gebhart/patrepeval huggingface dataset:
PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: The presence of multiple Bacillus anthracis strains in different victims (1998)

An outbreak of human anthrax occurred in Sverdlovsk, Union of Soviet Socialists Republic (now Ekaterinburg, Russia) in April 1979. Officials attributed this to consumption of contaminated meat, but Western governments believed it resulted from inhalation of spores accidentally released from a nearby military research facility. Tissue samples from 11 victims were obtained and methods of efficiently extracting high-quality total DNA from these samples were developed. Extracted DNA was analyzed by using PCR to determine whether it contained Bacillus anthracis-specific sequences. Double PCR using "nested primers" increased sensitivity of the assay significantly. Tissue samples from 11 persons who died during the epidemic were examined. Results demonstrated that the entire complement of B. anthracis toxin and capsular antigen genes required for pathogenicity were present in tissues from each of these victims. Tissue from a vaccination site contained primarily nucleic acids from a live vaccine, although traces of genes from the infecting organisms were also present. PCR analysis using primers that detect the vrrA gene variable region on the B. anthracis chromosome demonstrated that at least four of the five known strain categories defined by this region were present in the tissue samples. Only one category is found in a single B. anthracis strain.
Metformin: A Therapeutic Opportunity in Breast Cancer (2010)

Two important, related pathways are involved in cancer growth: the insulin/insulin-like growth factor-1 (IGF1) signaling pathway, which is activated when nutrients are available, and the adenosine mono-phosphate-activated protein kinase (AMPK) pathway, activated when cells are starved for carbohydrates. Metformin inhibits transcription of key gluconeogenesis genes in the liver, increases glucose uptake in skeletal muscle, and decreases circulating insulin levels. Metformin reduces levels of circulating glucose, increases insulin sensitivity, and reduces insulin resistance-associated hyperinsulinemia. At the level of cell signaling, metformin activates AMPK. There are extensive preclinical data showing the anticancer effects of metformin in all breast cancer subtypes as well as in cytotoxic therapy-resistant models. These data, and the epidemiological and retrospective data supporting the antineoplastic effects of metformin, provide the rationale to study the role of metformin for breast cancer therapy in a variety of clinical settings.
A herpesvirus trans-activating protein interacts with transcription factor OTF-1 and other cellular proteins. (1988)

Immediate early genes of herpes simplex viruses contain one or more copies of the conserved TAAT-GARAT (where R is purine) DNA motif. A virus-encoded regulatory protein (Vmw65) is believed to stimulate transcription via this element, although the protein does not bind directly to DNA. Overlapping the TAATGARAT element in many cases is an octamer sequence (ATGCAAAT) that is involved both in transcription by RNA polymerases II and III and in adenovirus DNA replication. So far at least two proteins (OTF-1 and OTF-2) have been identified that bind to the octamer. We show that both affinity-purified OTF-1 and OTF-2 bind to the TAATGARAT sequence and that Vmw65 induces the formation of an additional complex that involves OTF-1 and that is further retarded in a band-shift gel assay. Complementation experiments involving addition of purified OTF-1 to nuclear extracts that have been depleted of endogenous OTF-1 show that at least one other cellular factor(s) is required for complex formation. This cellular factor may be involved in recognition of the GARAT sequence.
Robust backstepping control of robotic systems using neural networks (2002)

Neural network (NN) controllers for the robust backstepping control of robotic systems in both continuous and discrete-time are presented. Control input is selected to achieve tracking performance for unknown nonlinear systems. Tuning methods are derived for the NN based on the delta rule. Novel weight tuning algorithms for the NN are obtained that are similar to /spl epsiv/-modification in the case of continuous-time adaptive control. Uniform ultimate boundedness of the tracking error and the weight estimates are presented without using the persistency of excitation (PE) condition. Certainty equivalence is not used and a regression matrix is not computed. No learning phase is needed for the NN and initialization of the network weights is straightforward.
Laterally Mobile, Functionalized Self-Assembled Monolayers at the Fluorous−Aqueous Interface in a Plug-Based Microfluidic System: Characterization and Testing with Membrane Protein Crystallization (2009)

