gebhart/patrepeval huggingface dataset:
Parametric modelling and segmentation of vertebral bodies in 3D CT and MR spine images (2011)

Accurate and objective evaluation of vertebral deformations is of significant importance in clinical diagnostics and therapy of pathological conditions affecting the spine. Although modern clinical practice is focused on three-dimensional (3D) computed tomography (CT) and magnetic resonance (MR) imaging techniques, the established methods for evaluation of vertebral deformations are limited to measuring deformations in two-dimensional (2D) x-ray images. In this paper, we propose a method for quantitative description of vertebral body deformations by efficient modelling and segmentation of vertebral bodies in 3D. The deformations are evaluated from the parameters of a 3D superquadric model, which is initialized as an elliptical cylinder and then gradually deformed by introducing transformations that yield a more detailed representation of the vertebral body shape. After modelling the vertebral body shape with 25 clinically meaningful parameters and the vertebral body pose with six rigid body parameters, the 3D model is aligned to the observed vertebral body in the 3D image. The performance of the method was evaluated on 75 vertebrae from CT and 75 vertebrae from T(2)-weighted MR spine images, extracted from the thoracolumbar part of normal and pathological spines. The results show that the proposed method can be used for 3D segmentation of vertebral bodies in CT and MR images, as the proposed 3D model is able to describe both normal and pathological vertebral body deformations. The method may therefore be used for initialization of whole vertebra segmentation or for quantitative measurement of vertebral body deformations.
Short antisense oligonucleotide-mediated inhibition is strongly dependent on oligo length and concentration but almost independent of location of the target sequence. (1994)

The inhibitory effect of short antisense oligodeoxynucleotides (aODNs) on cRNA expression in Xenopus oocytes was measured using an electrophysiological assay based on subunit-specific block of cloned alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionate receptors. The effect of both phosphorothioate-modified (PS) and phosphodiester (PO) aODNs was strongly length dependent with a half-maximal inhibition calculated for an oligo length of 7.6 nucleotides (nt) and 9.9 nt, respectively. More than 95% inhibition was mediated by a PS aODN of 12 nt and by PO aODNs > or = 15 nt. At a given length PS and PO aODNs showed differential dependence of their inhibitory effect on the injected aODN concentration (half-maximal inhibition at 18 ng/microliter for a PO 12-mer and at 0.19 ng/microliter for a PS 12-mer) and differential saturation behavior. The inhibitory effect of aODNs, even as short as 8 nt for PS oligomers, was highly sequence specific, but almost independent of the position of the respective target site on the cRNA (for PS 8-mers, > or = 70% expression inhibition throughout the tested target sites from the translation initiation to the 3'-untranslated region). Thus, short PS aODNs can be reliably used in order to specifically inhibit protein expression in experiments addressing physiological, molecular biological, and perhaps even therapeutical issues.
Clearing the smoke: the science base for tobacco harm reduction—executive summary (2001)

Tobacco smoke is the cause of the most deadly epidemic of modern times. Smoking causes cancer (for example, lung, oral cavity, oesophagus, larynx, pancreas, bladder, kidney), chronic obstructive pulmonary disease (COPD), myocardial infarction, and stroke. The continuing toll of tobacco use has prompted the search for means of harm reduction for those who cannot or will not stop using tobacco. Numerous products that make implied or explicit claims to reduce the burden of smoking while allowing continued nicotine consumption are now entering the market. This report is concerned with the evaluation of these products.

Nearly one quarter of adult Americans—an estimated 47 million people—smoke cigarettes.1 Although this is far lower than the 42% recorded in 1965, the decline in the rates of smoking among adults appears to have levelled off during much of the 1990s.2 In a recent survey, 12.8% of middle school children and 34.8% of high school students reported some form of tobacco use during the month prior to their being interviewed.3 The vast majority of smokers begin tobacco use during adolescence.4 However, 70% of smokers say they want to quit5 and 34% of smokers make an attempt to quit each year. Thus, many but not all tobacco users find it very difficult to quit and continually expose themselves to known toxic agents.

