gebhart/patrepeval huggingface dataset:
A programmable method for massively parallel targeted sequencing (2014)

We have developed a targeted resequencing approach referred to as Oligonucleotide-Selective Sequencing. In this study, we report a series of significant improvements and novel applications of this method whereby the surface of a sequencing flow cell is modified in situ to capture specific genomic regions of interest from a sample and then sequenced. These improvements include a fully automated targeted sequencing platform through the use of a standard Illumina cBot fluidics station. Targeting optimization increased the yield of total on-target sequencing data 2-fold compared to the previous iteration, while simultaneously increasing the percentage of reads that could be mapped to the human genome. The described assays cover up to 1421 genes with a total coverage of 5.5 Megabases (Mb). We demonstrate a 10-fold abundance uniformity of greater than 90% in 1 log distance from the median and a targeting rate of up to 95%. We also sequenced continuous genomic loci up to 1.5 Mb while simultaneously genotyping SNPs and genes. Variants with low minor allele fraction were sensitively detected at levels of 5%. Finally, we determined the exact breakpoint sequence of cancer rearrangements. Overall, this approach has high performance for selective sequencing of genome targets, configuration flexibility and variant calling accuracy.
Comparison of Babcock and Ether Extraction Methods for Determination of Fat Content of Cream: Collaborative Study (1996)

Abstract A modified Mojonnier ether extraction method for determination of the fat content of cream was developed based on the method for milk (AOAC Official Method 989.05). The cream Babcock method (AOAC Official Method 920.111 B-C) was modified to harmonize with the milk Babcock method (AOAC Official Method 989.04) and to clarify procedural details. Using the AOAC collaborative study format, 10 laboratories tested 9 pairs of blind duplicate heat-treated cream samples with a fat range of 30-45% using both methods. The statistical performance (invalid and outlier data removed) was as follows: mean % fat = 37.932, sr = 0.125, sR = 0.151, RSDr = 0.330, RSDR = 0.398, r = 0.354, and R = 0.427 for the ether extraction method. For the Babcock method, mean % fat = 38.209, sr = 0.209, SR = 0.272, RSDr = 0.548, RSDR = 0.712, r = 0.592, and R = 0.769. Average test results for fat from the Babcock method were 0.277% (absolute fat) greater than for the Mojonnier ether extraction method. The difference between methods, as a percentage of the average fat content of the samples, was 0.73%. This agrees with differences observed between the 2 methods for milk when 10 to 17 laboratories tested 7 milk samples in blind duplicate at bimonthly intervals over a 4-year period (average difference 0.029% fat, 0.78% as a percentage of average fat content). The Mojonnier ether extraction and Babcock methods for fat in cream have been adopted by AOAC INTERNATIONAL. The new Babcock method replaced the AOAC Official Method 920.111 B-C.
Varying Coefficients Model with Measurement Error (2007)

We propose a semiparametric partially varying coefficient model to study the relationship between serum creatinine concentration and the glomerular filtration rate (GFR) among kidney donors and patients with chronic kidney disease. A regression model is used to relate serum creatinine to GFR and demographic factors in which coefficient of GFR is expressed as a function of age to allow its effect to be age dependent. GFR measurements obtained from the clearance of a radioactively labeled isotope are assumed to be a surrogate for the true GFR, with the relationship between measured and true GFR expressed using an additive error model. We use locally corrected score equations to estimate parameters and coefficient functions, and propose an expected generalized cross-validation (EGCV) method to select the kernel bandwidth. The performance of the proposed methods, which avoid distributional assumptions on the true GFR and residuals, is investigated by simulation. Accounting for measurement error using the proposed model reduced apparent inconsistencies in the relationship between serum creatinine and GFR among different clinical data sets derived from kidney donor and chronic kidney disease source populations.
Purified ryanodine receptor from skeletal muscle sarcoplasmic reticulum is the Ca2+-permeable pore of the calcium release channel. (1987)