This paper describes a method to generate functionalizable, mobile self-assembled monolayers (SAMs) in plug-based microfluidics. Control of interfaces is advancing studies of biological interfaces, heterogeneous reactions, and nanotechnology. SAMs have been useful for such studies, but they are not laterally mobile. Lipid-based methods, though mobile, are not easily amenable to setting up the hundreds of experiments necessary for crystallization screening. Here we demonstrate a method, complementary to current SAM and lipid methods, for rapidly generating mobile, functionalized SAMs. This method relies on plugs, droplets surrounded by a fluorous carrier fluid, to rapidly explore chemical space. Specifically, we implemented his-tag binding chemistry to design a new fluorinated amphiphile, RfNTA, using an improved one-step synthesis of RfOEG under Mitsunobu conditions. RfNTA introduces specific binding of protein at the fluorous-aqueous interface, which concentrates and orients proteins at the interface, even in the presence of other surfactants. We then applied this approach to the crystallization of a his-tagged membrane protein, Reaction Center from Rhodobacter sphaeroides, performed 2400 crystallization trials, and showed that this approach can increase the range of crystal-producing conditions, the success rate at a given condition, the rate of nucleation, and the quality of the crystal formed.
Thalidomide produces transfusion independence in long-standing refractory anemias of patients with myelodysplastic syndromes (2001)

Thalidomide was administered to 83 patients with myelodysplastic syndrome (MDS), starting at 100 mg by mouth daily and increasing to 400 mg as tolerated. Thirty-two patients stopped therapy before 12 weeks (minimum period for response evaluation), and 51 completed 12 weeks of therapy. International Working Group response criteria for MDS were used to evaluate responses. Intent-to-treat (ITT) analysis classified all off-study patients as nonresponders. Off-study patients belonged to a higher risk category (P =.002) and had a higher percentage of blasts in their pretherapy bone marrow than patients who completed 12 weeks of therapy (P =.003). No cytogenetic or complete responses were seen, but 16 patients showed hematologic improvement, with 10 previously transfusion-dependent patients becoming transfusion independent. Responders had lower pretherapy blasts (P =.016), a lower duration of pretherapy platelet transfusions (P =.013), and higher pretherapy platelets (P =.003). Among responders, 9 had refractory anemia (RA); 5 had RA with ringed sideroblasts; and 2 had RA with excess blasts. By ITT analysis, 19% of patients (16 of 83) responded, and when only evaluable patients were analyzed, 31% (16 of 51) responded. It was concluded that thalidomide, as a single agent, is effective in improving cytopenias of some MDS patients, especially those who present without excess blasts. (Blood. 2001;98:958-965)
Stable and heritable inhibition of the expression of nopaline synthase in tobacco expressing antisense RNA (1987)

Antisense nopaline synthase (nos) (D-nopaline synthase; EC 1.5.1.19) RNA is stably expressed from the cauliflower mosaic virus 35S promoter in transformed tobacco plants. The expression of a previously introduced wild-type nos gene is inhibited by the antisense RNA, with less nos enzyme activity detected (by a factor of 8-50) depending on the tissue analyzed. The steady-state levels of nos mRNA are reduced in the presence of the antisense RNA, implying that mRNA degradation is probably the main mode of action for the decrease in expression in this system. The antisense RNA-expressing gene and its inhibition of nos expression are shown to be heritable, demonstrating that it is a potentially useful method for the modification of phenotype.
Endotoxin content in Haemophilus influenzae type b vaccine. (2004)

Haemophilus influenzae type b (Hib) is a major cause of bacterial meningitis among children. Hib conjugate vaccines have effectively prevented Hib infection, and routine immunization with Hib conjugate vaccine has diminished the incidence of the disease in the United States and European countries. Introduction of Hib conjugate vaccines is also required in Japan. However, endotoxin that can carry over from Gram-negative H. influenzae with a purified component may contribute to adverse events following Hib vaccination. In the present study, we examined the endotoxin content in Hib conjugate vaccines. The Hib conjugate vaccine batches, which were produced by a European vaccine manufacturer, were shown to have considerably high endotoxin activity and to vary from 13.9 to 173.7 endotoxin units/dose. These results suggest that it is necessary to monitor the endotoxin content of the vaccine batches to ensure the quality and safety of the vaccines.
Conceptual information retrieval using RUBRIC (1987)

