gebhart/patrepeval huggingface dataset:
Genome‐scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertion (2008)

Abstract BACKGROUND: Cyanobacterium Synechocystis sp. PCC 6803 has been used widely as a model system for the study of photosynthetic organisms and higher plants. The aim of this work was to integrate the genomic information, biochemistry and physiological information available for Synechocystis sp. PCC 6803 to reconstruct a metabolic network for system biology investigations. RESULTS: A genome‐scale Synechocystis sp. PCC 6803 metabolic network, including 633 genes, 704 metabolites and 831 metabolic reactions, was reconstructed for the study of optimal Synechocystis growth, network capacity and functions. Heterotrophic, photoautotrophic and mixotrophic growth conditions were simulated. The Synechocystis model was used for in silico predictions for the insertion of ethanol fermentation pathway, which is a novel approach for bioenergy and biofuels production developed in the authors' laboratory. Simulations of Synechocystis cell growth and ethanol production were compared with actual metabolic measurements which showed a satisfactory agreement. CONCLUSION: The Synechocystis metabolic network developed in this study is the first genome‐scale mathematical model for photosynthetic organisms. The model may be used not only in global understanding of cellular metabolism and photosynthesis, but also in designing metabolic engineering strategies for desirable bio‐products. Copyright © 2008 Society of Chemical Industry
Cutaneous Wound Healing (1999)

The primary function of the skin is to serve as a protective barrier against the environment. Loss of the integrity of large portions of the skin as a result of injury or illness may lead to major disability or even death. Every year in the United States more than 1.25 million people have burns1 and 6.5 million have chronic skin ulcers caused by pressure, venous stasis, or diabetes mellitus.2 The primary goals of the treatment of wounds are rapid wound closure and a functional and aesthetically satisfactory scar. Recent advances in cellular and molecular biology have greatly expanded our understanding . . .
Structure and Function of Rat Parietal Cells during Treatment with Omeprazole, SCH 28080, SCH 32651, or Ranitidine (1990)

For 2 weeks four groups of adult female rats were given daily peroral doses of 400 mumols/kg of one of the following inhibitors of gastric acid secretion: omeprazole, SCH 28080, SCH 32651, or ranitidine; additional control rats were given vehicle only. Six rats in each group were killed 2 h after the last dose and another six in each group at 48 h. Samples of the gastric corpus wall were processed for light and electron microscopy. The maximal reduction of stimulated acid secretion in parallel gastric fistula rats was 100%, 90%, 40%, and 85%, respectively. Forty-eight hours after the last dose only SCH 28080 produced significant inhibition of acid secretion. 'Vacuolation' of parietal cells was occasionally observed in paraffin sections. Such 'vacuoles', which were not found in plastic sections, probably represent dilated secretory canaliculi. A small number of lucid parietal cells--presumably in the process of desquamation--were seen in all groups of rats; their proportion was significantly higher 2 h after the last dose of ranitidine, SCH 28080, or SCH 32651 than in the controls. Forty-eight hours after the last dose the proportion of such degenerating parietal cells was about the same in all groups.
Copper(I) Iodide: A Catalyst for the Improved Synthesis of Aryl Propargyl Ethers (1995)

Copper(I) iodide catalyses the reaction between phenols and dialkylpropargyl chlorides to give aryl 1,1-dialkylpropargyl ethers 5a-k and 7a-e in good yields and purity. These ethers are important as precursors to the 2H-1-benzopyrans 8a-l and 9a-e.
On the synthesis of dynamic scenes from reference views (2002)

We consider a scene, containing many objects moving with constant velocity along straight line paths, seen from three reference viewpoints at three different times. The scene may even consist only of moving objects with no static features. We wish to create a new image sequence showing the scene from arbitrary viewing position and arbitrary time. We make use of a newly discovered tool, the "dual Htensor" that connects together three views of a coplanar configuration of (unlabeled) static and moving points. The newly synthesized images use constant velocity in the world to achieve realistic and physically correct images.
The role of interleukin-1 in host responses to infectious diseases. (1992)