The ryanodine receptor of rabbit skeletal muscle sarcoplasmic reticulum was purified by immunoaffinity chromatography as a single approximately 450,000-Da polypeptide and it was shown to mediate single channel activity identical to that of the ryanodine-treated Ca2+ release channel of the sarcoplasmic reticulum. The purified receptor had a [3H]ryanodine binding capacity (Bmax) of 280 pmol/mg and a binding affinity (Kd) of 9.0 nM. [3H]Ryanodine binding to the purified receptor was stimulated by ATP and Ca2+ with a half-maximal stimulation at 1 mM and 8-9 microM, respectively. [3H]Ryanodine binding to the purified receptor was inhibited by ruthenium red and high concentrations of Ca2+ with an IC50 of 2.5 microM and greater than 1 mM, respectively. Reconstitution of the purified receptor in planar lipid bilayers revealed the Ca2+ channel activity of the purified receptor. Like the native sarcoplasmic reticulum Ca2+ channels treated with ryanodine, the purified receptor channels were characterized by (i) the predominance of long open states insensitive to Mg2+ and ruthenium red, (ii) a main slope conductance of approximately 35 pS and a less frequent 22 pS substate in 54 mM trans-Ca2+ or Ba2+, and (iii) a permeability ratio PBa or PCa/PTris = 8.7. The approximately 450,000-Da ryanodine receptor channel thus represents the long-term open "ryanodine-altered" state of the Ca2+ release channel from sarcoplasmic reticulum. We propose that the ryanodine receptor constitutes the physical pore that mediates Ca2+ release from the sarcoplasmic reticulum of skeletal muscle.
An approach to image retrieval from large image databases (1987)

In this paper we address the problem of retrieving images from large image databases, giving a partial description of the image content. This approach allows a limited automatic analysis for image belonging to a domain described in advance to the system using a formalism based on fuzzy sets. The image query processing is based on special access structures generated from the image analysis process.
Antibodies recognizing different domains of the polymeric immunoglobulin receptor. (1985)

The receptor responsible for the transepithelial transport of IgA dimer antibodies is a transmembrane glycoprotein known as membrane secretory component (SCm). During transport, the membrane anchoring domain is cleaved and the ectoplasmic domain of the receptor (SCs) remains tightly bound to the IgA dimer in exosecretions. We have produced monoclonal antibodies with distinct specificities against both cytoplasmic and ectoplasmic epitopes of rabbit SCm. One antibody (anti-SC303) reacted both with SCm and free SCs but not with SCs bound to IgA dimer (SIgA). Therefore, it recognized an epitope close to the IgA dimer binding site. The other monoclonal antibody (anti-SC166), which was unable to react with SCs, bound to the 15-kDa cytoplasmic extension of the membrane-spanning domain of the receptor. A polyclonal antibody (GaR-SC), raised in a goat against rabbit milk SCs, reacted with a subpopulation of SCs not recognized by the anti-SC303 monoclonal antibody and in addition also reacted with covalently bound sIgA. The three antibodies cross-reacted with rat SCm. We demonstrate the ability of the anti-SC166 monoclonal antibody to immunoadsorb subcellular organelles as a result of the cytoplasmic orientation of its epitope. Our data indicate that there are functional differences between the high- and low-molecular-weight families of SC in terms of IgA dimer binding.
In vivo expansion of CD4+CD45RO-CD25+ T cells expressing foxP3 in IL-2-treated HIV-infected patients (2005)

Administration of IL-2 to HIV-infected patients leads to expansion of a unique subset of CD4CD45ROCD25 cells. In this study, the origin, clonality, and function of these cells were investigated. Analysis of TCR excision circles revealed that the CD4CD45ROCD25 cells were the product of peripheral expansion but remained polyclonal as determined by TCR repertoire analysis. Phenotypically, these cells were distinct from naturally occurring Tregs; they exhibited intermediate features, between those of memory and naive cells, and had lower susceptibility to apoptosis than CD45ROCD25 or memory T cells. Studies of intracellular cytokine production and proliferation revealed that cytokine-expanded naive CD25 cells had low IL-2 production and required costimulation for proliferation. Despite elevated expression of forkhead transcription factor P3 (foxP3), they exerted only weak suppression compared with CD45ROCD25 cells (Tregs). In summary, in vivo IL-2 administration to HIV-infected patients leads to peripheral expansion of a population of long-lived CD4CD45ROCD25 cells that express high levels of foxP3 but exert weak suppressive function. These CD4CD25 cytokine-expanded naive cells, distinct from antigen-triggered cells and Tregs, play a role in the maintenance of a state of low turnover and sustained expansion of the CD4 T cell pool.
DNA vaccines for the treatment of autoimmune disease (1997)

