Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening for genes up-regulated in 5/6 nephrectomized mouse kidney.

BACKGROUND In diabetic and nondiabetic renal diseases, glomerular hyperfiltration is believed to play a central role in the subsequent progression of glomerulosclerosis and interstitial renal scarring. To identify genes involved in the process of hyperfiltration and hypertrophy, a polymerase chain reaction (PCR)-based subtraction method, that is, representational difference analysis of cDNA (cDNA-RDA), was employed. METHODS Ten-week-old ICR mice were 5/6 nephrectomized and sham operated. After two weeks, mRNAs were isolated from control and remnant kidneys and were subjected to the cDNA-RDA procedure. RESULTS We identified 10 known and 9 novel genes. Among 19 clones, 12 clones (8 known and 4 novel) showed 1.5- to 6-fold up-regulation by Northern blot analyses. The remaining seven clones were rarely expressed genes and were barely detected by Northern blot analyses, and their up-regulated expression was confirmed by Southern blot analysis using the PCR-amplified representative amplicons. The known genes included kidney androgen-regulated protein, major urinary protein, lysozyme M, metalloproteinase-3 tissue inhibitor, chaperonin 10, cytochrome oxidase I, epsilon-sarcoglycan, ribosomal protein S3a, G-proteingamma10 subunit, and splicing factor 9G8. All of the isolated known genes have not been reported to be up-regulated in the nephrectomized mouse kidney and suggest the possible role of androgen action, mitochondrial functions, matrix metabolism, cell-matrix interactions, and intracellular signaling events in the initiation of the progressive renal injury of the remnant kidney. Furthermore, cDNA-RDA facilitates the discovery of novel genes, including two kidney-specific genes. CONCLUSIONS The isolated known and novel genes may be involved in the pathobiological process of initial hyperfiltration and hypertrophy of remnant kidney.
Induction of Steatohepatitis (NASH) with Insulin Resistance in Wild-type B6 Mice by a Western-type Diet Containing Soybean Oil and Cholesterol

Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are hepatic manifestations of the metabolic syndrome. Many currently used animal models of NAFLD/NASH lack clinical features of either NASH or metabolic syndrome such as hepatic inflammation and fibrosis (e.g., high-fat diets) or overweight and insulin resistance (e.g., methionine-choline-deficient diets), or they are based on monogenetic defects (e.g., ob/ob mice). In the current study, a Western-type diet containing soybean oil with high n-6-PUFA and 0.75% cholesterol (SOD + Cho) induced steatosis, inflammation and fibrosis accompanied by hepatic lipid peroxidation and oxidative stress in livers of C57BL/6-mice, which in addition showed increased weight gain and insulin resistance, thus displaying a phenotype closely resembling all clinical features of NASH in patients with metabolic syndrome. In striking contrast, a soybean oil-containing Western-type diet without cholesterol (SOD) induced only mild steatosis but not hepatic inflammation, fibrosis, weight gain or insulin resistance. Another high-fat diet, mainly consisting of lard and supplemented with fructose in drinking water (LAD + Fru), resulted in more prominent weight gain, insulin resistance and hepatic steatosis than SOD + Cho, but livers were devoid of inflammation and fibrosis. Although both LAD + Fru- and SOD + Cho-fed animals had high plasma cholesterol, liver cholesterol was elevated only in SOD + Cho animals. Cholesterol induced expression of chemotactic and inflammatory cytokines in cultured Kupffer cells and rendered hepatocytes more susceptible to apoptosis. In summary, dietary cholesterol in the SOD + Cho diet may trigger hepatic inflammation and fibrosis. SOD + Cho-fed animals may be a useful disease model displaying many clinical features of patients with the metabolic syndrome and NASH.
The influence of complexing agents on the solubility and absorption of aluminium in rats exposed to aluminium in water

