gebhart/patrepeval huggingface dataset:
Direct method for quantitation of extreme polymerase error frequencies at selected single base sites in viral RNA (1986)

Methods are described which allow direct quantitation and sequence analysis of base substitution levels at predetermined single nucleotide positions in cloned pools of an RNA virus genome or in its RNA transcripts in vitro. Base substitution frequencies for vesicular stomatitis virus (VSV) at one highly conserved site examined were reproducible and extremely high, averaging between 10(-4) and 4 X 10(-4) substitutions per base incorporated at this single site. If polymerase error frequencies averaged as high at all other sites in the 11-kilobase VSV genome, then every member of a cloned VSV population would differ from most other genomes in that clone at a number of different nucleotide positions. The preservation of a consensus sequence in such variable RNA virus genomes then could only result from strong biological selection (in a single host or multihost environment) for the most fit and competitive representatives of extremely heterogeneous virus populations.
Evolution of polymerase chain reaction to a quantitative laboratory tool (1995)

Journal Article Evolution of polymerase chain reaction to a quantitative laboratory tool Get access R A McPherson R A McPherson Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 41, Issue 8, 1 August 1995, Pages 1065–1067, https://doi.org/10.1093/clinchem/41.8.1065 Published: 01 August 1995
Calcium Binds to Leptospiral Immunoglobulin-like Protein, LigB, and Modulates Fibronectin Binding (2008)

Pathogenic Leptospira spp. express immunoglobulin-like proteins, LigA and LigB, which serve as adhesins to bind to extracellular matrices and mediate their attachment on host cells. However, nothing is known about the mechanism by which these proteins are involved in pathogenesis. We demonstrate that LigBCen2 binds Ca(2+), as evidenced by inductively coupled plasma optical emission spectrometry, energy dispersive spectrometry, (45)Ca overlay, and mass spectrometry, although there is no known motif for Ca(2+) binding. LigBCen2 binds four Ca(2+) as determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The dissociation constant, K(D), for Ca(2+) binding is 7 mum, as measured by isothermal titration calorimetry and calcium competition experiments. The nature of the Ca(2+)-binding site in LigB is possibly similar to that seen in the betagamma-crystallin superfamily, since structurally, both families of proteins possess the Greek key type fold. The conformation of LigBCen2 was significantly influenced by Ca(2+) binding as shown by far- and near-UV CD and by fluorescence spectroscopy. In the apo form, the protein appears to be partially unfolded, as seen in the far-UV CD spectrum, and upon Ca(2+) binding, the protein acquires significant beta-sheet conformation. Ca(2+) binding stabilizes the protein as monitored by thermal unfolding by CD (50.7-54.8 degrees C) and by differential scanning calorimetry (50.0-55.7 degrees C). Ca(2+) significantly assists the binding of LigBCen2 to the N-terminal domain of fibronectin and perturbs the secondary structure, suggesting the involvement of Ca(2+) in adhesion. We demonstrate that LigB is a novel bacterial Ca(2+)-binding protein and suggest that Ca(2+) binding plays a pivotal role in the pathogenesis of leptospirosis.
The burden of prostate cancer in Asian nations (2012)

Efforts to systematically collect cancer incidence data in Asian nations must be expanded. Current CI5 data indicate a rise in PCa ASIR in several populous Asian countries. If these rates continue to rise, it is uncertain whether there will be sufficient resources in place, in terms of trained personnel and infrastructure for medical treatment and continuum of care, to handle the increase in PCa patient volume. The recommendation by some experts to initiate PSA screening in Asian nations could compound a resource shortfall. Obtaining accurate estimates of PCa incidence in these countries is critically important for preparing for a potential shift in the public health burden posed by this disease.
Dietary myristic acid modifies the HDL-cholesterol concentration and liver scavenger receptor BI expression in the hamster (2002)

