gebhart/patrepeval huggingface dataset:
Redox Control of Cell Death (2002)

Cellular redox is controlled by the thioredoxin (Trx) and glutathione (GSH) systems that scavenge harmful intracellular reactive oxygen species (ROS). Oxidative stress also evokes many intracellular events including apoptosis. There are two major pathways through which apoptosis is induced; one involves death receptors and is exemplified by Fas-mediated caspase-8 activation, and another is the stress- or mitochondria-mediated caspase-9 activation pathway. Both pathways converge on caspase-3 activation, resulting in nuclear degradation and cellular morphological change. Oxidative stress induces cytochrome c release from mitochondria and activation of caspases, p53, and kinases, including apoptosis signal-regulating kinase 1 (ASK1), c-Jun N-terminal kinase, and p38 mitogen-activated protein kinase. Trx inhibits apoptosis signaling not only by scavenging intracellular ROS in cooperation with the GSH system, but also by inhibiting the activity of ASK1 and p38. Mitochondria-specific thioredoxin (Trx-2) and Trx peroxidases (peroxiredoxins) are suggested to regulate cytochrome c release from mitochondria, which is a critical early step in the apoptotis-signaling pathway. dATP/ATP and reducing factors including Trx determine the manifestation of cell death, apoptosis or necrosis, by regulating the activation process and the activity of redox-sensitive caspases. As mitochondria are the most redox-active organelle and indispensable for cells to initiate or inhibit the apoptosis process, the regulation of mitochondrial function is the central focus in the research field of apoptosis and redox.
Recurrent Neural Networks With Limited Numerical Precision (2016)

Recurrent Neural Networks (RNNs) produce state-of-art performance on many machine learning tasks but their demand on resources in terms of memory and computational power are often high. Therefore, there is a great interest in optimizing the computations performed with these models especially when considering development of specialized low-power hardware for deep networks. One way of reducing the computational needs is to limit the numerical precision of the network weights and biases. This has led to different proposed rounding methods which have been applied so far to only Convolutional Neural Networks and Fully-Connected Networks. This paper addresses the question of how to best reduce weight precision during training in the case of RNNs. We present results from the use of different stochastic and deterministic reduced precision training methods applied to three major RNN types which are then tested on several datasets. The results show that the weight binarization methods do not work with the RNNs. However, the stochastic and deterministic ternarization, and pow2-ternarization methods gave rise to low-precision RNNs that produce similar and even higher accuracy on certain datasets therefore providing a path towards training more efficient implementations of RNNs in specialized hardware.
Effect of controlled ovarian hyperstimulation in IVF on endometrial gene expression profiles (2004)

Controlled ovarian hyperstimulation (COH) used in IVF produces lower implantation rates per embryo transferred compared to natural cycles utilized in ovum donation, suggesting a suboptimal endometrial development. Endometrial receptivity has recently been investigated in natural menstrual cycles with the aid of microarray technology. The aim of this study is to investigate the impact of COH using urinary gonadotrophins with a long protocol with GnRH agonists without progesterone supplementation (similar to the natural cycle) on endometrial gene expression profiles during the window of implantation by comparing the profiles at day hCG + 7 of COH versus LH + 7 of a previous natural cycle in the same women. For this purpose we have used microarray technology by Affymetrix (GeneChip HG_U133A), which allows more than 22,000 genes to be tested simultaneously. Results were validated by semi-quantitative PCR and quantitative PCR experiments. We found that more than 200 genes showed a differential expression of more than 3-fold when COH and normal cycles were compared at hCG + 7 versus LH + 7. We simultaneously re-analysed the LH + 2 versus LH + 7 endometrial gene expression profiles in previous natural cycles in the same subject using this specific GeneChip, the results obtained were consistent with our own published results. This is the first time that gene expression profiles of the endometrium during COH are reported. The large degree of gene expression disturbance is surprising and highlights the need for further efforts to optimize COH protocols.
Filling gaps in the boundary of a polyhedron (1995)

In this paper we present an algorithm for detecting and repairing defects in the boundary of a polyhedron. These defects, usually caused by problems in CAD software, consist of small gaps bounded by edges that are incident to only one polyhedron face. The algorithm uses a partial curve matching technique for matching parts of the defects, and an optimal triangulation of 3-D polygons for resolving the unmatched parts. It is also shown that finding a consistent set of partial curve matches with maximum score, a subproblem which is related to our repairing process, is NP-hard. Experimental results on several polyhedra are presented.
Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond (2017)

