gebhart/patrepeval huggingface dataset:
A bacterial artificial chromosome-based framework contig map of human chromosome 22q. (1996)

We have constructed a physical map of human chromosome 22q using bacterial artificial chromosome (BAC) clones. The map consists of 613 chromosome 22-specific BAC clones that have been localized and assembled into contigs using 452 landmarks, 346 of which were previously ordered and mapped to specific regions of the q arm of the chromosome by means of chromosome 22-specific yeast artificial chromosome clones. The BAC-based map provides immediate access to clones that are stable and convenient for direct genome analysis. The approach to rapidly developing marker-specific BAC contigs is relatively straightforward and can be extended to generate scaffold BAC contig maps of the rest of the chromosomes. These contigs will provide substrates for sequencing the entire human genome. We discuss how to efficiently close contig gaps using the end sequences of BAC clone inserts.
High-Dose Cysteine Administration Does Not Increase Synthesis of the Antioxidant Glutathione Preterm Infants (2009)

Administration of a high dose of cysteine (81 mg/kg per day) to preterm infants seems clinically safe but does not stimulate glutathione synthesis, compared with a lower dose (45 mg/kg per day). Further research is required to determine whether there is significant benefit associated with cysteine supplementation.
Global genomic approaches to the iron-regulated proteome. (2005)

Iron interacts with cells to regulate the proteome through complex effects on gene expression. In simple organisms such as bacteria and yeast, intra- and extra-cellular iron influences gene expression through defined signal transduction pathways. In higher organisms, effects are probably mediated at the transcriptional level through secondary effects of reactive oxygen species, while post-transcriptional effects operate through well-defined pathways involving iron-regulatory proteins. To investigate the impact of iron levels on gene expression and the proteome, approaches such as differential display and subtractive hybridization have the advantage of surveying the entire genome. However, they are technically demanding and have given way to microarray techniques. To date, numerous microarray experiments with various organisms have not yielded any definitive picture of the role of iron. Common themes throughout such studies are that both iron excess and iron depletion influence expression of proteins related to energy metabolism, cell proliferation, matrix structure, and the metabolism of iron itself. That no consistent set of genes is involved from one study to the next probably results both from the uncertainties inherent in the technique and the biological variability of the systems under study. We briefly describe two types of iron-dependent microarray experiments from our laboratory to examine major cellular targets of iron toxicity. Using Affymetrix oligonucleotide arrays with cardiac cells, we found several hundred genes whose mRNA levels were affected by iron, including an increase in several genes responding to oxidative stress and a decrease in several kinases and phosphatases. In a simpler experiment using a human liver cell line with a limited cDNA array, we targeted 13 genes affected by iron chelation. Metabolic pathway analysis shows links of 5 of these through phorbol ester responsiveness, and additional links through prostaglandin E2. We conclude that definitive understanding of the complex iron-regulated proteome requires global gene approaches and rigorous interlaboratory standardization.
Hemoglobin-AGE: A Circulating Marker of Advanced Glycosylation (1992)

Advanced glycosylation end products (AGEs) form spontaneously from glucose-derived Amadori products and accumulate on long-lived tissue proteins. AGEs have been implicated in the pathogenesis of several of the complications of aging and diabetes, including atherosclerosis and renal disease. With the use of recently developed AGE-specific antibodies, an AGE-modified form of human hemoglobin has been identified. Termed hemoglobin-AGE (Hb-AGE), this modified species accounts for 0.42 percent of circulating hemoglobin in normal individuals but increases to 0.75 percent in patients with diabetes-induced hyperglycemia. In a group of diabetic patients treated with the advanced glycosylation inhibitor aminoguanidine, Hb-AGE levels decreased significantly over a 1-month period. Hemoglobin-AGE measurements may provide an index of long-term tissue modification by AGEs and prove useful in assessing the contribution of advanced glycosylation to a variety of diabetic and age-related complications.
Role of Solution Structure in Solid Electrolyte Interphase Formation on Graphite with LiPF6 in Propylene Carbonate (2013)

