gebhart/patrepeval huggingface dataset:
Anatomy and Physiology: Understanding the Human Body (2005)

In this colorful, accessible text for undergraduates, Clark (Cumberland County College) combines enough detail to satisfy well-prepared students with a conversational writing style and reader-friendly presentation to keep less-prepared students motivated. Organized into seven sections, the text begins with an explanation of basic chemistry and the
How much aerosol reaches the lungs of wheezy infants and toddlers? (1990)

Using sodium cromoglycate as a non-toxic marker, we assessed the delivery of aerosol to nine wheezy infants and seven healthy adults. The drug was delivered to the infants by face mask and spacer device from a metered dose inhaler, and by face mask and nebuliser to the infants and the adults who breathed though their noses. The concentration of sodium cromoglycate was estimated in timed urine collections to find out how much of the dose was absorbed from the lung. Only 0.13% to 0.61% of the 20 mg nominal dose was detected in the urine, representing an estimated 0.3% to 1.5% deposited in the lung. Nasal filtration of aerosol could be a critical factor in reducing lung deposition.
Inferring subnetworks from perturbed expression profiles (2001)

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways.
First Application of Geospatial Semantic Graphs to SAR Image Data (LDRD Final Report) (2013)

Modeling geospatial information with semantic graphs enables search for sites of interest based on relationships between features, without requiring strong a priori models of feature shape or other intrinsic properties. Geospatial semantic graphs can be constructed from raw sensor data with suitable preprocessing to obtain a discretized representation. This report describes initial work toward extending geospatial semantic graphs to include temporal information, and initial results applying semantic graph techniques to SAR image data. We describe an efficient graph structure that includes geospatial and temporal information, which is designed to support simultaneous spatial and temporal search queries. We also report a preliminary implementation of feature recognition, semantic graph modeling, and graph search based on input SAR data. The report concludes with lessons learned and suggestions for future improvements.
Cloning and sequencing of the alkaline extracellular protease gene of Yarrowia lipolytica (1987)

The XPR2 gene encoding an alkaline extracellular protease (AEP) from Yarrowia lipolytica was cloned, and its complete nucleotide sequence was determined. The amino acid sequence deduced from the nucleotide sequence reveals that the mature AEP consists of 297 amino acids with a relative molecular weight of 30,559. The gene codes for a putative 22-amino-acid prepeptide (signal sequence) followed by an additional 135-amino-acid propeptide containing a possible N-linked glycosylation site and two Lys-Arg peptidase-processing sites. The final Lys-Arg site occurs at the junction with the mature, extracellular form. The mature protease contains two potential glycosylation sites. AEP is a member of the subtilisin family of serine proteases, with 42.6% homology to the fungal proteinase K. The functional promoter is more than 700 base pairs long, allowing for the observed complex regulation of this gene. The 5' and 3' flanking regions of the XPR2 gene have structural features in common with other yeast genes.
Cryogenic Technology for Processing High-CO2 and -H2S Gas Reserves (2008)

This article, written by Assistant Technology Editor Karen Bybee, contains highlights of paper IPTC 12708, "Controlled Freeze ZoneTM Technology for Enabling Processing of High CO2 and H2S Gas Reserves," by J.A. Valencia, P.S. Northrop, and C.J. Mart, ExxonMobil, originally prepared for the 2008 International Petroleum Technology Conference, Kuala Lumpur, 3-5 December. The paper has not been peer reviewed. Global natural-gas reserves increasingly are reported with significant CO2 and/or H2S content. Concentrations of 20 to 40% are not uncommon. Commercialization of such resources poses significant economic and technical challenges. Approximately one-sixth of ExxonMobil's hydrocarbon resources are categorized as sour gas. With these volumes, ExxonMobil has the industry's largest sour-gas resource base and has more than 50 years experience in managing sour gas. Introduction Monetization of lesser amounts of saleable methane/hydrocarbons while at the same time producing, removing, and disposing of major quantities of acid-gas contaminants calls for technologies that can reduce capital and operating costs. The proper disposal of these contaminants adds to the challenge. Release of CO2 to the environment is not desirable, its geosequestration is a much better alternative, and it would be better yet if it can be turned into a product stream to be sold or used for enhanced-oil-recovery (EOR) purposes. Similarly, alternatives for the disposal of H2S are needed because the conventional conversion to elemental sulfur led to the saturation of many markets. While there has been a recent resurgence in the demand for sulfur, uncertainties about wide-spread demand sustainability encourages the development of alternative H2S-disposal options. The cryogenic technology, developed at ExxonMobil Upstream Research Company, is being advanced to the commercially ready stage in response to these needs. The first choice for many separations in the gas industry are those that take advantage of the simplicity provided by differing relative volatilities and phase behavior and are implemented by flash drums, separators, and distillation and fractionation towers. In the presence of methane, and to yield sales-quality gas, such separations imply very low, cryogenic temperatures of −120°F and lower, depending upon the operating pressure. CO2 solidifies at these low temperatures. The experimental measurement and analysis of CO2-solidification conditions in the presence of methane were pioneered in 1954. Shortly thereafter, a new process was proposed for freezing CO2 from natural gas by flashing a cooled gas stream into solidification conditions and using a cyclonic device to separate the resulting slurry into solid CO2 and liquid methane.
Stereotaxic Injection of IgG From Patients With Alzheimer Disease Initiates Injury of Cholinergic Neurons of the Basal Forebrain (2000)

