gebhart/patrepeval huggingface dataset:
Insecticidal and nematicidal properties of microbial metabolites (1987)

Metabolites from 942 microbial isolates were screened for insecticidal and nematicidal properties. The isolates included 302 streptomycetes, 502 'novel' actinomycetes including representatives of 18 genera, 28 unidentified aerobic actinomycetes, 70 fungi and 40 bacteria other than actinomycetes. When diluted 10-fold, the metabolites from 55 isolates caused nearly 100% mortality in mosquito larvae (Aedes aegypti) within 24 h. These isolates included 27 isolates of Streptornyces, four of Actinoplanes, three isolates each of Actinomadura and Streptoverticillium, two isolates each of Micromonospora, Bacillus and Paecilomyces, and one isolate each of Micropolyspora, Nocardiopsis, Streptosporangiurn, Oerskovia, Thermornonospora, Chainia, Pseudornonas, Fusarium, Monilia and Syncephalestrurn. Two fungal isolates could not be identified to the generic level. Extracts from the culture broth of 18 isolates caused 100% mortality in mosquito larvae within 15 min to 24 h at a concentration of 1000 ppm. The LCs0 of partially purified products from two isolates was 1-2.5 ppm and that of the semipurified preparations from four other isolates was _< 50 ppm. Valinomycin was identified as an active component in the culture broth from one isolate. The culture broth from 15 isolates of aerobic actinomycetes and 4 of fungi were toxic to PanagreIlus redivivus (Nematoda); these included 12 isolates with selective nematicidal properties.
DNA vaccine protection against challenge with simian/human immunodeficiency virus 89.6 in rhesus macaques. (2000)

Twelve Rhesus macaques were immunized by intramuscular injection of naked DNA encoding the SlVmac gag and nef genes, HIV-1 89.6 env and rev genes and the simian interleukin-12 (IL-12) gene. Six of the animals also received two intramuscular injections of gp140 89.6 formulated in QS21. The monkeys were challenged by the intrarectal route, in parallel with six control monkeys, using 750 TCID50 of SHIV-89.6. Virus recovery in PBMC by co-cultivation was as follows: controls: six out of six; DNA only: five out of six; DNA + protein: two out of six. The five animals that remained virus free after this first challenge were challenged a second time, again by the intrarectal route and in parallel with four naive controls, using 600 TCID50 of pathogenic SHIV-89.6P. A rapid CD4 cell count decline was observed in the four control monkeys as well as in the monkey vaccinated with DNA only, but in none of the four animals immunized with DNA + protein. No virus was recovered from PBMC in two of these monkeys, and viral RNA loads in plasma were greatly reduced in three of them as compared with the controls. Absence of virus in PBMC was ascertained by whole blood transfusion to naive recipients. Altogether, this shows that the DNA prime-protein boost vaccine regimen could provide some protection against mucosal SHIV infection in rhesus monkeys, whereas DNA alone was ineffective.
ChemInform Abstract: A New Reaction Surface for Concerted Reactions: The Metal Ion Catalyzed Addition of Enolpyruvate to Pyruvate. (1989)

Abstract It is assumed that in the title reaction C‐C bond formation is concerted with proton transfer and occurs within the coordination sphere of (I).
Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria. (1996)

DNA repair alkyltransferases protect organisms against the cytotoxic, mutagenic, and carcinogenic effects of alkylating agents by transferring alkyl adducts from DNA to an active cysteine on the protein, thereby restoring the native DNA structure. We used random sequence substitutions to gain structure-function information about the human O6-methylguanine-DNA methyltransferase (EC 2.1.1.63), as well as to create active mutants. Twelve codons surrounding but not including the active cysteine were replaced by a random nucleotide sequence, and the resulting random library was selected for the ability to provide alkyltransferase-deficient Escherichia coli with resistance to the methylating agent N-methyl-N'-nitro-N-nitrosoguanidine. Few amino acid changes were tolerated in this evolutionarily conserved region of the protein. One mutation, a valine to phenylalanine change at codon 139 (V139F), was found in 70% of the selected mutants; in fact, this mutant was selected much more frequently than the wild type. V139F provided alkyltransferase-deficient bacteria with greater protection than the wild-type protein against both the cytotoxic and mutagenic effects of N-methyl-N'-nitro-N-nitrosoguanidine, increasing the D37 over 4-fold and reducing the mutagenesis rate 2.7-5.5-fold. This mutant human alkyltransferase, or others similarly created and selected, could be used to protect bone marrow cells from the cytotoxic side effects of alkylation-based chemotherapeutic regimens.
Effect of Severe Burn Injury on Substrate Cycling by Glucose and Fatty Acids (1987)

