Miracle-dz/UniFAR-FTUs huggingface dataset:
Multivariate Gaussian Process Emulators With Nonseparable Covariance Structures

The Gaussian process regression model is a popular type of “emulator” used as a fast surrogate for computationally expensive simulators (deterministic computer models). For simulators with multivariate output, common practice is to specify a separable covariance structure for the Gaussian process. Though computationally convenient, this can be too restrictive, leading to poor performance of the emulator, particularly when the different simulator outputs represent different physical quantities. Also, treating the simulator outputs as independent can lead to inappropriate representations of joint uncertainty. We develop nonseparable covariance structures for Gaussian process emulators, based on the linear model of coregionalization and convolution methods. Using two case studies, we compare the performance of these covariance structures both with standard separable covariance structures and with emulators that assume independence between the outputs. In each case study, we find that only emulators with nonseparable covariances structures have sufficient flexibility both to give good predictions and to represent joint uncertainty about the simulator outputs appropriately. This article has supplementary material online.
Nutritional supplementation with the mushroom Agaricus sylvaticus reduces oxidative stress in children with HIV

Oxidative stress has been implicated in the progression of HIV and other diseases. The authors of this article aimed to evaluate the effects of supplementation with a mushroom known to exhibit antioxidant properties on the oxidative status of children with HIV. Extensive measurements of oxidative stress markers and antioxidant capacity were obtained before and after 90 days of supplementation with the mushroom extract.
Orientifold, geometric transition and large N duality for SO/Sp gauge theories

We extend the large N duality of four dimensional = 1 supersymmetric Yang-Mills theory with additional chiral fields and arbitrary superpotential recently proposed by Cachazo, Intriligator and Vafa to the case of SO/Sp gauge groups. By orientifolding the geometric transition, we investigate a large N duality between = 1, SO/Sp supersymmetric theories with arbitrary superpotential and an abelian = 2 theory with supersymmetry broken to = 1 by electric and magnetic Fayet-Iliopoulos terms.
A Retrieval Mechanism for Multi-versioned Digital Collection Using TAG

As the marvellous growth of the digital library in each year, the problems with indexing and searching a digital library is increased in a high rate. When the researchers search for the earlier versions, only a few recent versions in the back volumes can be retrieved soon. It is unpredictable that researchers require the earlier versions in a specific boundary. In order to facilitate the researchers, who may access any version at any time, we propose a VTAG technique for indexing. Our experiments indicate that the proposed retrieval technique, VTAG, effectively retrieves any version in considerable amount of time than the existing method.
Hamster Cells-deoxyuridine to Chinese ′ Mutagenicity of 5-Hydroxymethyl-2 Updated Version

5-Hydroxymethyluracil (HmUra) is formed from thymine in DNA through the action of ionizing radiation or reactive oxygen species gen erated by activated leukocytes. HmUra is removed from DNA by a specific DNA glycosylase, suggesting that it is also formed from endogenously generated reactive oxygen species and that its formation in DNA is potentially deleterious. To determine whether HmUra residues in DNA are mutagenic, hamster V79 cells were grown in the presence of 5hydroxymethyl-2'-deoxyuridine (HmdUrd) which is incorporated into DNA, and mutagenicity at the ouabainand thioguanine-resistant loci was determined. Levels of substitution ranged from 1/500 to 1/5,000 HmUra residues/thymine residues. There was slight mutagenicity at the thioguanine-resistant locus but none at the ouabain-resistant locus. The mutagenicity of HmdUrd, expressed as a function of HmUra substitution in DNA, was 1/30,000 in the hypoxanthine-guanine-phosphoribosyltransferase target gene. This low frequency indicates that the oxidation of thymine to HmUra in a preexisting AT base pair does not contribute significantly to the mutagenicity of ionizing radiation, because the yield of HmUra formed in DNA at mutagenic doses of radiation is too low. To determine whether repair of HmUra might be inhibited by ionizing radiation, cells were grown in medium containing HmdUrd and exposed to as much as 5 Gy of -y-irradiation, and the removal of HmUra from DNA was measured. No inhibition of repair was noted. Preirradiation of cells neither accelerated the rate of repair nor raised the level of HmUraDNA glycosylase activity, indicating that repair of HmUra was not induced by this type of oxidative stress. Although the mutagenicity of HmUra residues in DNA is low, even a rare mutation might be sufficiently deleterious to higher organisms to promote the development of HmUraDNA glycosylase activity.
Identifying Positive and Negative Expressions-a Step towards more “ sensitive ” eLearning Systems

The lack of face to face communication in eLearning is sometimes considered to be the main problem in the communication between students and teachers with respect to the proper and fast feedback, which both would like to receive from one another concerning learning material, learning environment, even the role of the teacher in the learning process. Systems of eLearning capable in one way or another to catch at least part of these sentiments could probably fill this gap and lead to more successful teaching and learning. The paper presents an application, which identifies positive and negative phrases in text. The main stress is on sentiment phrases, but modules for discovering their sources and targets and linking all of them in sentiment statements are implemented as well.
COMPETITION BETWEEN CALCIUM, STRONTIUM, AND MAGNESIUM FOR ABSORPTION IN THE ISOLATED RAT INTESTINE.

