gebhart/patrepeval huggingface dataset:
Anisotropic diffusion for Monte Carlo noise reduction (1999)

Monte Carlo sampling can be used to estimate solutions to global light transport and other rendering problems. However, a large number of observations may be needed to reduce the variance to acceptable levels. Rather than computing more observations within each pixel, if spatial coherence exists in image space it can be used to reduce visual error by averaging estimators in adjacent pixels. Anisotropic diffusion is a space-variant noise reduction technique that can selectively preserve texture, edges, and other details using a map of image coherence. The coherence map can be estimated from depth and normal information as well as interpixel color distance. Incremental estimation of the reduction in variance, in conjunction with statistical normalization of interpixel color distances, yields an energy-preserving algorithm that converges to a spatially nonconstant steady state.
Identification of microorganisms based on headspace analysis of volatile organic compounds by gas chromatography–mass spectrometry (2014)

The identification of specific volatile organic compounds (VOCs) produced by microorganisms may assist in developing a fast and accurate methodology for the determination of pulmonary bacterial infections in exhaled air. As a first step, pulmonary bacteria were cultured and their headspace analyzed for the total amount of excreted VOCs to select those compounds which are exclusively associated with specific microorganisms. Development of a rapid, noninvasive methodology for identification of bacterial species may improve diagnostics and antibiotic therapy, ultimately leading to controlling the antibiotic resistance problem. Two hundred bacterial headspace samples from four different microorganisms (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Klebsiella pneumoniae) were analyzed by gas chromatography-mass spectrometry to detect a wide array of VOCs. Statistical analysis of these volatiles enabled the characterization of specific VOC profiles indicative for each microorganism. Differences in VOC abundance between the bacterial types were determined using ANalysis of VAriance-principal component analysis (ANOVA-PCA). These differences were visualized with PCA. Cross validation was applied to validate the results. We identified a large number of different compounds in the various headspaces, thus demonstrating a highly significant difference in VOC occurrence of bacterial cultures compared to the medium and between the cultures themselves. Additionally, a separation between a methicillin-resistant and a methicillin-sensitive isolate of S. aureus could be made due to significant differences between compounds. ANOVA-PCA analysis showed that 25 VOCs were differently profiled across the various microorganisms, whereas a PCA score plot enabled the visualization of these clear differences between the bacterial types. We demonstrated that identification of the studied microorganisms, including an antibiotic susceptible and resistant S. aureus substrain, is possible based on a selected number of compounds measured in the headspace of these cultures. These in vitro results may translate into a breath analysis approach that has the potential to be used as a diagnostic tool in medical microbiology.
Genetic Variations and Diseases in UniProtKB/Swiss‐Prot: The Ins and Outs of Expert Manual Curation (2014)

During the last few years, next-generation sequencing (NGS) technologies have accelerated the detection of genetic variants resulting in the rapid discovery of new disease-associated genes. However, the wealth of variation data made available by NGS alone is not sufficient to understand the mechanisms underlying disease pathogenesis and manifestation. Multidisciplinary approaches combining sequence and clinical data with prior biological knowledge are needed to unravel the role of genetic variants in human health and disease. In this context, it is crucial that these data are linked, organized, and made readily available through reliable online resources. The Swiss-Prot section of the Universal Protein Knowledgebase (UniProtKB/Swiss-Prot) provides the scientific community with a collection of information on protein functions, interactions, biological pathways, as well as human genetic diseases and variants, all manually reviewed by experts. In this article, we present an overview of the information content of UniProtKB/Swiss-Prot to show how this knowledgebase can support researchers in the elucidation of the mechanisms leading from a molecular defect to a disease phenotype.
The lysosomal cysteine protease, cathepsin S, is increased in Alzheimer's disease and Down syndrome brain. An immunocytochemical study. (1995)

