Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Subdiffusion Using Reaction Diffusion Systems

In many types of media, particularly within living cells or within their membranes, diffusing species do not follow Fick's laws but instead show transient subdiffusive behavior. Formulating spatiotemporal models that take this behavior into account is a delicate matter, as one is faced with the choice of resorting either to fractional calculus or to microscopic descriptions. In this article, we provide an alternative designed to be easier to handle analytically and numerically than the existing approaches. Specifically, starting from the continuous time random walk model, we construct linear reaction diffusion systems that can be used as components within such a model and which capture the defining properties of subdiffusion. We show how to impose physically relevant parameters, and prove stability and mass conservation. While applications to cellular biology are our main motivation, our approach is abstract and should thus be applicable to any situation where anomalous subdiffusion is observed.
Inverse Optimization for the Recovery of Market Structure from Market Outcomes: An Application to the MISO Electricity Market

We propose an inverse optimization-based methodology to determine market structure from commodity and transportation prices. The methods are appropriate for locational marginal price-based electricity markets where prices are shadow prices in the centralized optimization used to clear the market. We apply the inverse optimization methodology to outcome data from the Midcontinent ISO electricity market (MISO) and, under noise-free assumptions, recover parameters of transmission and related constraints that are not revealed to market participants but explain the price variation. We demonstrate and evaluate analytical uses of the recovered structure including reconstruction of the pricing mechanism and investigations of locational market power through the transmission constrained residual demand derivative. Prices generated from the reconstructed mechanism are highly correlated to actual MISO prices under a wide variety of market conditions. In a case study, the residual demand derivative is shown to be corr.
Detection of human respiratory syncytial virus sequences in peripheral blood mononuclear cells

Peripheral blood mononuclear cells (PBMC) obtained from patients with lower respiratory infections were examined for the detection of human respiratory syncytial virus (RSV) sequences in the N region using the reverse transcription polymerase chain reaction (RT‐PCR). RSV infection was confirmed by at least one method, i.e., virus isolation, enzyme immunoassay for viral antigen, and RT‐PCR of nasopharyngeal secretions (NPS) samples. The detection rate for RSV RNA in PBMC obtained from RSV‐infected patients was 40% (38/94), compared to 5% (1/20) in controls (P = 0.002). Between the groups positive (38) and negative (56) for RSV RNA in PBMC, there was no significant difference in clinical parameters. Seven patients had eight episodes of reinfection and RSV RNA was detected in 50% (4/8) during consecutive infections. Sequences of their PBMC samples were distinct from those of prototype strains of subgroup A and B. However, they were not always consistent with those of paired NPS samples. The findings suggested that RSV RNA could be detected in PBMC even during reinfection and as might have the possibility of quasispecies dynamics, reflecting the nature of RNA viruses. J. Med. Virol. 70:481–489, 2003. © 2003 Wiley‐Liss, Inc.
The Diagnostic Yield of Array Comparative Genomic Hybridization Is High Regardless of Severity of Intellectual Disability/Developmental Delay in Children

Microarray-based comparative genomic hybridization is a method of molecular analysis that identifies chromosomal anomalies (or copy number variants) that correlate with clinical phenotypes. The aim of the present study was to apply a clinical score previously designated by de Vries to 329 patients with intellectual disability/developmental disorder (intellectual disability/developmental delay) referred to our tertiary center and to see whether the clinical factors are associated with a positive outcome of aCGH analyses. Another goal was to test the association between a positive microarray-based comparative genomic hybridization result and the severity of intellectual disability/developmental delay. Microarray-based comparative genomic hybridization identified structural chromosomal alterations responsible for the intellectual disability/developmental delay phenotype in 16% of our sample. Our study showed that causative copy number variants are frequently found even in cases of mild intellectual disability (30.77%). We want to emphasize the need to conduct microarray-based comparative genomic hybridization on all individuals with intellectual disability/developmental delay, regardless of the severity, because the degree of intellectual disability/developmental delay does not predict the diagnostic yield of microarray-based comparative genomic hybridization.
Transcriptional Regulation of Activating Transcription Factor 3 Involves the Early Growth Response-1 Gene