For the purposes of this report, a product is harm reducing if it lowers total tobacco related mortality and morbidity even though use of that product may involve continued exposure to tobacco related toxicants. Many different policy strategies may contribute to harm reduction. However, this report focuses on tobacco products that may be less harmful or on pharmaceutical preparations that may be used alone or concomitantly with decreased use of conventional tobacco. The committee does not use the term “safer …
Partially unfolded proteins efficiently penetrate cell membranes — implications for oral drug delivery (1998)

We have previously reported on the biological activity of members of a library of low molecular weight compounds (carriers) that enable the oral delivery of proteins (Milstein, Proceedings of the 1995 Miami Bio/Technology Winter Symposium on Protein Engineering and Structural Biology, IRL Press at Oxford University Press, 1995, p. 13; Leone-Bay et al., J. Med. Chem. 38 (1995) 4263-4269; Leone-Bay et al., J. Med. Chem. 39 (1996) 2571-2578; [1-3]). When rats or primates are orally administered a solution of carrier and either recombinant human alpha-interferon (rhIFN), insulin or recombinant human growth hormone (rhGH) significant serum concentrations of the proteins are detectable. The transport activity of these compounds is positively correlated with their structural effects on the protein molecules. Direct measurement of the interaction of these carrier molecules with the proteins indicates that they reversibly destabilize the native state of the molecule favoring a partially unfolded conformation. Apparently these intermediate protein conformations are transport competent and are able to be absorbed through the intestinal tissue and into the bloodstream. Since the measured binding of the carriers to the partially unfolded proteins is relatively weak (Kb = 100 M(-1)) and the systemic activity of the proteins appears to be unaffected, the changes in the structure of the proteins are manifestly reversible.
Phenotypic mixing between different hepadnavirus nucleocapsid proteins reveals C protein dimerization to be cis preferential (1994)

Hepadnaviruses encode a single core (C) protein which assembles into a nucleocapsid containing the polymerase (P) protein and pregenomic RNA during viral replication in hepatocytes. We examined the ability of heterologous hepadnavirus C proteins to cross-oligomerize. Using a two-hybrid assay in HepG2 cells, we observed cross-oligomerization among the core proteins from hepatitis B virus (HBV), woodchuck hepatitis virus, and ground squirrel hepatitis virus. When expressed in Xenopus oocytes, in which hepadnavirus C proteins form capsids, the C polypeptides from woodchuck hepatitis virus and ground squirrel hepatitis virus, but not duck hepatitis B virus, can efficiently coassemble with an epitope-tagged HBV core polypeptide to form mixed capsids. However, when two different core mRNAs are coexpressed in oocytes the core monomers show a strong preference for forming homodimers rather than heterodimers. This holds true even for coexpression of two HBV C proteins differing only by an epitope tag, suggesting that core monomers are not free to diffuse and associate with other monomers. Thus, mixed capsids result from aggregation of different species of homodimers.
Phenotypic variation of mutations in the human lipoprotein-lipase gene (1993)

We have described a large number of different mutations in the LPL gene that result in completely catalytically defective LPL protein. More recently exonic polymorphisms in the LPL gene have been described that do not result in the catalytic activity of LPL being significantly impaired. Furthermore we have recently described a patient who is homozygous for a mutation in the LPL gene in a conserved region of exon 5 that results only in partial residual activity and a very mild clinical phenotype. This may suggest that the frequency of mutations in the LPL gene is greater than has been previously recognized. Recognition and selection of patients for analysis was based on the phenotype of chylomicronaemia. However, the existence of the Ser172-Cys mutation in the LPL gene that results in only moderate hypertriglyceridaemia in the absence of environmental factors might suggest that mutations in this gene are more frequent and could be seen in patients with a milder clinical phenotype. The clue to detecting these changes in the LPL gene might be to investigate patients who present with chylomicronaemia due to different environmental triggers while, in the absence of these environmental factors, they have only moderate hypertriglyceridaemia.
Purification and properties of L-Aspartate-alpha-decarboxylase, an enzyme that catalyzes the formation of beta-alanine in Escherichia coli. (1979)

L-Aspartate-alpha-decarboxylase, an enzyme that catalyzes the production of beta-alanine, has been purified to apparent homogeneity from Escherichia coli. The properties of the enzyme are: (a) pH optimum of 6.8 to 7.5, (b) temperature optimum of 55 degrees C, (c) Km for L-aspartate of 0.16 mM, and (d) molecular weight of 58,000. The activity of the enzyme is inhibited by reagents (hydroxylamine, phenylhydrazine, and sodium borohydride) that react with carbonyl groups, but no pyridoxal phosphate is present. The compound containing the carbonyl group has been identified as covalently bound pyruvate. Approximately 1 mol of pyruvate was found/mol of enzyme. That the enzyme has a biosynthetic function rather than a catabolic role is indicated by the observations that a mutant (designated as E. coli 99-2) which requires either beta-alanine or pantothenic acid for growth contains only trace amounts of enzyme activity, whereas it is present in substantial amounts in the parent strain (E. coli W) and in a spontaneous revertant of the mutant.
Nicotinic Acid, Nicotinamide, and Nicotinamide Riboside: A Molecular Evaluation of NAD+ Precursor Vitamins in Human Nutrition (2008)

