gebhart/patrepeval huggingface dataset:
DiskSeen: exploiting disk layout and access history to enhance I/O prefetch (2007)

Current disk prefetch policies in major operating systems track access patterns at the level of the file abstraction. While this is useful for exploiting application-level access patterns, file-level prefetching cannot realize the full performance improvements achievable by prefetching. There are two reasons for this. First, certain prefetch opportunities can only be detected by knowing the data layout on disk, such as the contiguous layout of file metadata or data from multiple files. Second, non-sequential access of disk data (requiring disk head movement) is much slower than sequential access, and the penalty for mis-prefetching a ‘random ’ block, relative to that of a sequential block, is correspondingly more costly. To overcome the inherent limitations of prefetching at the logical file level, we propose to perform prefetching directly at the level of disk layout, and in a portable way. Our technique, called DiskSeen, is intended to be supplementary to, and to work synergistically with, filelevel prefetch policies, if present. DiskSeen tracks the locations and access times of disk blocks, and based on analysis of their temporal and spatial relationships, seeks to improve the sequentiality of disk accesses and overall prefetching performance. Our implementation of the DiskSeen scheme in the Linux 2.6 kernel shows that it can significantly improve the effectiveness of prefetching, reducing execution times by 20%-53 % for micro-benchmarks and real applications such as grep, CVS, and TPC-H. 1
Imbalance Fault Detection of Direct-Drive Wind Turbines Using Generator Current Signals (2012)

Imbalance faults constitute a significant portion of all faults in wind turbine generators (WTGs). WTG imbalance fault detection using generator current measurements has advantages over traditional vibration-based methods in terms of cost, implementation, and system reliability. However, there are challenges in using current signals for imbalance fault detection due to low signal-to-noise ratio of the useful information in current signals and nonstationary characteristic frequencies of imbalance faults. This paper proposes a method of using generator stator currents for imbalance fault detection of direct-drive WTGs. In the proposed method, the variable shaft rotating frequency of a WTG is estimated from one phase stator current measured from the generator terminal by using a phase-locked loop method. The estimated shaft rotating frequency is then processed by using appropriate upsampling and variable-rate downsampling algorithms. Consequently, the variable characteristic frequencies of imbalance faults in the spectrum of the estimated shaft rotating frequency are converted to constant values. Therefore, the signatures of wind turbine imbalance faults can be clearly identified from power spectral density analysis of the converted shaft rotating frequency signal. Simulation and experimental results show that the proposed method is effective to detect various imbalance faults in direct-drive WTGs.
Degradation of Tau Protein by Puromycin-Sensitive Aminopeptidase in Vitro (2006)

Tau, a microtubule associated protein, aggregates into intracellular paired helical filaments (PHFs) by an unknown mechanism in Alzheimer's disease (AD) and other tauopathies. A contributing factor may be a failure to metabolize free cytosolic tau within the neuron. The buildup of tau may then drive the aggregation process through mass action. Therefore, proteases that normally degrade tau are of great interest. A recent genetic screen identified puromycin-sensitive aminopeptidase (PSA) as a potent modifier of tau-induced pathology and suggested PSA as a possible tau-degrading enzyme. Here we have extended these observations using human recombinant PSA purified from Escherichia coli. The enzymatic activity and characteristics of the purified PSA were verified using chromogenic substrates, metal ions, and several specific and nonspecific protease inhibitors, including puromycin. PSA was shown to digest recombinant human full-length tau in vitro, and this activity was hindered by puromycin. The mechanism of amino terminal degradation of tau was confirmed using a novel N-terminal cleavage-specific tau antibody (Tau-C6g, specific for cleavage between residues 13-14) and a C-terminal cleavage-specific tau antibody (Tau-C3). Additionally, PSA was able to digest soluble tau purified from normal human brain to a greater extent than either soluble or PHF tau purified from AD brain, indicating that post-translational modifications and/or polymerization of tau may affect its digestion by PSA. These results are consistent with observations that PSA modulates tau levels in vivo and suggest that this enzyme may be involved in tau degradation in human brain.
Pharmacokinetics of SCH 56592, a New Azole Broad-Spectrum Antifungal Agent, in Mice, Rats, Rabbits, Dogs, and Cynomolgus Monkeys (2000)