An investigation of the interrelationship of cycling performance, solution structure, and electrode surface film structure has been conducted for electrolytes composed of different concentrations of LiPF6 in propylene carbonate (PC) with a binder-free (BF) graphite electrode. Varying the concentration of LiPF6 changes the solution structure, altering the predominant mechanism of electrolyte reduction at the electrode interface. The change in mechanism results in a change in the structure of the solid electrolyte interface (SEI) and the reversible cycling of the cell. At low concentrations of LiPF6 in PC (1.2 M), electrochemical cycling and cyclic voltammetry (CV) of BF graphite electrodes reveal continuous electrolyte reduction and no lithiation/delithiation of the graphite. The solution structure is dominated by solvent-separated ion pairs (Li+(PC) 4//PF6-), and the primary reduction product of the electrolyte is lithium propylene dicarbonate (LPDC). At high concentrations of LiPF6 in PC (3.0-3.5 M), electrochemical cycling and CV reveal reversible lithiation/delithiation of the graphite electrode. The solution structure is dominated by contact ion pairs (Li+(PC) 3PF6-), and the primary reduction product of the electrolyte is LiF. © 2013 American Chemical Society.
Animal Models of Huntington's Disease (2007)

Huntington's disease (HD) is a neurological disorder caused by a genetic mutation in the IT15 gene. Progressive cell death in the striatum and cortex, and accompanying declines in cognitive, motor, and psychiatric functions, are characteristic of the disease. Animal models of HD have provided insight into disease pathology and the outcomes of therapeutic strategies. Earlier studies of HD most often used toxin-induced models to study mitochondrial impairment and excitotoxicity-induced cell death, which are both mechanisms of degeneration seen in the HD brain. These models, based on 3-nitropropionic acid and quinolinic acid, respectively, are still often used in HD studies. The discovery in 1993 of the huntingtin mutation led to the creation of newer models that incorporate a similar genetic defect. These models, which include transgenic and knock-in rodents, are more representative of the HD progression and pathology. An even more recent model that uses a viral vector to encode the gene mutation in specific areas of the brain may be useful in nonhuman primates, as it is difficult to produce genetic models in these species. This article examines the aforementioned models and describes their use in HD research, including aspects of the creation, delivery, pathology, and tested therapies for each model.
Oral chemotherapy: rationale and future directions. (1998)

Oral chemotherapy represents a fundamental change in contemporary oncology practice, driven by pharmacoeconomic issues, patient convenience, and the potential for improved patient quality of life. Novel cytostatic therapies that require protracted drug administration periods will also favor an oral formulation. While the use of oral chemotherapy may initially be limited to metastatic disease palliation, demonstration of equivalent efficacy would allow for its subsequent use in adjuvant settings. This efficacy is contingent on circumventing bioavailability limitations and patient noncompliance. The development of specific, low-toxicity inhibitors of CYP3A4, P-glycoprotein (P-gp), and other drug metabolizing enzymes such as dihydropyrimidine dehydrogenase represents a major innovative step in the successful formulation of oral chemotherapy.
Assay of excised oxidative DNA lesions: isolation of 8-oxoguanine and its nucleoside derivatives from biological fluids with a monoclonal antibody column. (1992)

An immunoaffinity column is described that facilitates the analysis of oxidative damage products of DNA and RNA in urine, blood plasma, and medium isolated from cultures of Escherichia coli. In intact animals, lesions (adducts) excised from DNA are transported from the cell through the circulation and excreted in urine. In bacteria, DNA adducts are excreted directly into the medium. In either case, the adducts can be assayed as a measure of oxidative damage to DNA. A monoclonal antibody that recognizes 8-oxo-7,8-dihydro-2'-deoxyguanosine (oxo8dG;8-hydroxy-2'-deoxyguanosine), a bio-marker of oxidative damage to DNA, has been isolated, and its substrate binding properties have been characterized. The relative binding affinities of this monoclonal antibody for oxo8dG, unmodified nucleosides, or derivatives of Gua made it suitable for the preparation of immunoaffinity columns that greatly facilitate the isolation of oxo8dG, 8-oxo-7,8-dihydroguanine, and 8-oxo-7,8-dihydroguanosine from various biological fluids. Quantitative analysis of these adducts in urine of rats fed a nucleic acid-free diet and in the medium from cultures of E. coli suggests that oxo8-7,8-dihydroguanine is the principal repair product from oxo8-dG in DNA of both eukaryotes and prokaryotes. The results support our previous estimate of about 10(5) oxidative lesions to DNA being formed and excised in an average rat cell per day.
Photoaffinity labeling as an approach to study supramolecular nucleoprotein complexes (1998)

