gebhart/patrepeval huggingface dataset:
Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing (2012)

High-throughput sequencing (HTS) yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig) genes, which are variable and often highly mutated. This paper describes Ig High-Throughput Sequencing Cleaner (Ig-HTS-Cleaner), a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig Insertion-Deletion Identifier (Ig-Indel-Identifier), a program for identifying legitimate and artifact insertions and/or deletions (indels). Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.
Current Therapy for Brain Tumors (1999)

In the last 30 years, while considerable progress has been made in laboratory research of malignant gliomas, fewer clinical breakthroughs can be highlighted. Laboratory research has improved our understanding of the biology, and especially the molecular genetics of this disease. Unfortunately, these successes highlight the difficulties in translating laboratory results into substantive clinical improvements. In part, these difficulties stem from a schizophrenic view of the development and evolution of brain tumors. We believe either that (1) brain tumors are local and therefore the most important research should have as its goal local control, or (2) brain tumors are diffuse, which is to say that the cells rapidly grow beyond their initial locus, and our research goal is the prevention or treatment of the advancing tumor front. Clearly both hypotheses have merit and, in fact, almost certainly, both are true. The question becomes, should we devote our research energies to one hypothesis at the exclusion of the other?
Water Enhancement of CO2Conversion on Silver in 1-Ethyl-3-Methylimidazolium Tetrafluoroborate (2012)

Electrochemical recycling of carbon dioxide back to fuels and chemicals could be a viable method for CO2 remediation if the efficiency of the process could be improved. One of the key challenges, though, is that the faradaic efficiency is low in the presence of water because water electrolysis is much easier than CO2 electrolysis on most transition metal catalysts. Previous investigators have found that one can eliminate water conversion, by eliminating water from the system, but this has not proven to be practical. Here we present an alternate route, where EMIM-BF4 is used to suppress water electrolysis. We observe that the addition of water to 1-ethyl-3-methyl imidazolium tetrafluoroborate (EMIM-BF4) actually increased the efficiency of CO2 conversion to CO. Indeed we find that little hydrogen is produced on silver in EMIM-Water solutions, provided the water concentration is no more than about 90% by mole. We observe an increase in rate of carbon monoxide (CO) production on silver and platinum as water is added to the electrolyte. We attribute this increase to the hydrolysis of tetrafluoroborate, which releases protons when mixed with water. Protons are shown to accelerate the reduction of CO2 until a critical mole fraction of water is reached.
Latent semantic indexing (1998)

Article Free Access Share on Latent semantic indexing: a probabilistic analysis Authors: Christos H. Papadimitriou Computer Science Division, U. C. Berkeley Computer Science Division, U. C. BerkeleyView Profile , Hisao Tamaki Computer Science Department, Meiji University Computer Science Department, Meiji UniversityView Profile , Prabhakar Raghavan IBM Almaden Research Center IBM Almaden Research CenterView Profile , Santosh Vempala Department of Mathematics, M.I.T. Department of Mathematics, M.I.T.View Profile Authors Info & Claims PODS '98: Proceedings of the seventeenth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systemsMay 1998 Pages 159–168https://doi.org/10.1145/275487.275505Published:01 May 1998Publication History 277citation2,760DownloadsMetricsTotal Citations277Total Downloads2,760Last 12 Months261Last 6 weeks43 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Engineering eukaryotic signal transduction with RNAi: Enhancing Drosophila S2 cell growth and recombinant protein synthesis via silencing of TSC1 (2006)