Increases in metabolic rate and core temperature are common responses to severe injury. We have investigated the hypothesis that these responses are due to increases in substrate cycling. A substrate cycle exists when opposing, nonequilibrium reactions catalyzed by different enzymes are operating simultaneously. At least one of the reactions must involve the hydrolysis of ATP. Thus, a substrate cycle both liberates heat and increases energy expenditure, yet there is not net conversion of substrate to product. In studies in volunteers (n = 18) and in patients with severe burns who were in a hypermetabolic state (n = 18), we used stable-isotope tracers to quantify substrate cycling in the pathways of glycolysis and gluconeogenesis and a cycle involving the simultaneous breakdown and synthesis of stored triglyceride (triglyceride-fatty acid cycle). The total rates of triglyceride-fatty acid and glycolytic-gluconeogenic cycling were elevated in the patients by 450 and 250 percent, respectively (P less than 0.01). An infusion of propranolol in the patients greatly reduced triglyceride-fatty acid cycling but did not affect gluconeogenic-glycolytic cycling. We conclude that increased substrate cycling contributes to the increased thermogenesis and energy expenditure following severe burns and that the increased triglyceride-fatty acid cycling is due to beta-adrenergic stimulation.
Prediction of Preceding Driver Behavior for Fuel Efficient Cooperative Adaptive Cruise Control (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Advanced driver assistance systems like cooperative adaptive cruise control (CACC) are designed to exploit information provided by vehicle-to-vehicle (V2V) and/or infrastructure-to-vehicle (I2V) communication systems to achieve desired objectives such as safety, traffic fluidity or fuel economy. In a day to day traffic scenario, the presence of unknown disturbances complicates achieving these objectives. In particular, CACC benefits in terms of fuel economy require the prediction of the behavior of a preceding vehicle during a finite time horizon. This paper suggests an estimation method based on actual and past inter-vehicle distance data as well as on traffic and upcoming traffic lights. This information is used to train a set of nonlinear, autoregressive (NARX) models. Two scenarios are investigated, one of them assumes a V2V communication with the predecessor, the other uses only data acquired by on-board vehicle sensors. Depending on the applied approach and the moving space of the controlled vehicle, the thus obtained (imperfect) prediction allows fuel benefits in a range of 5% to 25% in the case of moderate, non-congested traffic. This is confirmed both by simulation and measurement. Compared to existing prediction methods, the proposed strategy delivers quite promising results.&lt;/div&gt;&lt;/div&gt;
1918 Spanish influenza: The secrets remain elusive (1999)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Electrophoretic methods for process monitoring and the quality assessment of recombinant glycoproteins (1998)

In many ways electrophoretic techniques appear ideal for quality monitoring of proteins and are thus well suited for the analysis of recombinant glycoproteins. The requirements of high throughput, comparative analysis and resolution of many variants are met by several electrophoretic techniques. A wide variety of such techniques are available to biotechnologists in the rapidly developing area of recombinant glycoproteins. It is the aim of this review to specifically cover recent work which has been applied to the analysis of DNA-derived glycoproteins, both from a process control standpoint and final product validation. All major areas of electrophoresis including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing and techniques utilizing capillary electrophoresis are covered, with emphasis on analysis of glycoforms and oligosaccharide profiles of recombinant glycoproteins. As illustration, actual examples rather than standard glycoproteins are given to indicate the potential and limitations which may be encountered. It is anticipated that this review will prove a useful and practical guide to the latest developments by indicating the relevant merits of different methods.
Improvement of CHO Cell Culture Medium Formulation: Simultaneous Substitution of Glucose and Glutamine (2000)

The formulation of the culture medium for a Chinese hamster ovary (CHO) cell line has been investigated in terms of the simultaneous replacement of glucose and glutamine, the most commonly employed carbon and nitrogen sources, pursuing the objective of achieving a more efficient use of these compounds, simultaneously avoiding the accumulation of lactate and ammonium in the medium. The key factor in this process is the selection of compounds that are slowly metabolized. Among the different compounds studied, galactose and glutamate provide the best results, allowing support of cell growth with an optimal balance between nutrient uptake and cell requirements and the generation of minimal quantities of lactate and ammonium. The attained results also highlight the capacity of the cells to redistribute their metabolism as a response to the changes in medium composition.
Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers (2017)

Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.
Studies on the active site of rat glutathione S‐transferase isoenzyme 4–4 (1989)