Data document that IgG from patients with AD can target a stereotaxically induced immune/inflammatory injury to cholinergic neurons in the rat basal forebrain in vivo.
Potential of the proteasomal inhibitor MG-132 as an anticancer agent, alone and in combination. (2002)

Proteasomal activity is required for normal cellular functions including cell division, where entry and exit from mitosis is strictly regulated by cyclins and cyclin-dependent kinases which are among the important substrates of the proteasomal degradative machinery. Inhibitors of proteasomal activity have been shown to be effective inducers of apoptosis in tumor cells and may be useful as anticancer agents, either alone or in combination with other drugs. We have examined the effect of MG-132, a dipeptide proteasomal inhibitor, on various human cancer cell lines. We have also examined the effect of MG-132 on normal CD34+ enriched primary human peripheral blood stem cells. Our results indicate that MG-312 is a potent anticancer agent with cytotoxic effects on a variety of human cancer cell lines irrespective of their p53 status. MG-132 was found to be more effective in combination with drugs such as doxorubicin and etoposide that act in the S/G2-phase of the cell cycle via a mechanism that involves stabilization of cyclin B1 and increased expression of Bax. Further, MG-132 inhibits CFU-GM colony formation of the CD34+ enriched PBSC population and this inhibition correlates with release of cyt C into the cytosol.
ARC, an inhibitor of apoptosis expressed in skeletal muscle and heart that interacts selectively with caspases (1998)

We have identified and characterized ARC, apoptosis repressor with caspase recruitment domain (CARD). Sequence analysis revealed that ARC contains an N-terminal CARD fused to a C-terminal region rich in proline/glutamic acid residues. The CARD domain of ARC exhibited significant homology to the prodomains of apical caspases and the CARDs present in the cell death regulators Apaf-1 and RAIDD. Immunoprecipitation analysis revealed that ARC interacts with caspase-2, -8, and Caenorhabditis elegans CED-3, but not with caspase-1, -3, or -9. ARC inhibited apoptosis induced by caspase-8 and CED-3 but not that mediated by caspase-9. Further analysis showed that the enzymatic activity of caspase-8 was inhibited by ARC in 293T cells. Consistent with the inhibition of caspase-8, ARC attenuated apoptosis induced by FADD and TRADD and that triggered by stimulation of death receptors coupled to caspase-8, including CD95/Fas, tumor necrosis factor-R1, and TRAMP/DR3. Remarkably, the expression of human ARC was primarily restricted to skeletal muscle and cardiac tissue. Thus, ARC represents an inhibitor of apoptosis expressed in muscle that appears to selectively target caspases. Delivery of ARC by gene transfer or enhancement of its endogenous activity may provide a strategy for the treatment of diseases that are characterized by inappropriately increased cell death in muscle tissue.
Role of ceramide as a lipid mediator of 1 alpha,25-dihydroxyvitamin D3-induced HL-60 cell differentiation. (1990)

The treatment of HL-60 myelocytic leukemia cells with 1 alpha,25-dihydroxyvitamin D3 (1,25-(OH)2D3) resulted in the activation of a neutral sphingomyelinase and in sphingomyelin turnover (Okazaki, T., Bell, R., and Hannun, Y. (1989) J. Biol. Chem. 264, 19076-19080). In this paper, the effects of 1,25-(OH)2D3 on the product of sphingomyelin hydrolysis, ceramide, and the possible function of ceramide as a lipid mediator of the effects of 1,25-(OH)2D3 on HL-60 cell differentiation were investigated. Treatment of HL-60 cells with 1,25-(OH)2D3 resulted in a time- and dose-dependent increase in ceramide mass levels. Ceramide levels peaked at 2 h following treatment of HL-60 cells with 100 nM 1,25-(OH)2D3 with an increase of 41% over base line. The mass of generated ceramide (13 +/- 2 pmol/nmol of phospholipid) agreed with the mass of hydrolyzed sphingomyelin (17 +/- 4 pmol/nmol of phospholipid). Cell-permeable ceramides with shorter N-acyl chains induced HL-60 cell differentiation at subthreshold concentrations of 1,25-(OH)2D3. Higher concentrations of cell-permeable ceramides potently induced HL-60 cell differentiation independent of 1,25-(OH)2D3. A 2-h exposure of HL-60 cells to N-acetyl-sphingosine was sufficient to cause differentiation. Morphologically, N-acetylsphingosine caused a similar monocytic differentiation of HL-60 cells as did 1,25-(OH)2D3. Exogenous ceramide was further metabolized to sphingomyelin and other sphingolipids, but no conversion to sphingosine was detected. Moreover, sphingosine and its analogs failed to affect monocytic differentiation of HL-60 cells in response to subthreshold 1,25-(OH)2D3, indicating that the effect of ceramide was independent of sphingosine generation. These studies demonstrate that ceramide is a lipid mediator that may transduce the action of 1,25-(OH)2D3 on HL-60 cell differentiation.
The Product of the Vaccinia Virus L5R Gene Is a Fourth Membrane Protein Encoded by All Poxviruses That Is Required for Cell Entry and Cell-Cell Fusion (2005)