Article Free Access Share on Conceptual information retrieval using RUBRIC Authors: R. Tong Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CA Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CAView Profile , L. Appelbaum Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CA Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CAView Profile , V. Askman Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CA Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CAView Profile , J. Cunningham Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CA Advanced Decision Systems, 201 San Antonio Circle, Suite 286, Mountain View, CAView Profile Authors Info & Claims SIGIR '87: Proceedings of the 10th annual international ACM SIGIR conference on Research and development in information retrievalNovember 1987 Pages 247–253https://doi.org/10.1145/42005.42033Online:01 November 1987Publication History 24citation577DownloadsMetricsTotal Citations24Total Downloads577Last 12 Months9Last 6 weeks2 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
Identification and modulation of a naturally processed T cell epitope from the diabetes-associated autoantigen human glutamic acid decarboxylase 65 (hGAD65) (2001)

T cell recognition of autoantigens is critical to progressive immune-mediated destruction of islet cells, which leads to autoimmune diabetes. We identified a naturally presented autoantigen from the human islet antigen glutamic acid decarboxylase, 65-kDa isoform (GAD65), by using a combination of chromatography and mass spectrometry of peptides bound by the type I diabetes (insulin-dependent diabetes mellitus, IDDM)-associated HLA-DR4 molecule. Peptides encompassing this epitope-stimulated GAD65-specific T cells from diabetic patients and a DR4-positive individual at high risk for developing IDDM. T cell responses were antagonized by altered peptide ligands containing single amino acid modifications. This direct identification and manipulation of GAD65 epitope recognition provides an approach toward dissection of the complex CD4(+) T cell response in IDDM.
A new stroke volume equation for thoracic electrical bioimpedance (1986)

A new stroke volume equation for thoracic electrical bioimpedance is proposed. This empirically derived formula differs from previous equations in that: the thoracic volume conductor is modeled geometrically as a frustum (truncated cone), rather than a cylinder; the specific resistivity of blood, rho, is appropriately eliminated as an independent variable; the equation employs a percentage of overall body height in lieu of a measured thoracic length; and a new term, delta, is introduced to scale the parent equation for deviation from ideal body weight.
Ion Transport Phenomena in Insulating Films (1965)

It is shown that changes in the capacitance-voltage characteristic of a metal-insulator-semiconductor structure provide a powerful tool for the observation of ion motion in thin insulating films. Using this method, a detailed study of the kinetics of alkali ion migration in thermally grown silicon dioxide films has been made. Alkali ions were initially deposited at the metal-oxide interface and their transport through the oxide was studied as a function of time, temperature and applied voltage. When the metal is biased positively the number of ions accumulated at the oxide-silicon interface is initially proportional to the square root of time and then approaches a saturation value. The temperature dependence is exponential and leads to an activation energy for the diffusion coefficient of 32 kcal/mole for Na and 22 kcal/mole for Li. A simple model is developed which is based on the division of the insulator into two regions: a thin boundary layer near the metal-insulator interface in which ion transport is by diffusion, and the remainder of the insulator where field transport dominates. It is shown that most features of this model are in excellent agreement with the experimental results.
Meldrum’s Acids and 5-Alkylidene Meldrum’s Acids in Catalytic Carbon−Carbon Bond-Forming Processes (2009)