The active site of glutathione S-transferase isoenzyme 4-4, purified from rat liver, was studied by chemical modification. Tetrachloro-1,4-benzoquinone, a compound previously shown to inactivate glutathione S-transferases very efficiently by covalent binding in or close to the active site, completely prevented the alkylation of the enzyme by iodoacetamide, indicating that the reaction had taken place with cysteine residues. Both from radioactive labeling and spectral quantification experiments, evidence was obtained for the covalent binding of three benzoquinone molecules per subunit, i.e. equivalent to the number of cysteine residues present. This threefold binding was achieved with a fourfold molar excess of the benzoquinone, illustrating the high reactivity of this compound. Comparison of the number of amino acid residues modified by tetrachloro-1,4-benzoquinone with the decrease of catalytic activity revealed an almost complete inhibition after modification of one cysteine residue. Chemical modification studies with diethylpyrocarbonate indicated that all four histidine residues of the subunit are ethoxyformylated in an at least partially sequential manner. Modification of the second histidine residue resulted in complete loss of catalytic activity. Preincubation of the transferase with the glutathione conjugate of tetrachloro-1,4-benzoquinone resulted in 78% protection against this modification. However, glutathione itself hardly protected against the reaction with diethylpyrocarbonate. The intrinsic fluorescence properties of the enzyme were affected by covalent binding of tetrachloro-1,4-benzoquinone. The concentration dependency of the fluorescence quenching is strongly correlated with the inactivation of the enzyme, indicating that covalent binding of the benzoquinone occurs in the vicinity of at least one tryptophan residue. Finally, the binding of bilirubin, as measured by means of circular dichroism, was inhibited by preincubation of the enzyme with tetrachloro-1,4-benzoquinone in a manner which strongly correlated with the loss of enzymatic activity, the protection against inactivation by diethylpyrocarbonate, and the fluorescence quenching. All processes showed a 70-80% decrease after incubation of the enzyme with an equimolar amount of the benzoquinone. Thus, evidence is presented for the presence of a cysteine, a histidine and a tryptophan residue in, or in the vicinity of, the active site of the glutathione S-transferase 4 subunit.
Inhibition of trans-Retinoic Acid-Resistant Human Breast Cancer Cell Growth by Retinoid X Receptor-Selective Retinoids (1997)

All-trans-retinoic acid (trans-RA) and other retinoids exert anticancer effects through two types of retinoid receptors, the RA receptors (RARs) and retinoid X receptors (RXRs). Previous studies demonstrated that the growth-inhibitory effects of trans-RA and related retinoids are impaired in certain estrogen-independent breast cancer cell lines due to their lower levels of RAR alpha and RARbeta. In this study, we evaluated several synthetic retinoids for their ability to induce growth inhibition and apoptosis in both trans-RA-sensitive and trans-RA-resistant breast cancer cell lines. Our results demonstrate that RXR-selective retinoids, particularly in combination with RAR-selective retinoids, could significantly induce RARbeta and inhibit the growth and induce the apoptosis of trans-RA-resistant, RAR alpha-deficient MDA-MB-231 cells but had low activity against trans-RA-sensitive ZR-75-1 cells that express high levels of RAR alpha. Using gel retardation and transient transfection assays, we found that the effects of RXR-selective retinoids on MDA-MB-231 cells were most likely mediated by RXR-nur77 heterodimers that bound to the RA response element in the RARbeta promoter and activated the RARbeta promoter in response to RXR-selective retinoids. In contrast, growth inhibition by RAR-selective retinoids in trans-RA-sensitive, RAR alpha-expressing cells most probably occurred through RXR-RAR alpha heterodimers that also bound to and activated the RARbeta promoter. In MDA-MB-231 clones stably expressing RAR alpha, both RARbeta induction and growth inhibition by RXR-selective retinoids were suppressed, while the effects of RAR-selective retinoids were enhanced. Together, our results demonstrate that activation of RXR can inhibit the growth of trans-RA-resistant MDA-MB-231 breast cancer cells and suggest that low cellular RAR alpha may regulate the signaling switch from RAR-mediated to RXR-mediated growth inhibition in breast cancer cells.
Isolation and sequence of a human apolipoprotein CII cDNA clone and its use to isolate and map to human chromosome 19 the gene for apolipoprotein CII. (1984)

cDNA clones encoding human apolipoprotein CII (apo CII) were identified by screening an adult human liver cDNA library with a mixed oligonucleotide probe corresponding to all possible codons for apo CII amino acid 6-10. One clone with an approximately equal to 500-base-pair (bp) insert, designated pCII -711, was selected for DNA sequence analysis. This clone contained a DNA sequence that corresponded with the previously reported amino acid sequence of apo CII with only minor differences. The DNA sequence specified a polypeptide of 79 amino acids, compared to the 78 amino acids previously reported. The pCII -711 clone contains a 36-bp DNA sequence upstream from that specifying the NH2-terminal threonine which, when read in frame, specifies the amino acid sequence Leu-Val-Leu-Leu-Val-Leu-Gly-Phe-Glu-Val-Gln-Gly and may be part of an apo CII signal peptide. The pCII -711 clone also contains a 144-bp region that corresponds to the 3' untranslated region of apo CII mRNA as well as a portion of the poly(A) tail. Clone pCII -711 was used to isolate and characterize by restriction endonuclease digestion the gene for apo CII from a human genomic library. In addition, through Southern blot analysis of DNA from human-rodent somatic cell hybrids, clone pCII -711 also was used to provisionally map the gene for apo CII to human chromosome 19.
Outsourcing coordination and management of home wireless access points through an open API (2015)