The influence of citrate (0–31mm), fluoride (0 or 2.6mM) and silicate (0 or 2.6mM) on the absorption of Al (0–18mM) was studied in rats. We tested the hypothesis that the solubility and absorption of Al increases in the gastrointestinal (GI) tract in the presence of the complexing agents. Male rats were exposed for 6 or 7 weeks to soluble Al in acidic drinking water (pH 2.5–3.0) with or without the complexing agents. At the end of exposure Al was fractionated in the stomach content, in order to study if the solubility of Al was changed after ingestion. Al absorption was estimated by Al analysis of the right femur bone. Speciation calculations indicated that citrate and fluoride caused formation of soluble Al-citrate (97%) and -fluoride (>60%) complexes in the water. Silicate did not affect the theoretical speciation. In all cases, a large fraction of soluble Al became insoluble in the stomach after ingestion. The concentration of soluble Al increased only in the presence of citrate or a mixture of fluoride and silicate, but citrate was the only complexing agent that influenced the absorption of Al in the rat. This indicates that the form of Al may be changed in the GI tract when soluble drinking-water Al is ingested, and that the solubility of Al in drinking water and GI tract may not be good predictors of the bioavailability of Al even when chelating agents are present.
Self-Healing for Self-Organizing Cluster Sensor Networks

Self-healing approach enables sensor network configuration robust to node failures. Fault-tolerance of k-connected network can be achieved using threshold of critical transmission range and node density. A self-healing scheme for clusterhead failure in k-connected cluster sensor network is presented in this work. Clusterhead failure triggers re-clustering in existing clustering schemes for wireless sensor networks (WSN). Re-clustering being a global operation in sensor network, incurs high energy overhead in constrained battery powered WSN. An alternative framework for WSN is based on localized scheme, called 'clusterhead-clique', taken in this work for self-healing. The clusterhead-clique is nearest neighborhood of clusterhead within half transmission radius, results a localized scheme for clusterhead position transfer. The simulation of the protocol based on our approach self-healing achieves 35% energy-efficiency in reconfiguring clusterheads over the existing re-clustering scheme
Using adjusted relative risks to calculate attributable fractions.

Leveille et al.1 estimated population attributable fraction (PAF) values for arthritis attributable to obesity by using multivariate-adjusted relative risks and the body mass index distribution in the US population aged 40 through 74 years. It is important to adjust relative risk estimates for confounding factors such as age and gender that are associated with both arthritis and obesity. However, when relative risks are adjusted for confounding factors, it is also necessary to use properly adjusted estimators of attributable fraction to avoid bias. The PAF formula cited by Leveille et al. is appropriate only for use with relative risks that are unadjusted for confounding2; the use of adjusted relative risks in this formula is incorrect and could lead to bias.3–5 There are ways to produce attributable fraction estimates that are properly adjusted for confounding and effect modification.3,4 In addition, Leveille et al. used the method of Zhang and Yu6 to calculate a relative risk estimate from a multivariate-adjusted odds ratio. This method is not valid when the estimated odds ratio is adjusted for confounding factors.7 Leveille et al. compared risk estimates and PAF values over time from the series of National Health and Nutrition Examination Surveys (NHANES), but without confidence intervals or statistical tests. Methods for statistical inference using data from multiple cross-sectional surveys are available.8 A recent article provides a method of calculating standard errors for attributable fractions from surveys with complex sample designs such as that of the NHANES.9
Ridgelet transform with application in ground penetrating radar processing

Ridgelet is the new development of wavelet dealing with line singularities in signals. In goundpenetrating radar (GPR) signal, the direct wave is a strong noise which has line singularity. In time-space domain, the useful information in GPR signal is badly polluted by strong direct wave so that the underground targets can not be recognized correctly. Ridgelet overcomes the disadvantages of wavelets in dealing with high dimensions that it can effectively represent singularities along lines or hyperplanes. Concerning the characteristics of GPR signals, the ridgelet transform is employed to remove the background noise and separate the direct wave. The simulation results for real GPR signals demonstrate its effectiveness.
Menopausal cardiomyopathy: Does it really exist? A case–control deformation imaging study

