gebhart/patrepeval huggingface dataset:
Molecular and biotechnological aspects of xylanases (1999)

Hemicellulolytic microorganisms play a significant role in nature by recycling hemicellulose, one of the main components of plant polysaccharides. Xylanases (EC 3.2.1.8) catalyze the hydrolysis of xylan, the major constituent of hemicellulose. The use of these enzymes could greatly improve the overall economics of processing lignocellulosic materials for the generation of liquid fuels and chemicals. Recently cellulase-free xylanases have received great attention in the development of environmentally friendly technologies in the paper and pulp industry. In microorganisms that produce xylanases low molecular mass fragments of xylan and their positional isomers play a key role in regulating its biosynthesis. Xylanase and cellulase production appear to be regulated separately, although the pleiotropy of mutations, which causes the elimination of both genes, suggests some linkage in the synthesis of the two enzymes. Xylanases are found in a cornucopia of organisms and the genes encoding them have been cloned in homologous and heterologous hosts with the objectives of overproducing the enzyme and altering its properties to suit commercial applications. Sequence analyses of xylanases have revealed distinct catalytic and cellulose binding domains, with a separate non-catalytic domain that has been reported to confer enhanced thermostability in some xylanases. Analyses of three-dimensional structures and the properties of mutants have revealed the involvement of specific tyrosine and tryptophan residues in the substrate binding site and of glutamate and aspartate residues in the catalytic mechanism. Many lines of evidence suggest that xylanases operate via a double displacement mechanism in which the anomeric configuration is retained, although some of the enzymes catalyze single displacement reactions with inversion of configuration. Based on a dendrogram obtained from amino acid sequence similarities the evolutionary relationship between xylanases is assessed. In addition the properties of xylanases from extremophilic organisms have been evaluated in terms of biotechnological applications.
Timing of Therapeutic Intervention Determines Functional and Survival Outcomes in a Mouse Model of Late Infantile Batten Disease (2007)

Classical late infantile neuronal ceroid lipofuscinosis (cLINCL) is a monogenic disorder caused by the loss of tripeptidyl peptidase 1 (TPP1) activity as a result of mutations in CLN2. Absence of TPP1 results in lysosomal storage with an accompanying axonal degeneration throughout the central nervous system (CNS), which leads to progressive neurodegeneration and early death. In this study, we compared the efficacies of pre- and post-symptomatic injections of recombinant adeno-associated virus (AAV) for treating the cellular and functional abnormalities of CLN2 mutant mice. Intracranial injection of AAV1-hCLN2 resulted in widespread human TPP1 (hTPP1) activity in the brain that was 10-100-fold above wild-type levels. Injections before disease onset prevented storage and spared neurons from axonal degeneration, reflected by the preservation of motor function. Furthermore, the majority of CLN2 mutant mice treated pre-symptomatically lived for at least 330 days, compared with a median survival of 151 days in untreated CLN2 mutant controls. In contrast, although injection after disease onset ameliorated lysosomal storage, there was evidence of axonal degeneration, motor function showed limited recovery, and the animals had a median lifespan of 216 days. These data illustrate the importance of early intervention for enhanced therapeutic benefit, which may provide guidance in designing novel treatment strategies for cLINCL patients.
Lysing Bacterial Spores by Sonication through a Flexible Interface in a Microfluidic System (2000)

Cell disruptions using ultrasonic energy transmitted through a flexible interface into a liquid region has limitations because the motion of the vibrating tip is not completely transferred into the liquid. To ensure that some degree of contact will be maintained between the ultrasonic horn tip and the flexible interface, the liquid must be pressurized. The pressure conditions that yield consistent coupling between the ultrasonic horn tip and the liquid region were explored in this study by using an analytical model of the system and test fixture experiments. The nature of the interaction between the horn tip and the flexible interface creates pulses of positive pressure rises, increase in temperature, streaming flow, and almost no cavitation in the liquid. There was sufficient energy to create a cloud of microspheres, or beads, that maintain a consistent pattern of ballistic motion in the liquid. The sonication was found to be repeatable by studying video recordings of bead motion and was shown to be statistically consistent using measurements of temperature rise. Sonication of bacterial spores to obtain measurements of released nucleic acid and SEM images of damaged spores were used to verify the effects of liquid pressure on the horn−interface−liquid coupling.
Rhythm complexity measures for music pattern recognition (2002)