The modern approaches for studying the detailed structure of nucleoprotein complexes involved in replication and transcription, based on the use of nucleic acids with photoreactive groups incorporated into definite positions of polynucleotide chain, are considered. Methods of preparation of photoreactive nucleic acids of this type are presented. Their use for positioning of RNA polymerase III and transcription factors as well as of the main participants of the replication machinery at the respective templates is described. A survey of the data concerning the amino acid residues modified in the course of photoaffinity labeling of proteins is also presented and some complications are discussed.
Mytilus edulis Adhesive Protein (MAP) as an Enzyme Immobilization Matrix in the Fabrication of Enzyme-Based Electrodes (1998)

A simple enzyme immobilization technique using an adhesive protein isolated from Mytilus edulis blue mussels was optimized for constructing a glucose oxidase (GOD) based electrode. Owing to the presence of 10–15 % of 3,4-dihydroxyphenylalanine residues, the mussel adhesive protein (MAP) was easily oxidized to form a stable protein film on platinum, gold and glassy carbon electrodes. Covalent attachment of glucose oxidase to adhesive protein modified electrodes was attained since the oxidized form of the L-Dopa moieties was very reactive towards various compounds containing amino, alcohol and thiol groups. Glucose detection was performed using MAP/GOD modified electrodes at +0.8 V in 0.1 M phosphate buffer, pH 5. Platinum modified electrodes (Pt/MAP/GOD) exhibited a considerably higher sensitivity (1.28 μA/mM) in comparison to its gold (Au/MAP/GOD, 2.92 nA/mM) or glassy carbon (GC/MAP/GOD, 2.62 nA/mM) counterparts. Tetrachloro-1,4-benzoquinone (TCBQ), an oxidation product of pentachlorophenol, was detected using MAP/GOD modified electrodes at +0.45 V in a deaerated 0.1 M tartaric acid buffer, pH 3.5 containing 40 mM glucose. In steady state, the current response of the Au/MAP/GOD electrode was higher (6.62 nA nM−1cm−2, t95 = 83 s, 5 nM) than the GC/MAP/GOD electrode (3.78 nA nM−1 cm−2, 8 nM). In flow injection analysis, GC/MAP/GOD electrodes exhibited a linear response for TCBQ ranging from 10 nM to 1 μM (3.96 nAs nM−1) with a detection limit of 10 nM. The modified glassy carbon enzyme based electrode retained 90 % and 87 % of its activity after 150 and 250 repeated injections.
Immunocytochemistry of cell surface heparan sulfate proteoglycan in mouse tissues. A light and electron microscopic study. (1987)

The core protein of the proteoglycan at the cell surface of NMuMG mouse mammary epithelial cells bears both heparan and chondroitin sulfate chains and is recognized by the monoclonal antibody 281-2. Using this antibody and the peroxidase-antiperoxidase staining technique in adult mouse tissues, we found that the antibody recognizes the antigen in a highly restricted distribution, staining a variety of epithelial cells but no cells derived from embryonic mesoderm or neural crest. The antibody fails to stain any stromal (mesenchymal) or neuronal cells, with the exception of plasma cells and Leydig cells. Squamous and transitional epithelia stain intensely over their entire surfaces, whereas cuboidal and columnar epithelia stain moderately and only at the lateral surface of the basal cells. Within squamous and transitional epithelial tissues that undergo physiological regeneration (e.g., epidermis), the most superficial and differentiated cell types fail to stain. Within glandular and branched epithelia (e.g., pancreas), the secretory alveolar cells fail to stain. When evaluated by electron microscopy, granular deposits of stain are seen on the plasma membrane, especially on lateral surfaces, but none are noted within the cells or the basement membrane. These results indicate that in adult tissues the core protein of this heparan sulfate-rich proteoglycan is expressed almost exclusively at epithelial cell surfaces. Expression appears to be lost as the cells become either mature or highly differentiated.
A 5-Year Surveillance Study of 44,691 Isolates of Haemophilus influenzae Project Beta-Alert 1993–1997 (1999)