We aimed to evaluate and compare the left ventricular (LV) functions of pre‐ and postmenopausal women at similar ages with none of the known cardiovascular risk factors, by both conventional and advanced echocardiographic methods such as 2‐D strain imaging via speckle tracking echocardiography.
Methodologic Considerations for Improving and Facilitating Human Milk Research

Over the past several decades, interest in using human milk as a biomonitoring matrix has increased. However, it is not always an easy matter for a new mother to provide a milk sample. In this article, guidance on facilitating collection of human milk is provided. This includes addressing the mother’s ease in expressing a milk sample, and engaging with many audiences to reduce the likelihood of negatively impacting the already low breastfeeding rates in the United States. In addition, this article covers concepts regarding long-term storage and integrity of human milk samples to maximize the utility of those samples, and proposed methods for improving public access to the full spectrum of human milk biomonitoring data, with context to understand the information presented. The environmental chemicals and chemical classes for which robust analytical methods exist are enumerated, and a process for prioritizing the development of analytical methods for additional environmental chemicals is described. We thank the following organizations for generously providing support for the Workshop: the American Chemistry Council; the Centers for Disease Control and Prevention (C13/CCU323635-01); the Department of Health and Human Services, Health Resources and Services Administration (HHSH240200415021P); Health Canada (H405-03-ExSD079/4500078209); 3M; Pennsylvania State University College of Medicine; the Research Foundation for Health and Environmental Effects; and the U.S. Environmental Protection Agency, Office of Children’s Health (CH-83213101-0). The opinions expressed in this article are those of the authors and do not necessarily reflect the views and/or policies of their affiliations.
Effects of recombinant bovine somatotrophin, insulin-like growth factor-I and insulin on bovine granulosa cell steroidogenesis in vitro.

Our previous studies have demonstrated that physiological concentrations of metabolic hormones, including recombinant bovine somatotrophin (BST), insulin-like growth factor-I (IGF-I) and insulin, can significantly stimulate the proliferation of bovine granulosa cells cultured under serum-free conditions. In this study we investigated the effects of these factors on bovine granulosa cell steroidogenesis using the same culture system. Bovine granulosa cells were obtained from antral follicles classified into three size classes: small, < 5 mm; medium-sized, 5-10 mm and large, > 10 mm in diameter. Whilst not affecting steroidogenesis by granulosa cells from small and medium-sized follicles, BST (10-1000 ng/ml) stimulated the secretion of both oestradiol and progesterone by granulosa cells from large follicles in a dose-dependent manner. Insulin (1-1000 ng/ml) and IGF-I (10-1000 ng/ml) stimulated the secretion of oestradiol and progesterone by granulosa cells from all three size categories of follicles in a dose-dependent manner. FSH (200 ng/ml) alone increased progesterone secretion by granulosa cells from all three size classes of follicles, but had no effect on oestradiol secretion by granulosa cells. Both IGF-I (200 ng/ml) and insulin (30 ng/ml) acted in synergy with FSH (200 ng/ml) to stimulate steroidogenesis by granulosa cells from all three size categories of follicles, but no such interaction was observed between BST (50 ng/ml) and FSH (200 ng/ml). In conclusion, BST, IGF-I and insulin significantly influence the steroidogenic activity of bovine granulosa cells cultured under serum-free conditions. (ABSTRACT TRUNCATED AT 250 WORDS)
Distributed Data Clustering via Opinion Dynamics

