gebhart/patrepeval huggingface dataset:
Image and Video Abstraction by Anisotropic Kuwahara Filtering (2009)

Abstract We present a non‐photorealistic rendering technique to transform color images and videos into painterly abstractions. It is based on a generalization of the Kuwahara filter that is adapted to the local shape of features, derived from the smoothed structure tensor. Contrary to conventional edge‐preserving filters, our filter generates a painting‐like flattening effect along the local feature directions while preserving shape boundaries. As opposed to conventional painting algorithms, it produces temporally coherent video abstraction without extra processing. The GPU implementation of our method processes video in real‐time. The results have the clearness of cartoon illustrations but also exhibit directional information as found in oil paintings.
Protein structure prediction by global optimization of a potential energy function (1999)

An approach based exclusively on finding the global minimum of an appropriate potential energy function has been used to predict the unknown structures of five globular proteins with sizes ranging from 89 to 140 amino acid residues. Comparison of the computed lowest-energy structures of two of them (HDEA and MarA) with the crystal structures, released by the Protein Data Bank after the predictions were made, shows that large fragments (61 residues) of both proteins were predicted with rms deviations of 4.2 and 6.0 A for the Calpha atoms, for HDEA and MarA, respectively. This represents 80% and 53% of the observed structures of HDEA and MarA, respectively. Similar rms deviations were obtained for approximately 60-residue fragments of the other three proteins. These results constitute an important step toward the prediction of protein structure based solely on global optimization of a potential energy function for a given amino acid sequence.
Characterization and chromosomal localization of JAM-1, a platelet receptor for a stimulatory monoclonal antibody (2001)

We have previously reported the purification and characterization of a 32 kDa platelet surface glycoprotein that is recognized by the stimulatory monoclonal antibody, F11. The cDNA has been cloned and found to encode the human homolog of the murine junctional adhesion molecule, JAM; we therefore named this human homolog JAM-1. Northern blot analysis indicated that JAM-1 mRNA is expressed as multiple species, the predominant transcript being approximately 4.0 kb in size. Genetic mapping analysis using fluorescence in situ hybridization (FISH) showed that it is localized to chromosome 1q21.1-21.3. Recombinant JAM-1, when expressed in Chinese hamster ovary (CHO) cells, localized to the cell membrane with intense staining where two adjacent cells actually made contact with each other, suggesting that, similar to murine JAM, human JAM-1 may also localize at the cell-cell junction. In well-spread cells, JAM-1 co-localized with F-actin at the cell-cell contacts and at the membrane ruffles, but not at the stress fibers. Interestingly, JAM-1 localizes only to the cell-cell junctions formed by two transfected cells and not to the cell-cell junctions formed by a transfected cell with an untransfected cell, suggesting that JAM-1 may facilitate cell adhesion through homophilic binding. In addition, human platelets specifically bind to a monolayer of CHO cells expressing human JAM-1, further supporting homophilic interactions. The results presented here indicate that JAM-1, a receptor for a platelet-activating antibody, is the human homolog of the junctional adhesion molecule. JAM-1 is a single copy gene, which is constitutively expressed on various tissues and cells, and may be involved in cell to cell adhesion through homophilic interaction.
Evaluation of Anticyclin B1 Serum Antibody as a Diagnostic and Prognostic Biomarker for Lung Cancer (2005)