The polypeptide cytokine interleukin-1 (IL-1) affects nearly every tissue and organ system. IL-1 is the prototype of the pro-inflammatory cytokines in that it induces the expression of a variety of genes and synthesis of several proteins which, in turn, induce acute and chronic inflammatory changes. Most studies on the biology of IL-1 have been carried out in animals, but human subjects have recently been injected with recombinant IL-1 and the results confirm IL-1 as being a mediator of disease as well as host defense. However, overproduction of IL-1 leads to debilitation of normal host functions; therefore, reduction of IL-1 synthesis or blockade of IL-1 activity becomes a target of therapy in many diseases. Agents for reducing the synthesis or antagonizing the effects of IL-1 have been sought, but the naturally occurring IL-1 receptor antagonist (IL-1Ra) has opened new experimental and clinical approaches. The ability of IL-1Ra to block IL-1 receptors without agonist activities has reduced the severity of diseases such as septic shock, lethal sepsis, inflammatory bowel disease, experimental arthritis, and the spontaneous proliferation of human leukemic cells.
Performance Analysis and Design Aspects of Mobile-Terminal Multiantenna Configurations (2008)

This paper presents a comprehensive study on the performance analysis and design aspects of mobile-terminal multiantenna configurations. Four realistic multiantenna terminals are studied in a large set of measured single-input-multiple-output (SIMO) and multiple-input-multiple-output (MIMO) environments. Several performance metrics, such as the total efficiencies of the antenna configurations, envelope correlation, effective array gain , eigenvalue dispersion, and capacity, are used in the performance evaluation. Emphasis has been put on increasing understanding on the power-transferring properties of mobile-terminal multiantenna configurations, for which purpose the is used. Furthermore, efficient theoretical ways of predicting the empirical results based on the simulated 3-D radiation patterns of an antenna configuration are proposed and studied. The results of this paper provide novel and useful information for the designers of future multiantenna terminals.
PPARs and the Cardiovascular System (2008)

Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone-receptor superfamily. Originally cloned in 1990, PPARs were found to be mediators of pharmacologic agents that induce hepatocyte peroxisome proliferation. PPARs also are expressed in cells of the cardiovascular system. PPAR gamma appears to be highly expressed during atherosclerotic lesion formation, suggesting that increased PPAR gamma expression may be a vascular compensatory response. Also, ligand-activated PPAR gamma decreases the inflammatory response in cardiovascular cells, particularly in endothelial cells. PPAR alpha, similar to PPAR gamma, also has pleiotropic effects in the cardiovascular system, including antiinflammatory and antiatherosclerotic properties. PPAR alpha activation inhibits vascular smooth muscle proinflammatory responses, attenuating the development of atherosclerosis. However, PPAR delta overexpression may lead to elevated macrophage inflammation and atherosclerosis. Conversely, PPAR delta ligands are shown to attenuate the pathogenesis of atherosclerosis by improving endothelial cell proliferation and survival while decreasing endothelial cell inflammation and vascular smooth muscle cell proliferation. Furthermore, the administration of PPAR ligands in the form of TZDs and fibrates has been disappointing in terms of markedly reducing cardiovascular events in the clinical setting. Therefore, a better understanding of PPAR-dependent and -independent signaling will provide the foundation for future research on the role of PPARs in human cardiovascular biology.
Novel Mechanistic Class of Fatty Acid Amide Hydrolase Inhibitors with Remarkable Selectivity (2007)

