gebhart/patrepeval huggingface dataset:
Impact of Recent Increase in Incidence on Future Diabetes Burden (2006)

n an earlier study, we had forecasted 39 million with diagnosed diabetes in 2050 in the U.S. (1,2). However, since then, national diabetes incidence increased (3) and the relative risk of death among people with diabetes declined (4,5). These changes will impact future forecasts.
The product of the adenovirus intermediate gene IX is a transcriptional activator (1997)

We have investigated the functional properties of the product of the adenovirus type 5 gene IX. This gene, which is expressed at intermediate times postinfection, encodes a small polypeptide (pIX) of 140 residues that has previously been shown to be incorporated into the viral capsid. Here, we show that pIX, in addition to its structural contribution, exhibits transcriptional properties. In transient transfection experiments, expression of pIX stimulated adenovirus major late promoter activity. The effect was independent of other viral proteins, but the level of promoter activation appeared strongly pIX dose dependent; similar levels of induction were observed with other cellular or viral TATA-containing (but not with TATA-less) promoters. This promoter specificity could be reproduced in a cell-free transcription system by the addition of purified recombinant pIX, further stressing the transcriptional nature of the phenomenon. A preliminary structural analysis of pIX indicated that the integrity of a putative leucine zipper at the carboxy-terminal end of the molecule, as well as elements within the amino-terminal half, was critical for pIX transcriptional activity. The relevance of these findings in adenovirus infection is discussed.
Coronary Plaque Erosion Without Rupture Into a Lipid Core (1996)

Erosion of proteoglycan-rich and smooth muscle cell-rich plaques lacking a superficial lipid core or plaque rupture is a frequent finding in sudden death due to coronary thrombosis, comprising 44% of cases in the present study. These lesions are more often seen in younger individuals and women, have less luminal narrowing and less calcification, and less often have foci of macrophages and T cells compared with plaque ruptures.
The Causes of Synonymous Rate Variation in the Rodent Genome: Can Substitution Rates Be Used to Estimate the Sex Bias in Mutation Rate? (1999)

Miyata et al. have suggested that the male-to-female mutation rate ratio (alpha) can be estimated by comparing the neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) genes. Rodent silent site X/A comparisons provide very different estimates from X/Y comparisons. We examine three explanations for this discrepancy: (1) statistical biases and artifacts, (2) nonneutral evolution, and (3) differences in mutation rate per germline replication. By estimating errors and using a variety of methodologies, we tentatively reject explanation 1. Our analyses of patterns of codon usage, synonymous rates, and nonsynonymous rates suggest that silent sites in rodents are evolving neutrally, and we can therefore reject explanation 2. We find both base composition and methylation differences between the different sets of chromosomes, a result consistent with explanation 3, but these differences do not appear to explain the observed discrepancies in estimates of alpha. Our finding of significantly low synonymous substitution rates in genomically imprinted genes suggests a link between hemizygous expression and an adaptive reduction in the mutation rate, which is consistent with explanation 3. Therefore our results provide circumstantial evidence in favor of the hypothesis that the discrepancies in estimates of alpha are due to differences in the mutation rate per germline replication between different parts of the genome. This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of alpha, obtained using this method, need to be treated with caution.
The use of Ignite (Basta;glufosinate;phosphinothricin) to select transformants of bar-containing plasmids in Neurospora crassa (1993)

The bacterial Basta-resistance (bar) gene has been previously adapted for use as a fungal selectable marker by Avalos et al. (1989 Curr. Genet. 16:369-372) and by Straubinger et al. (1992 Fungal Genet. Newsl. 39:82-83). Both bialaphos and Basta (Ignite) have been developed for use as herbicides and have only been available as free samples from the chemical companies that have been involved in this development.
Colchicine. Derivatives of Trimethylcolchicinic Acid1,2 (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTColchicine. Derivatives of Trimethylcolchicinic Acid1,2Robert F. Raffauf, Ann L. Farren, and Glenn E. UllyotCite this: J. Am. Chem. Soc. 1953, 75, 21, 5292–5294Publication Date (Print):November 1, 1953Publication History Published online1 May 2002Published inissue 1 November 1953https://pubs.acs.org/doi/10.1021/ja01117a044https://doi.org/10.1021/ja01117a044research-articleACS PublicationsRequest reuse permissionsArticle Views139Altmetric-Citations22LEARN 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
Plasma tumor necrosis factor and mortality in critically ill septic patients (1989)