The primary aims of this study were to establish a high-throughput assay and analytic procedures that would allow us to assess with accuracy and reproducibility the presence of anti-cyclin B1 antibodies in a large cohort of subjects at-risk for development of lung cancer. The overall goal is to identify factors significantly associated with immune responses against this lung tumor antigen and to evaluate the relationship between anticyclin B1 antibodies and lung cancer risk in a prospective cohort. Successful cancer treatment relies on early detection. The immune system could respond to tumor antigens arising from altered host factors and provide an early readout for cancer presence. This study examines immune responses to the tumor antigen cyclin B1. Lung cancer patients have antibodies against cyclin B1. Unscheduled overexpression of this cell cycle regulator occurs early in tumorigenesis and might be detected by the immune system long before clinical diagnosis of cancer. Antibodies recognizing cyclin B1 were measured using semiautomated ELISAs in sera samples from subjects without detectable lung cancer enrolled in the Pittsburgh Lung Screening Study (PLuSS), a longitudinal study of long-term smokers over age 50. Factors significantly associated with antibody presence were identified using linear regression analysis. We have established a highly reproducible, semiautomated ELISA-based assay for the high-throughput assessment of serum antibody titers. Using this technology and a small subset of PluSS subjects, cyclin B1 antibody levels were found to be high in a small proportion of subjects tested. Regression analysis identified gender as well as age in women smokers to be significant determinants of cyclin B1 antibody levels, association not seen in male subjects. This work represents an important first step toward defining the importance of the presence of anticyclin B1 antibodies in an at-risk population and assessing the predictive value of serum cyclin B1 antibody as relates to lung cancer risk.
Isolation of Yeast DNA (2003)

The problems often experienced with DNA isolated from yeast are mostly owing to the impurities remaining in DNA isolated according to certain isolation protocols. Incomplete cutting of chromosomal DNA with restriction endonucleases, or poor transformation of Escherichia coli with plasmid DNA from yeast are the difficulties most frequently encountered. The procedures given herein have been chosen since they have used successfully by many workers to obtain DNA that does not give these problems.
Polyvinyl alcohol enhances detection of low abundance transcripts in early stage quail embryos in a nonradioactive whole mount in situ hybridization technique. (1994)

We have tested the ability of polyvinyl alcohol (PVA) to enhance the indoxyl-nitro blue tetrazolium alkaline phosphatase color reaction in whole mount in situ hybridizations of early stage quail embryos. Using detection of the myogenic factor qmyoD in hybridizations of 13-14 somite-pair quail embryos as a test system, 10% solutions of 13-23 kDa and 31-50 kDa PVA optimally enhanced the alkaline phosphatase color reaction. With the enhanced detection conditions, we have been able to measure qmyoD expression as early as the 3 somite-pair stage, whereas previously we were unable to detect qmyoD prior to the 10 somite-pair stage. PVA-enhanced detection of somitic qmyoD expression was specific as no corresponding signal was found in control hybridizations with a sense qmyoD probe.
Conserved and non-conserved residues and their role in the structure and function of p-hydroxybenzoate hydroxylase (2013)

In order to elucidate the molecular mechanism of the catalytic reaction and enzyme conformation, we substituted 53 conserved residues identified by aligning 92 p-hydroxybenzoate hydroxylase sequences and 19 non-conserved residues selected from crystallographic studies of Pseudomonas fluorescens NBRC14160 p-hydroxybenzoate hydroxylase with 19 other naturally occurring amino acids, yielding a database of 619 active single mutants. The database contained 365 and 254 active single mutants for 44/53 conserved residues and 19 non-conserved residues, respectively; the data included main activity, sub-activity for NADPH and NADPH reaction specificity. Active mutations were not observed for the G14, Q102, G160, E198, R220, R246, N300, F342 and G387 conserved residues, and only one active mutant was obtained at the G9, G11, G187, D286, Y201, R214 and G295 conserved residues and the S13, E32 and R42 non-conserved residues. Only seven active mutants with higher activity than the wild-type enzyme were observed at conserved residues, and only two were observed at non-conserved residues. The 365 mutants at conserved residues included 64 active mutants with higher NADPH reaction specificity than the wild-type enzyme, and some Y181X single mutants exhibited considerable changes in NADPH reaction specificity. A Y181X/L268G double-mutant database was constructed to computationally analyze the effects of these substitutions on structural conformation and function. These results indicated that some conserved or non-conserved residues are important for structural stability or enzyme function.
Biomimetic temporal self-assembly via fuel-driven controlled supramolecular polymerization (2018)