Rats 1-2 mo. old were placed on a low calcium or a low calcium and low magnesium diet. Absorption in isolated rat intestine was studied in vitro. Duodenal segments which actively took up and actively transported Ca45++ well, actively took up and actively transported Sr85++ well; where Ca45++ active uptake and active transport was poor, that of Sr85++ was low. The uptakes of Ca45++, Sr85++, and Mg28++ by the gut tissue were greater than the amounts transported. Ca++, Sr++, and Mg++ decreased the active uptake of Ca45++ and Sr85++ by the duodenum. Ca++ decreased the rate of active transport to the serosal media of Ca40++ and Sr85++. Ca++ was more effective in decreasing the active uptake of Sr55++ than was Sr++. The active uptake of Ca45++ by the ileum was reduced by Mg++ and Sr++. The active uptake of Mg28++ by the ileum was reduced by Ca++. The rate at which Mg28++ crosses and is taken up by the small intestine increases as one progresses from the proximal duodenum to the distal ileum. Ca++ was actively transported by the colon. Ca++, Sr++, and Mg++ appear to share a common pathway for absorption by the gut, but in the various areas of the intestine the rate of absorption of a particular divalent cation and the degree of competition between the divalent cations varies. Therefore, the absorption of a particular cation may involve also other pathways.
Incidence of Transmitted Antiretroviral Drug Resistance in Treatment-Naive HIV-1-Infected Persons in a Large South Central United States Clinic

Background: Transmitted drug resistance (TDR) can limit effective treatment options to antiretroviral-naive HIV-infected persons and increase the risk of treatment failure. Limited estimates of TDR have been reported from the South Central United States. Objective: To describe the incidence of TDR in Oklahoma and to examine whether TDR rates have increased with time. Methods: This was a retrospective observational study of antiretroviral-naive patients at the Infectious Diseases Institute, a large infectious diseases clinic in Oklahoma City, Oklahoma, who had received baseline antiretroviral resistance testing. Mutations were screened using the 2011 International Antiviral Society-USA Drug Resistance Mutation (DRM) update, and categorized using the 2009 World Health Organization (WHO) Surveillance Drug Resistance Mutation (SDRM) list. Results: Genotypic sequences from 428 patients revealed a 6.0% to 13.6% incidence of SDRMs between 2007 and 2011, though no progression in the frequency was apparent during the study period. Primary DRMs were detected in 12.6% of the sampled patients, most commonly involving nonnucleoside reverse transcriptase inhibitors (NNRTIs; 8.2%), followed by protease inhibitors (PIs; 3.5%) and nucleoside reverse transcriptase inhibitors (NRTIs; 3.3%). The K103N/S and E138A reverse transcriptase mutations were the most common DRMs identified, both present in 3.5% of patients. The L90M mutation was the most frequently observed PI SDRM (1.6%), while the T215C/D/I mutation was the most common NRTI SDRM identified (1.9%). This study was limited by the fact that the WHO SDRM list was last updated in 2009. Conclusions: The frequency of DRMs in central and western Oklahoma is similar to recently reported rates in the United States which lack data from this region. However, the frequency of second-generation NNRTI DRMs (4.4%) suggests the need to closely monitor epidemiologic trends for increasing resistance rates to individual classes of ARVs in order to predict the impact of TDR on therapeutic options.
Radiative and Auger recombination in 1.3μm InGaAsP and 1.5μm InGaAs quantum-well lasers measured under high pressure at low and room temperatures

We report on the pressure dependence of the threshold current in 1. 3μm InGaAsP and 1. 5μm InGaAs quantum-well lasers measured at low temperatures ∼100K. It was found that the threshold current of both devices slowly increases with increasing pressure (i.e., increasing band gap) at ∼100K consistent with the calculated variation of the radiative current. In contrast, at room temperature we observed a reduction of the threshold current with increasing pressure. Our low-temperature, high-pressure data confirm the results of previous atmospheric pressure measurements on the same devices which indicated a transition in the dominant recombination mechanism from radiative to Auger as the device temperature is increased from ∼100 to 300K.
Extracellular Vesicles in Physiology, Pathology, and Therapy of the Immune and Central Nervous System, with Focus on Extracellular Vesicles Derived from Mesenchymal Stem Cells as Therapeutic Tools