Fatty acid amide hydrolase (FAAH) is an integral membrane enzyme that degrades the fatty acid amide family of signaling lipids, including the endocannabinoid anandamide. Genetic or pharmacological inactivation of FAAH leads to analgesic, anti-inflammatory, anxiolytic, and antidepressant phenotypes in rodents without showing the undesirable side effects observed with direct cannabinoid receptor agonists, indicating that FAAH may represent an attractive therapeutic target for treatment of pain, inflammation, and other central nervous system disorders. However, the FAAH inhibitors reported to date lack drug-like pharmacokinetic properties and/or selectivity. Herein we describe piperidine/piperazine ureas represented by N-phenyl-4-(quinolin-3-ylmethyl)piperidine-1-carboxamide (PF-750) and N-phenyl-4-(quinolin-2-ylmethyl)piperazine-1-carboxamide (PF-622) as a novel mechanistic class of FAAH inhibitors. PF-750 and PF-622 show higher in vitro potencies than previously established classes of FAAH inhibitors. Rather unexpectedly based on the high chemical stability of the urea functional group, PF-750 and PF-622 were found to inhibit FAAH in a time-dependent manner by covalently modifying the enzyme's active site serine nucleophile. Activity-based proteomic profiling revealed that PF-750 and PF-622 were completely selective for FAAH relative to other mammalian serine hydrolases. We hypothesize that this remarkable specificity derives, at least in part, from FAAH's special ability to function as a C(O)-N bond hydrolase, which distinguishes it from the vast majority of metabolic serine hydrolases in mammals that are restricted to hydrolyzing esters and/or thioesters. The piperidine/piperazine urea may thus represent a privileged chemical scaffold for the synthesis of FAAH inhibitors that display an unprecedented combination of potency and selectivity for use as potential analgesic and anxiolytic/antidepressant agents.
Bombesin-related peptides and their receptors: recent advances in their role in physiology and disease states (2008)

This receptor family is involved in an increasing number of central nervous system/peripheral processes physiologically and in disease states, and increased understanding of its role may lead to novel treatments.
Encoding of learned importance of sound by magnitude of representational area in primary auditory cortex (2005)

We hypothesized that learning-induced representational expansion in the primary auditory cortex (AI) directly encodes the degree of behavioral importance of a sound. Rats trained on an operant auditory conditioning task were variably motivated to the conditioned stimulus (CS) through different levels of water deprivation. Mean performance values correlated with deprivation level, validating them as a measure of the overall control and, therefore, behavioral importance of the CS. Electrophysiological mapping revealed expanded representations of the CS, compared with other frequencies in experimental subjects, but not in naive or visually trained controls that received noncontingent CS tones. Importantly, representational area showed a significant positive correlation with mean performance levels for only the CS band, with significant effects for relative area in contrast to only modest changes in absolute area. CS representational expansion was asymmetric into high-frequency zones, thus performance level also was significantly correlated with the relative anterior-posterior location of the enlarged representation. An increased representation of low frequencies, related to the acoustic spectrum of the reward delivery equipment, also was discovered in both experimental and control trained subjects, supporting the conclusion that behaviorally important sounds gain representational area. Furthermore, there was a surprising reduction in total AI area for the experimental and control groups, compared with untrained naive subjects, indicating that the functional dimensions of AI are not fixed. Overall, the findings support the encoding of acquired stimulus importance based on representational size in AI.
Single-Chip Silicon Photonics 100-Gb/s Coherent Transceiver (2014)

We demonstrate a monolithic silicon photonics integrated circuit that contains all the optics for a 100-Gb/s coherent transceiver, except the laser. Co-packaged with linear drivers and transimpedance amplifiers, the 27 × 35.5 mm2 module consumes only 4.5W.
Blood-Brain Barrier Genomics (2007)

Blood-brain barrier (BBB) genomics begins with the isolation of capillaries from fresh animal or human brain and is followed on the same day with the purification of capillary-derived RNA. The identification of microvascular-enriched genes from a whole brain gene microarray is unlikely because the brain capillary endothelial volume is <0.1% of total brain. Libraries of partial cDNAs corresponding to genes that are selectively expressed at the BBB are generated with polymerase chain reaction-based approaches such as subtractive suppressive hybridization. The availability of these partial cDNAs, in conjunction with production of animal or human BBB cDNA libraries, enables the cloning of the full-length cDNAs and a functional analysis of the BBB-enriched genes. The development of BBB genomics technologies enables the acquisition of a large body of new knowledge about the BBB and the brain microvasculature.
Arrays of silicon microdischarge devices with multicomponent dielectrics (2001)