Tumor necrosis factor (TNF) cachectin has been implicated as an important host mediator responsible for shock and multiple organ failure (MOF) observed during sepsis. Using a sensitive enzyme-linked immunosorbent assay, we measured plasma TNF levels in 43 septic patients suffering from a broad range of diseases. Measurements were taken on the day that sepsis was diagnosed. Eleven patients had detectable TNF plasma levels ranging from 10 to 100 pg/ml (TNF-positive group); in 32 patients circulating TNF could not be detected (TNF-negative group). The groups did not differ significantly as to age, underlying disease, percentage positive bacteremia and bacteriologic profile, sepsis score, and extent of MOF. Eight (73%) of 11 TNF-positive patients died from sepsis during ICU stay, vs. 11 (34%) of 32 TNF-negative patients (p less than .05). This study demonstrates that sepsis is accompanied by detectable circulating TNF in 25% of the cases, and for these patients mortality is twice that for comparable TNF-negative patients.
Regulation and Function of NF-κB Transcription Factors in the Immune System (2009)

The mammalian Rel/NF-kappaB family of transcription factors, including RelA, c-Rel, RelB, NF-kappaB1 (p50 and its precursor p105), and NF-kappaB2 (p52 and its precursor p100), plays a central role in the immune system by regulating several processes ranging from the development and survival of lymphocytes and lymphoid organs to the control of immune responses and malignant transformation. The five members of the NF-kappaB family are normally kept inactive in the cytoplasm by interaction with inhibitors called IkappaBs or the unprocessed forms of NF-kappaB1 and NF-kappaB2. A wide variety of signals emanating from antigen receptors, pattern-recognition receptors, receptors for the members of TNF and IL-1 cytokine families, and others induce differential activation of NF-kappaB heterodimers. Although work over the past two decades has shed significant light on the regulation of NF-kappaB transcription factors and their functions, much progress has been made in the past two years revealing new insights into the regulation and functions of NF-kappaB. This recent progress is covered in this review.
Polo-like kinase isoform expression is a prognostic factor in ovarian carcinoma (2004)

The Polo-like kinase (PLK) family comprises three serine/threonine kinases, functionally involved in signal transduction pathways essential for the accomplishment of mitosis in both normal and malignant cells. Moreover, certain PLKs have been functionally linked to cytoskeletal reorganisation. In this study, the expression of PLK1 and PLK3 was determined immunohistochemically in tissue specimen of normal ovaries (n=9), cystadenomas (n=17), borderline tumours (n=13) and ovarian carcinomas (n=77). PLK 1 and PLK3 expression was low in normal ovarian surface epithelium and borderline tumours, with moderately higher expression levels in cystadenomas. In ovarian carcinomas, 26% of cases were PLK1 positive and 50.6% of cases were PLK3 positive. A positive correlation of both PLK1 and PLK3 expression with indicators of mitotic frequency could be established. The overexpression of either isoenzyme had an impact on patient prognosis with shortened survival time for patients with tumours positive for PLK1 (P=0.02) and PLK3 (P=0.02), but only PLK1 expression remained a prognostic factor in multivariate survival analysis (P=0.03). The results of this study, if interpreted in the context of recently published functional data, suggest that inhibition of PLKs might represent an interesting new targeted approach for chemotherapy of epithelial ovarian cancer. Furthermore, this study suggests that PLK1 is a novel independent prognostic marker in ovarian carcinomas.
Organoboron Compounds, and the Study of Reaction Mechanisms. Primary Aliphatic Boronic Acids1 (1938)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganoboron Compounds, and the Study of Reaction Mechanisms. Primary Aliphatic Boronic Acids1H. R. Snyder, J. A. Kuck, and John R. JohnsonCite this: J. Am. Chem. Soc. 1938, 60, 1, 105–111Publication Date (Print):January 1, 1938Publication History Published online1 May 2002Published inissue 1 January 1938https://doi.org/10.1021/ja01268a033RIGHTS & PERMISSIONSArticle Views2069Altmetric-Citations122LEARN 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 (875 KB) Get e-Alerts Get e-Alerts
A new device to reduce the consumption of a halogenated anaesthetic agent* (2001)