Expression of cathepsin (cat) S, a lysosomal cysteine protease, has recently been shown to cause an increase in production of amyloid beta-peptides in transfected human cells. In this study, we examined the presence and localization of cat S by immunocytochemistry in 21 control, 24 Alzheimer's disease (AD), and 10 Down syndrome (DS) postmortem brains. An antiserum to a human cat S fusion protein was affinity purified and its specificity confirmed by abolition of immunoreactivity after adsorption with cat S but not cat L fusion protein. A small minority of control cases showed light, focal staining of scattered cortical neurons. Many control cases, as well as most AD and DS cases, showed prominent staining of vascular smooth muscle cells, particularly in leptomeningeal vessels. Both AD and DS brain tissue showed increased immunoreactivity in a subset of neocortical and hippocampal neurons and glia. Cat S immunoreactivity occurred in a granular, cytoplasmic pattern in some neurons or in a more dense staining pattern in certain neurofibrillary tangle-bearing neurons. Cat S-positive neurons were also present in amygdala and basal forebrain in AD brains. A subset of astrocytes were immunoreactive with the cat S antibody in AD and DS but not in control brains. In rare AD cases, cat S immunostaining was observed in astrocytes in the periphery of amyloid-beta-containing plaques. These results suggest that cat S is up-regulated in AD and DS brain. The association of cat S immunoreactivity with tangle-bearing neurons, astrocytes, and rare senile plaques implies a role for altered cat S activity in the pathogenesis of AD.
Involvement of cysteine residues in catalysis and inhibition of human aldose reductase. Site-directed mutagenesis of Cys-80, -298, and -303. (1992)

In order to study the potential role of cysteinyl residues in catalysis and inhibition of human aldose reductase, mutants containing cysteine to serine substitution at positions 80 (ALR2:C80S), 298 (ALR2:C298S), and 303 (ALR2:C303S) were constructed. Mutation of Cys298 resulted in the most profound changes, as ALR2:C298S displayed 4- to 5-fold elevation in K'm(NADPH), K'm(DL-glyceraldehyde), and kcat(DL-glyceraldehyde) relative to wild type aldose reductase as well as a 10-fold higher Ki for the aldose reductase inhibitor sorbinil. Wild type and mutant reductases were equally sensitive to tolrestat, a structurally different reductase inhibitor. Carboxymethylation of the wild type enzyme or the C80S and C303S mutants led to a modest decrease in kcat as well as an increase in K'm(DL-glyceraldehyde) and Ki(sorbinil). These parameters were not significantly changed when ALR2:C298S was subjected to carboxymethylation. Lithium sulfate caused activation of ALR2:WT, C80S, and C303S but did not significantly affect the activity of ALR2:C298S. The differential sensitivity of wild type and mutant reductases to inhibition by sorbinil and tolrestat, before and after carboxymethylation, indicates that these inhibitors bind at different sites. These results suggest that Cys-298 is present near the active site and constitutes a regulatory group which controls the catalytic activity and inhibitor sensitivity of the enzyme.
Population Pharmacokinetic Modeling of Ustekinumab, a Human Monoclonal Antibody Targeting IL‐12/23p40, in Patients With Moderate to Severe Plaque Psoriasis (2009)

The population pharmacokinetics of ustekinumab are characterized in patients with moderate to severe plaque psoriasis in 2 Phase 3 studies (PHOENIX 1 and PHOENIX 2). Serum concentration data from 1937 patients are analyzed to determine pharmacokinetic characteristics of ustekinumab and to assess factors that may contribute to their variability. The population typical mean (percentage relative standard error) values for apparent clearance, apparent volume of distribution, and absorption rate constant from the final covariate model are 0.465 L.day(-1) (2.0%), 15.7 L (2.0%), and 0.354 day(-1) (16.2%), respectively. The interindividual variabilities for apparent clearance and apparent volume of distribution are 41.0% and 33.2%, respectively. Of the factors evaluated in this analysis, body weight, diabetes, and positive immune response (antibodies to ustekinumab) are important covariates affecting the apparent clearance and/or apparent volume of distribution of ustekinumab. To fully understand the clinical relevance of these results, the covariate findings need to be evaluated concurrently with the efficacy and safety data.
Surface Energy and Adhesion Studies on Acrylic Pressure Sensitive Adhesives (2001)