RNAi has been useful in the study of biochemical pathways, but has not been widely used as a tool in metabolic engineering. The work described here makes use of double-stranded RNA (dsRNA) for the post-transcriptional gene silencing of TSC1 in Drosophila S2 cells. TSC1 downregulates the insulin-mediated signal transduction pathway, and serves as a metabolic control to guard against cellular overproliferation and tumorogenesis in both flies and mammals. By silencing TSC1 with in vitro-synthesized dsRNA, we have created a tunable and specific metabolic "throttle" that, like insulin, apparently increases the specific growth rate of S2 cells in a dose-dependent manner. This "throttle," augments the benefits of insulin addition while apparently avoiding deleterious and pleiotropic effects which can lead to lysis. During the period wherein dsRNA was active, cell growth rate was increased by 11% by the addition of 15 microg/mL dsTSC1 and by over 20% by the addition of 30 microg/mL dsTSC1. Additionally, synthesis of recombinant green fluorescent protein (GFP) was increased nearly 50% in a stable S2 cell line inducibly expressing GFP. Accordingly, we have "tuned" a normally tumorogenic pathway in animals into an advantage for both growth and recombinant product synthesis in cell culture. Potential applications for improving eukaryotic cell culture are anticipated.
Raised serum levels of cachectin/tumor necrosis factor alpha in renal allograft rejection. (1987)

A sensitive radioimmunoassay was used for monitoring serum levels of endogenous cachectin/tumor necrosis factor alpha (TNF) in 10 renal transplant recipients. Acute allograft rejections were associated with marked elevations of circulating TNF. The peak levels of TNF (median 140 pg/ml) were in the same concentration range as previously reported in parasitic infections. The results show that the release of TNF into circulation is an early event in renal allograft rejection and that raised levels of TNF in man can also be induced by noninfectious stimuli.
Association Awards Presented at Annual Meeting in Chicago (1987)

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Utah Fruit Pest Control Handbook (1998)

azinphosmethyl Guthion 50WP 2-3 lbs ^^^^^^^^)) Bacillus thuringiensis (Bt) Biobit, Dipel, Javelin, MVP 1-2 lbs 2-3 qt ^^^^ arbaryl Sevin 50WP 2 lbs ^^^^^^^^^^^^^^Usually no problems if applied early in the season (before June) chlorpyrifos Lorsban 4E Lorsban 50WP 2-4 pts 3-4 lbs ^^^^^^^^^) ) )) Limit use because of high toxicity Limit use because of high toxicity clofentezine Apollo 50SC 4-8 fl oz ^^)) )) )) diazinon Diazinon 50WP 4 lbs ^^^^^^^^^d imethoate Dimethoate 2.67EC 2 qts ^^^^^^^^^^^Limit use because of high toxicity encapsulated methyl parathion Penncap-M 2F 6-8 pts ^^^^^)) )) endosulfan Thiodan 50WP 3 lbs ^^^^^^^^^^ sfenvalerate Asana 0.66EC 1 pt ^^^^^^^^^^^ )) Limit use because of high toxicity fenbutatin-oxide Vendex 4L Vendex 50WP 2 pts 1.5 lbs ^^^^^^^)) ^^^^)))) Limit use because of high toxicity formetanate hydrochloride Carzol 92SP1.5 lbs ^^^^^^^))))Best if used early in the season (before June).Highly toxic to bees
A 0.18-$\mu$m CMOS SoC for a 100-m-Range 10-Frame/s 200$\,\times\,$96-Pixel Time-of-Flight Depth Sensor (2013)

