatile memory for the main memory. To adopt a new memory technology, we discuss a new file system based on tmpfs with three aspects that need to be included, and evaluate its performance against popular file systems such as ext4.
Supervised Lazy Random Walk for Topic-Focused Multi-document Summarization

Topic-focused multi-document summarization aims to produce a summary given a specific topic description and a set of related documents. It has become a crucial text processing task in many real applications that can help users consume the massive information. This paper presents a novel extractive approach based on supervised lazy random walk (Super Lazy). This approach naturally combines the rich features of sentences with the intrinsic sentence graph structure in a principled way, and thus enjoys the advantages of both the existing supervised and unsupervised approaches. Moreover, our approach can achieve the three major goals of topic-focused multi-document summarization (i.e. relevance, salience and diversity) simultaneously with a unified ranking process. Experiments on the benchmark dataset TAC2008 and TAC2009 are performed and the ROUGE evaluation results demonstrate that our approach can significantly outperform both the state-of-the-art supervised and unsupervised methods.
Evaluating evapotranspiration at local and regional scales

Combining remotely sensed data with ground-based meteorological data allows the evaluation of evapotranspiration (the evaporation of water from soil and plant surfaces) at local and regional scales. Remote sensors can provide information on reflected solar radiation and surface temperatures. The remaining variables in the energy balance equations must be measured at ground level, estimated, modeled, or ignored. It is how these variables are evaluated that distinguish the several approaches to estimating evapotranspiration. In general, regional scale methods would apply to part or all of a satellite image, and use meteorological data from local weather stations. Local scale techniques would rely largely on airborne remote sensors and on-site measurements of the pertinent meteorological factors at the time of remote-data collection. In this paper, methods for estimating evapotranspiration on both local and regional scales are reviewed, and some factors that complicate its measurement are discussed.
Alcohol management practices in community football clubs: Association with risky drinking at the club and overall hazardous alcohol consumption.

INTRODUCTION AND AIMS Across the world, it has been estimated that approximately 270 million people participate in community football clubs. However, the community sports club setting is associated with high levels of risky alcohol consumption. The study examined if sporting club alcohol management practices are associated with risky consumption of alcohol by club members while at the club, and also whether such consumption is directly and indirectly associated with club member overall hazardous alcohol consumption. DESIGN AND METHODS Telephone surveys were conducted with a representative from 72 community football clubs in New South Wales, Australia, and 1428 club members. A path and mediation analysis was undertaken to determine the association between 11 club alcohol management practices and member alcohol consumption, at the club and overall hazardous consumption. RESULTS Three alcohol management practices were associated with an increased probability of risky drinking while at the club: having alcohol promotions; serving intoxicated patrons; and having bar open longer than 4 h. A mediation analyses identified that risky drinking at the club as a result of these three practices was also linked to increase risk in being an overall hazardous drinker. DISCUSSION AND CONCLUSION Modifying alcohol management practices in community football clubs has the potential to reduce both risky alcohol consumption by members in this setting and the prevalence of overall hazardous alcohol consumption. Coordinated, multi-strategic interventions are required to support community football clubs to modify their alcohol management practices and hence contribute to reducing the burden of alcohol-related harm in the community.
Question Answering with Lexical Chains Propagating Verb Arguments

This paper describes an algorithm for propagating verb arguments along lexical chains consisting of WordNet relations. The algorithm creates verb argument structures using VerbNet syntactic patterns. In order to increase the coverage, a larger set of verb senses were automatically associated with the existing patterns from VerbNet. The algorithm is used in an in-house Question Answering system for re-ranking the set of candidate answers. Tests on factoid questions from TREC 2004 indicate that the algorithm improved the system performance by 2.4%.
A novel DRD2 single-nucleotide polymorphism associated with schizophrenia predicts age of onset: HapMap tag-single-nucleotide polymorphism analysis.

BACKGROUND Dopamine D2 receptor (DRD2) is thought to be critical in regulating the dopaminergic pathway in the brain, which is known to be important in the etiology of schizophrenia. It is, therefore, not surprising that most antipsychotic medication acts on DRD2. DRD2 is widely expressed in the brain; levels are reduced in the brains of patients with schizophrenia, and DRD2 polymorphisms have been associated with reduced brain expression. We have previously identified a genetic variant in DRD2, rs6277 to be strongly implicated in schizophrenia susceptibility. METHODS To identity new associations in the DRD2 gene with disease status and clinical severity, we genotyped seven single-nucleotide polymorphisms (SNPs) in DRD2 by using a multiplex mass spectrometry method. SNPs were chosen by using a haplotype block-based gene-tagging approach; so, the entire DRD2 gene was represented. RESULTS One polymorphism, rs2734839 was found to be significantly associated with schizophrenia as well as late onset age. Individuals carrying the genetic variation were more than twice as likely to have schizophrenia compared with controls. CONCLUSIONS Our results suggest that DRD2 genetic variation is a good indicator for schizophrenia risk and may also be used as a predictor of age of onset.
The Cross-sectional and Longitudinal Associations of Diabetic Retinopathy With Cognitive Function and Brain MRI Findings: The Action to Control Cardiovascular Risk in Diabetes (ACCORD) Trial

OBJECTIVE Longitudinal evidence linking diabetic retinopathy with changes in brain structure and cognition is sparse. We used data from the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial to determine whether diabetic retinopathy at baseline predicted changes in brain structure or cognition 40 months later. RESEARCH DESIGN AND METHODS Participants from the ACCORD-MIND and ACCORD-Eye substudies were included in analyses of cognition (n = 1,862) and MRI-derived brain variables (n = 432). Retinopathy was categorized as none, mild nonproliferative, or moderate/severe. Tests of cognition included the Mini-Mental State Examination (MMSE), Digit Symbol Substitution Test (DSST), Rey Auditory Verbal Learning Test, and Stroop test. Primary brain outcomes were gray matter and abnormal white matter volumes. RESULTS Baseline retinopathy was associated with lower gray matter volume (adjusted means of 470, 466, and 461 cm3 for none, mild, and moderate/severe retinopathy, respectively; P = 0.03). Baseline retinopathy also predicted a greater change in MMSE and DSST scores at 40 months in each retinopathy category (MMSE: −0.20, −0.57, and −0.42, respectively [P = 0.04]; DSST: −1.30, −1.84, and −2.89, respectively [P = 0.01]). CONCLUSIONS Diabetic retinopathy is associated with future cognitive decline in people with type 2 diabetes. Although diabetic retinopathy is not a perfect proxy for diabetes-related brain and cognitive decline, patients with type 2 diabetes and retinopathy represent a subgroup at higher risk for future cognitive decline.