Extracellular vesicles (EVs) are membrane-surrounded structures released by most cell types. They are characterized by a specific set of proteins, lipids and nucleic acids. EVs have been recognized as potent vehicles of intercellular communication to transmit biological signals between cells. In addition, pathophysiological roles of EVs in conditions like cancer, infectious diseases and neurodegenerative disorders are well established. In recent years focus has been shifted on therapeutic use of stem cell derived-EVs. Use of stem cell derived-EVs present distinct advantage over the whole stem cells as EVs do not replicate and after intravenous administration, they are less likely to trap inside the lungs. From the therapeutic perspective, the most promising cellular sources of EVs are mesenchymal stem cells (MSCs), which are easy to obtain and maintain. Therapeutic activity of MSCs has been shown in numerous animal models and the beneficial paracrine effect of MSCs may be mediated by EVs. The various components of MSC derived-EVs such as proteins, lipids, and RNA might play a specific therapeutic role. In this review, we characterize the role of EVs in immune and central nervous system (CNS); present evidences for defective signaling of these vesicles in neurodegeneration and therapeutic role of EVs in CNS.
Investigation of reflection properties of reactive impedance substrates

In this paper, reflection properties of a reactive impedance surface are investigated. An equivalent circuit model of the reactive impedance surfaces is discussed in more details in comparison with previous introduced models, and its consistency with the models addressed in frequency selective surface studies is presented. The feasibility of obtaining the circuit components of the model is also investigated
Galectin-7 is epigenetically-regulated tumor suppressor in gastric cancer

Gastric cancer is the second leading cause of cancer death and remains a major clinical challenge due to poor prognosis and limited treatment options. Therefore, the basic mechanisms underlying gastric tumorigenesis deserve investigation. Although regulation of the galactoside-binding lectin galectin-7 in cancer has been studied, its role in tumor formation and progression remains controversial. In this study, we investigated galectin-7 expression and its role in gastric cancer. Immunohistochemical staining using a tissue microarray of gastric cancer patients revealed significantly low expression levels of galectin-7 in malignant tissues compared with matched normal tissues, and decreased expression of galectin-7 in malignant tissues was associated with advanced TMN stage disease (p =0.034). Importantly, low expression of galectin-7 in normal tissues was associated with a poor survival rate (p =0.0561). Over-expression of galectin-7 in AGS gastric adenocarcinoma cells suppressed cell proliferation, migration, and invasion, whereas ablation of galectin-7 in KATO III gastric carcinoma cells reversed these properties. AGS cells that overexpressed galectin-7 could not form gastric tumors in xenografted mice. More than 70% hypermethylation was observed in 7 of 9 gastric cancer cell lines tested and 5-aza-cytidine treatment lowered galectin-7 expression by reducing methylation in 24 cancer cell lines from five different organ origins. We analyzed CpG islands in the galectin-7 genomic region and detected hypermethylation at +1566bp of exon 2, the predicted p53 binding region. DNA hypermethylation of this region was also detected in gastric cancer tissues from 20 patients. Taken together, our data indicate that galectin-7 has a tumor suppressive function, and that the gene is epigenetically modified by DNA methylation and significantly down-regulated in gastric cancer. Further study of galectin-7 regulation may lead to improved gastric cancer diagnosis and therapy.
Wikipedia and the Semantic Web The Missing Links ?

Wikipedia is the biggest collaboratively created source of encyclopaedic knowledge. Growing beyond the borders of any traditional encyclopaedia, it is facing new problems of knowledge management: The current excessive usage of article lists and categories witnesses the fact that 19th century content organization technologies like inter-article references and indices are no longer sufficient for today’s needs. Rather, it is necessary to allow knowledge processing in a computer assisted way, for example to intelligently query the knowledge base. To this end, we propose the introduction of typed links as an extremely simple and unintrusive way for rendering large parts of Wikipedia machine readable. We provide a detailed plan on how to achieve this goal in a way that hardly impacts usability and performance, propose an implementation plan, and discuss possible difficulties on Wikipedia’s way to the semantic future of the World Wide Web. The possible gains of this endeavor are huge; we sketch them by considering some immediate applications that semantic technologies can provide to enhance browsing, searching, and editing Wikipedia.
Staphylococcus aureus: Screening for Nasal Carriers in a Community Setting with Special Reference to MRSA

