gebhart/patrepeval huggingface dataset:
Suppression of metastasis through inhibition of chitinase 3-like 1 expression by miR-125a-3p-mediated up-regulation of USF1 (2018)

<b>Rationale:</b> Chitinase 3-like 1 (Chi3L1) protein is up-regulated in various diseases including solid cancers. According to Genome-Wide Association Study (GWAS)/Online Mendelian Inheritance in Man (OMIM)/Differentially Expressed Gene (DEG) analyses, Chi3L1 is associated with 38 cancers, and more highly associated with cancer compared to other oncogenes such as EGFR, TNFα, etc. However, the mechanisms and pathways by which Chi3L1 is associated with cancer are not clear. In current study, we investigated the role of Chi3L1 in lung metastasis. <b>Methods:</b> We performed the differentially expressed gene analysis to explore the genes which are associated with Chi3L1 using the web-based platform from Biomart. We investigated the metastases in lung tissues of C57BL/6 mice injected with B16F10 melanoma following treatment with Ad-shChi3L1. We also investigated the expression of USF1 and Chi3L1 in Chi3L1 KD mice lung tissues by Western blotting and IHC. We also analyzed lung cancer cells metastases induced by Chi3L1 using migration and cell proliferation assay in human lung cancer cell lines. The involvement of miR-125a-3p in Chi3L1 regulation was determined by miRNA qPCR and luciferase reporter assay. <b>Results:</b> We showed that melanoma metastasis in lung tissues was significantly reduced in Chi3L1 knock-down mice, accompanied by down-regulation of MMP-9, MMP-13, VEGF, and PCNA in Chi3L1 knock-down mice lung tissue, as well as in human lung cancer cell lines. We also found that USF1 was conversely expressed against Chi3L1. USF1 was increased by knock-down of Chi3L1 in mice lung tissues, as well as in human lung cancer cell lines. In addition, knock-down of USF1 increased Chi3L1 levels in addition to augmenting metastasis cell migration and proliferation in mice model, as well as in human cancer cell lines. Moreover, in human lung tumor tissues, the expression of Chi3L1 was increased but USF1 was decreased in a stage-dependent manner. Finally, Chi3L1 expression was strongly regulated by the indirect translational suppressing activity of USF1 through induction of miR-125a-3p, a target of Chi3L1. <b>Conclusion:</b> Metastases in mice lung tissues and human lung cancer cell lines were decreased by KD of Chi3L1. USF1 bound to the Chi3L1 promoter, however, Chi3L1 expression was decreased by USF1, despite USF1 enhancing the transcriptional activity of Chi3L1. We found that USF1 induced miR-125a-3p levels which suppressed Chi3L1 expression. Ultimately, our results suggest that lung metastasis is suppressed by knock-down of Chi3L1 through miR-125a-3p-mediated up-regulation of USF1.
Treatment of depression with selective serotonin inhibitors: the role of fluvoxamine (2007)

The advent of the selective serotonin reuptake inhibitors (SSRIs) is generally considered to have improved the treatment of depression. Head-to-head trials comparing SSRIs to each other have shown little difference in efficacy among agents. The main differences between the SSRIs relate to safety and tolerability profiles, reflecting the fact that the SSRIs possess significant and variable secondary pharmacological properties. This heterogeneity contributes to clinically relevant differences that clinicians are increasingly using to select antidepressant treatment more closely appropriate to specific patient populations and circumstances. This review assesses the place of fluvoxamine amongst the SSRIs in the context of current issues and concerns with drug therapy. Fluvoxamine has a proven efficacy and safety profile in treating elderly patients with depression. The beneficial effects of fluvoxamine in obsessive-compulsive disorder (OCD) are also well documented. On the other hand, its σ1-receptor binding profile may account for the observed high level of efficacy in psychotic depression and may explain the benefit of fluvoxamine in treating depression comorbid with anxiety/stress. There is no definitive evidence that suicide risk is higher with SSRIs than with other antidepressants or nonpharmacological treatments and postmarketing surveillance indicates that fluvoxamine is not associated with a higher level of suicidality.
Personalized tag suggestion for flickr (2008)