DNA vaccines represent one of the most significant developments in vaccine technology in recent years. Although, in general, studies have primarily focused on the induction of protective immune responses against infectious pathogens, the technology may prove useful for other immune-related diseases, including autoimmunity. Autoimmune disease results from a breakdown in tolerance to self antigens; however, the same fundamental immunological reactions that control immune responses to foreign antigens are also likely to operate during the course of autoimmune disease. These include the reciprocal regulation of Th cell subsets. Th1 cells appear to be involved in many organ-specific autoimmune diseases while suppression of disease is associated with cells of the Th2 phenotype. It has been possible, therefore, to suppress many of the pathological consequences of autoimmunity by manipulating the Th1/Th2 cell balance. The induction of Th2 responses by DNA immunization might therefore be expected to have a profound effect on the course of autoimmune disease. Indeed, we have demonstrated that DNA immunization can protect animals against the autoimmune central nervous system inflammatory disease, experimental autoimmune encephalomyelitis (EAE). As many other autoantigens have now been identified, the application of this technology to other autoimmune diseases warrants investigation.
a-Series Gangliosides Mediate the Effects of Advanced Glycation End Products on Pericyte and Mesangial Cell Proliferation (2005)

Advanced glycation end products (AGEs) are involved in the development of microvascular complications, including alterations of retinal pericyte and renal mesangial cell growth occurring during diabetic retinopathy and diabetic nephropathy, respectively. Because gangliosides are implicated in the regulation of cell proliferation, we hypothesized that AGEs could exert cellular effects in part by modulating ganglioside levels. Results of the present study indicate that AGEs caused an inhibition of both bovine retinal pericyte (BRP) and rat renal mesangial cell (RMC) proliferation, associated with an increase of a-series gangliosides consecutive to GM3 synthase activity increase and GD3 synthase activity inhibition. Similar modifications were also found in the renal cortex of diabetic db/db mice compared with controls. Treatment of BRP and RMC with exogenous a-series gangliosides decreased proliferation and blockade of a-series gangliosides with specific antibodies partially protecting the two cell types from the AGE-induced proliferation decrease. Further, inhibition of GM3 synthase using specific SiRNA partially reversed the AGE effects on mesangial cell proliferation. These results suggest that a-series gangliosides are mediators of the adverse AGE effects on BRP and RMC proliferation. They also raise the hypothesis of common mechanisms involved in the development of diabetic retinopathy and diabetic nephropathy.
Composite image formation inz-shimmed functional MR imaging (1999)

A challenge in functional magnetic resonance imaging (fMRI) is to develop imaging methods that are highly sensitive to microscopic field inhomogeneities [the blood oxygenation level-dependent (BOLD) effect] and minimally sensitivity to macroscopic fields. z-Shimming compensates for the through-plane dephasing that arises in gradient-echo images due to magnetic field inhomogeneities. To date, an analysis of the formation of composite images from multiple z-shim acquisitions has not been presented. This work compares three strategies for forming composite images, one of which is introduced for the first time, against the nominal image acquisition. True-versus false-positive rates of activation detection are considered, in addition to the time efficiency of the methods. It is shown that z-shimming can provide uniform spatial sensitivity, resulting in increased activation detectability, in many cases outperforming the nominal imaging approach. Time efficiency is shown to be dependent on field uniformity. Theory, computer simulations, and results from fMRI studies are used to demonstrate the performance of these methods.
Effects of Therapeutic Hypothermia on Inflammasome Signaling after Traumatic Brain Injury (2012)