With the emerging need for high-resolution light detection and ranging (LIDAR) technologies in advanced driver assistance systems (ADAS), we introduce a system-on-a-chip (SoC) that performs time-correlated single-photon counting and complete digital signal processing for a time-of-flight (TOF) sensor. At the core of the 0.18- <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\mu$</tex> </formula> m CMOS SoC, we utilize linear arrays of 16 TOF and 32 intensity-only macro-pixels based on single-photon avalanche diodes in an original look-ahead concept, thus acquiring active TOF and passive intensity images simultaneously. The SoC also comprises an array of circuits capable of generating precise triggers upon spatiotemporal correlation events, an array of 64 12-b time-to-digital converters, and 768 kb of SRAM memory. The SoC provides the system-level electronics with a serial and low-bit-rate digital interface for: 1) multi-echo distance; 2) distance reliability; 3) intensity; and 4) passive-only intensity, thus mitigating system-level complexity and cost. A proof-of-concept prototype that achieves depth imaging up to 100 m with a resolution of 202 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\,\times\,$</tex> </formula> 96 pixels at 10 frames/s has been implemented. Quantitative evaluation of the TOF sensor under strong solar background illuminance, i.e., 70 klux, revealed a repeatability error of 14.2 cm throughout the distance range of 100 m, thus leading to a relative precision of 0.14%. Under the same conditions, the relative nonlinearity error was 0.11%. In order to show the suitability of our approach for ADAS-related applications, experimental results in which the depth sensor was operated in typical traffic situations have also been reported.
Efficacy of GAD-alum immunotherapy associated with HLA-DR3-DQ2 in recently diagnosed type 1 diabetes (2020)

GAD65-specific immunotherapy has a significant effect on C-peptide retention in individuals with recent-onset type 1 diabetes who have the DR3-DQ2 haplotype. Graphical abstract.
Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro. (1989)

tat, the trans-activator protein for human immunodeficiency virus 1 (HIV-1), has been expressed in Escherichia coli from synthetic genes. Purified tat binds specifically to HIV-1 trans-activation-responsive region (TAR) RNA in gel-retardation, filter-binding, and immunoprecipitation assays. tat does not bind detectably to antisense TAR RNA sequences, cellular mRNA sequences, variant TAR RNA sequences with altered stem-loop structures, or TAR DNA.
On the Kinetics of the Reaction between Human Antiplasmin and Plasmin (1978)

The reaction between antiplasmin (A) and plasmin (P) proceeds in at least two steps: a very fast reversible second-order reaction followed by a slower irreversible first-order reaction, and may be represented by: . The two forms of plasmin with different affinities for lysine-Sepharose (plasmin I and plasmin II) react at different rates with antiplasmin. The k1 is (3.8±0.3)×107 M−1 s−1, for the reaction between plasmin I and antiplasmin, and (1.8±0.2) × 107 M−1 s−1 for plasmin II and antiplasmin. This reaction rate is one of the fastest so far described for protein-protein interactions. The k1 for trypsin and antiplasmin is (1.8±0.2) × 10−10 M for plasmin II with antiplasmin. The second step has a half-time of approximately 165 s for both types of plasmin, corresponding to a k2 of 4.2×10−3 s−1. Plasmin which has 6-aminohexanoic acid bound to its lysine binding site or the substrate d-valyl-l-lysyl-p-nitroanilide bound to its active site does not react, or reacts very slowly, with antiplasmin. From these findings we postulate that plasmin formed in the circulating blood is rapidly neutralized by antiplasmin, but plasmin bound to fibrin is not. This hypothesis may provide a molecular basis for the mechanism of thrombolysis in vivo.
Glucose and Insulin Stimulate Heparin-releasable Lipoprotein Lipase Activity in Mouse Islets and INS-1 Cells (2001)

Lipoprotein lipase (LpL) provides tissues with triglyceride-derived fatty acids. Fatty acids affect beta-cell function, and LpL overexpression decreases insulin secretion in cell lines, but whether LpL is regulated in beta-cells is unknown. To test the hypothesis that glucose and insulin regulate LpL activity in beta-cells, we studied pancreatic islets and INS-1 cells. Acute exposure of beta-cells to physiological concentrations of glucose stimulated both total cellular LpL activity and heparin-releasable LpL activity. Glucose had no effect on total LpL protein mass but instead promoted the appearance of LpL protein in a heparin-releasable fraction, suggesting that glucose stimulates the translocation of LpL from intracellular to extracellular sites in beta-cells. The induction of heparin-releasable LpL activity was unaffected by treatment with diazoxide, an inhibitor of insulin exocytosis that does not alter glucose metabolism but was blocked by conditions that inhibit glucose metabolism. In vitro hyperinsulinemia had no effect on LpL activity in the presence of low concentrations of glucose but increased LpL activity in the presence of 20 mm glucose. Using dual-laser confocal microscopy, we detected intracellular LpL in vesicles distinct from those containing insulin. LpL was also detected at the cell surface and was displaced from this site by heparin in dispersed islets and INS-1 cells. These results show that glucose metabolism controls the trafficking of LpL activity in beta-cells independent of insulin secretion. They suggest that hyperglycemia and hyperinsulinemia associated with insulin resistance may contribute to progressive beta-cell dysfunction by increasing LpL-mediated delivery of lipid to islets.
Improvement of ground radiation antenna performance using compact EBG in presence of battery effects (2018)