The influence of myristic acid in a narrow physiological range (0·5 to 2·4 % of total dietary energy) on the plasma and hepatic cholesterol metabolism was investigated in the hamster. The hamsters were fed on a diet containing 12·5 g fat/100 g and 0·05 g cholesterol/100 g with 0·5 % myristic acid (LA diet) for 3 weeks (pre-period). During the following 3 weeks (test period), they were divided into four dietary groups with 0·5 % (LA), 1·2 % (LM), 1·8 % (ML) or 2·4 % (M) myristic acid. Finally, half the hamsters in each group were again fed the LA diet for another 3 weeks (post-period). At the end of the test period, the hepatic expression of the scavenger receptor BI (SR-BI) was lower in the LM, ML and M groups than in the LA group whereas the hepatic cholesteryl ester concentration was higher. Cholesterol 7α hydroxylase activity was lower in the ML and M groups than in the LA and LM groups while the sterol 27 hydroxylase and 3-hydroxy-3-methyl glutaryl coenzyme A reductase activities were not modulated by dietary myristic acid. This is the first time a negative correlation has been observed between the HDL-cholesterol concentration and the hepatic mass of SR-BI ( r -0·69; P &lt;0·0001) under physiological conditions. An inverse linear regression was also shown between SR-BI and the percentage of myristic acid in the diet ( r -0·75; P &lt;0·0001). The hepatic mass of SR-BI in the M group had increased at the end of the post-period compared with the test-period values. The present investigation shows that myristic acid modulates HDL-cholesterol via a regulation of the SR-BI expression.
A New Multi-vehicle Trajectory Generator to Simulate Vehicle-to-Vehicle Encounters (2018)

Generating multi-vehicle trajectories from existing limited data can provide rich resources for autonomous vehicle development and testing. This paper introduces a multi-vehicle trajectory generator (MTG) that can encode multi-vehicle interaction scenarios (called driving encounters) into an interpretable representation from which new driving encounter scenarios are generated by sampling. The MTG consists of a bi-directional encoder and a multi-branch decoder. A new disentanglement metric is then developed for model analyses and comparisons in terms of model robustness and the independence of the latent codes. Comparison of our proposed MTG with $β$-VAE and InfoGAN demonstrates that the MTG has stronger capability to purposely generate rational vehicle-to-vehicle encounters through operating the disentangled latent codes. Thus the MTG could provide more data for engineers and researchers to develop testing and evaluation scenarios for autonomous vehicles.
Improved leukemia-free survival after postconsolidation immunotherapy with histamine dihydrochloride and interleukin-2 in acute myeloid leukemia: results of a randomized phase 3 trial (2006)

The primary objective of this phase 3 study was to determine whether postconsolidation immunotherapy with interleukin-2 (IL-2) and histamine dihydrochloride (HDC) improved the leukemia-free survival (LFS) of adult patients with acute myeloid leukemia (AML) in complete remission (CR). Three hundred twenty patients with AML (median age, 57 years; range, 18-84 years) were stratified by CR1 or subsequent CR (CR > 1) and randomly assigned to treatment with HDC/IL-2 or no treatment (control). Treatment comprised 10 21-day cycles with IL-2 (16 400 U/kg) plus HDC (0.5 mg); both compounds were administered by subcutaneous injection twice daily. Study arms were balanced for age, sex, previous treatment, leukemic karyotypes, time from CR to inclusion, and frequency of secondary leukemia. Three years after enrollment of the last patient, treatment with HDC/IL-2 was found to improve LFS over control in the study population (CR1 + CR > 1, n = 320; P < .01, log-rank test). For patients in CR1 (n = 261), treatment significantly improved LFS (P = .01) with 3-year LFS estimates of 40% (HDC/IL-2) compared with 26% (control). Side effects were typically mild to moderate. These results indicate that HDC/IL-2 treatment offers an efficacious and tolerable treatment for patients with AML in remission.
A Novel Role of Follistatin, an Activin-binding Protein, in the Inhibition of Activin Action in Rat Pituitary Cells (1997)