Temporal control of supramolecular assemblies to modulate the structural and transient characteristics of synthetic nanostructures is an active field of research within supramolecular chemistry. Molecular designs to attain temporal control have often taken inspiration from biological assemblies. One such assembly in Nature which has been studied extensively, for its well-defined structure and programmable self-assembly, is the ATP-driven seeded self-assembly of actin. Here we show, in a synthetic manifestation of actin self-assembly, an ATP-selective and ATP-fuelled, controlled supramolecular polymerization of a phosphate receptor functionalised monomer. It undergoes fuel-driven nucleation and seeded growth that provide length control and narrow dispersity of the resultant assemblies. Furthermore, coupling via ATP-hydrolysing enzymes yielded its transient characteristics. These results will usher investigations into synthetic analogues of important biological self-assembly motifs and will prove to be a significant advancement toward biomimetic temporally programmed materials.
Anti‐interleukin 2 receptor monoclonal antibodies. Respective role of epitope mapping and monoclonal antibody‐receptor interactions in their antagonist effects on interleukin 2‐dependent T cell growth (1986)

Functional studies, using mainly interleukin 2 (IL2)-dependent growth of human T cell lines or clones but also mixed lymphocyte cultures and mitogen T cell activation, allowed a collection of locally produced anti-IL2 receptor monoclonal antibodies (mAb) to be classified. They fell into two groups: one with strong to moderate inhibition of IL2, the other without any detectable functional activity in in vitro assays. Direct and sequential immunoprecipitation as well as peptide mapping confirm that all the mAb recognize the same surface molecule. The parameters responsible for such functional dichotomy were characterized: the main parameter was found to be linked to the epitopic cluster recognized on the molecule by the mAb. All functional mAb pertained to a given epitopic cluster and all the nonfunctional ones to an alternative cluster. Studies on mAb receptor and IL2 receptor interactions confirmed these findings and strongly suggest that functional mAb interact with a region on the IL2 receptor identical or very close to the site of ligand-receptor interaction. These data could facilitate the choice of mAb to be used in therapeutical approaches in vivo when ethical objections could be overcome by appropriate committees.
Neurotrophic factors in Alzheimer’s disease: role of axonal transport (2008)

Neurotrophic factors (NTF) are small, versatile proteins that maintain survival and function to specific neuronal populations. In general, the axonal transport of NTF is important as not all of them are synthesized at the site of its action. Nerve growth factor (NGF), for instance, is produced in the neocortex and the hippocampus and then retrogradely transported to the cholinergic neurons of the basal forebrain. Neurodegenerative dementias like Alzheimer's disease (AD) are linked to deficits in axonal transport. Furthermore, they are also associated with imbalanced distribution and dysregulation of NTF. In particular, brain-derived neurotrophic factor (BDNF) plays a crucial role in cognition, learning and memory formation by modulating synaptic plasticity and is, therefore, a critical molecule in dementia and neurodegenerative diseases. Here, we review the changes of NTF expression and distribution (NGF, BDNF, neurotrophin-3, neurotrophin-4/5 and fibroblast growth factor-2) and their receptors [tropomyosin-related kinase (Trk)A, TrkB, TrkC and p75(NTR)] in AD and AD models. In addition, we focus on the interaction with neuropathological hallmarks Tau/neurofibrillary tangle and amyloid-beta (Abeta)/amyloid plaque pathology and their influence on axonal transport processes in order to unify AD-specific cholinergic degeneration and Tau and Abeta misfolding through NTF pathophysiology.
Genetic Models of Mechanotransduction: The NematodeCaenorhabditis elegans (2004)