Three measures of rhythm complexity are considered. It is suggested that these measures be used in a system for machine recognition of music patterns as determinants of relative weights assigned to pitch and rhythm errors. The three measures are characterized and a procedure for determining parameters of one of the measures is described.
Pretarget radiotherapy with an anti-CD25 antibody-streptavidin fusion protein was effective in therapy of leukemia/lymphoma xenografts (2003)

Although radioimmunotherapy with radiolabeled intact monoclonal antibodies has demonstrated efficacy in the treatment of lymphoma, it provides low tumor-to-normal-tissue radionuclide target ratios and unwanted prolonged radiation exposure to the bone marrow. To overcome these obstacles, the administration of the radionuclide was separated from that of the antibody by using an anti-IL-2 receptor alpha antibody single chain Fv-streptavidin fusion protein, followed by radiolabeled biotin to treat lymphoma or leukemia xenografted mice. This Pretarget approach provided extremely rapid and effective tumor targeting, permitting the use of short-lived alpha-emitting radionuclides. With the beta-emitter (90)Y, all of the 10 lymphoma-xenografted mice were cured. With the alpha-emitter (213)Bi, significant efficacy was obtained in treating leukemic mice, and, furthermore, when combined with immunotherapy, 7 of 10 leukemic mice were cured. Thus, Pretarget radioimmunotherapy is very promising and could represent the next generation in the treatment of lymphoma and leukemia.
Naltrexone and Alcohol Dependence (1997)

Naltrexone is clinically effective relative to placebo in individuals who comply with the treatment protocol and take medication. The modest treatment effects in the entire sample suggest that the clinical efficacy of naltrexone could be improved by enhancing treatment compliance.
EIO: error handling is occasionally correct (2008)

Abstract The reliability of file systems depends in part on howwell they propagate errors. We develop a static analysis technique, EDP, that analyzes how file systems andstorage device drivers propagate error codes. Running our EDP analysis on all file systems and 3 major storagedevice drivers in Linux 2.6, we find that errors are often incorrectly propagated; 1153 calls (13%) drop an errorcode without handling it. We perform a set of analyses to rank the robustnessof each subsystem based on the completeness of its error propagation; we find that many popular file systemsare less robust than other available choices. We confirm that write errors are neglected more often than readerrors. We also find that many violations are not cornercase mistakes, but perhaps intentional choices. Finally,we show that inter-module calls play a part in incorrect error propagation, but that chained propagations do not.In conclusion, error propagation appears complex and hard to perform correctly in modern systems. 1 Introduction The robustness of file systems and storage systems isa major concern, and rightly so [32]. Recent work has shown that file systems are especially unreliablewhen the underlying disk system does not behave as expected [20]. Specifically, many modern commodity filesystems, such as Linux ext3 [31], ReiserFS [23], IBM&amp;apos;s JFS [1], and Windows NTFS [27], all have serious bugsand inconsistencies in how they handle errors from the storage system. However, the question remains unan-swered as to why these fault-handling bugs are present.
Metabolic Sources of Hydrogen Peroxide in Aerobically Growing Escherichia coli (1995)

