gebhart/patrepeval huggingface dataset:
Shape distributions (2002)

Measuring the similarity between 3D shapes is a fundamental problem, with applications in computer graphics, computer vision, molecular biology, and a variety of other fields. A challenging aspect of this problem is to find a suitable shape signature that can be constructed and compared quickly, while still discriminating between similar and dissimilar shapes.In this paper, we propose and analyze a method for computing shape signatures for arbitrary (possibly degenerate) 3D polygonal models. The key idea is to represent the signature of an object as a shape distribution sampled from a shape function measuring global geometric properties of an object. The primary motivation for this approach is to reduce the shape matching problem to the comparison of probability distributions, which is simpler than traditional shape matching methods that require pose registration, feature correspondence, or model fitting.We find that the dissimilarities between sampled distributions of simple shape functions (e.g., the distance between two random points on a surface) provide a robust method for discriminating between classes of objects (e.g., cars versus airplanes) in a moderately sized database, despite the presence of arbitrary translations, rotations, scales, mirrors, tessellations, simplifications, and model degeneracies. They can be evaluated quickly, and thus the proposed method could be applied as a pre-classifier in a complete shape-based retrieval or analysis system concerned with finding similar whole objects. The paper describes our early experiences using shape distributions for object classification and for interactive web-based retrieval of 3D models.
Cellulase Recovery via Membrane Filtration (2001)

A combined sedimentation and membrane filtration process was investigated for recycling cellulase enzymes in the biomass-to-ethanol process. In the first stage, lignocellulose particles longer than approx 50µm were removed by means of sedimentation in an inclined settler. Microfiltration was then utilized to remove the remaining suspended solids. Finally, the soluble cellulase enzymes were recovered by ultrafiltration. The permeate fluxes obtained in microfiltration and ultrafiltration were approx 400 and 80 L/(m2 h), respectively. A preliminary economic analysis shows that the cost benefit of enzyme recycling may be as much as 18 cents/gal of ethanol produced, provided that 75% of the enzyme is recycled in active form.
Viral nanomotors for packaging of dsDNA and dsRNA (2007)

While capsid proteins are assembled around single-stranded genomic DNA or RNA in rod-shaped viruses, the lengthy double-stranded genome of other viruses is packaged forcefully within a preformed protein shell. This entropically unfavourable DNA or RNA packaging is accomplished by an ATP-driven viral nanomotor, which is mainly composed of two components, the oligomerized channel and the packaging enzymes. This intriguing DNA or RNA packaging process has provoked interest among virologists, bacteriologists, biochemists, biophysicists, chemists, structural biologists and computational scientists alike, especially those interested in nanotechnology, nanomedicine, AAA+ family proteins, energy conversion, cell membrane transport, DNA or RNA replication and antiviral therapy. This review mainly focuses on the motors of double-stranded DNA viruses, but double-stranded RNA viral motors are also discussed due to interesting similarities. The novel and ingenious configuration of these nanomotors has inspired the development of biomimetics for nanodevices. Advances in structural and functional studies have increased our understanding of the molecular basis of biological movement to the point where we can begin thinking about possible applications of the viral DNA packaging motor in nanotechnology and medical applications.
Detection of Streptococcus pneumoniae DNA in blood cultures by PCR (1994)

We have developed a PCR assay, with primers derived from the autolysin (lyt) gene, for the detection of Streptococcus pneumoniae DNA in blood cultures. The predicted fragment of 247 bp was detected in all strains of pneumococci, embracing 12 different serotypes that were tested. Although DNA extracted from four viridans streptococci spp. Streptococcus oralis, Streptococcus mitis, Streptococcus sanguis, and Streptococcus parasanguis) gave amplification products, these were quite different from the predicted fragment for S. pneumoniae. Application of the assay for diagnosis of septicemia caused by S. pneumoniae showed concordance between PCR and culture results. However, on four occasions PCR was positive in supernatants from both paired culture bottles while pneumococci were cultured from only one. Performing PCR on negative cultures in controlled studies such as vaccine trials may provide a sensitive tool for increasing case detection.
In Vivo Islet Protection by a Nuclear Import Inhibitor in a Mouse Model of Type 1 Diabetes (2010)

These results indicate that a novel form of immunotherapy that targets nuclear import can arrest inflammation-driven destruction of insulin-producing beta cells at the site of autoimmune attack within pancreatic islets during the progression of T1D.
EV20, a Novel Anti-ErbB-3 Humanized Antibody, Promotes ErbB-3 Down-Regulation and Inhibits Tumor Growth In Vivo (2013)