Although baseline requirements for nicotinamide adenine dinucleotide (NAD+) synthesis can be met either with dietary tryptophan or with less than 20 mg of daily niacin, which consists of nicotinic acid and/or nicotinamide, there is growing evidence that substantially greater rates of NAD+ synthesis may be beneficial to protect against neurological degeneration, Candida glabrata infection, and possibly to enhance reverse cholesterol transport. The distinct and tissue-specific biosynthetic and/or ligand activities of tryptophan, nicotinic acid, nicotinamide, and the newly identified NAD+ precursor, nicotinamide riboside, reviewed herein, are responsible for vitamin-specific effects and side effects. Because current data suggest that nicotinamide riboside may be the only vitamin precursor that supports neuronal NAD+ synthesis, we present prospects for human nicotinamide riboside supplementation and propose areas for future research.
Yeast mRNA Cap Methyltransferase Is a 50-Kilodalton Protein Encoded by an Essential Gene (1995)

RNA (guanine-7-)methyltransferase, the enzyme responsible for methylating the 5' cap structure of eukaryotic mRNA, was isolated from extracts of Saccharomyces cerevisiae. The yeast enzyme catalyzed methyl group transfer from S-adenosyl-L-methionine to the guanosine base of capped, unmethylated poly(A). Cap methylation was stimulated by low concentrations of salt and was inhibited by S-adenosyl-L-homocysteine, a presumptive product of the reaction, but not by S-adenosyl-D-homocysteine. The methyltransferase sedimented in a glycerol gradient as a single discrete component of 3.2S. A likely candidate for the gene encoding yeast cap methyltransferase was singled out on phylogenetic grounds. The ABD1 gene, located on yeast chromosome II, encodes a 436-amino-acid (50-kDa) polypeptide that displays regional similarity to the catalytic domain of the vaccinia virus cap methyltransferase. That the ABD1 gene product is indeed RNA (guanine-7-)methyltransferase was established by expressing the ABD1 protein in bacteria, purifying the protein to homogeneity, and characterizing the cap methyltransferase activity intrinsic to recombinant ABD1. The physical and biochemical properties of recombinant ABD1 methyltransferase were indistinguishable from those of the cap methyltransferase isolated and partially purified from whole-cell yeast extracts. Our finding that the ABD1 gene is required for yeast growth provides the first genetic evidence that a cap methyltransferase (and, by inference, the cap methyl group) plays an essential role in cellular function in vivo.
LTCC Packages With Embedded Phased-Array Antennas for 60 GHz Communications (2011)

A low-cost, fully-integrated antenna-in-package solution for 60 GHz phased-array systems is demonstrated. Sixteen patch antennas are integrated into a 28 mm × 28 mm ball grid array together with a flip-chip attached transmitter or receiver IC. The packages have been implemented using low temperature co-fired ceramic technology. 60 GHz interconnects, including flip-chip transitions and via structures, are optimized using full-wave simulation. Anechoic chamber measurement has shown ~ 5 dBi unit antenna gain across all four IEEE 802.15.3c channels, achieving excellent model-to-hardware correlation. The packaged transmitter and receiver ICs, mounted on evaluation boards, have demonstrated beam-steered, non-line-of-sight links with data rates up to 5.3 Gb/s.
Emulsifying properties of proteins: evaluation of a turbidimetric technique (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEmulsifying properties of proteins: evaluation of a turbidimetric techniqueKevin N. Pearce and John E. KinsellaCite this: J. Agric. Food Chem. 1978, 26, 3, 716–723Publication Date (Print):May 1, 1978Publication History Published online1 May 2002Published inissue 1 May 1978https://doi.org/10.1021/jf60217a041RIGHTS & PERMISSIONSArticle Views8983Altmetric-Citations1731LEARN 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 (989 KB) Get e-Alertsclose Get e-Alerts
Model-Based Image Reconstruction for MRI (2010)

Magnetic resonance imaging (MRI) is a sophisticated and versatile medical imaging modality. Traditionally, MR images are reconstructed from the raw measurements by a simple inverse 2D or 3D fast Fourier transform (FFT). However, there are a growing number of MRI applications where a simple inverse FFT is inadequate, e.g., due to non-Cartesian sampling patterns, non-Fourier physical effects, nonlinear magnetic fields, or deliberate under-sampling to reduce scan times. Such considerations have led to increasing interest in methods for model-based image reconstruction in MRI.
Aromatic Fluorine Compounds. VIII. Plant Growth Regulators and Intermediates1,2 (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAromatic Fluorine Compounds. VIII. Plant Growth Regulators and Intermediates1,2G. C. Finger, M. J. Gortatowski, R. H. Shiley, and R. H. WhiteCite this: J. Am. Chem. Soc. 1959, 81, 1, 94–101Publication Date (Print):January 1, 1959Publication History Published online1 May 2002Published inissue 1 January 1959https://pubs.acs.org/doi/10.1021/ja01510a021https://doi.org/10.1021/ja01510a021research-articleACS PublicationsRequest reuse permissionsArticle Views2071Altmetric-Citations29LEARN 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
Intervening the Diabetes Patients' Exercise Engagement: A Transtheoretical Model Perspective (2011)