Exposure of cells to hydrogen peroxide (H2O2) mediates adaptive responses or oxidative damage, depending on the magnitude of the challenge. Determining the threshold for peroxide-mediated oxidative stress thus requires quantitation of the changes in endogenous H2O2 production. The intracellular steady-state concentrations of H2O2 were measured in intact Escherichia coli under different conditions. Compounds that block electron transport at NADH dehydrogenase (rotenone) or between ubiquinone and cytochrome b (antimycin) showed that univalent reduction of O2 can occur at these sites in vivo to form superoxide anion (O2-), in agreement with reports for mammalian mitochondria. Mutational inactivation of different components of the respiratory chain showed that H2O2 production also depended on the energy status of the cell and on the arrangement of respiratory chain components corresponding to particular growth conditions. Production rates for O2- and H2O2 were linearly related to the number of active respiratory chains that reached maximal values during exponential growth. In the strains defective in respiratory chain components, catalase activity was regulated to compensate for changes in the H2O2 production rates, which maintained intracellular H2O2 at 0.1-0.2 microM during aerobic growth over a wide range of cell densities. The expression of a katG'::lacZ fusion (reporting transcriptional control of the catalase-hydroperoxidase I gene) was increased by H2O2 given either as a pulse or as a steady production. This response not only depended on the type and severity of the stimulus but was also strongly influenced by the growth phase of the cells.
Bioorganometallic chemistry: a future direction for transition metal organometallic chemistry? (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBioorganometallic chemistry: a future direction for transition metal organometallic chemistry?Gerard Jaouen, Anne Vessieres, and Ian S. ButlerCite this: Acc. Chem. Res. 1993, 26, 7, 361–369Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/ar00031a002https://doi.org/10.1021/ar00031a002research-articleACS PublicationsRequest reuse permissionsArticle Views1136Altmetric-Citations271LEARN 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
Ergot alkaloids are not essential for endophytic fungus-associated population suppression of the lesion nematode, Pratylenchus scribneri, on perennial ryegrass (2006)

Abstract Several endophytic fungi of the genus Neotyphodium form symbiotic associations with Lolium spp. grasses and are renowned for production of bioactive alkaloids such as ergot alkaloids. Some of these endophytes make their grass partners less suitable as hosts for endoparasitic nematodes, including Pratylenchus spp. The potential for ergot alkaloids to affect nematode motility was investigated in vitro. Ergovaline, the ergot alkaloid pathway end product of several Neotyphodium spp., was the only ergot alkaloid tested that inhibited motility of Pratylenchus scribneri. The association of ergot alkaloids with nematode population suppression was examined in glasshouse experiments with strains of the perennial ryegrass endophyte Neotyphodium sp. isolate Lp1 (syn. Neotyphodium lolii × Epichloë typhina) that have been genetically modified to lack ergot alkaloids or to have an altered ergot alkaloid profile. Populations of P. scribneri were significantly smaller in pots of perennial ryegrass containing the wild-type, ergot alkaloid-producing endophyte than in pots of endophyte-free perennial ryegrass. Elimination of certain complex ergot alkaloids (ergovaline and lysergic acid amides) in one gene knockout strain, or complete elimination of ergot alkaloids in another, did not affect the ability of the endophyte to suppress populations of nematode. Presence and concentrations of ergot alkaloids in pseudostems were as expected based on presence and genotype of endophyte in each plant, but frequently were undetectable or in low concentration in roots. The data indicate that ergot alkaloids do not contribute significantly to the endophyte-associated suppression of Pratylenchus spp.
The Relationship between the Initial Gas Ratios and the Condensed Phase Composition in the CVD of B<sub>x</sub>C with BCl<sub>3</sub>-CH<sub>4</sub>-H<sub>2</sub> Precursors (2011)

For the preparation of the self-healing phase B x C with BCl 3 -CH 4 -H 2 precursors, the production has been examined as a function of the initial gas ratios of BCl 3 /(BCl 3 +CH 4 ) and H 2 /(BCl 3 +CH 4 ) at given temperature and pressure. The results show that the composition of the condensed phase is quite sensitive to the molar ratio of BCl 3 /(BCl 3 +CH 4 ) and H 2 /(BCl 3 +CH 4 ). The ideal condition for the deposition of B x C is that the ratio of BCl 3 /(BCl 3 +CH 4 ) is 0.8 and the H 2 /(BCl 3 +CH 4 ) ratio ranges from 10 to 10 5.2 . The carbon or boron-rich material is mainly controlled by the ratios of BCl 3 /(BCl 3 +CH 4 ) and H 2 /(BCl 3 +CH 4 ). The deposition condition of carbon-rich phase should be in low BCl 3 /(BCl 3 +CH 4 ) (0.0~0.8) and H 2 /(BCl 3 +CH 4 ) (10 -2 &lt;10 2 ) ratios, whereas that of the boron-rich phase needs high BCl 3 /(BCl 3 +CH 4 ) (0.8~1.0) and H 2 /(BCl 3 +CH 4 ) (10 4 ~10 5 ) ratios.
Raf-1 protein kinase activates the NF-kappa B transcription factor by dissociating the cytoplasmic NF-kappa B-I kappa B complex. (1993)