The L5R gene of vaccinia virus is conserved among all sequenced members of the Poxviridae but has no predicted function or recognized nonpoxvirus homolog. Here we provide the initial characterization of the L5 protein. L5 is expressed following DNA replication with kinetics typical of a viral late protein, contains a single intramolecular disulfide bond formed by the virus-encoded cytoplasmic redox pathway, and is incorporated into intracellular mature virus particles, where it is exposed on the membrane surface. To determine whether L5 is essential for virus replication, we constructed a mutant that synthesizes L5 only in the presence of an inducer. The mutant exhibited a conditional-lethal phenotype, as cell-to-cell virus spread and formation of infectious progeny were dependent on the inducer. Nevertheless, all stages of replication occurred in the absence of inducer and intracellular and extracellular progeny virions appeared morphologically normal. Noninfectious virions lacking L5 could bind to cells, but the cores did not enter the cytoplasm. In addition, virions lacking L5 were unable to mediate low-pH-triggered cell-cell fusion from within or without. The phenotype of the L5R conditional lethal mutant is identical to that of recently described mutants in which expression of the A21, A28, and H2 genes is repressed. Thus, L5 is the fourth component of the poxvirus cell entry/fusion apparatus that is required for entry of both the intracellular and extracellular infectious forms of vaccinia virus.
Pulsed Electroreduction of  CO 2 on Copper Electrodes‐ II (1994)

The pulsed method newly developed by the present authors was applied to electroreduction of on Cu electrodes. It was found that the optimum cathodic bias for generating and was −2.6 V vs. SCE, and the optimum anodic bias for the generation of was slightly more anodic than that of . Total faradaic efficiency for the generation of and became a maximum at 10°C and reached about 65%. Furthermore, increased with increasing reduction time in strong contrast with the conventional potentiostatic electroreduction in which decreased drastically with the reduction time due to the poisoning effect of the products. It was proposed that some surface intermediate formed by the interaction between and the thin oxide layer on a Cu electrode is finally reduced to or , depending on the anodic reactions taking place during the anodic period.
Transcranial magnetic stimulation modulates the brain's intrinsic activity in a frequency-dependent manner (2011)

Intrinsic activity in the brain is organized into networks. Although constrained by their anatomical connections, functional correlations between nodes of these networks reorganize dynamically. Dynamic organization implies that couplings between network nodes can be reconfigured to support processing demands. To explore such reconfigurations, we combined repetitive transcranial magnetic stimulation (rTMS) and functional connectivity MRI (fcMRI) to modulate cortical activity in one node of the default network, and assessed the effect of this upon functional correlations throughout the network. Two different frequencies of rTMS to the same default network node (the left posterior inferior parietal lobule, lpIPL) induced two topographically distinct changes in functional connectivity. High-frequency rTMS to lpIPL decreased functional correlations between cortical default network nodes, but not between these nodes and the hippocampal formation. In contrast, low frequency rTMS to lpIPL did not alter connectivity between cortical default network nodes, but increased functional correlations between lpIPL and the hippocampal formation. These results suggest that the default network is composed of (at least) two subsystems. More broadly, the finding that two rTMS stimulation regimens to the same default network node have distinct effects reveals that this node is embedded within a network that possesses multiple, functionally distinct relationships among its distributed partners.
The Clinical Significance of Tumor Cell-Lined Vasculature in Ovarian Carcinoma: Implications for Anti-Vasculogenic Therapy (2002)