SCH 56592 is a new broad-spectrum azole antifungal agent that is in phase 3 clinical trials for the treatment of serious systemic fungal infections. The pharmacokinetics of this drug candidate were evaluated following its intravenous (i.v.) or oral (p.o.) administration as a solution in hydroxypropyl-beta-cyclodextrin (HPbetaCD) or oral administration as a suspension in 0.4% methylcellulose (MC) in studies involving mice, rats, rabbits, dogs, and cynomolgus monkeys. SCH 56592 was orally bioavailable in all species. The oral bioavailability was higher with the HPbetaCD solution (range, 52 to approximately 100%) than from the MC suspension (range, 14 to 48%) and was higher in mice ( approximately 100% [HPbetaCD] and 47% [MC]), rats ( approximately 66% [HPbetaCD] and 48% [MC]), and dogs (72% [HPbetaCD] and 37% [MC]) than in monkeys (52% [HPbetaCD] and 14% [MC]). In rabbits, high concentrations in serum suggested good oral bioavailability with the MC suspension. The i.v. terminal-phase half-lives were 7 h in mice and rats, 15 h in dogs, and 23 h in monkeys. In rabbits, the oral half-life was 9 h. In species given increasing oral doses (mice, rats, and dogs), serum drug concentrations were dose related. Food produced a fourfold increase in serum drug concentrations in dogs. Multiple daily doses of 40 mg of SCH 56592/kg of body weight for eight consecutive days to fed dogs resulted in higher concentrations in serum, indicating accumulation upon multiple dosing, with an accumulation index of approximately 2.6. Concentrations above the MICs and minimum fungicidal concentrations for most organisms were observed at 24 h following a single oral dose in MC suspension in all five species studied (20 mg/kg for mice, rats, and rabbits and 10 mg/kg for dogs and monkeys), suggesting that once-daily administration of SCH 56592 in human subjects would be a therapeutically effective dosage regimen.
SYNTHESIS AND REACTION OF NEW TYPE I–N YLIDE, N-TOSYLIMINOIODINANE (1975)

Abstract (Diacetoxyiodo)arene reacts with p-toluenesulfonamide in the presence of base to give the new type I–N ylide, N-tosyliminoaryliodinane. In the decomposition of this ylide, the nitrene intermediate is proposed to be formed and react with nucleophiles to afford the imine compounds.
WAFTL: A workload adaptive flash translation layer with data partition (2011)

Current FTL schemes have inevitable limitations in terms of memory requirement, performance, garbage collection overhead, and scalability. To overcome these limitations, we propose a workload adaptive flash translation layer referred to as WAFTL. WAFTL explores either page-level or block-level address mapping for normal data block based on access patterns. Page Mapping Block (PMB) is used to store random data and handle large number of partial updates. Block Mapping Block (BMB) is utilized to store sequential data and lower overall mapping table. PMB or BMB is allocated on demand and the number of PMB or BMB eventually depends on workload. An efficient address mapping is designed to reduce overall mapping table and quickly conduct address translation. WAFTL explores a small part of flash space as Buffer Zone to log writes sequentially and migrate data into BMB or PMB based on threshold. Static and dynamic threshold setting are proposed to balance performance and mapping table size. WAFTL has been extensively evaluated under various enterprise workloads. Benchmark results conclusively demonstrate that proposed WAFTL is workload adaptive and achieves up to 80% performance improvement, 83% garbage collection overhead reduction and 50% mapping table reduction compared to existing FTL schemes.
THE USE OF ELECTRICAL DEVICES FOR THE TREATMENT OF BLADDER DYSFUNCTION: A REVIEW OF METHODS (2004)

Randomized clinical trials to compare different techniques and evaluate placebo effects are urgently needed, as are further studies to elucidate modes of action to improve stimulation application and therapy results. The introduction of new stimulation methods may provide treatment alternatives as well as help answer more basic questions on electrical neurostimulation and neuromodulation.
Evaluation of the effects of porcine genogroup 1 torque teno virus in gnotobiotic swine (2008)