Beta-Alert is a surveillance program developed in 1993 to monitor the percentage of beta-lactamase-producing Haemophilus influenzae isolates obtained from specimens submitted to regional commercial laboratories. The results of this study demonstrate that levels of beta-lactamase producers have remained between 31 and 38% in the United States over the past 5 years.
The skin fungus‐induced Th1‐ and Th2‐related cytokine, chemokine and prostaglandin E2 production in peripheral blood mononuclear cells from patients with atopic dermatitis and psoriasis vulgaris (2002)

AD patients manifest Th2-skewed responses to MF, CA and TR, which may be partially attributable to the enhanced PGE2 responses to these fungi. PV patients manifest Th1-skewed responses to MF.
High-performance signal peptide prediction based on sequence alignment techniques (2008)

Abstract Summary: The accuracy of current signal peptide predictors is outstanding. The most successful predictors are based on neural networks and hidden Markov models, reaching a sensitivity of 99% and an accuracy of 95%. Here, we demonstrate that the popular BLASTP alignment tool can be tuned for signal peptide prediction reaching the same high level of prediction success. Alignment-based techniques provide additional benefits. In spite of high success rates signal peptide predictors yield false predictions. Simple sequences like polyvaline, for example, are predicted as signal peptides. The general architecture of learning systems makes it difficult to trace the cause of such problems. This kind of false predictions can be recognized or avoided altogether by using sequence comparison techniques. Based on these results we have implemented a public web service, called Signal-BLAST. Predictions returned by Signal-BLAST are transparent and easy to analyze. Availability: Signal-BLAST is available online at http://sigpep.services.came.sbg.ac.at/signalblast.html Contact: sippl@came.sbg.ac.at
Electrical Stimulation of a Denervated Muscle Promotes Selective Reinnervation by Native Over Foreign Motoneurons (2002)

The effect of electrical stimulation of the denervated posterior cricoarytenoid (PCA) muscle on its subsequent reinnervation was explored in the canine. Eight animals were implanted with a planar array of 36 electrodes for chronic stimulation and recording of spontaneous and evoked electromyographic (EMG) potentials across the entire fan-shaped surface of a muscle pair. Normative EMG data were recorded from each electrode site before unilateral nerve section, and from the innervated partner after nerve section. After randomizing the animals to experimental and control groups, the right recurrent laryngeal nerve innervating the PCA abductor muscle and its adductor antagonists was sectioned and reanastomosed. The PCA muscle in four experimental animals was continuously stimulated during the 11-mo experiment, using a 1-s, 30-pps, biphasic pulse train composed of 1-ms pulses 2-6 mA in amplitude and repeated every 10 s. The remaining four animals served as nonstimulated controls. Appropriate reinnervation by native inspiratory motoneurons was indexed behaviorally by the magnitude of vocal fold opening and electromyographically by the potential across all electrode sites. Inappropriate reinnervation by foreign adductor motoneurons was quantitated by recording EMG potentials evoked reflexly by stimulation of sensory afferents of the laryngeal mucosa. All four experimental animals showed a greater level of correct PCA muscle reinnervation (P < 0.0064) and a lesser level of incorrect reinnervation (P < 0.0084) than the controls. Direct muscle stimulation also appeared to enhance the overall magnitude of reinnervation, but the effect was not as strong (P < 0.113). These findings are consistent with a previous report and suggest that stimulation of a mammalian muscle may profoundly affect its receptivity to reinnervation by a particular motoneuron type.
Express cubes: improving the performance of k-ary n-cube interconnection networks (1991)