There are two types of the activin-binding protein follistatin (FS), FS-288 and FS-315. These result from alternative splicing of mRNA. FS-288 exhibits high affinity for cell-surface heparan sulfate proteoglycans, whereas FS-315 shows low affinity. To understand the physiological role of cell-associated FS, we investigated the binding of activin to cell-associated FS and its behavior on the cell surface using primary cultured rat pituitary cells. Affinity cross-linking experiments using 125I-activin A demonstrated that activin bound to rat pituitary cells via FS as well as to their receptors on the cell surface. FS-288 promoted the binding of activin A to the cell surface more markedly than FS-315. When the cells were incubated with 125I-activin A in the presence of FS-288, significant degradation of activin A was observed, and this was dependent on the FS-288 concentration. This activin degradation was abolished by heparan sulfate, chloroquine, and several lysosomal enzyme inhibitors. Moreover, FS-288 stimulated cellular uptake of activin A, whereas chloroquine suppressed lysosomal degradation following internalization, as demonstrated by microscopic autoradiography. These results suggest that cell-associated FS-288 accelerates the uptake of activin A into pituitary cells, leading to increased degradation by lysosomal enzymes, and thus plays a role in the activin clearance system.
Mathematical Models of Tumour Invasion Mediated by Transformation‐Induced Alteration of Microenvironmental pH (2001)

The invasive phenotype, characteristic of malignancy, is found in multiple transformed populations with widely varying genotypes. The authors hypothesize that this genetic heterogeneity and instability precludes mechanisms of tumour invasion requiring consistent, coordinated production of one or more proteins or other macromolecules. Instead, this model assumes that the genetically disordered, unstable populations found in tumours must employ a simple mechanism of invasion that arises from one common trait of all transformed cells--reversion to a phenotype more primitive (less differentiated) than the tissue of origin. Specifically, this approach focuses on primitive metabolic pathways with preferential use of glycolysis for energy production. Mathematical models of invasive cancer based on tumour-induced acidification of the microenvironment are presented. Using population ecology and diffusion-reaction models, it is shown that normal tissue adjacent to the tumour edge is subjected to an extracellular pH that is significantly lower than normal. This leads to degradation of the interstitial matrix, loss of intercellular gap junctions and cell necrosis. Tumour cells have an optimal extracellular pH less than that of normal cells and are thus able to thrive in the acidic microenvironment expanding into the space of the dying normal tissue. The model is consistent with extant data on the tumour microenvironment as well as clinical data relating increasing tumour invasiveness with elevated glucose utilization and lactate content. It predicts well-established phenomena in tumorigenesis such as the adenoma-carcinoma sequence and the critical role of angiogenesis in the invasive phenotype. An acellular gap at the tumour host interface is also predicted and can be demonstrated in pathologic specimens. Novel treatment approaches based on this model are discussed.
An Aromatization Reaction of a Cross-conjugated Dienone System with Zinc. II. Aromatization of Steroidal 1,4-Dien-3-one and 1,4,6-Trien-3-one System with Zinc1 (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn Aromatization Reaction of a Cross-conjugated Dienone System with Zinc. II. Aromatization of Steroidal 1,4-Dien-3-one and 1,4,6-Trien-3-one System with Zinc1K. Tsuda, E. Ohki, and S. NozoeCite this: J. Org. Chem. 1963, 28, 3, 783–785Publication Date (Print):March 1, 1963Publication History Published online1 May 2002Published inissue 1 March 1963https://pubs.acs.org/doi/10.1021/jo01038a046https://doi.org/10.1021/jo01038a046research-articleACS PublicationsRequest reuse permissionsArticle Views533Altmetric-Citations41LEARN 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
Not-So-Latent Dirichlet Allocation: Collapsed Gibbs Sampling Using Human Judgments (2010)

Probabilistic topic models are a popular tool for the unsupervised analysis of text, providing both a predictive model of future text and a latent topic representation of the corpus. Recent studies have found that while there are suggestive connections between topic models and the way humans interpret data, these two often disagree. In this paper, we explore this disagreement from the perspective of the learning process rather than the output. We present a novel task, tag-and-cluster, which asks subjects to simultaneously annotate documents and cluster those annotations. We use these annotations as a novel approach for constructing a topic model, grounded in human interpretations of documents. We demonstrate that these topic models have features which distinguish them from traditional topic models.
Bone-implant interface with simulated insertion stress around an immediately loaded dental implant in the anterior maxilla: a three-dimensional finite element analysis. (2012)

