gebhart/patrepeval huggingface dataset:
Pharmacologic management of neuropathic pain: Evidence-based recommendations (2007)

Patients with neuropathic pain (NP) are challenging to manage and evidence-based clinical recommendations for pharmacologic management are needed. Systematic literature reviews, randomized clinical trials, and existing guidelines were evaluated at a consensus meeting. Medications were considered for recommendation if their efficacy was supported by at least one methodologically-sound, randomized clinical trial (RCT) demonstrating superiority to placebo or a relevant comparison treatment. Recommendations were based on the amount and consistency of evidence, degree of efficacy, safety, and clinical experience of the authors. Available RCTs typically evaluated chronic NP of moderate to severe intensity. Recommended first-line treatments include certain antidepressants (i.e., tricyclic antidepressants and dual reuptake inhibitors of both serotonin and norepinephrine), calcium channel alpha2-delta ligands (i.e., gabapentin and pregabalin), and topical lidocaine. Opioid analgesics and tramadol are recommended as generally second-line treatments that can be considered for first-line use in select clinical circumstances. Other medications that would generally be used as third-line treatments but that could also be used as second-line treatments in some circumstances include certain antiepileptic and antidepressant medications, mexiletine, N-methyl-D-aspartate receptor antagonists, and topical capsaicin. Medication selection should be individualized, considering side effects, potential beneficial or deleterious effects on comorbidities, and whether prompt onset of pain relief is necessary. To date, no medications have demonstrated efficacy in lumbosacral radiculopathy, which is probably the most common type of NP. Long-term studies, head-to-head comparisons between medications, studies involving combinations of medications, and RCTs examining treatment of central NP are lacking and should be a priority for future research.
Getting to know Moses (2007)

We present results and experiences from our experiments with phrase-based statistical machine translation using Moses. The paper is based on the idea of using an off-the-shelf parser to supply linguistic information to a factored translation model and compare the results of German---English translation to the shared task baseline system based on word form. We report partial results for this model and results for two simplified setups. Our best setup takes advantage of the parser's lemmatization and decompounding. A qualitative analysis of compound translation shows that decompounding improves translation quality.
Site-Specific N- and C-Terminal Labeling of a Single Polypeptide Using Sortases of Different Specificity (2009)

The unique reactivity of two sortase enzymes, SrtA(staph) from Staphylococcus aureus and SrtA(strep) from Streptococcus pyogenes, is exploited for site-specific labeling of a single polypeptide with different labels at its N and C termini. SrtA(strep) is used to label the protein's C terminus at an LPXTG site with a fluorescently labeled dialanine nucleophile. Selective N-terminal labeling of proteins containing N-terminal glycine residues is achieved using SrtA(staph) and LPXT derivatives. The generality of N-terminal labeling with SrtA(staph) is demonstrated by near-quantitative labeling of multiple protein substrates with excellent site specificity.
Genetic Algorithm−Assisted Combinatorial Search for a New Green Phosphor for Use in Tricolor White LEDs (2005)

An evolutionary optimization process involving a genetic algorithm and combinatorial chemistry was employed for the development of green phosphors which are suitable for tricolor white-light-emitting diodes. To accomplish a high luminescent efficiency at 400 nm excitation, we screened a seven-cation oxide system including Tb, Gd, Ce, Mg, Si, Al, and B. The combination of a genetic algorithm and combinatorial chemistry enhanced the searching efficiency when applied for phosphor screening. As a result, the optimized composition was Tb(0.01)Gd(0.02)Ce(0.04)B(0.1)Si(0.83)O(delta), The luminance of this borosilicate glass was 67% that of ZnS:Cu,Al at 400-nm excitation.
Separable image warping with spatial lookup tables (1989)

Image warping refers to the 2-D resampling of a source image onto a target image. In the general case, this requires costly 2-D filtering operations. Simplifications are possible when the warp can be expressed as a cascade of orthogonal 1-D transformations. In these cases, separable transformations have been introduced to realize large performance gains. The central ideas in this area were formulated in the 2-pass algorithm by Catmull and Smith. Although that method applies over an important class of transformations, there are intrinsic problems which limit its usefulness.The goal of this work is to extend the 2-pass approach to handle arbitrary spatial mapping functions. We address the difficulties intrinsic to 2-pass scanline algorithms: bottlenecking, foldovers, and the lack of closed-form inverse solutions. These problems are shown to be resolved in a general, efficient, separable technique, with graceful degradation for transformations of increasing complexity.
Functional analysis of the SH2 and SH3 domains of the lck tyrosine protein kinase. (1992)