Infections with flaviviruses, such as dengue, West Nile virus and the recently re-emerging Zika virus, are an increasing and probably lasting global risk. This Review summarizes and comments on the opportunities for broad-spectrum agents that are active against multiple flaviviruses. Broad-spectrum activity is particularly desirable to prepare for the next flaviviral epidemic, which could emerge from as-yet unknown or neglected viruses. Potential molecular targets for broad-spectrum antiflaviviral compounds include viral proteins, such as the viral protease or polymerase, and host targets that are exploited by these viruses during entry and replication, including α-glucosidase and proteins involved in nucleoside biosynthesis. Numerous compounds with broad-spectrum antiviral activity have already been identified by target-specific or phenotypic assays. For other compounds, broad-spectrum activity can be anticipated because of their mode of action and molecular targets.
Colitis in chronic granulomatous disease (2001)

Colitis is a common cause of gastrointestinal symptoms in CGD and is caused by a non-infective inflammatory process. The histology has specific features, which are distinctive from those seen in Crohn's disease.
Developmental biology and tissue engineering (2007)

Morphogenesis implies the controlled spatial organization of cells that gives rise to tissues and organs in early embryonic development. While morphogenesis is under strict genetic control, the formation of specialized biological structures of specific shape hinges on physical processes. Tissue engineering (TE) aims at reproducing morphogenesis in the laboratory, i.e., in vitro, to fabricate replacement organs for regenerative medicine. The classical approach to generate tissues/organs is by seeding and expanding cells in appropriately shaped biocompatible scaffolds, in the hope that the maturation process will result in the desired structure. To accomplish this goal more naturally and efficiently, we set up and implemented a novel TE method that is based on principles of developmental biology and employs bioprinting, the automated delivery of cellular composites into a three-dimensional (3D) biocompatible environment. The novel technology relies on the concept of tissue liquidity according to which multicellular aggregates composed of adhesive and motile cells behave in analogy with liquids: in particular, they fuse. We emphasize the major role played by tissue fusion in the embryo and explain how the parameters (surface tension, viscosity) that govern tissue fusion can be used both experimentally and theoretically to control and simulate the self-assembly of cellular spheroids into 3D living structures. The experimentally observed postprinting shape evolution of tube- and sheet-like constructs is presented. Computer simulations, based on a liquid model, support the idea that tissue liquidity may provide a mechanism for in vitro organ building.
Quantitative and qualitative studies of chemical transformation of cloned C3H mouse embryo cells sensitive to postconfluence inhibition of cell division. (1973)

A line of C3H mouse embryo cells (C3H/10T1/2 clone 8) sensitive to postconfluence inhibition of cell division was used for a variety of quantitative and qualitative studies of chemical oncogenesis in culture. The polycyclic hydrocarbons (PH), 3-methylcholanthrene, dibenz[a,h]anthracene, and 7,12-dimethylbenz[a]anthracene, caused varying degrees of cytotoxicity and produced morphologically and malignantly transformed foci in these cells with a dose-dependent frequency, while N -methyl- N ′-nitro- N -nitrosoguanidine was toxic but did not transform under the same conditions. Transformation frequency was related to cell density at the time of treatment and to the duration of treatment with PH. After treatment of the cells with the PH, three types of morphologically altered foci were identified. Foci of each type were cloned and inoculated into irradiated syngeneic mice. Two of the three types of foci gave rise to fibrosarcomas when cells were inoculated at Passages 2 to 4 after cloning. The determination of transformation frequency in this system includes only these two types of malignantly transformed foci. The third type of focus was morphologically minimally altered but did not give rise to tumors under the same conditions. Control cells did not produce tumors. The saturation densities of several transformed lines were shown to be greater than the control line and did not correlate with the growth rate of the cells. The antimycotic agent amphotericin B (Fungizone) interfered with transformation when it was present in the medium at the time of exposure of the cells to the PH.
Fluoxetine in post-traumatic stress disorder (1999)

Fluoxetine was superior for measures of PTSD severity, disability, stress vulnerability, and high end-state function. The placebo-group response was low when viewed as a broad outcome based on a portfolio of ratings, but was higher with a traditional global rating criterion.
Antiviral defense in mice lacking both alpha/beta and gamma interferon receptors (1995)

Alpha/beta interferon (IFN) and gamma IFN exert widely overlapping biological effects. Still, mice with individually inactivated alpha/beta or gamma receptors exhibit variably severely reduced resistance to infection and altered immune responses. To investigate to what extent the two IFN systems are functionally redundant, we generated mice with a combined receptor defect (AG129 mice). Like mice with individual mutations, AG129 mice had no apparent anomalies, confirming that in the mouse the IFN system is not essential for normal development. These mice showed an additive phenotype with respect to antiviral defense and exhibited an increased susceptibility to lymphocytic choriomeningitis virus (LCMV) and notably vaccinia virus infection. Because of unlimited replication and subsequent rapid exhaustion of cytotoxic T lymphocyte (CTL) precursors, these mice were unable to mount a CTL response to LCMV. CD8(+)-mediated immunopathology was absent in LCMV-infected mice, and virus persisted. Vaccinia virus replicated much faster in AG129 mice, and a 10(4)-fold lower dose of vaccinia virus was sufficient to prime these mice. With the normal priming dose of 10(6) PFU, cytopathic effects and overwhelming infection possibly causing partial exhaustion of CTL interfered with the anti-vaccinia virus response. Even though global antiviral immunoglobulin G (IgG) titers were within normal ranges, the IgG subclass distribution was heavily biased toward IgG1.
Pressure‐induced Vasodilation and Reactive Hyperemia at Different Depths in Sacral Tissue Under Clinically Relevant Conditions (2014)