In the maxilla, when immediate loading is applied after implant placement, 11.5- and 13.0-mm-long single implants showed more favorable stress patterns than the others analyzed. If implants longer than 15.0 mm are used in immediate loading, sufficient bone volume in the recipient site should be considered an important factor.
Optimal weighted loop fusion for parallel programs (1997)

Article Free Access Share on Optimal weighted loop fusion for parallel programs Authors: Nimrod Megiddo IBM Almaden Research Center and Tel Aviv University IBM Almaden Research Center and Tel Aviv UniversityView Profile , Vivek Sarkar MIT Laboratory for Computer Science and IBM Software Solutions Division MIT Laboratory for Computer Science and IBM Software Solutions DivisionView Profile Authors Info & Claims SPAA '97: Proceedings of the ninth annual ACM symposium on Parallel algorithms and architecturesJune 1997 Pages 282–291https://doi.org/10.1145/258492.258520Online:01 June 1997Publication History 38citation550DownloadsMetricsTotal Citations38Total Downloads550Last 12 Months23Last 6 weeks6 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
Initial experience with a direct antithrombin, Hirulog, in unstable angina. Anticoagulant, antithrombotic, and clinical effects. (1993)

In unstable angina patients, Hirulog infusions quickly and reproducibly yield stable, dose-dependent anticoagulant and antithrombotic effects with a favorable clinical efficacy profile.
A hybrid portfolio theory model based on genetic algorithm and vector quantization (2002)

Portfolio theory considers a sequential portfolio selection procedure with the goal of best analyzing and predicting the performance of the market. Data compression techniques such as context-based modeling and vector quantization are based on a memoryless or near-memoryless prediction process and suit for the memoryless nature of the stock market data. In this paper, we propose a data compression-based portfolio prediction model hybridized with the fuzzy logic and genetic algorithm. This model exploits the prediction power of the lossy compression techniques such as vector quantization and context-based modeling and applies the prediction to the portfolio theory. In the model, the quantifiable microeconomic stock data are first optimized through the genetic algorithms to generate the most effective microeconomic data in relation to the stock market performance. The nonquantifiable microeconomic data are modeled with the fuzzification process. Then the previous stock market performance with the effective stock data and the fuzzified microeconomic data are processed based on the context-based modeling and vector quantization. Finally, the prediction of the stock market performance with the stock data is defuzzified using the fuzzification model to produce a portfolio performance prediction. The experiment on JF Asean Unit Trust using this portfolio theory model has shown a reliable prediction for the performance of the Trust for the past 5 years.
The Effect of Hyperthermia on Human Prostatic Carcinoma Cell Lines: Evaluation in Vitro (1989)

The effect of hyperthermia on established human prostate carcinoma cell lines (PC-3, DU-145) and related sublines (1-LN, 125-1L) was investigated in vitro. Cells were exposed to heat treatment at 43C or 37C for varying time intervals, (one hr or two hrs) and cell survival was evaluated by the colony formation assay and by measurement of cellular growth rate. While one hr exposure at 43C did show a mean inhibition of colony formation, ranging from 29 to 41%, a statistically significant increase in inhibition rate (p less than 0.001) was observed at two hr exposure, ranging from 57 to 92%. This study is a report of the cytotoxic effect of hyperthermia on established human prostatic tumor cell lines. These in vitro results indicate that hyperthermia may become a potentially useful form of adjunctive therapy for local control of prostatic cancer. However, the temperature and exposure time may have an important impact on cell kill when this new modality for cancer treatment is proposed for a clinical trial.
Prevention of Apoptotic Neuronal Death by GM1 Ganglioside (1995)