We provide a distributed method to partition a large set of data in clusters, characterized by small in-group and large out-group distances. We assume a wireless sensors network in which each sensor is given a large set of data and the objective is to provide a way to group the sensors in homogeneous clusters by information type. In previous literature, the desired number of clusters must be specified a priori by the user. In our approach, the clusters are constrained to have centroids with a distance at least ε between them and the number of desired clusters is not specified. Although traditional algorithms fail to solve the problem with this constraint, it can help obtain a better clustering. In this paper, a solution based on the Hegselmann-Krause opinion dynamics model is proposed to find an admissible, although suboptimal, solution. The Hegselmann-Krause model is a centralized algorithm; here we provide a distributed implementation, based on a combination of distributed consensus algorithms. A comparison with k-means algorithm concludes the paper.
Pramlintide: A Human Amylin Analogue Reduced Postprandial Plasma Glucose, Insulin, and C‐peptide Concentrations in Patients with Type 2 Diabetes

In order to determine the influence of a 5 h infusion of pramlintide compared to placebo on postprandial glucose, lactate, insulin, and C‐peptide concentrations in patients with Type 2 diabetes, a single‐blind, randomized, cross‐over study was conducted in 24 patients; 12 treated with exogenous insulin and 12 managed with diet and/or oral hypoglycaemic agents. One hour after initiation of infusion, patients consumed a Sustacal® test meal. The protocol was repeated on the following day with each patient receiving the alternate study medication. Pramlintide infusion in the insulin‐treated patients resulted in statistically significant reductions in mean glucose, insulin, C‐peptide, and lactate concentrations during the 4‐h period after the Sustacal® test meal. Pramlintide infusion also resulted in significant reductions of mean insulin, C‐peptide, and lactate concentrations, but not glucose concentrations, in the patients treated with diet and/or oral hypoglycaemic agents. Within this latter group, reduction in postprandial glucose concentrations in individual patients correlated with glycated haemoglobin values. These results suggest that administration of pramlintide may improve glycaemic control in patients with Type 2 diabetes treated with insulin or poorly controlled on diet and/or oral hypoglycaemic agents. © 1997 John Wiley & Sons, Ltd.
Hydrodynamic analysis of human swimming based on VOF method

Abstract A 3-D numerical model, based on the Navier-Strokes equations and the RNG k-ε turbulence closure, for studying hydrodynamic drag on a swimmer with wave-making resistance taken into account is established. The volume of fluid method is employed to capture the undulation of the free surface. The simulation strategy is evaluated by comparison of the computed results with experimental data. The computed results are in good agreement with data from mannequin towing experiments. The effects of the swimmer’s head position and gliding depth on the drag force at different velocities are then investigated. It is found that keeping the head aligned with the body is the optimal posture in streamlined gliding. Also wave-making resistance is significant within 0.3 m depth from the free surface.
Accurate prediction of interfacial residues in two‐domain proteins using evolutionary information: Implications for three‐dimensional modeling

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure–function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two‐domain proteins. We also use information from the three‐dimensional structures of individual domains of two‐domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain–domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain–domain interaction, rigid‐body docking was able to provide us with accurate full‐length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. Proteins 2014; 82:1219–1234. © 2013 Wiley Periodicals, Inc.
Ectopic corticospinal tract and corticothalamic tract neurons in the cerebral cortex of yotari and reeler mice

Reeler and yotari mice, which are mutant for Reelin or Dab1, respectively, show disorders of cerebral cortical lamination. We injected horseradish peroxidase (HRP) into the upper lumbar enlargement to label corticospinal tract (CST) neurons and wheat germ agglutinin‐conjugated HRP (WGA‐HRP) into the ventral lateral nucleus of the thalamus to label corticothalamic tract (CTT) neurons in both 19‐day‐old yotari and reeler mice with the aim of discovering whether or not they show differences in the distribution pattern of layer V or layer VI neurons. Similar injections of tracers were made in normal controls. HRP‐labeled CST neurons, which were exclusively distributed in layer V of the normal cortex, were radially scattered in the cortex of both mutants, but those in reeler were more deeply distributed than in yotari. WGA‐labeled CTT neurons, which were mainly located in layer VI in the normal cortex, were superficially distributed just beneath the pia mater in both reeler and yotari cortex. The present quantitative study shows that the distribution pattern of layer V neurons, but not layer VI neurons, differs between reeler and yotari mice, suggesting that the Reelin and Dab1 proteins may play different roles in the migration and cell positioning of layer V neurons. J. Comp. Neurol. 461:61–75, 2003. © 2003 Wiley‐Liss, Inc.
Polymorphonuclear leukocyte transverse migration induces rapid alterations in endothelial focal contacts