Vasculogenic mimicry reflects the plasticity of aggressive tumor cells that express vascular cell markers and line tumor vasculature; such has been demonstrated in aggressive ovarian carcinoma. This study measured the clinical significance of tumor cell-lined vasculature in ovarian carcinomas (n=77), which was detected in 23 (29.8%) tumors. The data show that tumor cell-lined vasculature was associated with aggressive tumor features and with shorter overall survival (p<0.001). Cox proportional hazards model revealed that tumor cell-lined vasculature (p=0.002) was independently associated with poor survival. This is the first study demonstrating the clinical implications of tumor cell-lined vasculature in ovarian carcinoma.
Toward a Versatile Allylation Reagent:  Practical, Enantioselective Allylation of Acylhydrazones Using Strained Silacycles (2003)

A highly practical method for the enantioselective allylation of acylhydrazones has been developed. The previously reported strained silacycle reagent 1 reacts with a wide variety of acylhydrazones to give the hydrazide products with good enantioselectivity (83-89% ee, typically). It has been demonstrated that the products may be isolated without chromatography by recrystallization in >/=98% ee.
Drug Therapy for Patients with Eating Disorders (2003)

The purpose of this article is to review the psychopharmacology treatment literature for patients with eating disorders including bulimia nervosa, anorexia nervosa and binge eating disorder. The best-developed treatment literature concerns bulimia nervosa, which has been studied now in several dozen pharmacological treatment studies. The agents most commonly used are the antidepressants, with particular focus on the selective serotonin reuptake inhibitors including fluoxetine hydrochloride. These agents clearly impact significantly on the frequency of abnormal eating behaviors such as binge eating and purging. However, subjects treated with these drugs rarely achieve remission. Pharmacotherapy of anorexia nervosa has also traditionally focused on the use of antidepressants and there is some evidence that the use of SSRIs may help in preventing relapse in weight restored patients. Recently interest has developed in the use of atypical neuroleptics to help with the obsessionality and resistance to treatment frequently seen in low weight patients, the most commonly employed agent being olanzapine. Pharmacotherapy of binge-eating disorder is now being intensively investigated. In general medication alone seems inferior to psychotherapy in the short term. Antidepressants can increase the amount of weight loss when combined with psychological treatment and also appear to benefit symptoms such as depression. Further data are needed, but a number of drugs appear promising.
Prodrugs and soft drugs. (2007)

This review focuses on a new approach to the development of drugs, namely on prodrugs and soft drugs. Nowadays, we try to design drugs that heal sick people having the best acceptance of patients. They must be efficient and selective on their site of action and must be metabolized to non-toxic derivatives. Both, prodrugs and soft drugs should have good distributive properties to enhance their quality. They are designed to maximize the amount of an active drug that reaches its target, through changing the physicochemical, biopharmaceutical or pharmacokinetic properties of drugs. Prodrugs are changed into the active drug within the body through enzymatic or non-enzymatic reactions. Soft drugs are novel and active analogues of already known therapeutic agents. It is expected that continued studies will improve drug properties so as to achieve the best drug delivery system.
Managing virtual data marts with metapointer tables (2003)

Although Internet/intranet topology has radically evolved communications for information workers, the access and transfer of large volumes of data through this topology is still inefficient and is not inherently conducive to point-in-time recall. Because information managers make real time decisions based on relevant subsets of an enterprise data warehouse, data marts are required for optimized data accessibility and use. Storage virtualization, based on pointer systems, has introduced new instant copy functions which do not require that data be actually stored outside the data warehouse even though it is referenced in a variety of contexts (e.g., multiple data marts utilizing overlapping subsets of the data warehouse). The purpose of this paper is to describe a method enabling users to access relevant subsets of large data populations residing in different data warehouses. This method enables the creation of data marts for use by local decision support software without requiring the data mart data population to be stored locally. This will save storage space and data transmission resources, and simplify synchronization of the data mart and the warehouse when updates occur.
Characterization of the herpes simplex virus type 1 glycoprotein D mRNA and expression of this protein in Xenopus oocytes (1983)

We have identified and characterized a 3.0 kilobase (kb) mRNA containing coding sequences of the herpes simplex virus type 1 (HSV-1) glycoprotein D (gD) gene. The synthesis of this 3.0 kb mRNA was unaffected by the presence of cytosine arabinoside, but was made in greatly reduced amounts in cells infected with HSV-1 in the presence of cycloheximide: it was, therefore, classified as an early mRNA. By nuclease protection experiments, it was found that the 3.0 kb mRNA is unspliced and, further, that it is 3' co-terminal with a smaller 1.6 kb early mRNA which is transcribed from a DNA sequence 3' to the gD coding sequence. We describe the use of the Xenopus laevis oocyte system to produce HSV-1 gD in vitro. Oocytes injected with mRNA isolated from HSV-1-infected Vero cells synthesized gD, which was identified by immunoprecipitation. Injection of a plasmid clone containing the HSV-1 BamHI J fragment (0.89 to 0.93 map units) into the nuclei of Xenopus oocytes also resulted in synthesis of gD.