Abstract The surface energy and adhesion dynamics of pressure sensitive adhesives-like networks (PSA-LNs) as mimics for PSAs were studied using JKR-based contact mechanics and peel tests. Acrylic acid (AA) was co-polymerized with 2-ethyl hexyl acrylate (2-EHA) and 1,6-hexane diol diacrylate (HDDA) to create PSA-LNs. The measured surface energy (27 to 31 mJ/m2) was sensible as surmised from their structure. Acrylic acid content increases the surface energy, threshold adhesion energy and adhesion hysteresis of PSA-LNs. Measurements of adhesion dynamics showed a dependence of adhesion energy to the 0.6–0.8 power of crack speed, depending upon the model chosen for analysis of the data. When compared with actual pressure-sensitive adhesive tape peel tests, the adhesion dynamics data predicted the peel strength. This study shows a direct relationship between threshold adhesion energy, crack propagation mechanics and peel strength measurements.
Peptide-based drug design : controlling transport and metabolism (1995)

Introduction: molecular biology of amino acid, peptide and oligopeptide transport, Rufus M. Williamson and Dale L. Oxender peptide metabolism at brush-border membranes, Roger H. Erickson peptide metabolism by gastric, pancreatic and lysosomal proteinases, Ramesh Krishnamoorthy and Ashim K. Mitra biopharmaceutical properties and pharmacokinetics of peptide drugs, Hye J. Lee intestinal peptide transport. Part 1 Intestinal absorption of B-lactam antibiotics, Akira Tsuji oral absorption of angiotensin-converting enzyme inhibitors and peptide prodrugs, Shiyin Yee and Gordon L. Amidon the intestinal oligopeptide transporter - molecular characterization and substrate specificity, Werner Kramer et al oral delivery of therapeutic proteins and peptides by the B12-uptake system, Gregory J. Russell-Jones prodrug approaches for improving peptidomimetic drug absorption, Barbra H. Stewart and Michael D. Taylor. Part 2 Liver peptide transport: hepatic processing of peptides, David L. Marks approaches to modulating liver transport of peptide drugs, Mary L. Ruwart. Part 3 Blood-brain barrier peptide transport: blood-brain barrier peptide transport and peptide drug delivery to the brain, William M. Pardridge oligopeptide drug delivery to the brain - importance of absorptive-mediated endocytosis and P-glycoprotein-associated active efflux transport at the blood-brain barrier, Tetsuya Terasaki and Akira Tsuji molecular packaging - peptide delivery to the central nervous system by sequential metabolism, Nicholas Bodor and Laszlo Prokai. Part 4 Peptide transport in micro-organisms: bacterial peptide permeases as a drug delivery target, J. W. Payne fungal peptide transport as a drug delivery system, Jeffrey M. Becker and Fred R. Naider. Part 5 Peptide metabolism: peptidomimetic design and chemistry approaches to peptide metabolism, T.K. Sawyer peptide prodrugs designed to limit metabolism, Judi Moss improving duration of action of peptide drugs, John J. Nestor Jr. Part 6 Methods and systems for evaluating transport and metabolism of peptide-based drugs - cell culture models for examining peptide absorption, Donald W. Miller et al Elsbeth G. Chikale and Ronald T. Borchardt gastrointestinal transport of peptides - experimental systems, David Fleisher in vitro models of hepatic uptake - methods to determine kinetic parameters for receptor-mediated hepatic uptake, Yuichi Sugiyama and Yukio Kato.
The Role of Molecular Dipole Orientation in Single‐Molecule Fluorescence Microscopy and Implications for Super‐Resolution Imaging (2013)

Numerous methods for determining the orientation of single-molecule transition dipole moments from microscopic images of the molecular fluorescence have been developed in recent years. At the same time, techniques that rely on nanometer-level accuracy in the determination of molecular position, such as single-molecule super-resolution imaging, have proven immensely successful in their ability to access unprecedented levels of detail and resolution previously hidden by the optical diffraction limit. However, the level of accuracy in the determination of position is threatened by insufficient treatment of molecular orientation. Here we review a number of methods for measuring molecular orientation using fluorescence microscopy, focusing on approaches that are most compatible with position estimation and single-molecule super-resolution imaging. We highlight recent methods based on quadrated pupil imaging and on double-helix point spread function microscopy and apply them to the study of fluorophore mobility on immunolabeled microtubules.
Biopsy using a Magnetic Capsule Endoscope Carrying, Releasing, and Retrieving Untethered Microgrippers (2013)