Pressure-induced vasodilation and RH can be observed at different tissue depths. A lack of these responses was found in healthy individuals as well as in patients indicating an innate susceptibility in some individuals, and are potential important factors to evaluate in order to better understand the etiology of pressure ulcers.
TBD: Trajectory-Based Data Forwarding for Light-Traffic Vehicular Networks (2009)

This paper proposes a trajectory-based data forwarding (TBD) scheme, tailored for the data forwarding in light- traffic vehicular ad-hoc networks. State-of-the-art schemes have demonstrated the effectiveness of their data forwarding strategies by exploiting known vehicular traffic statistics (e.g., densities and speeds) in these vehicular networks. These results are encouraging, however, further improvements can be made by taking advantage of the growing popularity of GPS-based navigation systems. This paper presents the first attempt to investigate how to effectively utilize vehicles" trajectory information in a privacy-preserving manner. In our design, the trajectory information is combined with the traffic statistics to improve the performance of data forwarding in road networks. Through theoretical analysis and extensive simulation, it is shown that our design outperforms the existing scheme.
Conversion of control dependence to data dependence (1983)

Program analysis methods, especially those which support automatic vectorization, are based on the concept of interstatement dependence where a dependence holds between two statements when one of the statements computes values needed by the other. Powerful program transformation systems that convert sequential programs to a form more suitable for vector or parallel machines have been developed using this concept [AllK 82, KKLW 80].The dependence analysis in these systems is based on data dependence. In the presence of complex control flow, data dependence is not sufficient to transform programs because of the introduction of control dependences. A control dependence exists between two statements when the execution of one statement can prevent the execution of the other. Control dependences do not fit conveniently into dependence-based program translators.One solution is to convert all control dependences to data dependences by eliminating goto statements and introducing logical variables to control the execution of statements in the program. In this scheme, action statements are converted to IF statements. The variables in the conditional expression of an IF statement can be viewed as inputs to the statement being controlled. The result is that control dependences between statements become explicit data dependences expressed through the definitions and uses of the controlling logical variables.This paper presents a method for systematically converting control dependences to data dependences in this fashion. The algorithms presented here have been implemented in PFC, an experimental vectorizer written at Rice University.
Temperature of polypeptide inverse temperature transition depends on mean residue hydrophobicity (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTemperature of polypeptide inverse temperature transition depends on mean residue hydrophobicityDan W. Urry, Chi Hao Luan, Timothy M. Parker, D. Channe Gowda, Kari U. Prasad, Michael C. Reid, and Ahmad SafavyCite this: J. Am. Chem. Soc. 1991, 113, 11, 4346–4348Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ja00011a057https://doi.org/10.1021/ja00011a057research-articleACS PublicationsRequest reuse permissionsArticle Views1542Altmetric-Citations300LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Pseudomonas aeruginosa AlgB, a two-component response regulator of the NtrC family, is required for algD transcription (1991)

Most strains of Pseudomonas aeruginosa isolated from the respiratory tracts of cystic fibrosis patients have a mucoid colony morphology due to the synthesis of an expolysaccharide called alginate. The algB gene product (AlgB) is necessary for the high-level production of alginate in mucoid P. aeruginosa. In this study, AlgB was shown to be involved in the transcription of algD, a gene previously demonstrated to be activated in mucoid P. aeruginosa. In vitro and in vivo expression studies reveal that algB encodes a protein with a molecular size of 49 kDa. The DNA sequence of a 2.2-kb P. aeruginosa fragment containing algB was also determined. The amino-terminal domain of AlgB was found to be conserved with the amino-terminal domains of the response regulator class of two-component regulatory proteins. The central domain of AlgB has sequences highly conserved with those in the NtrC subfamily of transcriptional activators (NtrC, NifA, HydG, DctD, FlbD, TyrR, and PgtA). The central domain of AlgB also contains a potential nucleotide binding site. AlgB is the first NtrC homolog described from P. aeruginosa. At the carboxy terminus of AlgB, a helix-turn-helix motif was observed, suggesting that AlgB is a DNA-binding protein. The strongly conserved NtrC-like central domain of AlgB is not present in AlgR, another alginate response regulator. This study therefore identifies and characterizes the second of at least two unique response regulators used by P. aeruginosa to control alginate gene expression.
Using spin images for efficient object recognition in cluttered 3D scenes (1999)