Meldrum's acid (2,2-dimethyl-1,3-dioxane-4,6-dione) is a molecule with a unique history, owing to its originally misassigned structure, as well as a unique place among acylating agents, owing to its high acidity and remarkable electrophilicity. In this Account, we outline the work of our group and others toward harnessing the reactivity of Meldrum's acid derivatives in catalytic C-C bond-forming reactions. Taking advantage of the ability of Meldrum's acid to decompose to CO(2) and acetone following acyl substitution, we have shown that intramolecular Friedel-Crafts acylations can be performed under mild Lewis acidic conditions to yield a variety of benzocyclic ketones. In a further expansion of this method, a domino Friedel-Crafts acylation/alpha-tert alkylation reaction was used to complete the first total synthesis of (+/-)-taiwaniaquinol B. The unique characteristics of Meldrum's acid extend to its alkylidene derivatives, which have also proven exceptionally useful for the development of new reactions not readily accessible from other unsaturated carbonyl electrophiles. By combining the electrophilicity and dienophilicity of alkylidene Meldrum's acid with our Friedel-Crafts chemistry, we have demonstrated new domino syntheses of coumarin derivatives and tetrahydrofluorenones by conjugate additions, Diels-Alder cycloadditions, and C-H functionalizations. Additionally, we have used these powerful acceptors to allow conjugate alkenylation with functionalized organostannanes, and conjugate allylation under very mild conditions. We have also shown that these molecules permit the asymmetric formation of all-carbon quaternary stereocenters via enantioselective conjugate additions. These reactions employ dialkylzinc nucleophiles, maximizing functional group compatibility, while the presence of a Meldrum's acid moiety in the product allows a variety of postaddition modifications. A full investigation of this reaction has determined the structural factors of the alkylidene that contribute to optimal enantioselectivity. We have also used these acceptors to form tertiary propargylic stereocenters in very high enantiomeric excess by an extremely mild, Rh(I)-catalyzed addition of TMS-acetylene. Overall, we demonstrate that Meldrum's acid and its derivatives provide access to a broad range of reactivities that, combined with their ease of handling and preparation, make them ideal electrophiles.
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. (1994)

We have previously reported that in four transcription factor families the DNA-recognition rules can be described as (i) chemical rules, which list possible pairings between the 20 amino acid residues and the four DNA bases, and (ii) stereochemical rules, which describe the base and amino acid positions in contact. We have incorporated these rules into a computer program and examined the nature of the rules. Here we conclude that the DNA recognition rules are simple, logical, and consistent. The rules are specific enough to predict DNA-binding characteristics from a protein sequence.
An Update on Therapeutic Management of Canine Demodicosis (2011)

Canine demodicosis is a common noncontagious parasitic dermatosis caused by different spp of Demodex mites including Demodex canis, Demodex injai and D. cornei. Generalized demodicosis can be one of the most frustrating skin diseases, one will ever treat. Conventional and newer miticidal therapies are available to veterinarian to treat this frustrating skin disease. All recognized Demodex mites in dogs appear to respond similarly to mite targeted therapy. Treatment for canine demodicosis includes amitraz, ivermectin, milbemicin oxime, moxidectin, and doramectin. The use of any glucocorticoid-containing products is contraindicated and could favour disease generalization. Conventional treatments will often appear to work however, but it relies heavily on a highly toxic method of treatment. Using natural remedies for mange, on the other hand, can enhance the dog's immune system, so that the body can fight off the mange mite infection by itself.
Heat Shock Protein 90 Mediates the Balance of Nitric Oxide and Superoxide Anion from Endothelial Nitric-oxide Synthase (2001)

The balance of nitric oxide (.NO) and superoxide anion (O(2)) plays an important role in vascular biology. The association of heat shock protein 90 (Hsp90) with endothelial nitric-oxide synthase (eNOS) is a critical step in the mechanisms by which eNOS generates.NO. As eNOS is capable of generating both.NO and O(2), we hypothesized that Hsp90 might also mediate eNOS-dependent O(2) production. To test this hypothesis, bovine coronary endothelial cells (BCEC) were pretreated with geldanamycin (GA, 10 microg/ml; 17.8 microm) and then stimulated with the calcium ionophore, (5 microm). GA significantly decreased -stimulated eNOS-dependent nitrite production (p < 0.001, n = 4) and significantly increased -stimulated eNOS-dependent O(2) production (p < 0.001, n = 8). increased phospho-eNOS(Ser-1179) levels by >1.6-fold over vehicle (V)-treated levels. Pretreatment with GA by itself or with increased phospho-eNOS levels. In unstimulated V-treated BCEC cultures low amounts of Hsp90 were found to associate with eNOS. Pretreatment with GA and/or increased the association of Hsp90 with eNOS. These data show that Hsp90 is essential for eNOS-dependent.NO production and that inhibition of ATP-dependent conformational changes in Hsp90 uncouples eNOS activity and increases eNOS-dependent O(2) production.
CINNAMYL ALCOHOL DEHYDROGENASE-C and -D Are the Primary Genes Involved in Lignin Biosynthesis in the Floral Stem of Arabidopsis (2005)