The author discusses express cubes, k-ary n-cube interconnection networks augmented by express channels that provide a short path for nonlocal messages. An express cube combines the logarithmic diameter of a multistage network with the wire-efficiency and ability to exploit locality of a low-dimensional mesh network. The insertion of express channels reduces the network diameter and thus the distance component of network latency. Wire length is increased, allowing networks to operate with latencies that approach the physical speed-of-light limitation rather than being limited by node delays. Express channels increase wire bisection in a manner that allows the bisection to be controlled independently of the choice of radix, dimension, and channel width. By increasing wire bisection to saturate the available wiring media, throughput can be substantially increased. With an express cube both latency and throughput are wire-limited and within a small factor of the physical limit on performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Regulation of phase 2 enzyme induction by oltipraz and other dithiolethiones (1994)

4-Methyl-5-pyrazinyl-3H-1,2-dithiole-3-thione (oltipraz) and several other dithiolethiones protect against the acute toxicities of many xenobiotics and are effective inhibitors of experimental carcinogenesis. These protective effects are mediated, in part, through elevation of glutathione S-transferase, NAD(P)H: quinone reductase and UDP-glucuronosyltransferase activities in the liver and other target tissues. The induction of these phase 2 enzymes by oltiprax results from enhanced transcription. In the present study, the molecular mechanisms of these inductions were analyzed utilizing a construct containing a 41 bp enhancer element derived from the 5'-upstream region of the mouse liver glutathione S-transferase Ya subunit gene ligated to the 5' end of the isolated promoter region of this gene, and inserted into a plasmid containing a human growth hormone reporter gene. When this construct was transfected into murine Hepa 1c1c7 hepatoma cells, the concentrations of 25 dithiolethiones and related analogs required to double growth hormone production were determined and spanned a range nearly three orders of magnitude. Concentrations of dithiolethiones required to double the specific activity of NAD(P)H: quinone reductase were also determined in Hepa 1c1c7 cells. There was a positive correlation (r = 0.78) between the potencies of the 21 active compounds as inducers of both NAD(P)H: quinone reductase activity and growth hormone production. Moreover, no dithiolethiones were inactive in only one system. It is probable, therefore, that the induction of NAD(P)H: quinone reductase and other phase 2 enzymes by oltipraz and other dithiolethiones is mediated entirely through the 41 bp enhancer element.
Virtual screening of GPCRs: An in silico chemogenomics approach (2008)

We propose new methods for in silico chemogenomics and validate them on the virtual screening of GPCRs. The methods represent an extension of a recently proposed machine learning strategy, based on support vector machines (SVM), which provides a flexible framework to incorporate various information sources on the biological space of targets and on the chemical space of small molecules. We investigate the use of 2D and 3D descriptors for small molecules, and test a variety of descriptors for GPCRs. We show that incorporating information about the known hierarchical classification of the target family and about key residues in their inferred binding pockets significantly improves the prediction accuracy of our model.
Definitions of Managed Objects for RObust Header Compression (ROHC) (2004)

This memo defines a portion of the Management Information Base (MIB) for use with network management protocols in the Internet community.In particular, it describes a set of managed objects that allow monitoring of running instances of RObust Header Compression (ROHC).The managed objects defined in this memo are grouped into three MIB modules.The ROHC-MIB module defines managed objects shared by all ROHC profiles, the ROHC-UNCOMPRESSED-MIB module defines managed objects specific to the ROHC uncompressed profile, the ROHC-RTP-MIB module defines managed objects specific to the ROHC RTP (Real-Time Transport Protocol) profile, the ROHC UDP (User Datagram Protocol) profile, the ROHC ESP (Encapsulating Security Payload) profile, and the ROHC LLA (Link Layer Assisted) profile.Quittek, et al.