We report the first clinical application of a new anaesthetic agent-saving device. The principles of a heat-moisture exchanger have been further developed to create a device that reduces inhalational agent consumption. Sixteen patients were randomly allocated to receive isoflurane through either a vaporiser or through the agent-saving device. A coaxial Mapleson D system (Bain) was used in both groups. A standard ventilatory setting was used, aiming for normocapnia. Mean (SD) isoflurane consumption was 24.5 (2.8) ml x MAC-hour(-1) with the vaporiser, compared with 15.2 (3.0) ml x MAC-hour(-1) with the new device (p < 0.05). This corresponded to a 40% saving in the consumption of isoflurane. The amount of isoflurane that was scavenged to the atmosphere was reduced by an average of 55%.
PROTEIN ISOLATES FROM <i>CHLORELLA</i> ALGAE, <i>TORULA</i> YEASTS, AND HYDROCARBON-ASSIMILATING MICROORGANISMS (1973)

Preparation of protein isolates from the cells of Chlorella, Torula yeasts, and hydrocarbon-assimilating microorganisms is described. Simple pretreatment of the cells with alkali, acid, or some organic solvents enhanced the protein extraction efficiency and made the following purification procedures easier. Bleached cells of Chlorella obtained by growing the algae in a culture medium with high C/N ratio at high temperature were found to release protein more easily than do the normal cells. Structural changes in the cell wall region detected under the electron microscope may be responsible for this. The extracted protein was further purified. Amino acid composition of the protein isolates was determined, and their nutritional values were calculated. Among the essential amino acids the sulfur-containing amino acids were found to be the first limiting amino acid. Supplementing the isolate with methionine resulted in a significant increase in its nutritional value (PER) which became comparable to those of egg albumin and milk casein. The digestibility of the protein isolate from the cells of a hydro-carbon-assimilating yeast, tested in vitro with pepsin, was as high as 80% of that of the reference protein, milk casein, whereas that of the dried cells of the yeast was less than 50%. Viscosity was measured in regard to possible processed forms of the protein isolates. A few methods for disposing of the extraction residues were tested.
DNA Conjugates as Novel Functional Oligonucleotides (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Hybridization Assays Using an Expressible DNA Fragment Encoding Firefly Luciferase as a Label (1996)

We report the use of a new label, an expressible enzyme-coding DNA fragment, for nucleic acid hybridization assays. The DNA label contains a firefly luciferase coding sequence downstream from a T7 RNA polymerase promoter. The target DNA (200 bp) is denatured and hybridized simultaneously with two oligonucleotide probes. One of the probes is immobilized in microtiter wells, via the digoxigenin/anti-digoxigenin interaction, and the other probe is biotinylated. After completion of the hybridization, the hybrids are reacted with a streptavidin-luciferase DNA complex. Subsequently, the solid-phase bound DNA is expressed by coupled transcription/ translation. The synthesized luciferase catalyzes the luminescent reaction of luciferin with O2 and ATP. The luminescence is linearly related to the amount of target DNA in the range of 5-5000 amol. The CVs obtained for 20 and 100 amol of target are 6.5% and 10.8%, respectively (n = 4).
Pedicle Screw Instrumentation of the Thoracic Spine in Idiopathic Scoliosis (1997)

Pedicle or vertebral body cortical penetration occurred with 25% of the screws but with no neurologic compromise. Curve correction was slightly greater than with hooks, but not to a statistically significant extent.
An In Vitro Assay for Testing Mosquito Repellents Employing a Warm Body and Carbon Dioxide as a Behavioral Activator (2010)

We describe here an in vitro behavioral assay for testing mosquito repellents applied in a dose-based manner to a warm body (34 degrees C) in test cages. The system was used to assess the sensitivity of 4-6-day-old Anopheles gambiae to the insect repellent diethyl methyl benzamide (deet). These tests were made in the absence and presence of additional carbon dioxide (CO2) applied as a pulse to activate mosquitoes in the cages. In the absence of the CO2 pulse the mosquitoes hardly responded to the warm body. Increasing the CO2 level in the cage by 1,000 parts per million caused a 25-fold increase in the number of landings by mosquitoes on the warm body in 2-min tests. This mosquito activation allowed the measurement of a significant reduction in the number of landings to bite on the warm body with increasing doses of deet (0.4 to 3.8 microg/cm2). An asymptotic nonlinear model fitted to the repellency data in the presence of CO2 allowed estimation of the effective dose of deet that reduced landings to bite by 50% (ED50) at 0.95 microg/cm2 (5 nmol/cm2) and the corresponding ED95 at 4.12 microg/cm2 (21.5 nmol/cm2). This in vitro bioassay has the advantage of permitting a fast throughput of test products under standardized conditions and is suitable for screenings designed for the purpose of discovering lead products with as yet unknown human toxicological and dermatological profiles.
Accurate estimation of neural population dynamics without spike sorting (2017)