Traumatic brain injury (TBI) activates the NALP1/NLRP1 inflammasome, which is an important component of the early innate inflammatory response to injury. We investigated the influence of therapeutic hypothermia on inflammasome activation after TBI. Adult male Sprague-Dawley rats were subjected to moderate fluid percussion brain injury. Temperature manipulation (33°C or 37°C) was initiated 30 minutes after TBI and maintained for 4 hours. At 4 or 24 hours after TBI, traumatized cortex and hippocampus were prepared for immunoblot or immunohistochemical analysis. In the normothermic groups, caspase-1, caspase-11 and expression of the purinergic receptor P2X7 increased at 24 hours after TBI. Posttraumatic hypothermia lead to decreased expression of these proteins at 24 hours compared with normothermic levels. Immunocytochemical studies showed that posttraumatic hypothermia also decreased caspase-1 staining in cerebral cortical neurons compared with normothermic TBI. Cultured cortical neurons subjected to stretch injury demonstrated significant secretion of caspase-1 into the culture medium and caspase-3 activation, both results reduced by hypothermic treatment. Posttraumatic hypothermia decreases inflammasome signaling in neurons and reduces the innate immune response to TBI at 24 hours after injury. Therapeutic hypothermia may protect the injured central nervous system by targeting the detrimental consequences of the innate immune response to injury.
Multiwavelength DFB laser array with integrated spot size converters (2000)

We describe the design, fabrication, and performance of a five-element quarterwave-shifted distributed feedback laser array with monolithically integrated spot size converters intended for use as a multiple-wavelength source in dense wavelength-division telecommunications systems. Facet power in excess of 10 mW with less than 150 mA bias and longitudinal side mode suppression greater than 40 dB were routinely achieved. Narrow far-field full-width at half-maximum angles of 6.9/spl deg//spl times/16.3/spl deg/ provided 3.5-dB coupling loss into single-mode fiber with 1.0-dB misalignment tolerances of /spl plusmn/2.0 /spl mu/m. With /spl plusmn/10/spl deg/C thermal tuning, 22 1555-nm channels spaced by 50 GHz were accessed with this device. Thorough field evaluation indicates that such a device is consistent with manufacturing requirements.
Critical Role of CD2 Co-stimulation in Adaptive Natural Killer Cell Responses Revealed in NKG2C-Deficient Humans (2016)

Infection by human cytomegalovirus (HCMV) leads to NKG2C-driven expansion of adaptive natural killer (NK) cells, contributing to host defense. However, approximately 4% of all humans carry a homozygous deletion of the gene that encodes NKG2C (NKG2C(-/-)). Assessment of NK cell repertoires in 60 NKG2C(-/-) donors revealed a broad range of NK cell populations displaying characteristic footprints of adaptive NK cells, including a terminally differentiated phenotype, functional reprogramming, and epigenetic remodeling of the interferon (IFN)-γ promoter. We found that both NKG2C(-) and NKG2C(+) adaptive NK cells expressed high levels of CD2, which synergistically enhanced ERK and S6RP phosphorylation following CD16 ligation. Notably, CD2 co-stimulation was critical for the ability of adaptive NK cells to respond to antibody-coated target cells. These results reveal an unexpected redundancy in the human NK cell response to HCMV and suggest that CD2 provides "signal 2" in antibody-driven adaptive NK cell responses.
T‐box transcription factor Tbx2 represses differentiation and formation of the cardiac chambers (2004)

Specific regions of the embryonic heart tube differentiate into atrial and ventricular chamber myocardium, whereas the inflow tract, atrioventricular canal, inner curvatures, and outflow tract do not. These regions express Tbx2, a transcriptional repressor. Here, we tested its role in chamber formation. The temporal and spatial pattern of Tbx2 mRNA and protein expression in mouse hearts was found to be complementary to that of chamber myocardium-specific genes Nppa, Cx40, Cx43, and Chisel, and was conserved in human. In vitro, Tbx2 repressed the activity of regulatory fragments of Cx40, Cx43, and Nppa. Hearts of transgenic embryos that expressed Tbx2 in the prechamber myocardium completely failed to form chambers and to express the chamber myocardium-specific genes Nppa, Cx40, and Chisel, whereas other cardiac genes were normally expressed. These findings provide the first evidence that Tbx2 is a determinant in the local repression of chamber-specific gene expression and chamber differentiation.
Shape and Temperature Memory of Nanocomposites with Broadened Glass Transition (2007)

