Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of LPS on transport of indocyanine green and alanine uptake in perfused rat liver.

Lipopolysaccharide (LPS) initiates cholestasis. Whether this process is mediated by tumor necrosis factor-α (TNF-α) and whether the cholestatic response to LPS is associated with intrahepatic accumulation of possibly toxic substances are under debate. To study these questions the hepatic uptake and biliary excretion of indocyanine green (ICG) was examined in the isolated perfused rat liver 18 h after intravenous treatment of rats with either saline, 1 mg/kg body wt LPS, or LPS and intraperitoneal pentoxifylline (POF) ( n = 6 in each group). POF inhibits TNF-α release after LPS administration. LPS induced a typical acute-phase response with increased mRNA for acute-phase proteins, reduced albumin mRNA, and increased hepatic uptake of alanine. Intrinsic hepatic clearance of ICG in controls (1.01 ± 0.05 ml ⋅ min-1 ⋅ g liver-1) was similarly decreased by LPS alone (0.62 ± 0.04 ml ⋅ min-1 ⋅ g-1; P = 0.002 vs. control) or combined with POF (0.66 ± 0.06 ml ⋅ min-1 ⋅ g-1). A kinetic analysis indicated that LPS reduced both uptake and excretion processes in a balanced manner, so that intrahepatic ICG content was unaffected or even slightly reduced, as confirmed by measurement of ICG contents in the perfused livers. In livers from parallel-treated nonperfused rats, mRNA for the organic anion transporting protein-1 (Oatp1, which is likely to mediate ICG uptake) was unaffected by LPS, whereas the concentration of Oatp1 protein was reduced. Thus LPS induced an acute-phase response that included downregulation of ICG uptake by reduction of Oatp1 protein concentration, possibly at a posttranscriptional level. TNF-α appears not to be the mediator because POF did not modify these LPS effects.
Multicenter evaluation of the phosphorylcholinecoated biodivYsio stent in short de novo coronary lesions: The SOPHOS study

AIMS: The BiodivYsio™ stent (Biocompatibles Ltd, Farnham, UK) is coated with a phosphorylcholine (PC)-containin copolymer to confer biocompatibility. The SOPHOS (Study Of PHosphorylcholine coating On Stents) study was designed to assess the safety and efficacy of this novel coronary stent and by indirect comparison to indicate equivalence with other formal stent studies. METHODS AND RESULTS: Patients with angina and a single short ( r 12 mm) de novo lesion in a native coronary artery of S 2.75 mm diameter were included. A total of 425 patients were allocated in 24 centers. Clinical data were collected at one-, six- and nine-month follow-up. Angiography was performed before and after the stent implantation. In addition, in the first 200 patients (SOPHOS A) angiography was routinely performed at six months. The following 225 patients (SOPHOS B) were merely followed up clinically. The primary end-point of the study, the six-month MACE-rate (MACE = Major Adverse Cardiac Events) was 13.4% (two cardiac death; five Q-wave/nine non-Qwave myocardial infarctions (MI); nine CABG and 32 target lesion revascularization (TLR), which is similar to the calculated 15% MACE-rate in comparable reference studies. Secondary end-points included among others restenosis at six months in the SOPHOS A population. The target vessel diameter was 2.98 - 0.48 mm. Minimal lumen diameter pre/post procedure and at follow-up was 1.00 - 0.32, 2.69 - 0.37, 1.91 - 0.71mm, respectively. The binary restenosis rate ( S 50% diameter stenosis at follow-up) was 17.7%. CONCLUSION: The coronary BiodivYsio stent is safe and effective as a primary device for the treatment of native coronary artery lesions in patients with stable or unstable angina pectoris. Clinical and angiographic results are in the statistical range of equivalence with comparable studies with other current stents. (Int J Cardiovasc Intervent 2000; 3: 215-225)
A Study of Dependency Features for Chinese Sentiment Classification