In Internet‐of‐things devices, to alleviate the performance degradation of the ground radiation antenna due to the large battery, two compact electromagnetic bandgap (EBG) unit cells are introduced between the ground radiation antenna and the battery. The ground radiation antenna is comprised a small loop‐type circuit that is designed within a 5‐mm × 5‐mm ground clearance for 2.4‐GHz WLAN applications. The compact EBG unit cell is a modified square split‐ring resonator that is designed by meandering‐line technology. The measurement results showed that the 3:1 VSWR impedance bandwidth of the ground radiation antenna increased from 30 to 90 MHz, and the average total efficiency increased from 19% to over 54% with and without the introduction of the EBG structure, respectively.
Management of Clinically Suspected Acute Venous Thrombosis in Outpatients With Serial Impedance Plethysmography in a Community Hospital Setting (1989)

The reported high sensitivity and specificity of impedance plethysmography (IPG) in the diagnosis of proximal vein thrombosis were evaluated in a prospective cohort follow-up study, in which IPG was performed three times over a period of seven days in 243 consecutive outpatients with clinically suspected deep venous thrombosis (DVT). The test was abnormal in 112 patients (46%). The positive predictive value of an abnormal IPG for venography-proved DVT was 90%. One hundred thirty-one patients (54%) with repeatedly normal tests were considered not to have DVT, and anticoagulants were withheld. During six months of follow-up, completed in all patients with repeatedly normal IPG, no patient died of venous thromboembolism and no patient returned with clinically suspected pulmonary embolism. One patient (0.8%) returned after two months with recurrent leg symptoms, and venous thrombosis was documented (95% confidence limits, 0.02% to 4.21%). Another patient, who was nonsymptomatic, had an abnormal IPG at the three-month follow-up visit, and venography revealed venous thrombosis. Patients sent by general practitioners to a community hospital, with clinically suspected acute DVT, can be effectively managed by serial IPG alone.
Interstitial diode laser hyperthermia in the treatment of subcutaneous tumor (1996)

ILH with a low power 830 nm diode laser is an efficient treatment of subcutaneous tumor model. Partial responses are attributed to an insufficient heating at the tumor periphery. More precise control of the peripheral tumor temperature will improve the ILH results.
Enzymatic RNA synthesis with deoxynucleoside 5'‐O‐(1‐thiotriphosphates) (1993)

We have investigated the incorporation of 2'-deoxynucleoside-5'-O-(1-thiotriphosphates) into RNA transcripts using T7 RNA polymerase. With the exception of [alpha-S]dGTP, we obtained full-length transcripts of pre-tRNA(Phe) and pre-tRNA(Tyr) using an appropriate mixture of 2'-deoxynucleoside 5'-O-(1-thiotriphosphate) and the corresponding normal nucleoside triphosphate. The yields of the transcripts were comparable to those obtained with unmodified NTPs. Both substrates, [alpha-S]dTTP and [alpha-S]dATP, were inserted specifically. However, [alpha-S]dCTP was excluded at specific sites. We could not obtain transcripts using the deoxyguanosine derivative.
Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints (1993)