During lignin biosynthesis in angiosperms, coniferyl and sinapyl aldehydes are believed to be converted into their corresponding alcohols by cinnamyl alcohol dehydrogenase (CAD) and by sinapyl alcohol dehydrogenase (SAD), respectively. This work clearly shows that CAD-C and CAD-D act as the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis thaliana by supplying both coniferyl and sinapyl alcohols. An Arabidopsis CAD double mutant (cad-c cad-d) resulted in a phenotype with a limp floral stem at maturity as well as modifications in the pattern of lignin staining. Lignin content of the mutant stem was reduced by 40%, with a 94% reduction, relative to the wild type, in conventional beta-O-4-linked guaiacyl and syringyl units and incorportion of coniferyl and sinapyl aldehydes. Fourier transform infrared spectroscopy demonstrated that both xylem vessels and fibers were affected. GeneChip data and real-time PCR analysis revealed that transcription of CAD homologs and other genes mainly involved in cell wall integrity were also altered in the double mutant. In addition, molecular complementation of the double mutant by tissue-specific expression of CAD derived from various species suggests different abilities of these genes/proteins to produce syringyl-lignin moieties but does not indicate a requirement for any specific SAD gene.
The rheumatoid arthritis patient in the clinic: comparing more than 1300 consecutive DMARD courses (2002)

MTX was the most commonly employed DMARD therapy for RA and was used increasingly as first therapy in newly diagnosed RA. Patients with high disease activity were given MTX therapy more often than other DMARDs, while those with low activity were more likely to receive SSZ or AM, and MTX on failure of these drugs. First DMARDs in new patients were retained longer than subsequent DMARDs, apparently because they are more effective.
Suppression of competing speech through entrainment of cortical oscillations (2013)

People are highly skilled at attending to one speaker in the presence of competitors, but the neural mechanisms supporting this remain unclear. Recent studies have argued that the auditory system enhances the gain of a speech stream relative to competitors by entraining (or "phase-locking") to the rhythmic structure in its acoustic envelope, thus ensuring that syllables arrive during periods of high neuronal excitability. We hypothesized that such a mechanism could also suppress a competing speech stream by ensuring that syllables arrive during periods of low neuronal excitability. To test this, we analyzed high-density EEG recorded from human adults while they attended to one of two competing, naturalistic speech streams. By calculating the cross-correlation between the EEG channels and the speech envelopes, we found evidence of entrainment to the attended speech's acoustic envelope as well as weaker yet significant entrainment to the unattended speech's envelope. An independent component analysis (ICA) decomposition of the data revealed sources in the posterior temporal cortices that displayed robust correlations to both the attended and unattended envelopes. Critically, in these components the signs of the correlations when attended were opposite those when unattended, consistent with the hypothesized entrainment-based suppressive mechanism.
Categorical Data Analysis - Logistic Regression (2014)

Corresponding author: Shengping Yang Contact Information: Shengping.yang@ttuhsc.edu. DOI: 10.12746/swrccc2014.0207.094 Case-control studies are widely used in investigating the potential relationship of a suspected risk factor and a disease or outcome of interest. By looking retrospectively and comparing how frequently the exposure to a risk factor is present in subjects who have that disease (case) with those who do not have that disease (control), the relationship can be evaluated. The outcome variable can only take exactly two values, conventionally labeled as “case” and “control”. In fact, this type of variable is called a categorical/nominal variable1 (data that have two or more categories, but there is no intrinsic ordering to the categories).