Arrays as large as 15x15 of microdischarge devices having inverted pyramidal silicon cathodes (50mumx50mum) and SiO(2)- Si(3)N(4)- polymer composite dielectrics have been fabricated and characterized with Ne gas. The lifetimes, reliability, and ignition characteristics of the arrays are superior to those of earlier designs having a single polymer dielectric. Operating voltages as low as 150 V for a 10x10 pixel array and 1000 Torr of Ne have been measured. Single (50mumx50mum) pyramidal cathode devices operate at voltages as low as 113 V when the Ne pressure is 900 Torr.
Characterization of Promoter Function and Cell-Type-Specific Expression from Viral Vectors in the Nervous System (2000)

Viral vectors have become important tools to effectively transfer genes into terminally differentiated cells, including neurons. However, the rational for selection of the promoter for use in viral vectors remains poorly understood. Comparison of promoters has been complicated by the use of different viral backgrounds, transgenes, and target tissues. Adenoviral vectors were constructed in the same vector background to directly compare three viral promoters, the human cytomegalovirus (CMV) immediate-early promoter, the Rous sarcoma virus (RSV) long terminal repeat, and the adenoviral E1A promoter, driving expression of the Escherichia coli lacZ gene or the gene for the enhanced green fluorescent protein. The temporal patterns, levels of expression, and cytotoxicity from the vectors were analyzed. In sensory neuronal cultures, the CMV promoter produced the highest levels of expression, the RSV promoter produced lower levels, and the E1A promoter produced limited expression. There was no evidence of cytotoxicity produced by the viral vectors. In vivo analyses following stereotaxic injection of the vector into the rat hippocampus demonstrated differences in the cell-type-specific expression from the CMV promoter versus the RSV promoter. In acutely prepared hippocampal brain slices, marked differences in the cell type specificity of expression from the promoters were confirmed. The CMV promoter produced expression in hilar regions and pyramidal neurons, with minimal expression in the dentate gyrus. The RSV promoter produced expression in dentate gyrus neurons. These results demonstrate that the selection of the promoter is critical for the success of the viral vector to express a transgene in specific cell types.
Absence of interaction between porcine endogenous retrovirus and porcine cytomegalovirus in pig‐to‐baboon renal xenotransplantation in vivo (2018)

PCMV coinfection does not alter the replication of PERV in life-supporting renal xenotransplantation in vivo in baboons.
Enhanced Metabolic Stability and Protein‐Binding Properties of Artificial α Helices Derived from a Hydrogen‐Bond Surrogate: Application to Bcl‐xL (2005)

Artificial α helices prepared by the replacement of a hydrogen bond between residues i and i+4 with a carbon–carbon bond can stabilize biologically relevant peptides in helical conformations (1, internal constraint shaded in gray). α Helices based on hydrogen-bond surrogates that mimic Bak BH3 (2, yellow) can bind their expected protein receptor, Bcl-xL (2, green), with high affinity and resist proteolytic degradation. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501603_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Multiplex Single Nucleotide Polymorphism Genotyping Utilizing Ligase Detection Reaction Coupled Surface Enhanced Raman Spectroscopy (2010)

