gebhart/patrepeval huggingface dataset:
Reactive Nitrogen Intermediates Promote Low Density Lipoprotein Oxidation in Human Atherosclerotic Intima (1997)

Oxidized low density lipoprotein (LDL) may be of central importance in triggering atherosclerosis. One potential pathway involves the production of nitric oxide (NO) by vascular wall endothelial cells and macrophages. NO reacts with superoxide to form peroxynitrite (ONOO-), a potent agent of LDL oxidation in vitro. ONOO- nitrates the aromatic ring of free tyrosine to produce 3-nitrotyrosine, a stable product. To explore the role of reactive nitrogen species such as ONOO- in the pathogenesis of vascular disease, we developed a highly sensitive and specific method involving gas chromatography and mass spectrometry to quantify 3-nitrotyrosine levels in proteins. In vitro studies demonstrated that 3-nitrotyrosine was a highly specific marker for LDL oxidized by ONOO-. LDL isolated from the plasma of healthy subjects had very low levels of 3-nitrotyrosine (9 +/- 7 micromol/mol of tyrosine). In striking contrast, LDL isolated from aortic atherosclerotic intima had 90-fold higher levels (840 +/- 140 micromol/mol of tyrosine). These observations strongly support the hypothesis that reactive nitrogen species such as ONOO- form in the human artery wall and provide direct evidence for a specific reaction pathway that promotes LDL oxidation in vivo. The detection of 3-nitrotyrosine in LDL isolated from vascular lesions raises the possibility that NO, by virtue of its ability to form reactive nitrogen intermediates, may promote atherogenesis, counteracting the well-established anti-atherogenic effects of NO.
Historical overview: Searching for replication help in all of the rec places (2001)

For several decades, research into the mechanisms of genetic recombination proceeded without a complete understanding of its cellular function or its place in DNA metabolism. Many lines of research recently have coalesced to reveal a thorough integration of most aspects of DNA metabolism, including recombination. In bacteria, the primary function of homologous genetic recombination is the repair of stalled or collapsed replication forks. Recombinational DNA repair of replication forks is a surprisingly common process, even under normal growth conditions. The new results feature multiple pathways for repair and the involvement of many enzymatic systems. The long-recognized integration of replication and recombination in the DNA metabolism of bacteriophage T4 has moved into the spotlight with its clear mechanistic precedents. In eukaryotes, a similar integration of replication and recombination is seen in meiotic recombination as well as in the repair of replication forks and double-strand breaks generated by environmental abuse. Basic mechanisms for replication fork repair can now inform continued research into other aspects of recombination. This overview attempts to trace the history of the search for recombination function in bacteria and their bacteriophages, as well as some of the parallel paths taken in eukaryotic recombination research.
BIOELECTRICAL IMPEDANCE ANALYSIS OF MUSCLE FUNCTION AND ACTIVITY: (BIODYNAMIC ANALYSIS) (2008)

Abstract There is a need in medicine and research for noninvasive, painless, safe and simple bed-side techniques to measure physiological processes associated with muscle function and activity. Bioelectrical Impedance Analysis (BIA) is a widely used, noninvasive, painless, safe and simple procedure for the measurement of body composition. However, although capable of producing accurate and reproducible data, it is known to be prone to movement artifacts. This poses the interesting question “Could impedance changes be used to monitor movement and, consequently, be related to muscle function or activity?” This project investigated the utility of impedance change as a monitoring technique for physiological processes that involve movement such as muscular contraction, the calf muscle pump, and swallowing. The impedance of leg muscle segments during locomotion, whilst riding a stationary exercise cycle, was measured at discrete frequencies and by bioimpedance spectroscopy to monitor muscle function or activity. Impedance traces were compared to information obtained by electromyography (EMG). Impedance, at a discrete frequency, was able to measure the cadence of cycling and its magnitude was related to the position of the pedal during the pedal cycle. When the cycling action was measured by bioimpedance spectroscopy, R0 and Zc showed a statistically significant difference, (p
Granulocyte/macrophage colony-stimulating factor and interleukin-4-induced dendritic cells. (2004)

We speculate that GM-CSF/IL-4-induced DC promotes Th2-dominated immunity in Balb/c mice. Consideration might be given to which combination of cytokines is appropriate for the ex vivo differentiation of DC in tumor immunotherapy.
Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF (2001)

"Real time" molecular dynamics simulations of water permeation through human aquaporin-1 (AQP1) and the bacterial glycerol facilitator GlpF are presented. We obtained time-resolved, atomic-resolution models of the permeation mechanism across these highly selective membrane channels. Both proteins act as two-stage filters: Conserved fingerprint [asparagine-proline-alanine (NPA)] motifs form a selectivity-determining region; a second (aromatic/arginine) region is proposed to function as a proton filter. Hydrophobic regions near the NPA motifs are rate-limiting water barriers. In AQP1, a fine-tuned water dipole rotation during passage is essential for water selectivity. In GlpF, a glycerol-mediated "induced fit" gating motion is proposed to generate selectivity for glycerol over water.
Sequence-Specific and Synergistic Binding of Drugs to DNA (1999)