Syntactic dependency features, which encode long-range dependency relations and word order information, have been employed in sentiment classification. However, much of the research has been done in English, and researches conducted on exploring how features based on syntactic dependency relations can be utilized in Chinese sentiment classification are very rare. In this study, we present an empirical study of syntactic dependency features for Chinese sentiment classification. First, we consider two types of feature sets (word unigrams and word-dependency relations), three commonly-used feature weighting schemes (term presence, term frequency, and TF-IDF), and two well-known learning methods (Naive Bayes and SVM) to evaluate the performance of different classifiers. Then, we use ensemble technique to combine different types of features and classification algorithms. Specifically, two types of ensemble methods, namely average combination method and meta-learning combination method, are evaluated for two ensemble strategies. Through a wide range of comparative experiments conducted on two widely-used datasets in Chinese sentiment classification, finally, some in-depth discussion is presented and conclusions are drawn about the effectiveness of dependency features for Chinese sentiment classification.
Statistical significance and statistical power in hypothesis testing

Experimental design requires estimation of the sample size required to produce a meaningful conclusion. Often, experimental results are performed with sample sizes which are inappropriate to adequately support the conclusions made. In this paper, two factors which are involved in sample size estimation are detailed—namely type I (α) and type II (β) error. Type I error can be considered a “false positive” result while type II error can be considered a “false negative” result. Obviously, both types of error should be avoided. The choice of values for α and β is based on an investigator's understanding of the experimental system, not on arbitrary statistical rules. Examples relating to the choice of α and β are presented, along with a series of suggestions for use in experimental design.
Tolerability and efficacy of glycemic control with saxagliptin in older patients (aged ≥ 65 years) with inadequately controlled type 2 diabetes mellitus

Purpose To assess safety and efficacy of saxagliptin in older patients with type 2 diabetes mellitus (T2DM). Patients and methods This was a post hoc analysis of pooled data from older patients (≥65 years of age) from five 24-week phase III trials: three studies of saxagliptin versus placebo as an add-on therapy to metformin, glyburide, or a thiazolidinedione; and two studies of saxagliptin versus placebo as monotherapy in drug-naïve patients. Separate analyses were conducted on one study of initial combination therapy with saxagliptin plus metformin versus metformin monotherapy in drug-naïve patients. The safety analysis population for the five-study pool included 428 patients ≥ 65 years of age with baseline glycated hemoglobin (HbA1c) 7.0% to 10.5% who received saxagliptin 2.5 or 5 mg or placebo, and for the study of initial combination therapy included 69 patients ≥ 65 years of age with baseline HbA1c 8.0% to 12.0% who received saxagliptin 5 mg in combination with metformin or metformin monotherapy. The primary efficacy endpoint was change from baseline HbA1c. Results In the five-study pool, the differences in the adjusted mean change from baseline HbA1c among older patients receiving saxagliptin versus placebo were −0.60% (95% confidence interval [CI], −0.99% to −0.21%) for saxagliptin 2.5 mg and −0.55% (−0.97% to −0.14%) for saxagliptin 5 mg; in the initial combination study, the difference was −1.22% (−2.27% to −0.17%) among older patients receiving saxagliptin 5 mg plus metformin versus metformin monotherapy. The results were generally similar in older and younger patients. Saxagliptin was well tolerated; the incidence and types of adverse events were similar for saxagliptin and comparators. Hypoglycemia was reported in 3.0% to 9.4% of patients receiving saxagliptin (0%–8.0% for comparators) and was confirmed (finger stick glucose ≤ 50 mg/dL, with associated symptoms) in 0% to 0.7% (0%–0.7% for comparators); hypoglycemic episodes did not vary by age category and did not require medical intervention. Conclusion Saxagliptin was effective and well tolerated, with a low risk of hypoglycemia, when used as monotherapy, add-on therapy, or initial combination therapy with metformin in older patients with T2DM.
Congenital scrotal agenesis: description of a rare anomaly and management strategies.

Anomalies of the scrotum are uncommon. The most frequent malformations include bifid scrotum, scrotal ectopia and penile scrotal transposition. Congenital scrotal agenesis (CSA) is an extremely rare phenomenon, with only 3 cases reported in the worldwide literature. We report a case of CSA in an infant and review the current literature to identify possible congenital associations, diagnostic approaches and surgical reconstructive options. A MEDLINE search was performed for the period January 1965 to December 2003 using the National Center for Biotechnology Information PubMed Internet site.
Histopathologic characterization of human breast cancer in correlation with estrogen receptor status. A comparison of immunocytochemical and biochemical analysis