We present a system for personalized tag suggestion for Flickr: While the user is entering/selecting new tags for a particular picture, the system is suggesting related tags to her, based on the tags that she or other people have used in the past along with (some of) the tags already entered. The suggested tags are dynamically updated with every additional tag entered/selected. We describe three algorithms which can be applied to this problem. In experiments, our best-performing method yields an improvement in precision of 10-15% over a baseline method very similar to the system currently used by Flickr. Our system is accessible at http://ltaa5.epfl.ch/flickr-tags/.To the best of our knowledge, this is the first study on tag suggestion in a setting where (i) no full text information is available, such as for blogs, (ii) no item has been tagged by more than one person, such as for social bookmarking sites, and (iii) suggestions are dynamically updated, requiring efficient yet effective algorithms.
Transistor-Level Static Timing Analysis by Piecewise Quadratic Waveform Matching (2003)

While fast timing analysis methods, such as asymptotic waveform evaluation (AWE), have been well established for linear circuits, the timing analysis for non-linear circuits, which are dominant in digital CMOS circuits, is usually, performed by a SPICE like, time domain integration based approach, involving expensive Newton Raphson iterations at numerous time steps. In this paper we propose a new technique that leads to the transient solution of charge/discharge paths with a complexity equivalent to only K DC operating point calculations, where K is the number of transistors along the path. This is accomplished by approximating each nodal voltage as a piecewise quadratic waveform, whose characteristics can be determined by matching the charge/discharge currents. Experiments on a wide range of circuits show that a 31.6 times speed-up over SPICE transient simulation with 10 ps step size can be achieved, while maintaining an average accuracy of 99%.
Electrical and Thermal Conduction in Atomic Layer Deposition Nanobridges Down to 7 nm Thickness (2012)

While the literature is rich with data for the electrical behavior of nanotransistors based on semiconductor nanowires and carbon nanotubes, few data are available for ultrascaled metal interconnects that will be demanded by these devices. Atomic layer deposition (ALD), which uses a sequence of self-limiting surface reactions to achieve high-quality nanolayers, provides an unique opportunity to study the limits of electrical and thermal conduction in metal interconnects. This work measures and interprets the electrical and thermal conductivities of free-standing platinum films of thickness 7.3, 9.8, and 12.1 nm in the temperature range from 50 to 320 K. Conductivity data for the 7.3 nm bridge are reduced by 77.8% (electrical) and 66.3% (thermal) compared to bulk values due to electron scattering at material and grain boundaries. The measurement results indicate that the contribution of phonon conduction is significant in the total thermal conductivity of the ALD films.
The Ubiquitin Peptidase UCHL1 Induces G0/G1 Cell Cycle Arrest and Apoptosis Through Stabilizing p53 and Is Frequently Silenced in Breast Cancer (2012)

UCHL1 exerts its tumor suppressive functions by inducing G0/G1cell cycle arrest and apoptosis in breast tumorigenesis, requiring its deubiquitinase activity. Its frequent silencing by promoter CpG methylation may serve as a potential tumor marker for breast cancer.
A Piezoelectric Immunosensor for the Detection of Cortisol (1995)

A piezoelectric crystal immunosensor has been developed for the detection and determination of cortisol. Cortisol antibody was layered onto the gold electrodes of a 10 MHz piezoelectric crystal which was pre-coated with either protein A or gluteraldehyde. Crystals pre-coated with protein A showed the best results with respect to stability and sensitivity. The sensor was successfully used for the determination of cortisol in standard solutions from 36-3628 micrograms/L (part per billion). The advantages of the proposed sensor include simplicity, short analysis time, cost effectiveness and selectivity. The results demonstrate the feasibility of cortisol assay in clinical testing and in drug monitoring.
Vascular Smooth Muscle Cell Apoptosis - a Dangerous Phenomenon in Vascular Disease? (2000)

Apoptosis (programmed cell death) of vascular smooth muscle cells (VSMCs) has been recognised recently in the vessel wall in disease states such as atherosclerosis and restenosis after angioplasty, and also in physiological arterial remodelling. Although apoptosis has been observed, the role and importance of VSMC apoptosis has not been determined. Although VSMC apoptosis is undoubtedly one mechanism employed for changing VSMC mass in vessel remodelling, VSMC apoptosis appears to be almost entirely a detrimental phenomenon in vascular disease.
HIV-1 Protease and Reverse Transcriptase Mutation Patterns Responsible for Discordances Between Genotypic Drug Resistance Interpretation Algorithms (2003)