Abstract : Combination chemotherapy is one of the important strategies in cancer treatments. This is based on the observation that administering certain drugs together is more effective than giving individual drugs separately. Although the reason for such an effect is not understood, it may be related to the synergistic effect of their binding to biomacromolecules. Consequently, studies on the interplay among drugs capable of binding to different regions of DNA will be of considerable interest. Understanding the synergism of drugs at the molecular level may have important implication for designing more effective chemotherapeutic strategies in breast cancer treatments. Our proposal focuses on the sequence specific binding and synergistic effect of three drugs having distinctly different binding modes: actinomycin D (ACTD), a guanine specific intercalator; chromomycin A3 (CHR), a guanine specific minor groove binder; and distamycin A (DST), an AeT specific groove binder. In order to investigate the possible synergistic effects of drugs on DNA binding, it is essential that binding characteristics of each individual drug such as binding affinities, sequence specificities, and kinetic behaviors be thoroughly elucidated. Consistent with the Statement of Work outlined in the proposal, our laboratory has focused on the sequence specificity and binding mode studies of DST during the past year.
Enabling interaction with single user applications through speech and gestures on a multi-user tabletop (2006)

Co-located collaborators often work over physical tabletops with rich geospatial information. Previous research shows that people use gestures and speech as they interact with artefacts on the table and communicate with one another. With the advent of large multi-touch surfaces, developers are now applying this knowledge to create appropriate technical innovations in digital table design. Yet they are limited by the difficulty of building a truly useful collaborative application from the ground up. In this paper, we circumvent this difficulty by: (a) building a multimodal speech and gesture engine around the Diamond Touch multi-user surface, and (b) wrapping existing, widely-used off-the-shelf single-user interactive spatial applications with a multimodal interface created from this engine. Through case studies of two quite different geospatial systems -- Google Earth and Warcraft III -- we show the new functionalities, feasibility and limitations of leveraging such single-user applications within a multi user, multimodal tabletop. This research informs the design of future multimodal tabletop applications that can exploit single-user software conveniently available in the market. We also contribute (1) a set of technical and behavioural affordances of multimodal interaction on a tabletop, and (2) lessons learnt from the limitations of single user applications.
Thrombolytic activity of a novel plasminogen activator, LY210825, compared with recombinant tissue-type plasminogen activator in a canine model of coronary artery thrombosis. (1990)

LY210825, a recombinant tissue-type plasminogen activator (rt-PA), which contains the kringle-2 and serine protease functional domains of native tissue-type plasminogen activator, was previously produced by site-directed mutagenesis in a Syrian hamster cell line. We studied the thrombolytic potential of this molecule in a canine thrombosis model. Male hounds (16-22 kg) were anesthetized; a 2.0-cm segment of the left circumflex coronary artery (LCX) was isolated proximal to the first main branch, and the dogs were instrumented with an electromagnetic flow probe to measure coronary blood flow. An occlusive thrombus was formed after injury of the intimal surface of the LCX with an electrical current applied by a needle-tipped anode placed distal to the electromagnetic flow probe. After 1 hour of occlusion, either LY210825 or rt-PA was administered intravenously according to the following protocols: 1) a 1-hour infusion of either 0.25 mg/kg LY210825 or 0.4 mg/kg rt-PA, 2) single injections of 0.15-0.6 mg/kg LY210825, and 3) a single injection of 0.45 mg/kg LY210825 and a 3-hour infusion of 1.0 or 1.7 mg/kg rt-PA. Plasma half-lives of LY210825 and rt-PA were 58 +/- 7 and 3.3 +/- 0.3 minutes, respectively. LY210825 produced more rapid reperfusion of the LCX than did rt-PA. In the third study, 90% of the rt-PA-treated vessels reoccluded within 1 hour after cessation of drug, whereas only 25% of the LY210825-treated vessels reoccluded during a 4-hour washout period. There were significant, but relatively small, reductions produced by both plasminogen activators on plasma fibrinogen and plasminogen (25-35% decreases). Because of its longer plasma half-life, LY210825 could be administered intravenously as a single injection. In a canine model of coronary artery thrombosis, LY210825 was a more effective thrombolytic agent than was rt-PA.
Unipole method of electrical profiling (1963)