Mechanotransduction, the conversion of a mechanical stimulus into a biological response, constitutes the basis for a plethora of fundamental biological processes such as the senses of touch, balance, and hearing and contributes critically to development and homeostasis in all organisms. Despite this profound importance in biology, we know remarkably little about how mechanical input forces delivered to a cell are interpreted to an extensive repertoire of output physiological responses. Recent, elegant genetic and electrophysiological studies have shown that specialized macromolecular complexes, encompassing mechanically gated ion channels, play a central role in the transformation of mechanical forces into a cellular signal, which takes place in mechanosensory organs of diverse organisms. These complexes are highly efficient sensors, closely entangled with their surrounding environment. Such association appears essential for proper channel gating and provides proximity of the mechanosensory apparatus to the source of triggering mechanical energy. Genetic and molecular evidence collected in model organisms such as the nematode worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the mouse highlight two distinct classes of mechanically gated ion channels: the degenerin (DEG)/epithelial Na(+) channel (ENaC) family and the transient receptor potential (TRP) family of ion channels. In addition to the core channel proteins, several other potentially interacting molecules have in some cases been identified, which are likely parts of the mechanotransducing apparatus. Based on cumulative data, a model of the sensory mechanotransducer has emerged that encompasses our current understanding of the process and fulfills the structural requirements dictated by its dedicated function. It remains to be seen how general this model is and whether it will withstand the impiteous test of time.
NCSA Mosaic: A Global Hypermedia System (1994)

This paper reports on an Internet‐based system for hypermedia information discovery and retrieval and wide‐area distributed asynchronous collaboration designed and built at the National Center for Supercomputing Applications (NCSA). The system, called NCSA Mosaic, integrates cleanly into existing Internet protocols, formats, data sources, and environments, and provides powerful new capabilities for using and sharing information across the Internet.
The molecular control of blood cells (1988)

This book presents a masterful overview of the mechanics of blood cell formation and the factors that control blood cell growth. Cells circulating in the blood perform functions essential for the survival of organisms, yet blood cells and associated blood-cell-forming (hemopoietic) tissues have certain features that make them quite different from other vital organs in the body. These features include the short life span of mature blood cells, the multiplicity of blood cell types, and the wide dispersion of hemopoietic tissue in the body.The regulation of hemopoiesis in response to emergencies such as blood loss or infections is an exceedingly complex process. However, our knowledge of hemopoietic growth factors, known generally as colony-stimulating factors or CSFs, has made exciting advances in recent years. This book provides a leading authority's review of the purification and cloning of CSFs and their actions in regulating white blood cell production in the body. Donald Metcalf also examines the role of CSFs in controlling resistance to infections and in the initiation and suppression of myeloid leukemia.Metcalf's involvement at the center of this research from its inception to the present day enables him to give a historical view as well as a lucid summary of recent research. In addition, he addresses the broader question of the relation between growth control and cancer development. This excellent synopsis should be of particular interest to hematologists, virologists, general clinicians, and medical students.
The lysine‐rich H1 histones from the slime moulds, Physarum polycephalum and Dictyostelium discoideum lack phosphorylation sites recognised by cyclic AMP‐dependent protein kinase in vitro (1992)

Calcium chloride-extracted histones were prepared from nuclei of the slime moulds, Physarum polycephalum and Dictyostelium discoideum, and phosphorylation by purified preparations of cyclic AMP-dependent protein kinase (cAMP-d PK) and growth-associated H1 histone kinase (HKG) examined and compared. Among the major histone fractions and other proteins in the two preparations, the H1 histones from both organisms were found to be effective and exclusive substrates for HKG. cAMP-d PK, which phosphorylates mammalian H1 histone and certain, in particular H2B, of the mammalian core histones, phosphorylated several of the core histones from both slime moulds but did not phosphorylate H1 histone from either. The slime mould H1s remained ineffective substrates for cAMP-d PK even after extensive alkaline phosphatase treatment of the histone preparations. Additional studies demonstrated that the lack of slime mould H1 phosphorylation by cAMP-d PK was not due to competition of the H1 molecules with the core histones for the kinase. Our studies suggest that H1 histones from these organisms, whilst clearly containing sites for phosphorylation by HKG, apparently lack phosphorylation sites recognised by cAMP-d PK. Thus, the mediation of specific nuclear functions by cAMP-dependent phosphorylation of H1 in higher organisms may not occur or be required in these lower eukaryotes.
RNA interference‐induced reduction in CD98 expression suppresses cell fusion during syncytialization of human placental BeWo cells (2004)