Addition of mitogenic growth factors to quiescent cells triggers complex signal transduction cascades that result in the reprogramming of gene expression and entry into the cell cycle. We have found that an oncogenic variant of the c-Raf-1 protein kinase stimulated the expression of promoters containing NF-kappa B binding sites. In situ immunofluorescence analysis revealed elevated nuclear levels of the p65 subunit of NF-kappa B in v-raf-transformed NIH 3T3 cells. Incubation of HeLa cell cytoplasmic extracts with a purified recombinant glutathione S-transferase-raf fusion protein in the presence of ATP released active NF-kappa B that could be detected by electrophoretic gel mobility shift assay. Coincubation of purified recombinant I kappa B and glutathione S-transferase-raf in the presence of ATP resulted in the phosphorylation of I kappa B. Coexpression of GAL4 (activation domain)-I kappa B and GAL4 (DNA-binding domain)-raf fusion proteins in yeast resulted in stimulation of a GAL4-responsive reporter gene, indicating that I kappa B and Raf interact physically in vivo. These results indicate that the Raf-1 kinase functions in signal transduction in part by activating the NF-kappa B transcription factor by phosphorylating I kappa B in the cytoplasmic I kappa B-NF-kappa B complex to release active NF-kappa B.
Colonization in the fish intestinal tract and production of inhibitory substances in intestinal mucus and faecal extracts by Carnobacterium sp. strain K1 (1997)

A non‐virulent Carnobacterium sp., designated strain K1, isolated from the gastrointestinal tract of Atlantic salmon, Salmo salar L., which produced inhibitory substances against bacterial fish pathogens, was examined in vitro for characteristics important for the colonization of the fish gastrointestinal tract and in vivo for persistence in the tract after oral dosing. In vitro growth experiments showed that the cells of this strain were metabolically active in both the intestinal mucus and faeces from salmonids. The production of growth inhibitors against the two common fish pathogens Vibrio anguillarum and Aeromonas salmonicida by Carnobacterium sp. strain K1 was demonstrated in vitro in mucus and faecal extracts. Furthermore, it was demonstrated that the Carnobacterium cells remained viable in the gastrointestinal tract for several days and that no detrimental effect to the fish was observed as a result of the presence of the bacterium.
A two phase successive cancellation decoder architecture for polar codes (2013)

We propose a two-phase successive cancellation (TPSC) decoder architecture for polar codes that exploits the array-code property of polar codes by breaking the decoding of a length-TV polar code into a series of length-√ L decoding cycles. Each decoding cycle consists of two phases: a first phase for decoding along the columns and a second phase for decoding along the rows of the code array. The reduced decoder size makes it more affordable to implement the core decoder logic using distributed memory elements consisting of flip-flops (FFs), as opposed to slower random access memory (RAM), leading to a speed up in clock frequency. To minimize the circuit complexity, a single decoder unit is used in both phases with minor modifications. The re-use of the same decoder module makes it necessary to recall certain internal decoder state variables between decoding cycles. Instead of storing the decoder state variables in RAM, the decoder discards them and calculates them again when needed. Overall, the decoder has O(√ L) circuit complexity excluding RAM, and a latency of approximately 2.57V. A RAM of size O(N) is needed for storing the channel log-likelihood variables and the decoder decision variables. As an example of the proposed method, a length N = 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> bit polar code is implemented in an FPGA and the synthesis results are compared with a previously reported FPGA implementation. The results show that the proposed architecture has lower complexity, lower memory utilization with higher throughput, and a clock frequency that is less sensitive to code length.
Fundal dysaccommodation in functional dyspepsia: head-to-head comparison between the barostat and three-dimensional ultrasonographic technique (2006)

3DUS is a feasible non-invasive technique to measure gastric volumes and shows a distinct overlap with barostat data in healthy subjects and patients with functional dyspepsia. Fullness relates to distal gastric volumes when assessed by non-invasive 3DUS.
Comparison of the effects of tamoxifen and of a tamoxifen analogue that does not bind the estrogen receptor on serum lipid profiles in the cockerel (1990)