A central goal of systems neuroscience is to relate an organism’s neural activity to behavior. Neural population analysis often begins by reducing the dimensionality of the data to focus on the patterns most relevant to a given task. A major practical hurdle to data analysis is spike sorting, and this problem is growing rapidly as the number of neurons measured increases. Here, we investigate whether spike sorting is necessary to estimate neural dynamics. The theory of random projections suggests that we can accurately estimate the geometry of low-dimensional manifolds from a small number of linear projections of the data. We re-analyzed data from three previous studies and found that neural dynamics and scientific conclusions are quite similar using multi-unit threshold crossings in place of sorted neurons. This finding unlocks existing data for new analyses and informs the design and use of new electrode arrays for laboratory and clinical use.
PrimeDesign software for rapid and simplified design of prime editing guide RNAs (2021)

Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.
<title>Comparison of automated and manual segmentation of hippocampus MR images</title> (1995)

The precision and accuracy of area estimates from magnetic resonance (MR) brain images and using manual and automated segmentation methods are determined. Areas of the human hippocampus were measured to compare a new automatic method of segmentation with regions of interest drawn by an expert. MR images of nine normal subjects and nine schizophrenic patients were acquired with a 1.5-T unit (Siemens Medical Systems, Inc., Iselin, New Jersey). From each individual MPRAGE 3D volume image a single comparable 2-D slice (matrix equals 256 X 256) was chosen which corresponds to the same coronal slice of the hippocampus. The hippocampus was first manually segmented, then segmented using high dimensional transformations of a digital brain atlas to individual brain MR images. The repeatability of a trained rater was assessed by comparing two measurements from each individual subject. Variability was also compared within and between subject groups of schizophrenics and normal subjects. Finally, the precision and accuracy of automated segmentation of hippocampal areas were determined by comparing automated measurements to manual segmentation measurements made by the trained rater on MR and brain slice images. The results demonstrate the high repeatability of area measurement from MR images of the human hippocampus. Automated segmentation using high dimensional transformations from a digital brain atlas provides repeatability superior to that of manual segmentation. Furthermore, the validity of automated measurements was demonstrated by a high correlation with manual segmentation measurements made by a trained rater. Quantitative morphometry of brain substructures (e.g. hippocampus) is feasible by use of a high dimensional transformation of a digital brain atlas to an individual MR image. This method automates the search for neuromorphological correlates of schizophrenia by a new mathematically robust method with unprecedented sensitivity to small local and regional differences.
Extended levodopa release from a subcutaneously implanted polymer matrix in rats (1990)

It is well recognized that plasma fluctuations resulting from oral levodopa therapy may cause an unstable clinical response in parkinsonian patients. We have therefore developed a slow-release polymer matrix system that can deliver levodopa continuously for extended periods of time (at least 225 days) after subcutaneous implantation in rats. Advantages of this approach include (1) the elimination of levodopa plasma fluctuations and (2) the possibility of reducing the required dose due to constant plasma levels and because the gastrointestinal tract is circumvented. The peripheral implantation of polymer systems containing levodopa, dopamine receptor agonists, or other anti-Parkinson agents may constitute a novel technology of drug delivery to improve the care of patients with Parkinson's disease.
Spherical deformation of compliant substrates with semiconductor device islands (2003)

This article explores, through experiments and finite element analysis, the ability to plastically deform thin-film semiconductor structures on deformable substrates to spherical cap shapes without cracking the semiconductor layers. The major challenge involves contending with the large strain due to extreme deformation that will crack uniform stiff layers, such as silicon or silicon nitride. By patterning amorphous silicon and silicon nitride layers into islands, such problems can be avoided despite average strains in the substrate in excess of 5%. The strain in the device islands after deformation is a function of the island structure, size, and substrate material properties. Although the substrate is plastically expanded to a spherical dome, device islands can experience either tension or compression depending on the structure.
Molybdenum‐Based Complexes with Two Aryloxides and a Pentafluoroimido Ligand: Catalysts for Efficient Z‐Selective Synthesis of a Macrocyclic Trisubstituted Alkene by Ring‐Closing Metathesis (2013)

Olefin metathesis catalysts for controlling the formation of trisubstituted macrocyclic Z alkenes have been developed. The most effective complexes are Mo alkylidenes with a pentafluorophenylimido group and two large aryloxide ligands. The macrocyclic lactone precursor to anticancer agents epothilones B and D is obtained in 73 % yield and 91 % Z selectivity in less than 6 hours at room temperature. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.