p56lck is a lymphoid cell-specific member of the src family of cytoplasmic tyrosine kinases. In helper and cytotoxic T cells it is physically associated with the CD4 and CD8 surface antigens and appears to play a role in signal transduction during T-cell activation. p56lck contains both an SH3 and an SH2 Src homology domain. Such domains have been suggested to play a role in the regulation of the activity or function of both receptor and non-receptor tyrosine protein kinases. Deletion of either or both domains in p56lck was found here to activate the protein and to lead to increased phosphorylation of the autophosphorylation site, Tyr-394, in vivo. These findings are consistent with the hypothesis that these domains participate in repression of the kinase activity of p56lck. None of the deleted forms was capable of transformation of fibroblasts. Deletion of the SH3 domain of a constitutively activated form of p56lck, p56lckF505, did not diminish the transforming activity of this protein. This suggests that this domain is dispensable for the transformation of fibroblasts by p56lck. In contrast, deletion of the SH2 domain abolished the transforming potential of activated p56lckF505. However, interpretation of this effect is made somewhat difficult because the mutation also lowered the steady-state abundance of the protein.
Phenotypic selection and characterization of mutant alleles of a eukaryotic DNA topoisomerase I. (1990)

We have developed a simple, effective genetic screen for mutant alleles of eukaryotic DNA topoisomerase I that manifest severely depressed or complete loss of enzymatic function. The screen is based on the extreme toxicity of vaccinia topoisomerase expression in the Escherichia coli lysogen strain BL21(DE3) and is notable for its ease in distinguishing nonsense mutations (that result in truncated proteins) from missense mutations. The power of the method is evinced by our observation that 100% of the candidate alleles identified in the screen were ultimately found to have single-base changes at the DNA level that result in amino acid substitutions at the protein level. By mutagenizing plasmid DNA in vitro with hydroxylamine and applying this phenotypic screen, we have isolated five distinct single amino acid substitution mutants, each of which shows a biochemical phenotype, that is, greater than or equal to 90% reduction in specific DNA relaxing activity of the mutant protein relative to wild type. The amino acids thus implicated in topoisomerase function have identical or related counterparts at homologous positions in the topoisomerases from yeast and man. The same genetic screen has been applied to the selection of temperature-sensitive alleles of the vaccinia topoisomerase, leading to the isolation of two additional single-hit mutant alleles that display a temperature-sensitive growth phenotype in E. coli BL21(DE3). By broadening our mutagenesis procedures, we expect to generate a comprehensive map of vaccinia topoisomerase function and primary protein structure that should have direct application to eukaryotic cellular enzymes. Our methodology should be applicable to the selection of missense and conditional mutant alleles in other genes whose expression in bacteria is toxic.
Face location in wavelet-based video compression for high perceptual quality videoconferencing (1996)

We present a human face location technique based on contour extraction within the framework of a wavelet-based video compression scheme for videoconferencing applications. In addition to an adaptive quantization in which spatial constraints are enforced to preserve perceptually important information at low bit rates, semantic information of the human face is incorporated to design a hybrid compression scheme for videoconferencing since the human face is often the most important portion within a frame and should be coded with high fidelity. The human face is detected based on contour extraction and feature point analysis. An approximated face mask is then used in the quantization of the decomposed subbands. At the same total bit rate, coarser quantization of the background enables the face region to be quantized finer and coded with higher quality. Simulation results have shown that the perceptual image quality can be greatly improved using the proposed scheme.
Phenolics, fiber and fiber digestibility in bird resistant and non bird resistant sorghum grain (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhenolics, fiber and fiber digestibility in bird resistant and non bird resistant sorghum grainJess D. ReedCite this: J. Agric. Food Chem. 1987, 35, 4, 461–464Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/jf00076a005https://doi.org/10.1021/jf00076a005research-articleACS PublicationsRequest reuse permissionsArticle Views65Altmetric-Citations8LEARN 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
Kinetics of restitution of left ventricular relaxation. (1992)

Although the kinetics of cardiac systolic force restitution have been well described, the restitution kinetics of left ventricular relaxation have not been examined. To define relaxation restitution behavior, we studied seven dogs chronically instrumented with left ventricular high-fidelity micromanometers and piezoelectric dimension crystals. After a priming period at a basic cycle length of 375 msec, test extrastimuli were introduced after a range of extrasystolic intervals (ESIs). Relaxation behavior of control and extrasystolic beats was characterized by the time constant of isovolumic relaxation, tau. Relaxation restitution can be described by two concatenated monoexponential curves, an early phase described by a rapid time constant and a late phase described by a slower time constant (TC1, 36.21 +/- 7.90 msec; TC2, 75.94 +/- 10.65 msec; p less than 0.05). The first phase of relaxation restitution parallels systolic force restitution over the same range and displays faster recovery (TCs, 58.93 +/- 10.01 msec, p less than 0.05). Postextrasystolic restitution of test pulses after beats at fixed ESIs depends on the initial ESI. Relaxation recovery of postextrasystolic beats proceeds faster with smaller initial ESIs (TC1 for ESI of 300 msec, 13.27 +/- 4.05 msec; TC1 for ESI of 450 msec, 72.85 +/- 21.72 msec; p less than 0.0001). The monoexponential pattern of restitution was seen with model-independent descriptors of relaxation as well as with tau.
PYY inhibits CCK-stimulated pancreatic secretion through the area postrema in unanesthetized rats (2001)