Analysis of these data revealed that porcine g1-TTV was readily transmitted to TTV-naïve swine and that infection was associated with characteristic pathologic changes in gnotobiotic pigs inoculated with g1-TTV. Thus, g1-TTV could be an unrecognized pathogenic viral infectious agent of swine. This indicated a directly associated induction of lesions attributable to TTV infection in swine for a virus of the genus Anellovirus.
Solubilization, Partial Purification, and Immunodetection of Squalene Synthetase from Tobacco Cell Suspension Cultures (1992)

Squalene synthetase, an integral membrane protein and the first committed enzyme for sterol biosynthesis, was solubilized and partially purified from tobacco (Nicotiana tabacum) cell suspension cultures. Tobacco microsomes were prepared and the enzyme was solubilized from the lipid bilayer using a two-step procedure. Microsomes were initially treated with concentrations of octyl-beta-d-thioglucopyranoside and glycodeoxycholate below their critical micelle concentration, 4.5 and 1.1 millimolar, respectively, to remove loosely associated proteins. Complete solubilization of the squalene synthetase enzyme activity was achieved after a second treatment at detergent concentrations above or at their critical micelle concentration, 18 and 2.2 millimolar, respectively. The detergent-solubilized enzyme was further purified by a combination of ultrafiltration, gel permeation, and Fast Protein Liquid Chromatography anion exchange. A 60-fold purification and 20% recovery of the enzyme activity was achieved. The partially purified squalene synthetase protein was used to generate polyclonal antibodies from mice that efficiently inhibited synthetase activity in an in vitro assay. The apparent molecular mass of the squalene synthetase protein as determined by immunoblot analysis of the partially purified squalene synthetase protein separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was 47 kilodaltons. The partially purified squalene synthetase activity was optimal at pH 6.0, exhibited a K(m) for farnesyl diphosphate of 9.5 micromolar, and preferred NADPH as a reductant rather than NADH.
Improving laminar mixing in a stirred vessel using impeller speed modulations (2010)

Mixing of high viscous liquids at low Reynolds numbers often leadas to inefficient mixing due to the presence of isolated mixing regions (IMRs) formed above and below the impeller. Much research effort has gone in recent years into developing better mixing methods to destroy IMRs. This paper investigates the mixing effects of impeller speed modulation in a Newtonian viscous liquid. The impeller speed modulation was carried out using four different wave forms namely, square, sine, triangle and pulse. Glycerol solution was agitated with a\nstandard six-bladed Rushton turbine in an unbaffled mixing vessel. Direct visualization of an acid-base neutralization reaction with fluorescent green dye was used to measure the mixing time. Digital image analysis was performed to determine the volume of the IMRs at different intervals of the mixing process. Results show that the best mixing performance can be achieved by using square wave modulation. Mixing with pulse, sine wave and triangle wave modulations does help in destroying IMRs. IMRs were still visible after a long period of mixing for the sine wave modulation while they were completely destroyed by other types of modulations.
p38alpha-selective MAP kinase inhibitor reduces tumor growth in mouse xenograft models of multiple myeloma. (2009)

Multiple myeloma (MM) is a clonal plasma cell malignancy, which is currently incurable. Therefore, new mono- or combined therapy treatment regimens in the early and advanced phases of MM are urgently needed to combat this disease. Recently, p38 mitogen-activated protein kinase (MAPK) has been implicated as playing an important role in MM. Therefore, the effect of a p38alpha-selective MAPK inhibitor, SCIO-469 (indole-5-carboxamide, ATP-competitive inhibitor), or its structural analog, SD-282 (indole-5-carboxamide, ATP-competitive inhibitor) was examined in mouse xenograft models of MM using human RPMI-8226 or H-929 plasmacytoma inocula. Oral treatment with SCIO-469 (10, 30, 90 mg/kg) twice daily was initiated in mice with palpable tumors of RPMI-8226 origin, a condition that mimics early human myeloma disease. In mice with palpable tumors, 14 days of SCIO-469 treatment significantly reduced RPMI-8226 tumor growth in a dose-dependent manner. A significant dose-dependent reduction in RPMI-8226 tumor growth was also observed when SCIO-469 oral treatment at doses of 10, 30 and 90 mg/kg twice daily was initiated in mice with tumors of pronounced size, a condition that mimics advanced human myeloma disease. In a similar set of studies employing the SCIO-469 analogue SD-282 at 90 mg/kg/bid orally, histological assessment at the end of the study demonstrated a significant reduction in RPMI-8226 tumor growth and angiogenesis. SD-282 treatment was additionally shown to significantly reduced expression of heat-shock protein-27 (HSP-27) and phospho-p38 in the tumor cells. Furthermore, co-administration of SCIO-469 with dexamethasone elicited antitumor properties in dexamethasone-sensitive H-929 tumors at much lower than the typically effective doses of dexamethasone, suggesting its potential for combined therapy. In conclusion, p38 inhibitors reduced human myeloma cell growth in vivo both at early and advanced phases of the disease. The current study also provides evidence of potential for co-therapy with dexamethasone.
Nucleotide sequence of the Salmonella typhimurium mutS gene required for mismatch repair: homology of MutS and HexA of Streptococcus pneumoniae (1988)