This paper proposes a new wireless biopsy method where a magnetically actuated untethered soft capsule endoscope carries and releases a large number of thermo-sensitive, untethered microgrippers (μ-grippers) at a desired location inside the stomach and retrieves them after they self-fold and grab tissue samples. We describe the working principles and analytical models for the μ-gripper release and retrieval mechanisms, and evaluate the proposed biopsy method in ex vivo experiments. This hierarchical approach combining the advanced navigation skills of centimeter-scaled untethered magnetic capsule endoscopes with highly parallel, autonomous, submillimeter scale tissue sampling μ-grippers offers a multifunctional strategy for gastrointestinal capsule biopsy.
Fine specificity of IgG subclass response to group antigens in HIV-1-infected patients. (1989)

There is an association between the clinical stage of HIV-1 infection and the presence of antibodies against viral gag proteins (p17 and p24). The IgG subclass (G1 and G3) pattern against these antigens was analysed in stable patients and HIV patients progressing to AIDS. Antibodies were analysed with whole viral or peptide ELISA (using sequentially overlapping peptides) and Western Blots. IgG1 was found to be the dominant anti-HIV-1 IgG subclass and IgG1 antibodies declined in progressing patients against all HIV antigens evaluated in Western blot, including p17, p24, p31, gp41, p64, gp120 and gp160. In contrast IgG3 antibodies, which were found to be predominantly directed against gag proteins, and which could be detected in almost all patients, remained in the circulation during disease progression. By peptide assays distinct immunogenic regions were found in p17 in contrast to more evenly distributed epitopes in p24. A decreased divergence of antibody reactivity to both p17 and p24 peptides in the group of patients who developed AIDS was seen. No reaction to any single gag epitope related to disease progression. The difference between IgG1 and IgG3 anti-gag antibodies in relation to clearance during disease progression may depend on different properties of immune complexes formed by these two IgG subclasses.
Expression of the protein product of the prostaglandin synthase-2/TIS10 gene in mitogen-stimulated Swiss 3T3 cells. (1993)

TIS10/PGS-2 encodes a prostaglandin synthase (PGS) distinct from the previously described enzyme PGS-1 (EC 1.14.99.1). We have now generated antipeptide antisera, directed to an amino acid sequence unique to the murine TIS10/PGS-2 protein, which specifically recognize the TIS10/PGS-2 antigen. TIS10/PGS-2 protein was undetectable in quiescent Swiss 3T3 cells. The level of TIS10/PGS-2 protein peaked between 6 and 8 h following phorbol ester stimulation of cells, then declined to basal levels after 18-24 h. Synthesis of TIS10/PGS-2 protein was dramatically increased in the second hour following mitogen stimulation and remained elevated for several hours. The half-life of the TIS10/PGS-2 protein was 4 h. Immunofluorescence studies demonstrated a perinuclear and cytoplasmic localization of the TIS10/PGS-2 antigen. As expected, detection of induced TIS10/PGS-2 antigen was dependent on protein synthesis. Metabolically labeled TIS10/PGS-2 protein migrated as a 71/73-kDa doublet following immunoprecipitation. Dexamethasone blocked both the TPA- and serum-induced appearance of TIS10/PGS-2 antigen. These studies demonstrate the existence of a mitogen-inducible, glucocorticoid-inhibitable, immunologically distinct prostaglandin synthase protein.
A new mutation in the coding region of the bovine leptin gene associated with feed intake (2003)

An experimental cattle population was screened for polymorphisms in the leptin gene and five SNPs were found in the regions containing the coding sequences. The association of these polymorphisms with feed intake and fat-related traits was evaluated. The results suggest an association between a polymorphism in exon 2, described here for the first time, and feed intake. Individuals with genotype A/T at this position had 19% greater mean feed intake than individuals with genotype A/A. There was also evidence for a link between leptin haplotypes and some fat-related traits.
American Society of Clinical Oncology Recommendations on Adjuvant Chemotherapy for Stage II Colon Cancer (2004)

Direct evidence from randomized controlled trials does not support the routine use of adjuvant chemotherapy for patients with stage II colon cancer. Patients and oncologists who accept the relative benefit in stage III disease as adequate indirect evidence of benefit for stage II disease are justified in considering the use of adjuvant chemotherapy, particularly for those patients with high-risk stage II disease. The ultimate clinical decision should be based on discussions with the patient about the nature of the evidence supporting treatment, the anticipated morbidity of treatment, the presence of high-risk prognostic features on individual prognosis, and patient preferences. Patients with stage II disease should be encouraged to participate in randomized trials.
Relation Between the Pacing Induced Sequence of Activation and Left Ventricular Pump Function in Animals (2002)