The physiological importance of CD98 surface antigen in regulating placental trophoblast cell fusion has been studied in a cell model of syncytialization (the cytotrophoblast cell line BeWo following increased intracellular cAMP by forskolin treatment) using RNA interference. CD98 protein abundance (determined by Western blot) was decreased by 40–50% following double‐stranded small interfering RNA transfection. Cell fusion (determined by quantitative flow cytometry) was similarly inhibited and human chorionic gonadotropin secretion was suppressed. These findings show that CD98 is involved in the process of cell fusion necessary for syncytiotrophoblast formation.
Neurosteroid analogs: structure-activity studies of benz[e]indene modulators of GABAA receptor function. 1. The effect of 6-methyl substitution on the electrophysiological activity of 7-substituted benz[e]indene-3-carbonitriles (1993)

The effect of 6-methyl substitution of the ability of 7-(2-hydroxyethyl)benz[e]indene-3-carbonitriles to potentiate GABA-mediated chloride current and to directly gate a chloride current in the absence of GABA in cultured rat hippocampal neurons was investigated. Structurally analogous steroid 17-carbonitriles that either contained or did not contain a 19-methyl group were also investigated. Compounds were evaluated at 1 microM for their ability to potentiate GABA-mediated currents and at 10 microM for current activation in the absence of GABA. The benz[e]indene 3(R)-carbonitriles and analogous steroid 17 alpha-carbonitriles had no effects in either assay. The benz[e]indene-3(S)-carbonitriles and analogous steroid 17 alpha-carbonitriles were active in both assays. Relative to the 6-unsubstituted benz[e]indene 3(S)-carbonitrile, the following effects of 6-methyl substituents were observed: a 6(a)-methyl group increased both activities; a 6(e)-methyl group decreased both activities; and 6,6-dimethyl substituents had opposing effects so that both activities remained similar to those of the 6-unsubstituted compound. The activities of the steroid 17 beta-carbonitriles were not affected significantly by the presence or absence of a 19-methyl group. A conformational analysis using molecular modeling methods was also performed for the benz[e]indene 3S-carbonitriles and the steroid 17 beta-carbonitriles. The ability of the different 6-methyl substituents to differentially effect the conformations of the flexible benz[e]indenes and the inability of the steroid 19-methyl group to alter the conformations of the rigid steroid 17 beta-carbonitriles are suggested to explain the results.
Expression and characterization of the protein Rv1399c from Mycobacterium tuberculosis (2004)

The Mycobacterium tuberculosis genome contains an unusually high number of proteins involved in the metabolism of lipids belonging to the Lip family, including various nonlipolytic and lipolytic hydrolases. Driven by a structural genomic approach, we have biochemically characterized the Rv1399c gene product, LipH, previously annotated as a putative lipase. Rv1399c was overexpressed in E. coli as inclusion bodies and refolded. Rv1399c efficiently hydrolyzes soluble triacylglycerols and vinyl esters. It is inactive against emulsified substrate and its catalytic activity is strongly inhibited by the diethyl paranitrophenyl phosphate (E600). These kinetic behaviors unambiguously classify Rv1399c as a nonlipolytic rather than a lipolytic hydrolase. Sequence alignment reveals that this enzyme belongs to the alpha/beta hydrolase fold family and shares 30-40% amino acid sequence identity with members of the hormone-sensitive lipase subfamily. A model of Rv1399c derived from homologous three-dimensional structures reveals a canonical catalytic triad (Ser162, His290 and Asp260) located at the bottom of a solvent accessible pocket lined by neutral or charged residues. Based on this model, kinetic data of the Arg213Ala mutant partially explain the role of the guanidinium moiety, located close to His290, to confer an unusual low pH shift of the catalytic histidine in the wild type enzyme. Overall, these data identify Rv1399c as a new nonlipolytic hydrolase from M. tuberculosis and we thus propose to reannotate its gene product as NLH-H.