Abstract In the unipole method of resistivity prospecting, an electrode arrangement A M N A' with a third common electrode at infinity, is used as against the arrangement A M N B in the conventional bipole method. The electrodes A and A' are connected to one and the same pole of electric current. In the case of the unipole method, field intensity at the center of the spread is zero for a homogeneous ground. This results in a pure-anomaly method, increasing the depth of investigation and the sensitivity of field measurements considerably. The percentage of total current entering the deeper regions is larger in the unipole method than in the bipole method. The difference is further increased if a less resistive layer is present near the surface of the earth. Sensitivity of the unipole method to the near-surface inhomogeneities is less than that of the bipole method. But the unipole method is more sensitive to the deeper inhomogeneities of interest. The unipole arrangement introduces some focusing of the current within a particular range of the depth which can be controlled by altering the spacing between the current electrodes. In general, response curves for the unipole method are less complicated and admit more controls for interpretation than those for the bipole method. A theoretical and experimental comparison of the unipole method with the conventional bipole method shows that the former method is more effective than the latter in certain applications. The field instruments used at present for the bipolar measurements can be very easily adapted to the unipole method.
Selection for animal cells that express the Escherichia coli gene coding for xanthine-guanine phosphoribosyltransferase. (1981)

Cultured monkey (TC7) and mouse (3T6) cells synthesize an Excherichia coli enzyme, xanthine-guanine phosphoribosyltransferase (XGPRT; 5-phospho-alpha-D-ribose-1-diphosphate:xanthine phosphoribosyltransferase, EC 2.4.2.22), after transfection with DNA vectors carrying the corresponding bacterial gene, Ecogpt. In contrast to mammalian cells, which do not efficiently use xanthine for purine nucleotide synthesis, cells that produce E. coli XGPRT can synthesize GMP from xanthine via XMP. After transfection with vector-Ecogpt DNAs, surviving cells producing XGPRT can be selectively grown with xanthine as the sole precursor for guanine nucleotide formation in a medium containing inhibitors (aminopterin and mycophenolic acid) that block de novo purine nucleotide synthesis. Cells transformed for Ecogpt arise with a frequency of 10(-4) to 10(-5); they appear to be genetically stable in as much as there is no discernible decrease in XGPRT formation or loss on their ability to grow in selective medium after propagation in nonselective medium. Although several of the vector-gpt DNAs can replicate in monkey and mouse cells, none of the transformants contain autonomously replicating vector-gpt DNA. Rather, the gpt transformants contain one to five copies of the transfecting DNA associated with, and most probably integrated into, cellular DNA sequences. In several transformants, vector-coded gene products for which there was no selection are also synthesized. This suggests that recombinant DNAs containing Ecogpt as a selective marker can be useful for cotransformation of nonselectable genes.
Order and specificity of the Plasmodium falciparum hemoglobin degradation pathway. (1994)

The human malaria parasite, Plasmodium falciparum, degrades nearly all its host cell hemoglobin during a short segment of its intraerythrocytic development. This massive catabolic process occurs in an acidic organelle, the digestive vacuole. Aspartic and cysteine proteases have been implicated in this pathway. We have isolated three vacuolar proteases that account for most of the globin-degrading activity of the digestive vacuole. One is the previously described aspartic hemoglobinase that initiates hemoglobin degradation. A second aspartic protease is capable of cleaving hemoglobin with an overlapping specificity, but seems to prefer acid-denatured globin. The third is a cysteine protease that does not recognize native hemoglobin but readily cleaves denatured globin. It is synergistic with the aspartic hemoglobinase, both by in vitro assay of hemoglobin degradation, and by isobologram analysis of protease inhibitor-treated parasites in culture. The cysteine protease is highly sensitive to chloroquine-heme complex, suggesting a possible mechanism of 4-aminoquinoline antimalarial action. The data suggest an ordered pathway of hemoglobin catabolism that presents an excellent target for chemotherapy.
Embryonic stem cells injected into the mouse knee joint form teratomas and subsequently destroy the joint (2002)

It is currently not possible to use ES cells to repair joint tissues. Further optimization of donor ES cells to differentiate as well as inhibit tumour growth may help to meet these challenges.
Regioselective catalytic transfer hydrogenation of dimethyl bicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate, dimethyl bicyclo[2.2.1]hept-2-ene-2,3-dicarboxylate, and related compounds over palladium on carbon (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegioselective catalytic transfer hydrogenation of dimethyl bicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate, dimethyl bicyclo[2.2.1]hept-2-ene-2,3-dicarboxylate, and related compounds over palladium on carbonDerrick C. Tabor, Franklin White H., L. Warren Collier IV, and Slayton A. Evans Jr.Cite this: J. Org. Chem. 1983, 48, 10, 1638–1643Publication Date (Print):May 1, 1983Publication History Published online1 May 2002Published inissue 1 May 1983https://pubs.acs.org/doi/10.1021/jo00158a013https://doi.org/10.1021/jo00158a013research-articleACS PublicationsRequest reuse permissionsArticle Views857Altmetric-Citations26LEARN 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
Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems (2004)

Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the methionine metabolism in Gram-positive bacteria was known to be controlled by the S-box and T-box mechanisms, both acting on the level of premature termination of transcription. Using comparative analysis of genes, operons and regulatory elements, we described the methionine metabolic pathway and the methionine regulons in available genomes of Gram-positive bacteria. A large number of methionine-specific RNA elements were identified. S-boxes were shown to be widely distributed in Bacillales and Clostridia, whereas methionine-specific T-boxes occurred mostly in Lactobacillales. A candidate binding signal (MET-box) for a hypothetical methionine regulator, possibly MtaR, was identified in Streptococcaceae, the only family in the Bacillus/Clostridium group of Gram-positive bacteria having neither S-boxes, nor methionine-specific T-boxes. Positional analysis of methionine-specific regulatory sites complemented by genome context analysis lead to identification of new members of the methionine regulon, both enzymes and transporters, and reconstruction of the methionine metabolism in various bacterial genomes. In particular, we found candidate transporters for methionine (MetT) and methylthioribose (MtnABC), as well as new enzymes forming the S-adenosylmethionine recycling pathway. Methionine biosynthetic enzymes in various bacterial species are quite variable. In particular, Oceanobacillus iheyensis possibly uses a homolog of the betaine-homocysteine methyltransferase bhmT gene from vertebrates to substitute missing bacterial-type methionine synthases.
Structure and expression of an amylopullulanase gene from Bacillus stearothermophilus TS‐23 (2001)

An amylopullulanase gene (apuTS) from Bacillus stearothermophilus TS-23 was cloned and characterized. apuTS consisted of an open reading frame of 6054 bp encoding a protein of 2018 amino acids with a calculated M(r) of 223811. The deduced amino acid sequence revealed four highly conserved regions that are common among amylolytic enzymes. In the C-terminal region, a six-amino-acid sequence (Pro-Gly-Ser-Gly-Thr-Thr) is repeated nine times. It shared the highest degree of homology with the amylopullulanase of Bacillus sp. XAL601. The enzyme also had moderate homology with amylopullulanases from thermophilic anaerobic bacteria. Low levels of homology were observed between the ApuTS of B. stearothermophilus TS-23 and amylopullulanases of Pyrococcus abyssi Orsay, P. furiosus and Bacillus sp. KSM1378. When the intact coding region of apuTS was expressed in Escherichia coli under the control of the lac promoter, the product was degenerate, as revealed by amylase activity staining after SDS/PAGE. The largest active polypeptide had an M(r) of about 220000, while the smallest one had an M(r) of about 105000. Upstream of the apuTS gene, a gene orfX was fortuitously cloned. The putative OrfX protein was weakly related to the myosin heavy chain. It was predicted to contain a central, 179-residue-long, coiled-coil domain.
Polymerase errors accumulating during natural evolution of the glycoprotein gene of vesicular stomatitis virus Indiana serotype isolates (1990)

We report the entire glycoprotein (G) gene nucleotide sequences of 26 vesicular stomatitis virus Indiana serotype (VSV IND) type 1 isolates from North and Central America. These sequences are also compared with partial G gene sequences of VSV IND type 2 (Cocal) and type 3 (Alagoas) viruses and the complete G gene sequences of the more distantly related VSV New Jersey (NJ) and Chandipura viruses. Phylogenetic analysis of the G gene sequences by maximum parsimony revealed four major lineages or subtypes within the classical VSV IND (type 1) viruses, each with a distinct geographic distribution. A high degree of VSV genetic diversity was found in Central America, with several virus subtypes of both VSV IND and NJ serotypes existing in this mainly enzootic disease region. Nineteen percent sequence variation but no deletions or insertions were evident within the 5' noncoding and the coding regions of the VSV IND type 1 G genes. In addition to numerous base substitutions, the 3' noncoding regions of these viruses also contained numerous base insertions and deletions. This resulted in striking variation in G gene sizes, with gene lengths ranging from 1,652 to 1,868 nucleotides. As the VSV IND type 1 subtypes have diverged from the common ancestor with the NJ subtypes, their G mRNAs have accumulated more 3' noncoding sequence inserts, ranging up to 303 nucleotides in length. These primarily consist of an imprecise reiteration of the sequence UUUUUAA, apparently generated by a unique polymerase stuttering error. Analysis of the deduced amino acid sequence differences among VSV IND type 1 viruses revealed numerous substitutions within defined antigenic epitopes, suggesting that immune selection may play a role in the evolution of these viruses.