gebhart/patrepeval huggingface dataset:
A genotype calling algorithm for affymetrix SNP arrays (2005)

A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling genotypes on SNP arrays process all the features associated with one chip and one SNP at a time. Using a large training sample where the genotype labels are known, we develop a supervised learning algorithm to obtain more accurate classification results on new data. The method we propose, RLMM, is based on a robustly fitted, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variance is reduced through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as across thousands of SNPs for accurate classification. In this paper, we apply RLMM to Affymetrix 100 K SNP array data, present classification results and compare them with genotype calls obtained from the Affymetrix procedure DM, as well as to the publicly available genotype calls from the HapMap project.
Gold nanoparticle-doped biocompatible silk films as a path to implantable thermo-electrically wireless powering devices (2010)

In this paper, we report on gold nanoparticle (GNP) doped silk films as an implantable and degradable heating element activated by light, which can be potentially used for wireless powering of implanted microdevices. Proof-of-concept experiments have been conducted by casting a GNP doped silk film on a miniature thermal-power chip, which generates ∼20 mW when illuminated by a green laser with an output power of 450 mW/mm2 at 532 nm.
High resolution measurement of cerebral blood flow using intravascular tracer bolus passages. Part I: Mathematical approach and statistical analysis (1996)

The authors review the theoretical basis of determination of cerebral blood flow (CBF) using dynamic measurements of nondiffusible contrast agents, and demonstrate how parametric and nonparametric deconvolution techniques can be modified for the special requirements of CBF determination using dynamic MRI. Using Monte Carlo modeling, the use of simple, analytical residue models is shown to introduce large errors in flow estimates when actual, underlying vascular characteristics are not sufficiently described by the chosen function. The determination of the shape of the residue function on a regional basis is shown to be possible only at high signal-to-noise ratio. Comparison of several nonparametric deconvolution techniques showed that a nonparametric deconvolution technique (singular value decomposition) allows estimation of flow relatively independent of underlying vascular structure and volume even at low signal-to-noise ratio associated with pixel-by-pixel deconvolution.
Solvent polarity influences product selectivity of lipase‐mediated esterification reactions in microaqueous media (1996)

Abstract Esterification reactions were evaluated by using lipases from Rhizomucor miehei (Lipozyme IM20) and Pseudomonas cepacia (PS‐30) with equimolar levels (1.77 mmol) of undecanoic acid and glycerol or 1,3‐propanediol (1,3‐PD) or 1,2‐propanediol (1,2‐PD) in organic solvents of log P (partition coefficient between 1‐octanol/water) values of (−0.33–4.5. Reaction yields (percentage of esterified undercanoate) with glycerol ranged from 1.4 to 72%, with greatest yields observed in solvents of log P 4.0–4.5 for Lipozyme, whereas the PS‐30 lipase was similarly effective (27–38% yield) over the full range of solvent polarities. For both enzymes, as solvent apolarity increased, so did the extent of acylation of glycerol in the final product mixture. Reaction yields with 1,3‐PD ranged from 8.1 to 64% for Lipozyme and from 18 to 84% for PS‐30 lipase, with greatest yields observed for both enzymes in solvents of log P values in the range 1.2–5.0. For both lipases, the shift to greater solvent apolarity was accompanied by an increased molar ratio of diacylated‐1,3‐PD/monoacylated‐1,3‐PD in the product mixture. Reaction yields with 1,2‐PD ranged from 2.5 to 45% for Lipozyme and from 12 to 52% for PS‐30 lipase, with greatest yields observed in solvents of log P values in the ranges 1.4–1.9 and 1.4–4.5, respectively. The shift to greater solvent apolarity was accompanied by an increased molar ratio of diacylated‐1,2‐PD: monoacylated‐1,2‐PD in the product mixture, except for Lipozyme in the three most apolar solvents (log P of 3.5–4.5) in which there was a general attenuation of activity. These results suggest the existence of a solvent polarity influence on reaction product selectivity in multiproduct reactions, which can be partially explained on the basis of differential solvation and extraction properties of solvents.
Constitutive Expression of a 2′,5′-Oligoadenylate Synthetase cDNA Results in Increased Antiviral Activity and Growth Suppression (1989)