In dense wireless deployments at homes, such as apartment buildings, neighboring home WLANs share the same unlicensed spectrum by deploying consumer-grade access points in their individual homes. In such environments, WiFi networks can suffer from intermittent performance issues such as wireless packet losses, interference from WiFi and non-WiFi sources due to the rapid growth and increasing diversity of devices that share the spectrum. In this paper, we propose a vendor-neutral cloud-based centralized framework called COAP to configure, coordinate and manage individual home APs using an open API implemented by these commodity APs. The framework, implemented using OpenFlow extensions, allows the APs to share various types of information with a centralized controller - interference and traffic phenomenon and various flow contexts, and in turn receive instructions - configuration parameters (e.g., channel) and transmission parameters (through coarse-grained schedules and throttling parameters). This paper describes the framework and associated techniques, applications to motivate its potential benefits, such as, upto 47% reduction in channel congestion and our experiences from having deployed it in actual home environments.
The 67 kDa laminin receptor increases tumor aggressiveness by remodeling laminin-1 (2005)

The association between expression of the 67 kDa laminin receptor (67LR) and tumor aggressiveness has been convincingly demonstrated although the exact function of this molecule in the metastatic process has remained unclear. In this study, we tested whether the laminin-1, upon interaction with 67LR, promotes tumor cell aggressiveness; the investigation was based on: (i) the previous demonstration that soluble 67LR, as well as a 20-amino-acid peptide corresponding to the 67LR laminin binding site, changes the conformation of laminin upon interaction with this adhesion molecule and (ii) the known relevance of microenvironment remodeling by the tumor, leading to structural modification of extracellular matrix components in tumor progression. MDAMB231 breast carcinoma cells plated on peptide G-treated laminin-1 exhibited a polygonal array of actin filament bundles compared with cells seeded on native laminin-1 which presented the actin bundles organized as multiple cables parallel to margins. Furthermore, in cells seeded on peptide G-treated laminin-1, 67LR was distinct from the alpha6 integrin subunit in filopodia protrusions in addition to colocalizing with this integrin in focal adhesion plaques as it occurs when cells are plated on native laminin-1. In addition to differences in tumor cell adhesion and migration found in cells exposed to peptide G-treated vs native laminin-1, breast carcinoma cells seeded on modified laminin-1 showed a 6-fold increase in invasion capability compared with cells seeded on unmodified laminin-1. Alterations in actin organization as well as adhesion, migration and especially invasion observed in MDAMB231 cells in the presence of peptide G-treated laminin-1 were even found in MDAMB231 cells that, after selection for 67LR high expression, were seeded on native laminin-1. As the 67LR shedding is proportional to its expression level, these findings indicate a role for 67LR in changing laminin structure. Expression analysis of 97 genes encoding proteins that mediate cell matrix interactions, revealed significant differences between cells exposed to modified vs unmodified laminin-1 in 19 genes, 17 of which--including those encoding alpha3 integrin, extracellular matrix protein 1, proteolytic enzymes (such as MT1-MMP, stromelysin-3 and cathepsin L) and their inhibitors--were up-modulated in cells treated with modified laminin-1. Zymogram analysis clearly indicated a significant increase in the activity of the gelatinolytic enzyme MMP-2 in the culture supernatant from cells exposed to modified laminin-1, without an increase in mRNA abundance as observed in microarray analysis. Invasiveness of tumor cells conditioned by modified laminin-1, evaluated as the capability to cross Matrigel basement, was significantly more inhibited by MMPinhibitor TIMP-2 than invasiveness induced by native laminin-1. Taken together, our findings indicate that the role of 67LR in tumor aggressiveness rests in its ability to modify laminin-1 thereby activating proteolytic enzymes that promote tumor cell invasion through extracellular matrix degradation.
Circulating tumour‐associated plasma DNA represents an independent and informative predictor of prostate cancer (2006)

Our data suggest that plasma DNA level is a highly accurate and informative predictor in uni- and multivariate models for the presence of prostate cancer on needle biopsy. The predictive accuracy was substantially increased by adding plasma DNA level. However, larger-scale studies are needed to further confirm its clinical impact on prostate cancer detection.
Baclofen for Alcohol Dependence: A Preliminary Open‐Label Study (2004)

These findings suggest that baclofen is reasonably tolerated in an alcohol-dependent population, although the high dropout rate in the study is of concern. Baclofen may be effective for the reduction of drinking, anxiety, and craving for some alcohol-dependent individuals. A larger-scale placebo-controlled study is needed to further explore these effects and to determine the characteristics of those who respond to this medication.