Peptide YY (PYY) inhibits CCK-8-secretin-stimulated pancreatic secretion in vivo. To investigate whether CCK-8-secretin-stimulated pancreatic secretion is mediated through a vago-vagal pathway and whether PYY inhibits this pathway through the area postrema (AP), chronic pancreatic, biliary, and duodenal catheters were implanted in AP-lesioned (APX) or sham-operated rats. The effects of APX on pancreatic secretion stimulated by bethanechol, pancreatic juice diversion (PJD), or CCK-8-secretin, were tested, with and without background PYY infusion, in unanesthetized rats. APX reduced basal pancreatic secretion by 15-20% (P < 0.01). APX had no effect on bethanechol-stimulated secretion and potentiated protein secretion stimulated by PJD (396 vs. 284%) and exogenous CCK-8-secretin. In sham-operated rats, background PYY potently inhibited CCK-8-secretin-stimulated pancreatic fluid (1.8 vs. 48.2%) and protein secretion (3.7 vs. 45.8%) but potentiated fluid (52.9 vs. 43.1%) and protein (132.9 vs. 68.9%) secretion in APX rats. Our findings demonstrate that PYY inhibits CCK-8-secretin-stimulated pancreatic secretion through an AP-dependent mechanism in sham-operated rats. The AP also contributes to basal pancreatic secretion.
Proteophosphoglycan, a Major Secreted Product of IntracellularLeishmania mexicanaAmastigotes, Is a Poor B-Cell Antigen and Does Not Elicit a Specific Conventional CD4+T-Cell Response (1999)

Secreted and surface-exposed antigens of intracellular pathogens are thought to provide target structures for detection by the host immune system. The major secreted product of intracellular Leishmania mexicana amastigotes, a proteophosphoglycan (aPPG), is known to contribute to the establishment of the parasitophorous vacuole and is able to activate complement. aPPG belongs to a novel class of serine- and threonine-rich Leishmania proteins that are extensively modified by phosphodiester-linked phosphooligosaccharides and terminal mannooligosaccharides. Here we show that mice chronically infected with L. mexicana generally do not produce antibodies or Th cells specific for aPPG. Similarly, antibody titers are very low in mice vaccinated with aPPG, and specific CD4+ T cells are undetectable. Comparative analyses of other Leishmania glycoconjugates indicate that L. mexicana-specific carbohydrate structures are poorly immunogenic in mice and that the proteophosphoglycan aPPG behaved immunologically like a carbohydrate. The latter observation is explained by the lack of induction of aPPG-specific CD4+ T cells. In contrast, recombinant aPPG peptides stimulate CD4+ T-cell responses and high titers of specific antibodies are found in the sera of mice vaccinated with these peptides. Native aPPG is highly resistant to proteinases and apparently cannot be degraded by macrophages. It is concluded that conventional CD4+ T cells against the polypeptide backbone of aPPG are not induced because the molecule resists antigen processing due to its extensive and complex carbohydrate modification. The complex glycan chains of aPPG, which exhibit important biological functions for the parasite, may therefore also have evolved to evade detection by the immune system of the host organism.
Proteomics Comparison of Cerebrospinal Fluid of Relapsing Remitting and Primary Progressive Multiple Sclerosis (2010)

The main finding of this comparative study is the observation that the proteome profiles of CSF in PP and RR MScl patients overlap to a large extent. Still, a number of differences could be observed. Protein jagged-1 is a ligand for multiple Notch receptors and involved in the mediation of Notch signaling. It is suggested in literature that the Notch pathway is involved in the remyelination of MScl lesions. Aberration of normal homeostasis of Vitamin D, of which approximately 90% is bound to vitamin D-binding protein, has been widely implicated in MScl for some years now. Vitamin D directly and indirectly regulates the differentiation, activation of CD4+ T-lymphocytes and can prevent the development of autoimmune processes, and so it may be involved in neuroprotective elements in MScl.
The relationship between fibromyalgia and major depressive disorder: a comprehensive review (2008)

New methodological and theoretical approaches may lead to a better understanding of the link between FM and MDD, and to more effective psychological and psychopharmacological therapies for FM patients. In the meantime, clinicians should carefully screen for a history of MDD in patients with FM.
Characterization of mucin‐type core‐1 β1‐3 galactosyltransferase homologous enzymes in Drosophila melanogaster (2005)