We present a 3D shape-based object recognition system for simultaneous recognition of multiple objects in scenes containing clutter and occlusion. Recognition is based on matching surfaces by matching points using the spin image representation. The spin image is a data level shape descriptor that is used to match surfaces represented as surface meshes. We present a compression scheme for spin images that results in efficient multiple object recognition which we verify with results showing the simultaneous recognition of multiple objects from a library of 20 models. Furthermore, we demonstrate the robust performance of recognition in the presence of clutter and occlusion through analysis of recognition trials on 100 scenes.
Correlation between Musashi‐1 and c‐hairy‐1 expression and cell proliferation activity in the developing intestine and stomach of both chicken and mouse (2005)

Musashi-1 (Msi-1) is an RNA-binding protein that plays key roles in the maintenance of neural stem cell states and in their differentiation into neural cells. Msi-1 has also been proposed as a candidate marker gene of mammalian intestinal stem cells and their immediate lineages. In this study, we examined Msi-1 expression in the small intestine and the stomach of both chicken and mouse during embryonic, fetal and postnatal development. In addition, we analyzed the expression of c-hairy-1, a chicken homologue of mouse Hes1, and assessed the proliferative activity of the cells expressing both of these factors. Significantly, during the development of these digestive organs in both species Msi-1 expression showed dynamic changes, suggesting that it is important for digestive organ development, particularly for epithelial differentiation. Based on our observations of the expression patterns of Msi-1 and c-hairy-1 in the adult small intestine, we speculate that Msi-1 is also a stem cell marker of the chicken small intestinal epithelium.
Development of the methylotrophic yeast Pichia methanolica for the expression of the 65 kilodalton isoform of human glutamate decarboxylase (1998)

We describe a protein expression system in the methylotrophic yeast, Pichia methanolica. Methods for transformation and genetic manipulation of the organism were developed using an ade2 strain and the wild-type ADE2 gene. A vacuolar protease-deficient strain was constructed. Two genes encoding alcohol oxidases were found, yet a single isoform of alcohol oxidase was produced during methanol-fed fermentations. The promoter from this gene was used to drive expression. An integrating plasmid for the cytoplasmic expression of the 65 kDa isoform of human glutamate decarboxylase (human GAD65) was assembled. A strain harboring eight copies of this plasmid expressed enzymatically active human GAD65 at levels approaching 0·5 g/l. Identical amounts were made in Pichia pastoris. The recombinant GAD65 was purified to greater than 90% purity. © 1998 John Wiley & Sons, Ltd.
The use of adenovirus-mediated gene transfer to develop a rat model for photoreceptor degeneration. (2000)

These results demonstrate that recombinant adenovirus-mediated transient modulation of gene expression in retinal pigment epithelial (RPE) cells could induce changes in the retina, and, in spite of the low expression of endogenous CatS in RPE cells, this enzyme plays an important role in maintenance of normal retinal function.
Towards Testing Model Transformation Chains Using Precondition Construction in Algebraic Graph Transformation (2015)

Abstract. Complex model-based tools such as code generators are typi-cally designed as chains of model transformations taking as input a model of a software application and transforming it through several intermedi-ate steps and representations. The complexity of intermediate models is such that testing is more conveniently done on the integrated chain, with test models expressed in the input language. To achieve a high test cover-age, existing transformation analyses automatically generate constraints guiding the generation of test models. However, these so called test ob-jectives are expressed on the complex intermediate models. We propose to back-propagate test objectives along the chain into constraints and test models in the input language, relying on precondition construction in the theory of Algebraic Graph Transformation. This paper focuses on a one-step back-propagation.
Polyinosinlc acid as a carrier in the microscale purification of total RNA (1991)

Three different RNA carriers were compared for use in microscale RNA isolation and subsequent cDNA synthesis and amplification via the polymerase chain reaction. E.coli rRNA alone gave considerable cDNA synthesis which under standard carrier conditions overwhelmed cDNA synthesis from lymphocyte mRNA. Yeast tRNA caused inhibition of mRNA primed cDNA synthesis, giving low levels of cDNA synthesis when used without cellular RNA. In contrast, commercially available poly I alone did not prime detectable cDNA synthesis nor did it inhibit such synthesis primed by cellular mRNA. When RNA preparations were made using these three carriers and decreasing numbers of starting lymphocytes, poly I allowed the detection of cDNA from two orders of magnitude fewer lymphocytes than the other carriers. Thus poly I was found to be a superior carrier molecule for microscale RNA preparations suitable for reverse transcription and subsequent amplification using the polymerase chain reaction.