Several rules-based algorithms have been developed to interpret results of HIV-1 genotypic resistance tests. To assess the concordance of these algorithms and to identify sequences causing interalgorithm discordances, we applied four publicly available algorithms to the sequences of isolates from 2,045 individuals in northern California. Drug resistance interpretations were classified as S for susceptible, I for intermediate, and R for resistant. Of 30,675 interpretations (2,045 sequences x 15 drugs), 4.4% were completely discordant, with at least one algorithm assigning an S and another an R; 29.2% were partially discordant, with at least one algorithm assigning an S and another an I, or at least one algorithm assigning an I and another an R; and 66.4% displayed complete concordance, with all four algorithms assigning the same interpretation. Discordances between nucleoside reverse transcriptase inhibitor interpretations usually resulted from several simple, frequently occurring mutational patterns. Discordances between protease inhibitor interpretations resulted from a larger number of more complex mutation patterns. Discordances between nonnucleoside reverse transcriptase inhibitor interpretations were uncommon and resulted from a small number of individual drug resistance mutations. Determining the clinical significance of these mutation patterns responsible for interalgorithm discordances will improve interalgorithm concordance and the accuracy of genotypic resistance interpretation.
Scheduling crude oil operations in refineries with genetic algorithm (2016)

With the hybrid characteristics of a refinery, it is very challenging to schedule crude oil operations. This work intends to solve this scheduling problem by decomposing it into two sub-problems hierarchically. At the upper level, a refining schedule is found, while a detailed schedule is obtained to realize it at the lower level. Given a refining schedule at the upper level, this work focuses on the detailed scheduling problem at the lower level. Based on a control-theoretic perspective, the problem is transferred to a problem of assigning charging tanks to distillers such that meta-heuristics can be applied. Then, a genetic algorithm (GA) approach is innovatively developed to solve it. An industrial case study is used to show the application of the proposed approach. It shows that the method works well and is applicable to real-life problems.
Dry Chemistry Reagent Systems (1984)

Dry Chemistry Reagent Systems Get access Alfred H. Free, Alfred H. Free Search for other works by this author on: Oxford Academic PubMed Google Scholar Helen M. Free Helen M. Free Search for other works by this author on: Oxford Academic PubMed Google Scholar Laboratory Medicine, Volume 15, Issue 9, 1 September 1984, Pages 595–601, https://doi.org/10.1093/labmed/15.9.595 Published: 01 September 1984
Framework for explicit drift correction in multivariate calibration models (2010)

Abstract Latent‐variable calibrations using principal component regression and partial least‐squares regression are often compromised by drift such as systematic disturbances and offsets. This paper presents a two‐step framework that facilitates the evaluation and comparison of explicit drift‐correction methods. In the first step, the drift subspace is estimated using different types of correction data in a master/slave setting. The correction data are measured for the slave with drift and computed for the master with no drift. In the second step, the original calibration data are corrected for the estimated drift subspace using shrinkage or orthogonal projection. The two cases of no correction and drift correction by orthogonal projection can be seen as special cases of shrinkage. The two‐step framework is illustrated with four different experimental data sets. The first three examples study drift correction on one instrument (temperature effects, spectral differences between samples obtained from different plants, instrumental drift), while the fourth example studies calibration transfer between two instruments. Copyright © 2010 John Wiley & Sons, Ltd.
A widespread amino acid polymorphism at codon 905 of the glycogen-associated regulatory subunit of protein phosphatase-1 is associated with insulin resistance and hypersecretion of insulin (1995)