Mucin type O-glycosylation is a widespread modification of eukaryotic proteins. The transfer of N-acetylgalactosamine to selected serine or threonine residues is catalyzed by a family of polypeptide N-acetylgalactosaminyltransferases localized in the Golgi apparatus. The most abundant elongation of O-glycans is the addition of a beta1-3 linked galactose by the core-1 beta1-3 galactosyltransferase (core-1 beta3GalT), thereby building the T-antigen or core-1 structure Gal(beta1-3)GalNAc(alpha1-O). We have isolated four Drosophila melanogaster cDNAs encoding proteins structurally similar to the human core-1 beta3GalT enzyme and expressed them as FLAG-tagged proteins in Sf9 insect cells. The identity of these D. melanogasterbeta3GalT enzymes with a core-1 beta3GalT activity was confirmed by utilization of MUC5AC mucin derived O-glycopeptide acceptors. In addition to the core-1 beta3GalT activity toward O-glycoprotein substrates, one member of this enzyme family showed a strong activity towards glycolipid acceptors, thereby building the core-1 terminated Nz6 glycosphingolipid. Transcripts of the embryonically expressed core-1 beta3GalTs were found in the maternally deposited mRNA, in salivary glands and in the amnioserosa. The presence of multiple core-1 beta3GalT genes in D. melanogaster suggests an increased complexity of core-1 O-glycan expression, which is possibly related to multiple developmental and physiological functions attributable to this class of glycans.
Apoptosis: a basic biological phenomenon with wide‐ranging implications in human disease (2005)

Apoptosis is a highly regulated process of cell deletion and plays a fundamental role in the maintenance of tissue homeostasis in the adult organism. Numerous studies in recent years have revealed that apoptosis is a constitutive suicide programme expressed in most, if not all cells, and can be triggered by a variety of extrinsic and intrinsic signals. Many human diseases can be attributed directly or indirectly to a derangement of apoptosis, resulting in either cell accumulation, in which cell eradication or cell turnover is impaired, or cell loss, in which the apoptotic programme is inadvertently triggered. In addition, defective macrophage engulfment and degradation of cell corpses may also contribute to a dysregulation of tissue homeostasis. An increased understanding of the signalling pathways that govern the execution of apoptosis and the subsequent clearance of dying cells may thus yield novel targets for therapeutic intervention in a wide range of human maladies.
Iteratively Coupled Reservoir Simulation for Multiphase Flow (2007)

Abstract FIM (Fully Implicit Method) and IMPES (Implicit Pressure Explicit Saturation) are two of the most commonly used time-stepping schemes in present reservoir simulation. However, neither of them satisfies the requirements of accuracy and efficiency with increasing size and degree of complexity of highly heterogeneous reservoirs. In this paper, an iterative coupling scheme is developed and applied to multiphase reservoir problems, which aims to model and simulate realistic reservoirs accurately and efficiently. Numerical examples reflecting major difficulties in treating heterogeneities and simulating complex reservoir phenomena such as coning and countercurrent flow problems are presented in comparison studies of iterative coupling, FIM and IMPES methods. Our results indicate that for the same accuracy the iterative approach can reduce computational time by 30%-40% or even more over the FIM. In comparing with the IMPES method, the iterative method shows better stability for taking larger time steps, and superior local mass balance. In this paper, the iterative approach is also shown to be scalable in parallel. Another advantage of the iterative coupled approach over FIM is that different numerical schemes and even physical models can be incorporated into the algorithm thus allowing more flexibility in treating complicated problems, e.g. highly heterogeneous reservoirs with different subdomain stochastic properties.
Clinical trial participant characteristics and saliva and DNA metrics (2009)

COMPASS; registered as NCT00301145 at clinicaltrials.gov.
Ionizing radiation induces tumor cell lysyl oxidase secretion (2014)

These results indicate a differential regulation of LOX-expression and secretion in response to IR and hypoxia, and suggest that LOX may contribute towards an IR-induced migratory phenotype in sublethally-irradiated tumor cells and tumor progression.
Adenoviral DNA Replication: DNA Sequences and Enzymes Required for Initiation In vitro (1983)

The development of cell-free systems for the replication of DNA has enabled diverse mechanisms for the priming of DNA synthesis at replication origins to be determined. Such varied mechanisms are discussed in this volume, including the self-priming of replication by the template DNA, as for the autonomous parvoviruses (Astell et al., this volume) and the priming by an RNA synthesized either by primase (Stayton et al.; Brown et al.; both this volume) or by RNA polymerase (Fuller et al., this volume). The development of a cell-free system for the replication of adenoviral DNA (Challberg and Kelly 1979) has paved the way for a detailed examination of a novel mechanism for the initiation of DNA synthesis, namely, priming by a deoxynucleotide that is covalently attached to a protein. Several aspects of this mechanism are discussed in this paper and by Lichy et al. (this volume).