We have used serum-deprived cultures of wild type and genetically modified PC12 cells to investigate the molecular mechanisms by which monosialoganglioside (GM1) rescues neuronal cells from apoptotic death elicited by withdrawal of trophic support. Our findings indicate that GM1-promoted survival can be mediated in part by the Trk NGF receptor as well as by TrkB, and potentially by tyrosine kinase receptors for additional neurotrophic growth factors. Experiments employing K-252a, an inhibitor of Trk kinases, and PC12 cells overexpressing a dominant inhibitory form of Trk both indicate that a portion of the survival-promoting activity of GM1 is evoked by receptor dimerization and autophosphorylation. In consonance with this we find that GM1 stimulates Trk tyrosine autophosphorylation and Trk-associated protein kinase activity. These observations may provide a mechanism to account for the reported in vitro and in vivo trophic actions of GM1.
An Improved Kick Detection System for Floating Rigs (1991)

ABSTRACT Early detection of fluid influx from the formation (generally known as a "kick") is a key consideration for rig safety. The first indication of many kicks is given by a comparison of flow-in and flow-out of the well being drilled. Accurate flow measurement is therefore of crucial importance to the drilling industry. The heave motion of a floating rig, however, produces large instantaneous variation in flow-out. These fluctuations can simply be averaged over several heave periods but this leads to a delay in detecting an influx. This paper describes a new approach to obtain an improved flow-out indication by utilising measurements of rig movement in order to predict expected flow variations. This information is used to adaptively compensate flow-out readings from existing sensors for the effects of rig motion to provide a more accurate measure of the instantaneous flow from the well. The technique has been incorporated in a drilling contractor's computerised monitoring and alarm system which displays the compensated measurements in realtime and automatically warns the driller and other key personnel of any influx or loss. Field examples are presented to illustrate the effectiveness of the system and to show that a reliable alarm warns of changes in flow-out before they would normally be apparent with existing detection systems.
Fatty amidoamine derivatives: N,N‐dimethyl‐N‐(3‐alkylamidopropyl)amines and their salts (1968)

Abstract A group of cationic surfactants based on N‐alkylamidopropyl‐N,N‐dimethylamines, R‐CONHCH 2 CH 2 CH 2 N(CH 3 ) 2 , was studied. Caprylamidopropyl, capramidopropyl, lauramidopropyl, stearamidopropyl and oleamidopropyl dimethylamines were prepared, purified and characterized. NMR, IR, and pK b data are reported. The acetate and methylchloride quaternary salts of these amines were also prepared and evaluated as bactericides gelling agents, and foaming surfactants. Surface tensions, interfacial tensions, critical micelle concentrations and Ross‐Miles foam heights were determined. N‐(3‐dimethylaminopropyl)stearamide formed well structured gels in white mineral oil and deodorized kerosene. Further, these amidoamines and their salts showed excellent antistatic properties and were substantive to hair and skin.
Solution-Processed Graphene/MnO2 Nanostructured Textiles for High-Performance Electrochemical Capacitors (2011)

Large scale energy storage system with low cost, high power, and long cycle life is crucial for addressing the energy problem when connected with renewable energy production. To realize grid-scale applications of the energy storage devices, there remain several key issues including the development of low-cost, high-performance materials that are environmentally friendly and compatible with low-temperature and large-scale processing. In this report, we demonstrate that solution-exfoliated graphene nanosheets (∼5 nm thickness) can be conformably coated from solution on three-dimensional, porous textiles support structures for high loading of active electrode materials and to facilitate the access of electrolytes to those materials. With further controlled electrodeposition of pseudocapacitive MnO(2) nanomaterials, the hybrid graphene/MnO(2)-based textile yields high-capacitance performance with specific capacitance up to 315 F/g achieved. Moreover, we have successfully fabricated asymmetric electrochemical capacitors with graphene/MnO(2)-textile as the positive electrode and single-walled carbon nanotubes (SWNTs)-textile as the negative electrode in an aqueous Na(2)SO(4) electrolyte solution. These devices exhibit promising characteristics with a maximum power density of 110 kW/kg, an energy density of 12.5 Wh/kg, and excellent cycling performance of ∼95% capacitance retention over 5000 cycles. Such low-cost, high-performance energy textiles based on solution-processed graphene/MnO(2) hierarchical nanostructures offer great promise in large-scale energy storage device applications.