The interferon (IFN)-induced enzyme 2',5'-oligoadenylate (2-5A) synthetase has been implicated in the development of antiviral activity in human and animal cells. However, its role in IFN-mediated growth inhibition remains unclear. To elucidate the function of 2-5A synthetase, we have stably introduced a human 2-5A synthetase cDNA into a human glioblastoma cell line (T98G). Constitutive expression of the cDNA in these cells is associated with increased levels of resistance to infection by encephalomyocarditis virus. One transfected subclone, which expresses elevated levels of 2-5A synthetase enzyme activity, also shows a reduced rate of cellular proliferation.
A Tutorial on Automated Text Categorisation (2000)

The automated categorisation (or classification) of texts into topical categories has a long history, dating back at least to 1960. Until the late ’80s, the dominant approach to the problem involved knowledge-engineering automatic categorisers, i.e. manually building a set of rules encoding expert knowledge on how to classify documents. In the ’90s, with the booming production and availability of on-line documents, automated text categorisation has witnessed an increased and renewed interest. A newer paradigm based on machine learning has superseded the previous approach. Within this paradigm, a general inductive process automatically builds a classifier by “learning”, from a set of previously classified documents, the characteristics of one or more categories; the advantages are a very good effectiveness, a considerable savings in terms of expert manpower, and domain independence. In this tutorial we look at the main approaches that have been taken towards automatic text categorisation within the general machine learning paradigm. Issues of document indexing, classifier construction, and classifier evaluation, will be touched upon. 1 A definition of the text categorisation task
The effect of hypoxia on thallium kinetics in cultured chick myocardial cells. (1987)

To assess the effect of hypoxia on cellular thallium-201 (201Tl) uptake and washout independent of coronary flow, we studied thallium kinetics during normoxia and hypoxia in cultured chick ventricular cells. Monolayers of contracting ventricular cells grown on coverslips were placed in a chamber and perfused to asymptote with media containing 201Tl. Perfusates were equilibrated with 5% CO2-95% air or 5% CO2-95% nitrogen for normoxia and hypoxia, respectively. Washout thallium kinetics were then observed during perfusion with unlabeled media. Twenty paired experiments were performed, randomly alternating the sequence of normoxia and hypoxia. Pharmacokinetics for thallium were determined by computer using standard formulae. Thallium uptake and washout were best described by assuming that intracellular thallium was contained within a single compartment. Cellular thallium uptake, as well as transfer rate constants for thallium uptake and for thallium washout during normoxia and hypoxia, were compared using paired t-tests. During normoxia and hypoxia, respectively, thallium uptake was 22 +/- 7% and 19 +/- 7% of asymptote (p less than 0.01); the compartmental rate constant for uptake by the cell was 0.16 +/- 0.07 min-1 and 0.15 +/- 0.06 min-1 (N.S.); and the transfer rate constant for washout from the cell was 0.26 +/- 0.06 min-1 and 0.23 +/- 0.05 min-1 (p less than 0.01). We conclude that there was a small (14%) decrease in thallium uptake during hypoxia. The rate of thallium uptake and washout was slightly less during hypoxia, although only the rate of washout was significantly less. These data show that cellular accumulation of thallium and the rate of washout of thallium were minimally decreased by hypoxia independent of blood flow.
Phenazine Content in the Cystic Fibrosis Respiratory Tract Negatively Correlates with Lung Function and Microbial Complexity (2012)

Although much is known about how virulence factors affect pathogens and host tissues in vitro, far less is understood about their dynamics in vivo. As a step toward characterizing the chemistry of infected environments, we measured phenazine abundance in the lungs of patients with cystic fibrosis (CF). Phenazines are redox-active small molecules produced by Pseudomonas aeruginosa that damage host epithelia, curb the growth of competing organisms, and play physiologically important roles in the cells that produce them. Here, we quantify phenazines within expectorated sputum, characterize the P. aeruginosa populations responsible for phenazine production, and assess their relationship to CF lung microflora. Chemical analyses of expectorated sputum showed that the concentrations of two phenazines, namely, pyocyanin (PYO) and phenazine-1-carboxylic acid (PCA), were negatively correlated (ρ = -0.68 and -0.57, respectively) with lung function. Furthermore, the highest phenazine concentrations were found in patients whose pulmonary function showed the greatest rates of decline. The constituent P. aeruginosa populations within each patient showed diverse capacities for phenazine production. Early during infection, individual isolates produced more PYO than later during infection. However, total PYO concentrations in sputum at any given stage correlated well with the average production by the total P. aeruginosa population. Finally, bacterial community complexity was negatively correlated with phenazine concentrations and declines in lung function, suggesting a link to the refinement of the overall microbial population. Together, these data demonstrate that phenazines negatively correlate with CF disease states in ways that were previously unknown, and underscore the importance of defining in vivo environmental parameters to better predict clinical outcomes of infections.
Peroxiredoxin-6 protects against mitochondrial dysfunction and liver injury during ischemia-reperfusion in mice (2008)