The mutS gene product of Escherichia coli and Salmonella typhimurium is one of at least four proteins required for methyl-directed mismatch repair in these organisms. A functionally similar repair system in Streptococcus pneumoniae requires the hex genes. We have sequenced the S. typhimurium mutS gene, showing that it encodes a 96-kilodalton protein. Amino-terminal amino acid sequencing of purified S. typhimurium MutS protein confirmed the initial portion of the deduced amino acid sequence. The S. typhimurium MutS protein is homologous to the S. pneumoniae HexA protein, suggesting that they arose from a common ancestor before the gram-negative and gram-positive bacteria diverged. Overall, approximately 36% of the amino acids of the two proteins are identical when the sequences are optimally aligned, including regions of stronger homology which are of particular interest. One such region is close to the amino terminus. Another, located closer to the carboxy terminus, includes homology to a consensus sequence thought to be diagnostic of nucleotide-binding sites. A third one, adjacent to the second, is homologous to the consensus sequence for the helix-turn-helix motif found in many DNA-binding proteins. We found that the S. typhimurium MutS protein can substitute for the E. coli MutS protein in vitro as it can in vivo, but we have not yet been able to demonstrate a similar in vitro complementation by the S. pneumoniae HexA protein.
American Journal of Gastroenterology Lecture: Intestinal Microbiota and the Role of Fecal Microbiota Transplant (FMT) in Treatment of C. difficile Infection (2013)

The vital roles that intestinal flora, now called microbiota, have in maintaining our health are being increasingly appreciated. Starting with birth, exposure to the outside world begins the life-long intimate association our microbiota will have with our diet and environment, and initiates determination of the post-natal structural and functional maturation of the gut. Moreover, vital interactions of the microbiota with our metabolic activities, as well as with the immunological apparatus that constitutes our major defense system against foreign antigens continues throughout life. A perturbed intestinal microbiome has been associated with an increasing number of gastrointestinal and non-gastrointestinal diseases including Clostridium difficile infection (CDI). It has become recognized that fecal microbiota transplantation (FMT) can correct the dysbiosis that characterizes chronic CDI, and effect a seemingly safe, relatively inexpensive, and rapidly effective cure in the vast majority of patients so treated. In addition, FMT has been used to treat an array of other gastrointestinal and non-gastrointestinal disorders, although experience in these other non-CDI diseases is in its infancy. More work needs to be done with FMT to ensure its safety and optimal route of administration. There is a conceptual sea change that is developing in our view of bacteria from their role only as pathogens to that of being critical to health maintenance in a changing world. Future studies are certain to narrow the spectrum of organisms that need to be given to patients to cure disease. FMT is but the first step in this journey.
The Study of International Cooperation on Emergencies (2017)

International cooperation on emergencies is significant to the response of these emergencies. Firstly, the connotation and characteristics of international cooperation on emergencies were analyzed. Secondly, the typical types of emergencies in need of international cooperation, the types of countries involved in international cooperation and the typical types of international cooperation modes on emergencies were analyzed in order to explain the mechanism of international cooperation. Finally, some strategies of international cooperation on emergencies were proposed. The result shows that, in order to have a better international cooperation, international cooperation modes on emergencies should be determined according to the types of emergencies, the situations of countries and organizations involved in it.
Integrating natural language, query processing, and semantic data models (2002)