Single nucleotide polymorphisms (SNPs) are one of the key diagnostic markers for genetic disease, cancer progression, and pharmcogenomics. The ligase detection reaction (LDR) is an excellent method to identify SNPs, combining low detection limits and high specificity. We present the first multiplex LDR-surface enhanced Raman spectroscopy (SERS) SNP genotyping scheme. The platform has the advantage in that the diagnostic peaks of Raman are more distinct than fluorescence, and in theory, a clinically significant number of markers can be multiplexed in a single sample using different SERS reporters. Here we report LDR-SERS multiplex SNP genotyping of K-Ras oncogene alleles at 10 pM detection levels, optimization of DNA labeling as well as Raman conditions, and the linear correlation of diagnostic peak intensity to SNP target concentration in heterozygous samples. Genomic DNA from typed cells lines was obtained and scored for the K-Ras genotype. These advances are significant as we have further developed our new SNP genotyping platform and have demonstrated the ability to correlate genotype ratios directly to diagnostic Raman peak signal intensity.
Carcinogenicity studies of astemizole in mice and rats. (1995)

The histamine H1 antagonist astemizole (Hismanal) was tested for carcinogenicity in Swiss mice and Wistar rats. Astemizole was administered with the food to mice for 18 and to rats for 24 consecutive months. The doses given--approximately 5, 20, and 80 mg/kg body weight.day--were equivalent to 25, 100, and 400 times, respectively, the recommended human dose of 10 mg/day. Survival of both mice and rats was comparable between groups. Peto's age-adjusted, dose-related trend analysis for the tumor-bearing rats did not reveal a statistically significant difference for males or females. There was no evidence that astemizole led to an increased incidence of spontaneously or unusually occurring neoplastic lesions in either mice or rats. Special attention was given to the effect of astemizole on the progression of spontaneously occurring mammary gland adenomas and fibroadenomas. Peto's analysis applied to the number of female rats bearing these benign mammary gland tumors disclosed no statistically significant dose-related trend. There was no positive trend for the onset of this tumor type, and the median size of the tumor over time per rat was also not statistically significantly different in a comparison of the control group with each of the dosed groups. The findings from these carcinogenicity studies suggest that astemizole is not tumorigenic and that it does not promote tumor growth.
Cdc6 expression as a marker of proliferative activity in brain tumors (2001)

Antibodies against human proteins that regulate DNA replication such as Cdc6 and Mcm5 became available as a new marker of proliferation. We performed immunohistochemical analysis with MIB-1 and antibody against Cdc6 on 35 brain tumors, including tumors of neuroepithelial tissue, vestibular schwannomas, meningiomas, and pituitary adenomas. Median reactivity for MIB-1 was 8.8%, and that for Cdc6 was 55%. Reactivity in most brain tumors was significantly higher for Cdc6 than for MIB-1, but reactivity of Cdc6 was independent of tumor grade. Detection of Cdc6 expression might be useful for the estimation of proliferative activity in brain tumors.
A Model-Based Background Adjustment for Oligonucleotide Expression Arrays (2004)

High-density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of further preprocessing and data reduction occurs after the image-processing step. Statistical procedures developed by academic groups have been successful in improving the default algorithms provided by the Affymetrix system. In this article we present a solution to one of the preprocessing steps—background adjustment—based on a formal statistical framework. Our solution greatly improves the performance of the technology in various practical applications. These arrays use short oligonucleotides to probe for genes in an RNA sample. Typically, each gene is represented by 11–20 pairs of oligonucleotide probes. The first component of these pairs is referred to as a perfect match probe and is designed to hybridize only with transcripts from the intended gene (i. e., specific hybridization). However, hybridization by other sequences (i. e., nonspecific hybridization) is unavoidable. Furthermore, hybridization strengths are measured by a scanner that introduces optical noise. Therefore, the observed intensities need to be adjusted to give accurate measurements of specific hybridization. We have found that the default ad hoc adjustment, provided as part of the Affymetrix system, can be improved through the use of estimators derived from a statistical model that uses probe sequence information. A final step in preprocessing is to summarize the probe-level data for each gene to define a measure of expression that represents the amount of the corresponding mRNA species. In this article we illustrate the practical consequences of not adjusting appropriately for the presence of nonspecific hybridization and provide a solution based on our background adjustment procedure. Software that computes our adjustment is available as part of the Bioconductor Project (http://www.bioconductor.org).