Introduction. Emergence of MRSA infections among previously healthy persons in community settings (without exposure to health care facilities) has been noted recently. MRSA infections are now classified as health care-associated MRSA (HA-MRSA) and community-associated MRSA (CA-MRSA) infections. Its colonization is an important risk factor for subsequent MRSA infection. Aims and Objectives. The aim was to screen patients and health care workers for staphylococcal carriage, identify risk factors for MRSA colonization, and determine the sensitivity pattern. Materials and Methods. A total of 200 subjects were screened for nasal carriage after obtaining verbal consent. These were both healthy subjects attending various outpatient departments and health care workers. Specimens were collected from the anterior nares using premoistened sterile cotton swabs and inoculated onto blood agar and mannitol salt agar and incubated at 37°C for 24–48 h. Results. Staphylococcus aureus colonisation was found to be 12% (n = 24). MRSA was identified in 5% (n = 10) which represents 41.66% of SA. A total of 10 strains of MRSA were isolated from 200 subjects, giving an overall positivity rate of 5%. Discussion. Staphylococcal colonization was found to be 12% (MRSA 5%). Fluoroquinolone resistance was remarkable whereas all strains were sensitive to vancomycin, teicoplanin, linezolid, quinupristin-dalfopristin.
Recruitment Market Trend Analysis with Sequential Latent Variable Models

Recruitment market analysis provides valuable understanding of industry-specific economic growth and plays an important role for both employers and job seekers. With the rapid development of online recruitment services, massive recruitment data have been accumulated and enable a new paradigm for recruitment market analysis. However, traditional methods for recruitment market analysis largely rely on the knowledge of domain experts and classic statistical models, which are usually too general to model large-scale dynamic recruitment data, and have difficulties to capture the fine-grained market trends. To this end, in this paper, we propose a new research paradigm for recruitment market analysis by leveraging unsupervised learning techniques for automatically discovering recruitment market trends based on large-scale recruitment data. Specifically, we develop a novel sequential latent variable model, named MTLVM, which is designed for capturing the sequential dependencies of corporate recruitment states and is able to automatically learn the latent recruitment topics within a Bayesian generative framework. In particular, to capture the variability of recruitment topics over time, we design hierarchical dirichlet processes for MTLVM. These processes allow to dynamically generate the evolving recruitment topics. Finally, we implement a prototype system to empirically evaluate our approach based on real-world recruitment data in China. Indeed, by visualizing the results from MTLVM, we can successfully reveal many interesting findings, such as the popularity of LBS related jobs reached the peak in the 2nd half of 2014, and decreased in 2015.
Resilience of Coral-Associated Bacterial Communities Exposed to Fish Farm Effluent

Background The coral holobiont includes the coral animal, algal symbionts, and associated microbial community. These microbes help maintain the holobiont homeostasis; thus, sustaining robust mutualistic microbial communities is a fundamental part of long-term coral reef survival. Coastal pollution is one major threat to reefs, and intensive fish farming is a rapidly growing source of this pollution. Methodology & Principal Findings We investigated the susceptibility and resilience of the bacterial communities associated with a common reef-building coral, Porites cylindrica, to coastal pollution by performing a clonally replicated transplantation experiment in Bolinao, Philippines adjacent to intensive fish farming. Ten fragments from each of four colonies (total of 40 fragments) were followed for 22 days across five sites: a well-flushed reference site (the original fragment source); two sites with low exposure to milkfish (Chanos chanos) aquaculture effluent; and two sites with high exposure. Elevated levels of dissolved organic carbon (DOC), chlorophyll a, total heterotrophic and autotrophic bacteria abundance, virus like particle (VLP) abundances, and culturable Vibrio abundance characterized the high effluent sites. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed rapid, dramatic changes in the coral-associated bacterial communities within five days of high effluent exposure. The community composition on fragments at these high effluent sites shifted towards known human and coral pathogens (i.e. Arcobacter, Fusobacterium, and Desulfovibrio) without the host corals showing signs of disease. The communities shifted back towards their original composition by day 22 without reduction in effluent levels. Significance This study reveals fish farms as a likely source of pathogens with the potential to proliferate on corals and an unexpected short-term resilience of coral-associated bacterial communities to eutrophication pressure. These data highlight a need for improved aquaculture practices that can achieve both sustainable industry goals and long-term coral reef survival.
Serial-Probe Recognition for Gustatory Objects

ii Acknowledgments . iii List of Tables . vi List of Figures . vii Chapter 1: Introduction . 1 A Selective History of Working Memory . 2 Neurological Evidence for Independent Short-Term Stores . 6 Evidence from Neurological Impairment. 6 Evidence from Neuroimaging Techniques. 8 List Memory, Primacy, and Recency . 12 Taste: Perception and Memory . 19 Sensation and Perception of Taste . 19 Current Research in Taste Memory . 22 Chapter 2: Experiments . 29 Experimental Overview . 29 Experiment 1 . 30 Methods . 31 Apparatus . 31 Stimuli . 31 Procedure . 32 Memory Task . 32 Ratings Task . 37 Data Analysis . 39 Experiment 1 Results . 39 Recognition Task . 39 Within-Taste Trials . 40