Previously, our laboratory identified activating transcription factor 3 (ATF3) as up-regulated by nonsteroidal anti-inflammatory drugs using microarray analysis of mRNA from human colorectal cancer cells treated with sulindac sulfide. ATF3 is a transcription factor involved in cell growth, apoptosis, and invasion and is induced by a variety of anticancer and dietary compounds. However, the regulation of ATF3 by anticancer agents is not known. The promoter of ATF3 contains several transcription factor binding sites. We identified three putative Egr-1 binding sites in the promoter of ATF3 and report for the first time that the molecular mechanism responsible for the transcriptional regulation of ATF3 by two divergent pharmaceutical compounds, sulindac sulfide and troglitazone, involved the early growth response gene-1 (Egr-1). For example, overexpression of Egr-1 protein induced ATF3 mRNA 3.5-fold and transcriptional activity of an ATF3 promoter construct more than 20-fold. ATF3 and Egr-1 mRNA and protein and ATF3 promoter activity were induced by these compounds, whereas induction of ATF3 by these compounds was blocked by Egr-1 small interfering RNA. Sulindac sulfide and troglitazone regulated ATF3 promoter activity, which was suppressed when the two Egr-1 sites were mutated. These compounds induced phosphorylation of extracellular signal-regulated kinase1/2 (Erk1/2), whereas a dominant-negative inhibitor of mitogen-activate protein kinase kinase (MEK) 1 blocked the induction of ATF3. The MEK1/2 inhibitor PD98059 (2′-amino-3′-methoxyflavone) blocked the induction of ATF3 and Egr-1 mRNA expression and ATF3 promoter activity by these compounds. Therefore, this is a novel first report demonstrating that the expression of ATF3 occurs via Egr-1 downstream of Erk1/2.
Immunochemical characterization of native polysaccharides from group B streptococcus: the relationship of the type III and group B determinants.

Three polysaccharides were purified from a type III strain of Group B Streptococcus grown under conditions varying in exposure to acid by washing the cells with an EDTA buffer or extracting with cold 10% TCA. Extraction of cells grown in a medium buffered with a pH titrator resulted in a polysaccharide antigen of 1.2 × 106 daltons having only type III serologic specificity. The antigen extracted with EDTA from cells grown in a medium where acid accumulated had a molecular size of approximately 600,000, and demonstrated both type III and group B serologic activity. The antigen extracted with TCA had a molecular size of approximately 500,000 and also reacted with type III and group B sera. Chemical studies revealed that all three polysaccharides contained varying concentrations of galactose, glucose, glucosamine, and sialic acid. Only the TCA antigen contained rhamnose. Alcohol fractionation of the TCA antigen allowed separation of type III from group B serologic reactivity. However, this method failed to separate the two determinants of the EDTA-non-pH titrated antigen. Other physical, chemical, and immunologic methods similarly failed to separate these two determinants. Mild hydrolysis of the EDTA-pH-titrated antigen exposed a determinant immunologically identical to the formamide-extracted group B antigen. These studies as well as electron microscopy and affinity chromatography demonstrated that two determinants exist on the native polysaccharide antigen of type III, Group B Streptococcus. One is the superficial capsular type specific determinant, which in the most native state masks the second determinant, a common group B determinant. Quantitative precipitation inhibition studies confirmed that l-rhamnose was the immunodominant sugar for the formamide-extracted B antigen. No monosaccharide inhibited the cross-reactive determinant on the EDTA-non pH titrated antigen. Despite this observation, both the formamide-extracted B antigen and the EDTA-non pH titrated antigen were demonstrated to be precipitating antibodies of identical specificity.
Automated Regulation of Inspired Oxygen in Preterm Infants: Oxygenation Stability and Clinician Workload

Premature infants are at an increased risk of ophthalmic, neurologic, and respiratory sequelae related to inadequate maintenance of oxygenation and exposure to increased levels of inspired oxygen. Management of inspired oxygen is complicated in this population by an increased variability in oxygenation. Automated regulation of the fraction of inspired oxygen is a technology that has a potential of improving such outcomes as well as impacting personnel workload. This is a review of current experimental evidence on the effectiveness of automated regulation of inspired oxygen and its effects on oxygenation variability and personnel workload during the care of premature infants.
The Optimal Search for a Moving Target When the Search Path Is Constrained