A general scheme for the improvement of electron-density maps is described which combines information from real and reciprocal space. The use of Sayre's equation, solvent flattening and histogram matching within this scheme has been described previously [Main (1990). Acta Cryst. A46, 372-377]. Non-crystallographic symmetry averaging, the use of a partial structure and constraints on individual structure factors have now been added. A computer program, SQUASH, is described which applies all these constraints simultaneously. Its application to the maps of several structures has been successful, particularly so when non-crystallographic symmetry is present. Uninterpretable maps have been improved to the point where a significant amount of the structure can be recognized. Applying the constraints simultaneously is more powerful than applying them all in series.
Cytokines in the cotton top tamarin model of human ulcerative colitis. (1996)

The cotton top tamarin is a unique model of human ulcerative colitis. This disease is clinically and histologically similar. It is also complicated in some cases by colon cancer. The cotton top tamarin provides an appropriate animal model for assessing new treatments in inflammatory bowel disease.
Comparative analysis of mouse hepcidin 1 and 2 genes: evidence for different patterns of expression and co‐inducibility during iron overload 1 (2003)

In contrast to the human genome, the mouse genome contains two HEPC genes encoding hepcidin, a key regulator of iron homeostasis. Here we report a comparative analysis of sequence, genomic structure, expression and iron regulation of mouse HEPC genes. The predicted processed 25 amino acid hepcidin 2 peptide share 68% identity with hepcidin 1 with perfect conservation of eight cysteine residues. Both HEPC1 and HEPC2 genes have similar genomic organization and have probably arisen from a recent duplication of chromosome 7 region, including the HEPC ancestral gene and a part of the adjacent USF2 gene. Insertion of a retroviral intracisternal A-particle element was found upstream of the HEPC1 gene. Both genes are highly expressed in the liver and to a much lesser extent in the heart. In contrast to HEPC1, a high amount of HEPC2 transcripts was detected in the pancreas. Expression of both genes was increased in the liver during carbonyl-iron and iron-dextran overload. Overall our data suggest that both HEPC1 and HEPC2 genes are involved in iron metabolism regulation but could exhibit different activities and/or play distinct roles.
Syntheses of 6-oxodecahydroisoquinoline-3-carboxylates. Useful intermediates for the preparation of conformationally defined excitatory amino acid antagonists (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses of 6-oxodecahydroisoquinoline-3-carboxylates. Useful intermediates for the preparation of conformationally defined excitatory amino acid antagonistsPaul L. Ornstein, M. Brian Arnold, Nancy K. Augenstein, and Jonathan W. PaschalCite this: J. Org. Chem. 1991, 56, 14, 4388–4392Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://doi.org/10.1021/jo00014a012RIGHTS & PERMISSIONSArticle Views567Altmetric-Citations38LEARN 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 InReddit PDF (720 KB) Get e-Alertsclose Get e-Alerts
Cervical But Not Urinary Excretion Of Cytomegalovirus Is Related To Sexual Activity And Contraceptive Practices In Sexually Active Women (1995)

The relationship between sexual activity and genitourinary excretion of cytomegalovirus (CMV) was evaluated in 1481 women at a sexually transmitted disease (STD) clinic. Among 951 who were CMV-seropositive, 16.6% had CMV isolated, from cervix alone in 9.4%, urine alone in 3.8%, and both sites in 4.2%. Isolation rates were highest in young women (P < .001). Compared with those with only cervical infection, women shedding from both cervix and urine were younger, began sexual activity when younger, had more recent partners, and a higher frequency of CMV-specific IgM, suggesting recent CMV infection. By logistic regression, cervical CMV excretion was associated with concomitant gonococcal infection (P = .008) and was less frequent in those using barrier contraception (P = .036). Isolated urinary excretion of CMV was not associated with sexual activity, concomitant cervical infections, or use of contraception. Cervical CMV infection is related to sexual activity, acquisition of other STDs, or exogenous reinfection, and urinary CMV is not.