The main goal of this article was to review animal experimental work on the effect of asynchronous activation on ventricular pump function. During normal sinus rhythm and atrial pacing, the Purkinje system contributes significantly to the rapid electrical activation of the ventricles. In contrast, during ventricular pacing the impulse is almost exclusively conducted through the normal myocardium. As a consequence, electrical activation of the ventricles becomes asynchronous and has an abnormal sequence. The abnormal impulse conduction causes considerable disturbances to occur in regional systolic fiber shortening, mechanical work, blood flow, and oxygen consumption; low values occurring in early activated regions and values above normal being present in late activated regions. Many animal studies have now shown that the abnormal electrical activation, induced by ventricular pacing, leads to a depression of systolic and diastolic LV function. Pacing at the right ventricular apex (the conventional pacing site) reduces LV function more than pacing at the high ventricular septum or at LV sites. In canine hearts with experimental LBBB, LV pacing significantly improves LV pump function. Differences in LV pump function between (combinations of) pacing sites are poorly correlated with QRS duration. Therefore, the cause of the depression of LV function during abnormal electrical activation appears to be a combination of the asynchrony and the sequence of activation. These experimental findings justify continuing attention for optimizing the site(s) of ventricular pacing in patients with normal and abnormal ventricular impulse conduction.
Integrated acoustic and magnetic separation in microfluidic channels (2009)

With a growing number of cell-based biotechnological applications, there is a need for particle separation systems capable of multiparameter separations at high purity and throughput, beyond what is presently offered by traditional methods including fluorescence activated cell sorting and column-based magnetic separation. Toward this aim, we report on the integration of microfluidic acoustic and magnetic separation in a monolithic device for multiparameter particle separation. Using our device, we demonstrate high-purity separation of a multicomponent particle mixture at a throughput of up to 10(8) particleshr.
Aprataxin, poly-ADP ribose polymerase 1 (PARP-1) and apurinic endonuclease 1 (APE1) function together to protect the genome against oxidative damage (2009)

Aprataxin, defective in the neurodegenerative disorder ataxia oculomotor apraxia type 1 (AOA1), is a DNA repair protein that processes the product of abortive ligations, 5' adenylated DNA. In addition to its interaction with the single-strand break repair protein XRCC1, aprataxin also interacts with poly-ADP ribose polymerase 1 (PARP-1), a key player in the detection of DNA single-strand breaks. Here, we reveal reduced expression of PARP-1, apurinic endonuclease 1 (APE1) and OGG1 in AOA1 cells and demonstrate a requirement for PARP-1 in the recruitment of aprataxin to sites of DNA breaks. While inhibition of PARP activity did not affect aprataxin activity in vitro, it retarded its recruitment to sites of DNA damage in vivo. We also demonstrate the presence of elevated levels of oxidative DNA damage in AOA1 cells coupled with reduced base excision and gap filling repair efficiencies indicative of a synergy between aprataxin, PARP-1, APE-1 and OGG1 in the DNA damage response. These data support both direct and indirect modulating functions for aprataxin on base excision repair.
Room acoustic prediction based on a unified treatment of diffuse and specular reflection (1996)

A new general algorithm for room acoustic prediction is presented. The algorithm, based on approximate cone tracing, handles diffuse reflection by a splitup of cones incident on diffusing surfaces. The splitup of cones treats the interaction between specular and diffuse reflection in a physically sensible manner. A ‘‘brute-force’’ implementation of such an algorithm inevitably creates an exponential dependence of the calculation time on the number of reflection combinations between diffusely reflecting surfaces, and therefore results in extremely long processing times. By exploiting the properties of diffuse reflection, the described algorithm displays an essentially linear dependence resulting in processing times short enough also for personal computers. The algorithm adapts its behavior to the properties of each specific environment, relies on very few nonverifiable assumptions, and is designed to meet the specific requirements of auralization. The splitup of cones creates a myriad of weak diffuse reflections resulting in a very smooth late decay. The algorithm is described in detail and sample predictions are shown.