Hepatic ischemia-reperfusion (I/R) injury is an important complication of liver surgery and transplantation. Mitochondrial function is central to this injury. To examine alterations in mitochondrial function during I/R, we assessed the mitochondrial proteome in C57Bl/6 mice. Proteomic analysis of liver mitochondria revealed 234 proteins with significantly altered expression after I/R. From these, 13 proteins with the greatest expression differences were identified. One of these proteins, peroxiredoxin-6 (Prdx6), has never before been described in mitochondria. In hepatocytes from sham-operated mice, Prdx6 expression was found exclusively in the cytoplasm. After ischemia or I/R, Prdx6 expression disappeared from the cytoplasm and appeared in the mitochondria, suggesting mitochondrial trafficking. To explore the functional role of Prdx6 in hepatic I/R injury, wild-type and Prdx6-knockout mice were subjected to I/R injury. Prdx6-knockout mice had significantly more hepatocellular injury compared with wild-type mice. Interestingly, the increased injury in Prdx6-knockout mice occurred despite reduced inflammation and was associated with increased mitochondrial generation of H(2)O(2) and dysfunction. The mitochondrial dysfunction appeared to be related to complex I of the electron transport chain. These data suggest that hepatocyte Prdx6 traffics to the mitochondria during I/R to limit mitochondrial dysfunction as a protective mechanism against hepatocellular injury.
Affinity and Kinetics of the Interaction between Soluble Trimeric OX40 Ligand, a Member of the Tumor Necrosis Factor Superfamily, and Its Receptor OX40 on Activated T Cells (1997)

OX40 ligand (OX40L) and OX40 are members of the tumor necrosis factor and tumor necrosis factor receptor superfamilies, respectively. OX40L is expressed on activated B and T cells and endothelial cell lines, whereas OX40 is expressed on activated T cells. A construct for mouse OX40L was expressed as a soluble protein with domains 3 and 4 of rat CD4 as a tag (sCD4-OX40L). It formed a homotrimer as assessed by chemical cross-linking and gel filtration chromatography. Radiolabeled sCD4-OX40L bound to activated mouse T cells with a high affinity (KD = 0.2-0.4 nM) and dissociated slowly (koff = 4 x 10(-5) s-1). The affinity and kinetics of the OX40L/OX40 interactions were studied using the BIAcoreTM biosensor, which measures macromolecular interactions in real time. The extracellular part of the OX40 antigen was expressed as a soluble monomeric protein and immobilized on the BIAcore sensor chip. sCD4-OX40L bound the OX40 with a high affinity (KD = 3.8 nM), although this was lower than that determined on the surface of activated T cells (KD = 0.2-0.4 nM), where there is likely to be less restriction in mobility of the receptor. In the reverse orientation, sOX40 bound to immobilized sCD4-OX40L with a stoichiometry of 3.1 receptors to one ligand, with low affinity (KD = 190 nM) and had a relatively fast dissociation rate constant (koff = 2 x 10(-2) s-1). Thus if the OX40 receptor is cleaved by proteolysis, it will release any bound ligand and is unlikely to block re-binding of ligand to cell surface OX40 because of the low monomeric affinity.
Progress in the Development of Melanocortin Receptor Selective Ligands (2004)

The melanocortin pathway consists of endogenous agonists, antagonists, G-protein coupled receptors (GPCRs), and auxiliary proteins. This pathway has been identified to participate physiologically in numerous biological pathways including energy homeostasis, pigmentation, sexual function, inflammation, cardiovascular function, adrenal function, sebaceous gland lipid production, just to list a few. During this past decade, a clear link between the melanocortin-4 receptor (MC4R) and obesity, in both mice and humans via the regulation of food intake and energy homeostasis, has made this pathway the target of many academic and industrial research endeavors in attempts to develop potent and selective MC4R small molecules as anti-obesity therapeutic agents. Herein, we attempt to summarize the known proteins that constitute the melanocortin system and discuss advances in peptide and non-peptide drug discovery.
Diastereocontrol by a Hydroxyl Auxiliary in the Synthesis of Pyrrolidines via Radical Cyclization (2002)