Shape-memory polymers can revert to their original shape when they are reheated. The stress generated by shape recovery is a growing function of the energy absorbed during deformation at a high temperature; thus, high energy to failure is a necessary condition for strong shape-memory materials. We report on the properties of composite nanotube fibers that exhibit this particular feature. We observed that these composites can generate a stress upon shape recovery up to two orders of magnitude greater than that generated by conventional polymers. In addition, the nanoparticles induce a broadening of the glass transition and a temperature memory with a peak of recovery stress at the temperature of their initial deformation.
Effect of Erythromycin on Ethanol's Pharmacokinetics and Perception of Intoxication (1995)

Oral erythromycin base 1500 mg/day compared with placebo does not alter ethanol's pharmacokinetics or perception of intoxication in healthy volunteers.
A Specific, Highly Active Malate Dehydrogenase by Redesign of a Lactate Dehydrogenase Framework (1988)

Three variations to the structure of the nicotinamide adenine dinucleotide (NAD)-dependent L-lactate dehydrogenase from Bacillus stearothermophilus were made to try to change the substrate specificity from lactate to malate: Asp197----Asn, Thr246----Gly, and Gln102----Arg). Each modification shifts the specificity from lactate to malate, although only the last (Gln102----Arg) provides an effective and highly specific catalyst for the new substrate. This synthetic enzyme has a ratio of catalytic rate (kcat) to Michaelis constant (Km) for oxaloacetate of 4.2 x 10(6)M-1 s-1, equal to that of native lactate dehydrogenase for its natural substrate, pyruvate, and a maximum velocity (250 s-1), which is double that reported for a natural malate dehydrogenase from B. stearothermophilus.
Bimolecular chemistry of macromolecules: synthesis of bacterial polysaccharide conjugates with Neisseria meningitidis membrane protein (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBimolecular chemistry of macromolecules: synthesis of bacterial polysaccharide conjugates with Neisseria meningitidis membrane proteinS. Marburg, D. Jorn, R. L. Tolman, B. Arison, J. McCauley, P. J. Kniskern, A. Hagopian, and P. P. VellaCite this: J. Am. Chem. Soc. 1986, 108, 17, 5282–5287Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/ja00277a037https://doi.org/10.1021/ja00277a037research-articleACS PublicationsRequest reuse permissionsArticle Views535Altmetric-Citations96LEARN 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
Should We Use N -Acetyltransferase Type 2 Genotyping To Personalize Isoniazid Doses? (2005)

Isoniazid is metabolized by the genetically polymorphic arylamine N-acetyltransferase type 2 (NAT2). A greater number of high-activity alleles are related to increased acetylation capacity and in some reports to low efficacy and toxicity of isoniazid. The objective of this study was to assess individual isoniazid exposure based on NAT2 genotype to predict a personalized therapeutic dose. Isoniazid was administered to 18 healthy Caucasians (age 30 +/- 6 years, body weight 74 +/- 10 kg, five women) in random order as a 200-mg infusion, a 100-mg oral, and a 300-mg oral single dose. For the assessment of NAT2 genotype, common single nucleotide polymorphisms identifying 99.9% of variant alleles were characterized. Noncompartmental pharmacokinetics and compartmental population pharmacokinetics were estimated from isoniazid plasma concentrations until 24 h postdose by high-pressure liquid chromatography. The influence of NAT2 genotype, drug formulation, body weight, and sex on dose-normalized isoniazid pharmacokinetics was assessed by analysis of variance from noncompartmental data and confirmed by population pharmacokinetics. Eight high-activity NAT2*4 alleles were identified. Sex had no effect; the other factors explained 93% of the variability in apparent isoniazid clearance (analysis of variance). NAT2 genotype alone accounted for 88% of variability. Individual isoniazid clearance could be predicted as clearance (liters/hour) = 10 + 9 x (number of NAT2*4 alleles). To achieve similar isoniazid exposure, current standard doses presumably appropriate for patients with one high-activity NAT2 allele may be decreased or increased by approximately 50% for patients with no or two such alleles, respectively. Prospective clinical trials are required to assess the merits of this approach.