Administration of the nonsteroidal antiestrogen tamoxifen to cockerels results in dose- and time-dependent decreases in the levels of free and esterified cholesterol, phospholipids, and triglycerides in serum and in very low density and low density lipoprotein fractions. Similar changes can be elicited using a tamoxifen analogue, N,N-diethyl-2-[(4-phenylmethyl)phenoxy]ethanamine.HCl (DPPE). Like tamoxifen, this compound is capable of binding antiestrogen binding sites and exhibits a relative binding affinity of 90% compared with tamoxifen (Ki approximately 4-5 nM). Unlike tamoxifen, DPPE shows no measureable affinity for the cockerel liver nuclear estrogen receptor. Further, DPPE exhibits no estrogen agonist or antagonist activity as measured at the level of synthesis of apolipoprotein II of very low density lipoprotein by liver, synthesis of ovalbumin by oviduct, or growth of the oviduct. Although it is possible that the lipid-lowering effects of tamoxifen result from the opposition of endogenous estrogen action in the cockerel, the similarity of the effects of tamoxifen and DPPE on the lipid profiles suggests common mechanisms that do not involve the estrogen receptor.
Electrochemical and Surface Studies of Carbon Dioxide Reduction to Methane and Ethylene at Copper Electrodes in Aqueous Solutions (1989)

The electrochemical reduction of to and in aqueous alkaline solutions at Cu electrodes was studied under potentiostatic conditions at −2.00V vs. SCE. The current at the Cu electrodes and the rate of hydrocarbon formation were monitored as a function of time over a temperature range from 0 to 48°C. Solutions of formate, formaldehyde, and methanol, possible intermediates in the reduction process, were also electrolyzed. Surface analyses (XPS and AES) were also performed on the Cu electrodes following electrolysis to identify surface intermediates. In addition to hydrocarbon formation, a poisoning process occurred, causing a deposit of a black film on the surface of the Cu cathode. XPS and AES studies indicated that the black film was graphitic carbon, probably the result of a side reaction, the reduction of through formate to graphite. A tentative reaction mechanism for reduction, based upon the data here and those of previous investigators, involving the reaction path , is proposed.
Production of reovirus type-1 and type-3 from Vero cells grown on solid and macroporous microcarriers (1999)

Two strains of reovirus were propagated in Vero cells grown in stationary or microcarriers cultures. Vero cells grown as monolayers on T-flasks or in spinner cultures of Cytodex-1 or Cultispher-G microcarriers could be infected with reovirus serotype 1, strain Lang (T1L), and serotype 3, strain Dearing (T3D). A regime of intermittent low speed stirring at reduced culture volume was critical to ensure viral infection of cells in microcarrier cultures. The virus titre increased by 3 to 4 orders of magnitude over a culture period of 150 h. Titres of the T3D reovirus strain were higher (43%) compared to those of the T1L strain in all cultures. Titres were significantly higher in T-flask and Cytodex-1 microcarrier cultures compared to Cultispher-G cultures with respect to either reovirus type. The viral productivity in the microcarrier cultures was dependent upon the multiplicity of infection (MOI) and the cell/bead ratio at the point of infection. A combination of high MOI (5 pfu/cell) and high cell/bead loading (>400 for Cytodex-1 and >1,000 for Cultispher-G) resulted in a low virus productivity per cell. However, at low MOI (0.5 pfu/cell) the virus productivity per cell was significantly higher at high cell/bead loading in cultures of either microcarrier type. The maximum virus titre (8.5 x 10(9) pfu/mL) was obtained in Cytodex-1 cultures with a low MOI (0.5 pfu/cell) and a cell/bead loading of 1,000. The virus productivity per cell in these cultures was 4,000 pfu/cell. The lower viral yield in the Cultispher-G microcarrier cultures is attributed to a decreased accessibility of the entrapped cells to viral infection. The high viral productivity from the Vero cells in Cytodex-1 cultures suggests that this is a suitable system for the development of a vaccine production system for the Reoviridae viruses.