The regulatory G-subunit of the glycogen-associated form of protein phosphatase 1 (PP1) plays a crucial part in muscle tissue glycogen synthesis and breakdown. As impaired insulin stimulated glycogen synthesis in peripheral tissues is considered to be a pathogenic factor in subsets of non-insulin-dependent diabetes mellitus (NIDDM) and obesity, the G-subunit of PP1 should be viewed as a candidate gene for inherited insulin resistance. When applying heteroduplex formation analysis and nucleotide sequencing of PP1G-subunit cDNA from 30 insulin resistant white NIDDM patients two cases were identified as heterozygous carriers of an Asp905 --> Tyr substitution. The carrier prevalence of the PP1G-subunit variant was 18% in 150 healthy subjects and 13% in 313 NIDDM subjects (chi 2 = 1.94, p = 0.16). Twenty-seven healthy subjects volunteered for a 4 h euglycaemic, hyperinsulinaemic clamp in combination with indirect calorimetry in order to elucidate the potential impact of the Tyr905 substitution on the whole body glucose metabolism. Interestingly, the Tyr905 variant was associated with altered routing of glucose: a decreased insulin stimulated non-oxidative glucose metabolism of peripheral tissues (glycogen synthesis) (p < 0.04) and an increased basal glucose oxidation rate (p < 0.04) when compared with wild type carriers. A population-based sample of 380 unrelated young healthy Caucasians was examined during a combined intravenous glucose and tolbutamide test to address whether the Asp905/Tyr905 polymorphism was associated with alterations in insulin secretion which might be secondary to the insulin resistance of skeletal muscle.(ABSTRACT TRUNCATED AT 250 WORDS)
Interactive shader development (2007)

Since the introduction of programmable graphics hardware, the creation of shader programs has played an increasingly important role in real-time graphics. Programming shaders is no trivial task, and this has led to the introduction of graphical shader editor tools. Using these tools, shaders are authored by connecting nodes and building a shade tree.
Characterization of the sequential non-covalent and covalent interactions of the antitumour antibiotic hedamycin with double stranded DNA by NMR spectroscopy (1999)

Hedamycin, a member of the pluramycin class of antitumour antibiotics, consists of a planar anthrapyrantrione chromophore to which is attached two aminosugar rings at one end and a bisepoxide-containing sidechain at the other end. Binding to double-stranded DNA is known to involve both reversible and non-reversible modes of interaction. As a part of studies directed towards elucidating the structural basis for the observed 5'-pyGT-3' sequence selectivity of hedamycin, we conducted one-dimensional NMR titration experiments at low temperature using the hexadeoxyribonucleotide duplexes d(CACGTG)(2) and d(CGTACG)(2). Spectral changes which occurred during these titrations are consistent with hedamycin initially forming a reversible complex in slow exchange on the NMR timescale and binding through intercalation of the chromophore. Monitoring of this reversible complex over a period of hours revealed a second type of spectral change which corresponds with formation of a non-reversible complex.
High doses of siRNAs induce <i>eri-1</i> and <i>adar-1</i> gene expression and reduce the efficiency of RNA interference in the mouse (2005)

RNAi (RNA interference) is a gene-silencing mechanism that is conserved in evolution from worm to human and has been a powerful tool for gene functional research. It has been clear that the RNAi effect triggered by endogenous or exogenous siRNAs (small interfering RNAs) is transient and dose-dependent. However, there is little information on the regulation of RNAi. Recently, some proteins that regulate the RNA-silencing machinery have been identified. We have observed in previous work that the expression of target genes rebounds after being suppressed for a period of time by siRNAs. In the present study, we used secretory hepatitis B virus surface antigen gene as a reporter and compared its expression level in cell culture and mice challenged by different doses of siRNAs. A quicker and higher rebound of gene expression was observed in mice tail-vein-injected with higher doses of siRNA, and the rebound was associated with an increase in the mRNA level of meri-1 (mouse enhanced RNAi) and adar-1 (adenosine deaminase acting on RNA) genes encoding an exonuclease and RNA-specific adenosine deaminase respectively. Down-regulation of meri-1 by RNAi enhanced the sensitivity and efficiency of siRNA in inhibiting the expression of hepatitis B virus surface antigen. These results indicate that RNAi machinery may be under negative regulation, through the induction of a series of genes coding for destabilizing enzymes, by siRNAs introduced into the cell, and also suggest that a suitable amount of siRNA should be used for research or therapeutic applications.
Photodiode performance and nanostructure of polythiophene/C<sub>60</sub> blends (1997)

Highly efficient photovoltaic devices , constructed using polythiophene derivatives blended with fullerenes, are described. The photovoltaic behavior of the sandwich‐structure devices (current‐voltage characteristic, conversion efficiency) is reported and the electrical, optical (optical absorption, photoluminescence), and morphological properties of the blends are presented. The importance of the morphology of the films is pointed out: it can determine the photovoltaic properties of the devices.
The essential OST2 gene encodes the 16-kD subunit of the yeast oligosaccharyltransferase, a highly conserved protein expressed in diverse eukaryotic organisms. (1995)