A detailed histopathologic analysis of 399 primary breast carcinomas was performed, and several morphologic features were correlated with the estrogen receptor (ER) status. In all cases ER status was determined immunocytochemically by estrogen receptor immunocytochemical assay (ER‐ICA). In 359 carcinomas ER status was also biochemically determined. Invasive lobular, mucoid, and tubular carcinomas rather than ductal carcinomas were ER‐positive more frequently in ER‐ICA. Medullary and papillary carcinomas had corresponding lower or higher ER positivity, respectively, by both methods. The correlation of histologic grade and its single factors with ER status was statistically significant by both methods. Lymphocytic reaction to tumor showed a significant inverse relationship to ER status by both methods. A statistically significant higher number of ER‐positive carcinomas in ER‐ICA and dextran‐coated charcoal assay (DCC) occurred when elastic tissue was present. Different associations were found between stromal content, tumor diameter, and ER status in DCC and ER‐ICA, respectively.
Modeling Inhibitory Interneurons in Efficient Sensory Coding Models

There is still much unknown regarding the computational role of inhibitory cells in the sensory cortex. While modeling studies could potentially shed light on the critical role played by inhibition in cortical computation, there is a gap between the simplicity of many models of sensory coding and the biological complexity of the inhibitory subpopulation. In particular, many models do not respect that inhibition must be implemented in a separate subpopulation, with those inhibitory interneurons having a diversity of tuning properties and characteristic E/I cell ratios. In this study we demonstrate a computational framework for implementing inhibition in dynamical systems models that better respects these biophysical observations about inhibitory interneurons. The main approach leverages recent work related to decomposing matrices into low-rank and sparse components via convex optimization, and explicitly exploits the fact that models and input statistics often have low-dimensional structure that can be exploited for efficient implementations. While this approach is applicable to a wide range of sensory coding models (including a family of models based on Bayesian inference in a linear generative model), for concreteness we demonstrate the approach on a network implementing sparse coding. We show that the resulting implementation stays faithful to the original coding goals while using inhibitory interneurons that are much more biophysically plausible.
Seventy Million Years of Concerted Evolution of a Homoeologous Chromosome Pair, in Parallel, in Major Poaceae Lineages[W]

This work analyzes an ancient duplicated chromosome pair from grasses that has experienced very different evolution from all other such paleo-duplicated chromosome pairs. It finds chromosome structural stratification, enrichment of autoimmune response–related genes, and accelerated DNA rearrangement and gene loss that are reminiscent of the sex chromosomes of other taxa. Whole genome duplication ~70 million years ago provided raw material for Poaceae (grass) diversification. Comparison of rice (Oryza sativa), sorghum (Sorghum bicolor), maize (Zea mays), and Brachypodium distachyon genomes revealed that one paleo-duplicated chromosome pair has experienced very different evolution than all the others. For tens of millions of years, the two chromosomes have experienced illegitimate recombination that has been temporally restricted in a stepwise manner, producing structural stratification in the chromosomes. These strata formed independently in different grass lineages, with their similarities (low sequence divergence between paleo-duplicated genes) preserved in parallel for millions of years since the divergence of these lineages. The pericentromeric region of this homeologous chromosome pair accounts for two-thirds of the gene content differences between the modern chromosomes. Both intriguing and perplexing is a distal chromosomal region with the greatest DNA similarity between surviving duplicated genes but also with the highest concentration of lineage-specific gene pairs found anywhere in these genomes and with a significantly elevated gene evolutionary rate. Intragenomic similarity near this chromosomal terminus may be important in hom(e)ologous chromosome pairing. Chromosome structural stratification, together with enrichment of autoimmune response–related (nucleotide binding site–leucine-rich repeat) genes and accelerated DNA rearrangement and gene loss, confer a striking resemblance of this grass chromosome pair to the sex chromosomes of other taxa.
Detection of Plagiarism in University Projects Using Metrics-based Spectral Similarity

An original method of spectral similarity analysis for plagia- rism detection in university project is presented. The approach is based on a clone detection tool called CLAN that performs metrics based sim- ilarity analysis of source code fragments. Denitions and algorithms for spectral similarity analysis are presented and discussed. Experiments performed on university projects are presented. Experimental results include the distribution of similarity in C and C++ projects. Analy- sis of spectral similarity distribution identies the most similar pairs of projects that can be considered as candidates for plagiarism.
Transcriptomic and Proteomic Responses of Sweetpotato Whitefly, Bemisia tabaci, to Thiamethoxam