Diabetes can cause serious acute and chronic complications. Despite the diabetes is troublesome, good control on the patients' blood glucose can greatly help reducing complications and having a quality life. Exercise and diet control as well as medications are the iron triangle protecting the diabetes patients' health and quality life. This paper argues that effective intervention in the diabetes patient's daily life can do good help to ameliorate the case's health. Based on the transtheoretical model, this paper suggests a five-step approach with relevant strategies to be taken. This paper concludes with formulating an exercise program in accordance with the individual's cognition on behavior changes. This paper provides healthcare practices simple yet effective guidance while educating self-care of diabetes patients.
Induction of Persistent Colitis by a Human Commensal, EnterotoxigenicBacteroides fragilis, in Wild-Type C57BL/6 Mice (2009)

Enterotoxigenic Bacteroides fragilis (ETBF) causes diarrhea and is implicated in inflammatory bowel diseases and colorectal cancer. The only known ETBF virulence factor is the Bacteroides fragilis toxin (BFT), which induces E-cadherin cleavage, interleukin-8 secretion, and epithelial cell proliferation. A murine model for ETBF has not been characterized. Specific pathogen-free (SPF) C57BL/6J or germfree 129S6/SvEv mice were orally inoculated with wild-type ETBF (WT-ETBF) strains, a nontoxigenic WT strain of B. fragilis (WT-NTBF), WT-NTBF overexpressing bft (rETBF), or WT-NTBF overexpressing a biologically inactive mutated bft (rNTBF). In SPF and germfree mice, ETBF caused colitis but was lethal only in germfree mice. Colonic histopathology demonstrated mucosal thickening with inflammatory cell infiltration, crypt abscesses, and epithelial cell exfoliation, erosion, and ulceration. SPF mice colonized with rETBF mimicked WT-ETBF, whereas rNTBF caused no histopathology. Intestinal epithelial E-cadherin was rapidly cleaved in vivo in WT-ETBF-colonized mice and in vitro in intestinal tissues cultured with purified BFT. ETBF mice colonized for 16 months exhibited persistent colitis. BFT did not directly induce lymphocyte proliferation, dendritic cell stimulation, or Toll-like receptor activation. In conclusion, WT-ETBF induced acute then persistent colitis in SPF mice and rapidly lethal colitis in WT germfree mice. Our data support the hypothesis that chronic colonization with the human commensal ETBF can induce persistent, subclinical colitis in humans.
A Prospective Study in the Rational Design of Efficient Antisense Oligonucleotides for Exon Skipping in the DMD Gene (2012)

Antisense oligonucleotide (AON)-mediated exon skipping to restore dystrophin expression in Duchenne muscular dystrophy (DMD) therapy shown promise in a number of human clinical trials. Current AON design methods are semi-empirical, involving either trial-and-error and/or preliminary experimentations. Therefore, a rational approach to design efficient AONs to address the wide spectrum of patients' mutations is desirable. Retrospective studies have extracted many AON design variables, but they were not tested prospectively to design AONs for skipping DMD exons. Not only did the variables differ among the various studies, no numerical cutoff for each variable was inferred, which makes their use in AON design difficult. The challenge is to thus select a minimal set of key independent variables that can consistently design efficient AONs. In this prospective study, a novel set of design variables with respective cutoff values was used to design 23 novel AONs, each to skip one of nine DMD exons. Nineteen AONs were found to be efficacious in inducing specific exon skipping (83% of total), of which 14 were considered efficient (61% of total), i.e., they induced exon skipping in >25% of total transcripts. Notably, the satisfactory success rates were achieved by using only three design variables; namely, co-transcriptional binding accessibility of target site, presence of exonic splicing enhancers, and target length. Retrospective analyses revealed that the most efficient AON in every exon targeted has the lowest average cumulative position (ACP) score. Taking the prospective and retrospective studies together, we propose that design guidelines recommend using the ACP score to select the most efficient AON for each exon.
TROSPIUM CHLORIDE IMPROVES OVERACTIVE BLADDER SYMPTOMS: A MULTICENTER PHASE III TRIAL (2004)

Trospium was found to have sustained effectiveness beginning at the end of week 1 in decreasing the number of voids, urge incontinent episodes, total daily micturitions and urge severity, and in increasing volume per void. It also improved symptoms of OAB and quality of life.