[reaction: see text] Organoselenium precursors of 3-aza-5-hexenyl radicals carrying a 1-hydroxyalkyl group in the 2-position were prepared by addition of organometallic reagents to N-allyl-2-aziridinecarbonitrile, reduction of the resulting aziridine ketone, and regioselective benzeneselenol ring opening of the aziridine. Reductive radical cyclization was highly selective, affording the corresponding trans-2,4-disubstituted pyrrolidine (cis/trans ca. 1/10) as the major diastereomer. Recrystallization afforded material that was substantially more enriched in the trans isomer (cis/trans < 1/25).
Regulation of prostate cancer immunity-related genes in PC3 prostate cancer cells by ETS-1 (2011)

Prostate cancer (PCa) is one of the most prevalent forms of cancer affecting males worldwide, and knowledge of the immune defenses involved in PCa remains incomplete. Since the identification of immunity-related genes may have enormous implications for the understanding of PCa immunology, we recently reported the identification of immunity-related genes in PCa tissues and found potential binding sites for the ETS family prototype, ETS-1, in the majority of genes identified. Therefore, as a continuation of our previous study, we investigated whether ETS-1 regulates these genes in an in vitro PCa cell line model, PC3 cells. We specifically blocked ETS-1 in PC3 cells by transfection with an ETS-1 inverse antisense expression vector or a mock control vector. We then assessed the effect of the blockade on the expression of the recently identified PCa immunity-related genes using a comprehensive oligo gene expression microarray analysis. The results showed that ETS-1 is involved in the activation or repression of the recently identified immunity‑related genes in PCa. These findings provide insights into the regulation of immunity-related genes in PCa, and emphasize the importance of ETS-1 in prostate cancer immunology.
Cellular promoters incorporated into the adenovirus genome: cell specificity of albumin and immunoglobulin expression. (1986)

Recombinant adenoviruses were constructed in which the viral E1A gene was deleted and the E1B promoter was replaced by the rat albumin, mouse beta-major globin, or mouse immunoglobulin heavy-chain promoter. After infection of human or rat hepatoma cells, E1B-containing mRNAs could be detected only from the virus containing the albumin promoter. Conversely, only the immunoglobulin promoter was active in virus-infected myeloma cells. However, in hepatoma cells transcription from the albumin promoter in the virus was much less than that of the endogenous cellular albumin gene or of other viral genes. In primary mouse hepatocytes endogenous albumin gene transcription was high immediately after plating but declined within 24 h. Expression of the albumin promoter in the virus paralleled that of the cellular albumin gene. From these results it appears that cell-specific expression of albumin depends on the presence of tissue-specific trans-acting factors, but the presence of such factors does not suffice for a maximal rate of transcription, a conclusion that requires direct comparison within a differentiated cell of a newly introduced and preexisting active cell gene.
Linux programmer's toolbox (2008)

０１ オープンソースツールのダウンロードとインストール ０２ ソースからのビルド ０３ ヘルプの検索 ０４ ソースファイルの編集と管理 ０５ カーネルについて開発者が知るべきこと ０６ プロセスを理解する ０７ プロセス間通信 ０８ シェルコマンドによるＩＰＣのデバッグ ０９ パフォーマンスの調整 １０ デバッギング
<title>Generic web-based teleoperations architecture: details and experience</title> (1999)

Teleoperation of remote devices on the World Wide Web is becoming more common and feasible. Prices on devices ranging from digital cameras to LEGO RCXs(tm) have dropped, making them available to a much wider audience. Increasing availability of remotely operable devices removes one barrier to ubiquitous telepresence, but leaves others intact. One of the remaining barriers is the need for a user to develop and deploy an end-to-end solution for device manipulation. The goal of our research is to reduce this barrier by making a flexible end-to-end solution accessible to a wide audience of potential Web device developers.
Autoactivation of Transforming Growth Factor β-activated Kinase 1 Is a Sequential Bimolecular Process (2010)