The design and implementation of a natural language query processing system is described. The system is based on the CANDIDE object-oriented data model, which consists of a collection of instances and classes. Classes are arranged in a generalization hierarchy. Each instance belongs to one or more classes. CANDIDE includes a terminological reasoning capability, known as the Classifier, which is used to process queries. Natural language queries are converted into CANDIDE objects and then processed by the Classifier. Issues in natural language processing are discussed, including the lexical acquisition problem. The approach is unique in terms of aiding natural language processing with a semantic data model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Valyl-tRNA synthetase gene of Escherichia coli K12. Molecular genetic characterization. (1988)

We report the subcloning and characterization of the molecular elements necessary for the expression of the Escherichia coli valS gene which encodes the enzyme valyl-tRNA synthetase (EC 6.1.1.9). The valS gene was subcloned from the Clarke-Carbon plasmid pLC26-22 by genetic complementation of the valS temperature-sensitive mutant strain, AB4141. The protein-coding region of the valS structural gene was determined by in vitro DNA directed coupled transcription-translation assays. Assays of cellular extracts of cells transformed with a plasmid containing a full length copy of the valS gene enhanced in vivo valyl-tRNA synthetase-specific activity 12-fold. The DNA sequences of the 5'- and 3'-terminal regions of the valS structural gene are presented. The transcription initiation sites of the valS gene were determined, in vivo and in vitro, by S1 nuclease protection studies, primer-extension analysis and both alpha-32P labeled and gamma-32P-end-labeled in vitro transcription assays. In vivo, valS transcription initiates from tandem overlapping promoters separated by seven nucleotides. In vitro, only the upstream promoter is active. The presence of several regions of hyphenated dyad symmetry overlapping the tandem promoter region are noted. The valS translational start codon (AUG) is located 93 base pairs downstream from the major transcription initiation site. The valS transcriptional unit encodes only the valyl-tRNA synthetase gene since the 3' terminus of the amino acid-coding region of this gene is followed closely (26 base pairs) by an efficient rho-independent transcription termination site.
Improvement of Photosynthetic CO2 Fixation at High Light Intensity Through Reduction of Chlorophyll Antenna Size (2002)

At elevated light intensities (greater than ~200 μE/[m2·s]), the kinetic imbalance between the rate of photon excitation and thermally activated electron transport results in saturation of the rate of photosynthesis. Since maximum terrestrial solar radiation can reach 200 μE/(m2·s), a significant opportunity exists to improve photosynthetic efficiency at elevated light intensities by achieving a kinetic balance between photon excitation and electron transport, especially in designed large-scale photosynthetic reactors in which a low-cost and efficient biomass production system is desired. One such strategy is a reduction in chlorophyll (chl) antenna size in relation to the reaction center that it serves. In this article, we report recent progress in this area of research. Light-saturation studies for CO2 fixation were performed on an antenna-deficient mutant of Chlamydomonas (DS521) and the wild type (DES15) with 700 ppm of CO2 in air. The light-saturated rate for CO2 assimilation in the mutant DS521 was about two times higher (187 μmol/[h·mg of chl]) than that of the wild type, DES15 (95 μmol/[h·mg of chl]). Significantly, a partial linearization of the light-saturation curve was also observed. These results confirmed that DS521 has a smaller relative chl antenna size and demonstrated that reduction of relative antenna size can improve the overall efficiency of photon utilization at higher light intensities. The antenna-deficient mutant DS521 can provide significant resistance to photoinhibition, in addition to improvement in the overall efficiency of CO2 fixation at high light. The experimental data reported herein support the idea that reduction in chl antenna size could have significant implications for both fundamental understanding of photosynthesis and potential application to improve photosynthetic CO2 fixation efficiency.
Analysis of the T cell receptor repertoire in rheumatoid arthritis. (1997)

The V families found to be increased in 4 of the 8 patients studied were different, except for V beta 1 which was more highly expressed in 2 patients. The presence of conserved amino acid sequences in the CDR3 region is consistent with an antigen-driven T cell expansion at the site of autoimmune inflammation. These findings do not support our original hypothesis of the possible usefulness of therapy based on the inactivation or elimination of presumed pathogenic T cells using TCR-derived peptides or monoclonal antibodies against particular TCRs.