A search is conducted for a target moving in discrete time among a finite number of cells according to a known Markov process. The searcher must choose one cell in which to search in each time period. The set of cells available for search depends upon the cell chosen in the last time period. The problem is to find a searcher path, i.e., a sequence of search cells, that maximizes the probability of detecting the target in a fixed number of time periods. We formulate the problem as a partially observable Markov decision process and present a finite time horizon POMDP solution technique which is simpler than the standard linear programming methods.
Primary Cell Cultures in the Study of Human Muscle Metabolism

Skeletal muscle plays an important role in whole-body metabolism. Some research has used cell cultures raised from human biopsy tissue to study mechanisms that regulate skeletal muscle metabolism. The purpose of the current paper is to provide evidence indicating the efficacy of primary human skeletal muscle cell cultures as a tool to study substrate regulation and control in human tissue.
Does Seasonal Decline in Breeding Performance Differ for an African Raptor across an Urbanization Gradient?

As human populations have increased globally, so too has the transformation of natural landscapes into more urban areas. Within Africa, population growth rates and urbanisation rates are amongst the highest in the world, but the impacts of these processes on Africa’s wildlife are largely un-explored. In this study, we focus on a recently established population of black sparrowhawks Accipiter melanoleucus in Cape Town, South Africa. Using long-term data (16 years), we investigate the relationship between the timing of breeding and breeding performance along an urban gradient. We found no evidence for a direct effect of urbanisation on either timing of breeding or breeding performance. However we did find some evidence for a differential seasonal decline in breeding performance dependent on the levels of urbanisation. Thus, higher productivity was found in more urbanised habitats earlier in the season, but toward the end of the breeding season, birds in less urbanised habitats performed better. Our study represents one of the first to examine avian productivity in relation to urbanisation in Africa, and also represents one of the first studies to suggest that seasonal declines in productivity may differ according to levels of urbanisation. These results have considerable implications for potential changes in phenology or productivity for the regions’ avifauna as African urbanisation continues.
PV impacts on dynamic voltage stability

In this paper we discuss the impact of PV on dynamic voltage stability. The power system becomes more vulnerable as we add PV and displace conventional generation, and consequently inertia and VAR support. While PV inverters have the capability to provide reactive power, the fact that most PVs are connected at lower voltage levels limits its usefulness. We use the Dominion Virginia Power's system with different PV scenarios to show how dynamic voltage stability of the system was significantly affected. The purpose of this paper is to increase the awareness to the dynamic voltage stability issues the in case of significant PVs connected to the system.
Vitamin D Deficiency in Elderly Women in Nursing Homes: Investigation with Consideration of Decreased Activation Function from the Kidneys

To determine the approximate percentage of women in nursing homes who have vitamin D deficiency and to investigate whether, in assessing vitamin D status in elderly women, there are problems with measuring only 25 hydroxy‐vitamin D3 (25(OH)D3) and whether decreased vitamin D activation as a result of poor renal function needs to be considered.
Factors influencing outcome of Vitis vinifera (grapes, raisins, currants and sultanas) intoxication in dogs

INGESTION of the fruits of Vitis vinifera (grapes, raisins, currants and sultanas) causes acute renal failure in dogs. The mechanism of toxicity is currently unknown, although hypotheses include tannin intolerance in dogs ([Singleton 2001][1]), the contamination of the fruits with mycotoxins,
THE FORMATION OF SPHEROIDS IN EARLY-TYPE SPIRALS: CLUES FROM THEIR GLOBULAR CLUSTERS