Transforming growth factor-beta-activated kinase 1 (TAK1), an MAP3K, is a key player in processing a multitude of inflammatory stimuli. TAK1 autoactivation involves the interplay with TAK1-binding proteins (TAB), e.g. TAB1 and TAB2, and phosphorylation of several activation segment residues. However, the TAK1 autoactivation is not yet fully understood on the molecular level due to the static nature of available x-ray structural data and the complexity of cellular systems applied for investigation. Here, we established a bacterial expression system to generate recombinant mammalian TAK1 complexes. Co-expression of TAK1 and TAB1, but not TAB2, resulted in a functional and active TAK1-TAB1 complex capable of directly activating full-length heterotrimeric mammalian AMP-activated protein kinase (AMPK) in vitro. TAK1-dependent AMPK activation was mediated via hydrophobic residues of the AMPK kinase domain alphaG-helix as observed in vitro and in transfected cell culture. Co-immunoprecipitation of differently epitope-tagged TAK1 from transfected cells and mutation of hydrophobic alphaG-helix residues in TAK1 point to an intermolecular mechanism of TAB1-induced TAK1 autoactivation, as TAK1 autophosphorylation of the activation segment was impaired in these mutants. TAB1 phosphorylation was enhanced in a subset of these mutants, indicating a critical role of alphaG-helix residues in this process. Analyses of phosphorylation site mutants of the activation segment indicate that autophosphorylation of Ser-192 precedes TAB1 phosphorylation and is followed by sequential phosphorylation of Thr-178, Thr-187, and finally Thr-184. Finally, we present a model for the chronological order of events governing TAB1-induced TAK1 autoactivation.
Treatment of patients with advanced cancer using multiple long-term cultured lymphokine-activated killer (LAK) cell infusions and recombinant human interleukin-2. (1989)

Escalating doses of recombinant human interleukin-2 (rIL-2) were combined with long-term cultured rIL-2 activated killer cells to treat patients with disseminated melanoma, renal cell cancer, and colon cancer. Twenty-four patients were entered, 12 with renal cell cancer, 8 with colon cancer, and 4 with melanoma; 23 were evaluable for efficacy and toxicity. The (dose-related) toxicities were moderate to severe and consisted of fever, chills, rigors, weight gain, hypotension, mild confusion, elevation of liver enzymes and serum creatinine, thrombocytopenia, and eosinophilia. No cardiac events (arrhythmias or myocardial infarction) were recorded. None of the patients were admitted to the intensive care unit, and no deaths occurred. Two partial responses were observed, one at relatively low doses of rIL-2 in a patient with renal cell carcinoma and one at the highest dose level in a patient with malignant melanoma. The maximally tolerated dose level of rIL-2 for this study was 6 X 10(6) U/m2 i.v./day. The recommended dose for further studies is 3 X 10(6) U/m2 i.v./day in three divided doses.
TAPC-Promoted Oxidation of Sulfides and Deoxygenation of Sulfoxides (2010)

1,3,5-Triazo-2,4,6-triphosphorine-2,2,4,4,6,6-tetrachloride (TAPC) was found to be an efficient promoter for the oxidation of sulfides and deoxygenation of sulfoxides. Excellent yields, short reaction time, easy and quick isolation of the products, solvent-free process, and excellent chemoselectivity are the main advantages of this procedure.
Self-assembly of mono- and multilayers of polyconjugated conducting polymers (2000)

To obtain organised mono- and multilayers of policonjugated polymers or oligomers by self assembly techniques has recently attracted much attention. This is due to the simplicity of the method and to the fact that no sophisticated apparatus is required. In the present feature the state of the art in this field is discussed including our own research results. A survey on self assembly of thiols, disulfides, and alkylsilanes on gold or glass surfaces is presented as well as self assembly of ferrocenylalkyl-substituted heterocycle adsorbates on ITO surfaces. Carboxyalkyl bithiophenes and terthiophenes, in which the oligothiophene tail is either perpendicularly or linearly linked to the tethering carboxyalkyl chain form stable monolayers on ITO electrodes and are anodically oxidised to produce polymer layers or to couple with oligothiophenes in solution, depending on the structure. As for multilayers, an introductory survey on the self assembly technique usually employed is given. Several examples of multilayers constituted of electroconductive polymers are discussed. Finally our recent results concerning different multilayers from polythiophenes bearing anionic and cationic moieties are discussed.