Transmigrated polymorphonuclear leukocytes (PMNs) usually undergo subendothelial transverse migration before penetrating into inner tissue layers. Whether or how endothelial cells (ECs) respond to the PMN migrating underneath them is unknown. A tissue flow chamber was used to establish a fMLP gradient and to observe PMN transverse migration along with its associated endothelial responses in culture (on a collagen gel) or in vascular tissues. Our results indicated that transversely migrating PMNs were in direct contact with the basal side of ECs. Contrasting to focal adhesion kinase (FAK) or proteins with phosphorylated tyrosine, paxillin disappeared rapidly (<1 min) from endothelial focal contacts afterencountering the leukocyte's leading edge and soon rejoined them after the PMN had left. In addition, FAK moved away or became dephosphorylated when PMNs remained at the same subendothelial location for longer than 10 min, leaving actin filaments apparently unaltered. Unlike PMN transendothelial migration, PMN transverse migration did not induce any detectable endothelial calcium signaling. Taken together, our findings indicated that PMN transverse migration interrupted endothelial‐matrix interactions and induced rapid alterations in endothelial focal contact composition.
Biodegradation of trichloroethylene and toluene by indigenous microbial populations in soil

The biodegradation of trichloroethylene (TCE) and toluene, incubated separately and in combination, by indigenous microbial populations was measured in three unsaturated soils incubated under aerobic conditions. Sorption and desorption of TCE (0.1 to 10 micrograms ml-1) and toluene (1.0 to 20 micrograms ml-1) were measured in two soils and followed a reversible linear isotherm. At a concentration of 1 micrograms ml-1, TCE was not degraded in the absence of toluene in any of the soils. In combination, both 1 microgram of TCE ml-1 and 20 micrograms of toluene ml-1 were degraded simultaneously after a lag period of approximately 60 to 80 h, and the period of degradation lasted from 70 to 90 h. Usually 60 to 75% of the initial 1 microgram of TCE ml-1 was degraded, whereas 100% of the toluene disappeared. A second addition of 20 micrograms of toluene ml-1 to a flask with residual TCE resulted in another 10 to 20% removal of the chemical. Initial rates of degradation of toluene and TCE were similar at 32, 25, and 18 degrees C; however, the lag period increased with decreasing temperature. There was little difference in degradation of toluene and TCE at soil moisture contents of 16, 25, and 30%, whereas there was no detectable degradation at 5 and 2.5% moisture. The addition of phenol, but not benzoate, stimulated the degradation of TCE in Rindge and Yolo silt loam soils, methanol and ethylene slightly stimulated TCE degradation in Rindge soil, glucose had no effect in either soil, and dissolved organic carbon extracted from soil strongly sorbed TCE but did not affect its rate of biodegradation.
MHPS-Driven Early Design and Analysis of VLSI CPU Chips

JVe present (1 noid appsoaclz to carry per/i,rinancc analysis arid tiiiiitig of VLSI processors, don(? in the context of higlt-lewl source Iceriicls. U7e illustrate our rnetliodology in 1Crt71.r of a small (exaniph? ) super scalas RlSC J ~ S O C ~ S S I ~ S architecture. A pnrantetrized execution 17ic~cIeI is used fhr piforinance eslimniion. IJsing an iterative optimization techniqire, the parameter set can bc locally optiinizcd around a g i i w design point to genesare tlie ininii? itrtn cycles per. iiwtrttction ( V I ) . W e also iiicludc a ctirsory discussion on linking . rirclt a CI’I estiiizntor io an early jloorplanner jhr A f IPS-driven block layout for the processor chb.