We use deep Hubble Space Telescope images taken with the Advanced Camera for Surveys (ACS) in the F475W and F814W filters to investigate the globular cluster (GC) systems in four edge-on Sa spiral galaxies covering a factor of four in luminosity. The specific frequencies of the blue GCs in the galaxies in our sample fall in the range 0.34–0.84, similar to typical values found for later-type spirals. The number of red GCs associated with the bulges generally increases with the bulge luminosity, similar to what is observed for elliptical galaxies, although the specific frequency of bulge clusters is a factor of 2–3 lower for the lowest luminosity bulges than for the higher-luminosity bulges. We present a new empirical relation between the fraction of red GCs and total bulge luminosity based on the elliptical galaxies studied by ACSVCS (ACS Virgo Cluster Survey) and discuss how this diagram can be used to assess the importance of dissipative processes in building spiral bulges. Our results suggest a picture where dissipative processes, which are expected during gas-rich major mergers, were more important for building luminous bulges of Sa galaxies, whereas secular evolution may have played a larger role in building lower-luminosity bulges in spirals.
Gravity invasion percolation in two dimensions: Experiment and simulation.

We present experiments and computer simulations of slow drainage in a two-dimensional porous medium. The effect of gravity is systematically varied by tilting the system from the horizontal position. The width σ of the front between the fluids is found to scale with the dimensionless Bond number Bo (ratio between gravitational and capillary forces) as σ∼Bo -0.57 , as predicted by theory. The external perimeter of the invaded structure is shown to be fractal with the fractal dimension D e ≃1.34 for length scales smaller than the front width
PROLIFERATIVE EFFECTS OF CXC CHEMOKINES IN RAT HEPATOCYTES IN VITRO AND IN VIVO

ABSTRACT The CXC chemokines have well-documented neutrophil chemotactic, angiogenic, and mitogenic properties. The current investigations evaluate the effects of interleukin-8 (IL-8), epithelial neutrophil activating protein (ENA-78), and macrophage inflammatory peptide-2 (MIP-2) on hepatocyte proliferation in vitro and liver regeneration in vivo. Primary rat hepatocytes were isolated by collagenase digestion and exposed to incremental doses of IL-8, ENA-78, or MIP-2, and cellular proliferation was measured via tritiated thymidine incorporation. These experiments demonstrated significant increases in hepatocyte proliferation in response to IL-8, ENA-78, and MIP-2. Next, rats were sacrificed in a time-dependent manner following 70% hepatectomy or sham laparotomy, and hepatic tissue levels of MIP-2 and ENA-78 were measured using an ELISA. ENA-78 and MIP-2 were significantly elevated following 70% hepatectomy as compared with sham-operated control animals. Rats undergoing 70% hepatectomy were then treated with neutralizing anti-ENA-78 serum, anti-MIP-2 serum, or preimmune control serum, and liver regeneration was evaluated. These experiments demonstrated that neutralization of ENA-78 or MIP-2 slowed the rate of liver regeneration. These data suggest that the CXC chemokines may be important agents for the induction of hepatocyte proliferation and may be important molecules in vivo in the setting of liver injury, repair, and regeneration.
Hsc 70 Regulates Accumulation of Cyclin D 1 and Cyclin D 1-Dependent Protein Kinase

The Leonard and Madlyn Abramson Family Cancer Research Institute, Department of Cancer Biology, Abramson Cancer Center at the University of Pennsylvania, Philadelphia, Pennsylvania 19104; Department of Pharmacology and The Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska 68198; and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
A dynamic approach to detecting suspicious profiles on social platforms

The combined success of social networking sites and smartphones has changed the way people communicate. It is now possible to publish and track contents in real time at any time and from anywhere. The large number of users on social platforms constitutes an unprecedented opportunity for attack for malicious users. Social engineering techniques, spammers, phishing and malicious attacks are examples of threats that can lead to data loss, data theft, identity theft, etc. The detection of suspicious messages or profiles is mainly covered in the literature as a binary and static classification problem. In this paper, we propose a dynamic behavioral framework for identifying suspicious profiles on social networking sites. This approach is based on three indicators: balance, energy and anomaly, synthesized from daily activities of users. We demonstrate that sensing users regularly, even on few indicators, enables suspicious behaviour to be predicted with a high level of accuracy. The low calculation costs of the approach makes it embeddable into smartphones of social networking users for inferring trust scores to their contacts.
Analysis of PD-generated SF/sub 6/ decomposition gases adsorbed on carbon nanotubes