Background The sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), is one of the most widely distributed agricultural pests. Although it has developed resistance to many registered insecticides including the neonicotinoid insecticide thiamethoxam, the mechanisms that regulate the resistance are poorly understood. To understand the molecular basis of thiamethoxam resistance, “omics” analyses were carried out to examine differences between resistant and susceptible B. tabaci at both transcriptional and translational levels. Results A total of 1,338 mRNAs and 52 proteins were differentially expressed between resistant and susceptible B. tabaci. Among them, 11 transcripts had concurrent transcription and translation profiles. KEGG analysis mapped 318 and 35 differentially expressed genes and proteins, respectively, to 160 and 59 pathways (p<0.05). Thiamethoxam treatment activated metabolic pathways (e.g., drug metabolism), in which 118 transcripts were putatively linked to insecticide resistance, including up-regulated glutathione-S-transferase, UDP glucuronosyltransferase, glucosyl/glucuronosyl transferase, and cytochrome P450. Gene Ontology analysis placed these genes and proteins into protein complex, metabolic process, cellular process, signaling, and response to stimulus categories. Quantitative real-time PCR analysis validated “omics” response, and suggested a highly overexpressed P450, CYP6CX1, as a candidate molecular basis for the mechanistic study of thiamethoxam resistance in whiteflies. Finally, enzymatic activity assays showed elevated detoxification activities in the resistant B. tabaci. Conclusions This study demonstrates the applicability of high-throughput omics tools for identifying molecular candidates related to thiamethoxam resistance in an agricultural important insect pest. In addition, transcriptomic and proteomic analyses provide a solid foundation for future functional investigations into the complex molecular mechanisms governing the neonicotinoid resistance in whiteflies.
Visceral obesity and plasma glucose-insulin homeostasis: contributions of interleukin-6 and tumor necrosis factor-alpha in men.

OBJECTIVE This study examined the relationships of two inflammatory cytokines, IL-6 and TNF-alpha, to visceral adiposity and indices of plasma glucose-insulin homeostasis. RESEARCH DESIGN AND METHODS Plasma levels of IL-6 and TNF-alpha were measured in 189 untreated asymptomatic men (aged 43.7 +/- 7.8 yr; body mass index 29.0 +/- 4.3 kg/m(2); waist girth 98.6 +/- 10.3 cm). RESULTS Significant and positive associations were found between both cytokines with adiposity and adipose tissue distribution indices (0.15 < or = r < 0.32; P < 0.05) as well as plasma glucose-insulin homeostasis variables (0.22 < or = r < 0.28; P <0.05). Comparison of two subgroups, each composed of 32 overweight men (> or =25 kg/m(2)) with similar body mass index values (28.7 kg/m(2) in both groups) but with markedly different levels of visceral adipose tissue (< vs. > or = 130 cm(2)), revealed significant differences only for IL-6 levels (1.42 +/- 1.15 vs. 0.86 +/- 0.52 pg/ml; P < 0.02 for men with high vs. low visceral adipose tissue, respectively). Finally, when subjects were stratified on the basis of their respective concentrations of IL-6 and TNF-alpha (using the 50th percentile of their overall distribution), an ANOVA revealed an independent contribution of IL-6 to the variation of fasting insulin (P < 0.01) and each of these two cytokines to the variation of insulin levels measured after a 75-g oral glucose challenge (P <0.01 for IL-6 and P < 0.05 for TNF-alpha). CONCLUSIONS Because IL-6 appeared to be clearly associated with visceral adiposity, TNF-alpha rather showed associations with indices of total body fatness. Thus, TNF-alpha may contribute to the insulin resistance of overall obesity, whereas IL-6 may be one of the mediators of the hyperinsulinemic state specifically related to excess visceral adiposity.
On coefficients of powers of polynomials and their compositions over finite fields