Oligosaccharyltransferase catalyzes the transfer of a preassembled high mannose oligosaccharide from a dolichol-oligosaccharide donor to consensus glycosylation acceptor sites in newly synthesized proteins in the lumen of the rough endoplasmic reticulum. The Saccharomyces cerevisiae oligosaccharyltransferase is an oligomeric complex composed of six non-identical subunits (alpha-zeta). The alpha, beta, gamma, and delta subunits of the oligosaccharyltransferase are encoded by the OST1, WBP1, OST3, and SWP1 genes, respectively. Here we describe the functional characterization of the OST2 gene that encodes the epsilon-subunit of the oligosaccharyltransferase. Genomic disruption of the OST2 locus was lethal in haploid yeast showing that expression of the Ost2 protein is essential for viability. Overexpression of the Ost2 protein suppresses the temperature-sensitive phenotype of the wbp1-2 allele and increases in vivo and in vitro oligosaccharyltransferase activity in a wbp1-2 strain. An analysis of a series of conditional ost2 mutants demonstrated that defects in the Ost2 protein cause pleiotropic underglycosylation of soluble and membrane-bound glycoproteins. Microsomal membranes isolated from ost2 mutant yeast show marked reductions in the in vitro transfer of high mannose oligosaccharide from exogenous lipid-linked oligosaccharide to a glycosylation site acceptor tripeptide. Surprisingly, the Ost2 protein was found to be 40% identical to the DAD1 protein (defender against apoptotic cell death), a highly conserved protein initially identified in vertebrate organisms. The protein sequence of ost2 mutant alleles revealed mutations at highly conserved residues in the Ost2p/DAD1 protein sequence.
Structural Studies of the Interaction between Ubiquitin Family Proteins and Proteasome Subunit S5a (2002)

The 26S proteasome is essential for the proteolysis of proteins that have been covalently modified by the attachment of polyubiquitinated chains. Although the 20S core particle performs the degradation, the 19S regulatory cap complex is responsible for recognition of polyubiquitinated substrates. We have focused on how the S5a component of the 19S complex interacts with different ubiquitin-like (ubl) modules, to advance our understanding of how polyubiquitinated proteins are targeted to the proteasome. To achieve this, we have determined the solution structure of the ubl domain of hPLIC-2 and obtained a structural model of hHR23a by using NMR spectroscopy and homology modeling. We have also compared the S5a binding properties of ubiquitin, SUMO-1, and the ubl domains of hPLIC-2 and hHR23a and have identified the residues on their respective S5a contact surfaces. We provide evidence that the S5a-binding surface on the ubl domain of hPLIC-2 is required for its interaction with the proteasome. This study provides structural insights into protein recognition by the proteasome, and illustrates how the protein surface of a commonly utilized fold has highly evolved for various biological roles.
Ovarian function following marrow transplantation for aplastic anemia or leukemia. (1988)

One hundred eighty-seven women between 13 and 49 years of age had ovarian function evaluated from 1 to 15 years (median, 4) after marrow transplant for aplastic anemia or leukemia. Among 43 women transplanted for aplastic anemia following 200 mg/kg cyclophosphamide (CY), all 27 less than 26 years of age, but only five of 16 greater than 26 years of age recovered normal ovarian function. Nine of the 43 have had 12 pregnancies, resulting in eight live births, and two elective and two spontaneous abortions. All eight children are normal. Nine of 144 women transplanted for leukemia following 120 mg/kg CY and 9.20 to 15.75 Gy total body irradiation (TBI) recovered ovarian function. Two of these nine have had three pregnancies, resulting in two spontaneous and one elective abortion. The probability of having ovarian failure was 0.35 by 7 years for patients receiving CY alone and was 1.00 at 1 year for patients receiving CY plus TBI (P less than .0001). By 7 years after transplant the probabilities of having normal ovarian function were 0.92 after CY alone and 0.24 after CY plus TBI (P less than .0001). Multivariate analysis showed that TBI was the only factor significantly influencing ovarian failure and that both TBI and greater patient age at transplant were significantly associated with a decreased probability of recovering normal ovarian function. These data demonstrate that after high-dose CY, recovery of ovarian function occurs in younger women and in a minority of older women, but after CY and TBI, recovery occurs in only a few younger women and none of the older women.