Chemical byproducts analysis has been recognized as a powerful diagnosis method for SF6 gas-insulated switchgear (GIS). The authors have previously demonstrated that a carbon nanotube (CNT) gas sensor could detect partial discharge (PD) generated in SF6 gas. However, PD-generated decomposition gas species, which were responsible for the CNT gas sensor response, have not been identified yet. In this paper, two kinds of experiments were conducted in order to identify the responsible decomposition gas species. At first, the decomposition gas molecules adsorbed on CNTs were analyzed by Fourier transformation infrared (FTIR) spectroscopy. FTIR absorbance was observed around 735 cm-1 after CNTs were exposed to PD generated in SF6. In the second experiment, the CNT gas sensor responses to typical SF6 decomposition products (HF and SF4) were examined. The CNT gas sensor responded to these gases in the same way as to PD generated in SF6. SF4 response was larger than HF response. Based on these results, SF 4 and SOF2 emerged as candidates for the responsible decomposition gases. Electrochemical interactions between adsorbed gas molecules and CNT were discussed based on theoretical predictions of molecular orbital calculations. The calculation results suggested that both of SOF2 and SF4 could increase the CNT gas sensor conductance
Filtered bank based implementation for filtered OFDM

OFDM suffers from high spectrum sidelobes and lacks the ability to support an important feature of 5G and future wireless communications: flexible numerology. To overcome these shortcomings, we consider in this paper filtered OFDM (F-OFDM) as a candidate solution, which is able to provide greater flexibility and adaptability than traditional CP-OFDM. We propose filters constructed by filter banks to transmit and receive F-OFDM signals with different waveform parameters. The proposed architecture enjoys excellent spectrum shaping performance, and efficient implementation.
Heterogeneity testing in meta‐analysis of genome searches

Genome searches for identifying susceptibility loci for the same complex disease often give inconclusive or inconsistent results. Genome Search Meta‐analysis (GSMA) is an established non‐parametric method to identify genetic regions that rank high on average in terms of linkage statistics (e.g., lod scores) across studies. Meta‐analysis typically aims not only to obtain average estimates, but also to quantify heterogeneity. However, heterogeneity testing between studies included in GSMA has not been developed yet. Heterogeneity may be produced by differences in study designs, study populations, and chance, and the extent of heterogeneity might influence the conclusions of a meta‐analysis. Here, we propose and explore metrics that indicate the extent of heterogeneity for specific loci in GSMA based on Monte Carlo permutation tests. We have also developed software that performs both the GSMA and the heterogeneity testing. To illustrate the concept, the proposed methodology was applied to published data from meta‐analyses of rheumatoid arthritis (4 scans) and schizophrenia (20 scans). In the first meta‐analysis, we identified 11 bins with statistically low heterogeneity and 8 with statistically high heterogeneity. The respective numbers were 9 and 6 for the schizophrenia meta‐analysis. For rheumatoid arthritis, bins 6.2 (the HLA region that is a well‐documented susceptibility locus for the disease) and 16.3 (16q12.2‐q23.1) had both high average ranks and low between‐study heterogeneity. For schizophrenia, this was seen for bin 3.2 (3p25.3‐p22.1) and heterogeneity was still significantly low after adjusting for its high average rank. Concordance was high between the proposed metrics and between weighted and unweighted analyses. Data from genome searches should be synthesized and interpreted considering both average ranks and heterogeneity between studies. Genet. Epidemiol. 28:123–137, 2005. © 2004 Wiley‐Liss, Inc.
Pattern for Python

Pattern is a package for Python 2.4+ with functionality for web mining (Google + Twitter + Wikipedia, web spider, HTML DOM parser), natural language processing (tagger/chunker, n-gram search, sentiment analysis, WordNet), machine learning (vector space model, k-means clustering, Naive Bayes + k-NN + SVM classifiers) and network analysis (graph centrality and visualization). It is well documented and bundled with 30+ examples and 350+ unit tests. The source code is licensed under BSD and available from http://www.clips. ua.ac. be/pages/pattern.