For any given polynomial $f$ over the finite field $\mathbb{F}_q$ with degree at most $q-1$, we associate it with a $q\times q$ matrix $A(f)=(a_{ik})$ consisting of coefficients of its powers $(f(x))^k=\sum_{i=0}^{q-1}a_{ik} x^i$ modulo $x^q -x$ for $k=0,1,\ldots,q-1$. This matrix has some interesting properties such as $A(g\circ f)=A(f)A(g)$ where $(g\circ f)(x) = g(f(x))$ is the composition of the polynomial $g$ with the polynomial $f$. In particular, $A(f^{(k)})=(A(f))^k$ for any $k$-th composition $f^{(k)}$ of $f$ with $k \geq 0$. As a consequence, we prove that the rank of $A(f)$ gives the cardinality of the value set of $f$. Moreover, if $f$ is a permutation polynomial then the matrix associated with its inverse $A(f^{(-1)})=A(f)^{-1}=PA(f)P$ where $P$ is an antidiagonal permutation matrix. As an application, we study the period of a nonlinear congruential pseduorandom sequence $\bar{a} = \{a_0, a_1, a_2, . \}$ generated by $a_n = f^{(n)}(a_0)$ with initial value $a_0$, in terms of the order of the associated matrix. Finally we show that $A(f)$ is diagonalizable in some extension field of $\mathbb{F}_q$ when $f$ is a permutation polynomial over $\mathbb{F}_q$.
Upregulation of Cystathionine-β-Synthase in Colonic Epithelia Reprograms Metabolism and Promotes Carcinogenesis.

The trans-sulfuration enzyme cystathionine-β-synthase (CBS) and its product hydrogen sulfide (H2S) are aberrantly upregulated in colorectal cancers, where they contribute to tumor growth and progression by both autocrine and paracrine mechanisms. However, it is unknown whether the CBS/H2S axis plays a role in colorectal carcinogenesis. Here, we report upregulation of CBS in human biopsies of precancerous adenomatous polyps and show that forced upregulation of CBS in an adenoma-like colonic epithelial cell line is sufficient to induce metabolic and gene expression profiles characteristic of colorectal cancer cells. Differentially expressed metabolites (65 increased and 20 decreased) clustered into the glycolytic pathway, nucleotide sugars, intermediates of the pentose phosphate pathway, and lipogenesis, including primarily phospholipids, sphingolipids, and bile acids. CBS upregulation induced broad changes in the NCM356 cell transcriptome with over 350 differentially expressed genes. These genes overlapped significantly with gene sets related to glycolysis, hypoxia, and a colon cancer cell phenotype, including genes regulated by NF-κB, KRAS, p53, and Wnt signaling, genes downregulated after E-cadherin knockdown, and genes related to increased extracellular matrix, cell adhesion, and epithelial-to-mesenchymal transition. The CBS-induced switch to an anabolic metabolism was associated with increased NCM356 cell bioenergetics, proliferation, invasion through Matrigel, resistance to anoikis, and CBS-dependent tumorigenesis in immunocompromised mice. Genetic ablation of CBS in CBS heterozygous mice (CBS+/- ) reduced the number of mutagen-induced aberrant colonic crypt foci. Taken together, these results establish that activation of the CBS/H2S axis promotes colon carcinogenesis. Cancer Res; 77(21); 5741-54. ©2017 AACR.
Repeat 1 of TAL effectors affects target specificity for the base at position zero

AvrBs3, the founding member of the Xanthomonas transcription-activator-like effectors (TALEs), is translocated into the plant cell where it localizes to the nucleus and acts as transcription factor. The DNA-binding domain of AvrBs3 consists of 17.5 nearly-identical 34 amino acid-repeats. Each repeat specifies binding to one base in the target DNA via amino acid residues 12 and 13 termed repeat variable diresidue (RVD). Natural target sequences of TALEs are generally preceded by a thymine (T0), which is coordinated by a tryptophan residue (W232) in a degenerated repeat upstream of the canonical repeats. To investigate the necessity of T0 and the conserved tryptophan for AvrBs3-mediated gene activation we tested TALE mutant derivatives on target sequences preceded by all possible four bases. In addition, we performed domain swaps with TalC from a rice pathogenic Xanthomonas because TalC lacks the tryptophan residue, and the TalC target sequence is preceded by cytosine. We show that T0 works best and that T0 specificity depends on the repeat number and overall RVD-composition. T0 and W232 appear to be particularly important if the RVD of the first repeat is HD (‘rep1 effect’). Our findings provide novel insights into the mechanism of T0 recognition by TALE proteins and are important for TALE-based biotechnological applications.