ErbB-3 (HER-3) receptor is involved in tumor progression and resistance to therapy. Development of specific inhibitors impairing the activity of ErbB-3 is an attractive tool for cancer therapeutics. MP-RM-1, a murine monoclonal antibody targeting human ErbB-3, has shown anticancer activity in preclinical models. With the aim to provide novel candidates for clinical use, we have successfully generated a humanized version of MP-RM-1. The humanized antibody, named EV20, abrogates both ligand-dependent and ligand-independent receptor signaling of several tumor cell types, strongly promotes ErbB-3 down-regulation, and efficiently and rapidly internalizes into tumor cells. Furthermore, treatment with EV20 significantly inhibits growth of xenografts originating from prostatic, ovarian, and pancreatic cancers as well as melanoma in nude mice. In conclusion, we provide a novel candidate for ErbB-3-targeted cancer therapy.
On the role of burst buffers in leadership-class storage systems (2012)

The largest-scale high-performance (HPC) systems are stretching parallel file systems to their limits in terms of aggregate bandwidth and numbers of clients. To further sustain the scalability of these file systems, researchers and HPC storage architects are exploring various storage system designs. One proposed storage system design integrates a tier of solid-state burst buffers into the storage system to absorb application I/O requests. In this paper, we simulate and explore this storage system design for use by large-scale HPC systems. First, we examine application I/O patterns on an existing large-scale HPC system to identify common burst patterns. Next, we describe enhancements to the CODES storage system simulator to enable our burst buffer simulations. These enhancements include the integration of a burst buffer model into the I/O forwarding layer of the simulator, the development of an I/O kernel description language and interpreter, the development of a suite of I/O kernels that are derived from observed I/O patterns, and fidelity improvements to the CODES models. We evaluate the I/O performance for a set of multiapplication I/O workloads and burst buffer configurations. We show that burst buffers can accelerate the application perceived throughput to the external storage system and can reduce the amount of external storage bandwidth required to meet a desired application perceived throughput goal.
Beneficios de un programa de reeducación vesical en ancianos hospitalizados (2007)

Urinary incontinence is a geriatric syndrome of high prevalence in elderly people, which very frequently is not diagnosed and many times appears when suffering a sharp incapacitate Pathology. \nThe aim of the research is to discover the response to the treatment of vesicle re-education in patients with various pathologies and to observe if the benefit is permanent. \nA group of 372 patients of the “Middle-Stay Unit” of the Red Cross Hospital were evaluated from October 1, 2001 to December 31, 2002 using objective instruments of physical and mental evaluation. \nThe results showed that the prevalence of the incontinence at patients’ admission was very high and the vesicle re-education was proved to be very effective since the continence was recovered in a significant number of patients permanently.
Energy savings through compression in embedded Java environments (2003)

Limited energy and memory resources are important constraints in the design of an embedded system. Compression is an useful and widely employed mechanism to reduce the memory requirements of the system. As the leakage energy of a memory system increases with its size and because of the increasing contribution of leakage to overall system energy, compression also has a significant effect on reducing energy consumption. However, storing compressed data/instructions has a performance and energy overhead associated with decompression at runtime. The underlying compression algorithm, the corresponding implementation of the decompression and the ability to reuse decompressed information critically impact this overhead.In this paper, we explore the influence of compression on overall memory energy using a commercial embedded Java virtual machine (JVM) and a customized compression algorithm. Our results show that compression is effective in reducing energy even when considering the runtime decompression overheads for most applications.
Expression of tumor-specific antigen MAGE, GAGE and BAGE in ovarian cancer tissues and cell lines (2010)

Tumor-specific antigen MAGE, BAGE and GAGE may play a role in the occurrence and development of ovarian cancer. These genes can be used as one of the important indicators for early diagnosis, efficacy evaluation and prognostic determination of ovarian cancer.
Infection and Immunity (2004)

Even a cursory glance at science news confirms that research on transplantation and novel treatments for diseases such as cancer, HIV, and tuberculosis has been moving forward at an explosive pace. Copiously illustrated with line drawings, tables, and photographs, Infection and Immunity links current developments in basic science with the realities
A Potent, Selective and Cell‐Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3) (2015)

PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is essential for maturation of ribosomes, may have a role in lipogenesis, and is implicated in several diseases. A potent, selective, and cell-active PRMT3 inhibitor would be a valuable tool for further investigating PRMT3 biology. Here we report the discovery of the first PRMT3 chemical probe, SGC707, by structure-based optimization of the allosteric PRMT3 inhibitors we reported previously, and thorough characterization of this probe in biochemical, biophysical, and cellular assays. SGC707 is a potent PRMT3 inhibitor (IC50 =31±2 nM, KD =53±2 nM) with outstanding selectivity (selective against 31 other methyltransferases and more than 250 non-epigenetic targets). The mechanism of action studies and crystal structure of the PRMT3-SGC707 complex confirm the allosteric inhibition mode. Importantly, SGC707 engages PRMT3 and potently inhibits its methyltransferase activity in cells. It is also bioavailable and suitable for animal studies. This well-characterized chemical probe is an excellent tool to further study the role of PRMT3 in health and disease.
The Baltimore Sepsis Scale: measurement of sepsis in patients with burns using a new scoring system. (1992)

A new sepsis scale has been developed, and it consists of 13 parameters, each of which is measured daily on a variable point scale. In 41 patients with major burns the Baltimore Sepsis scale correlated well with death or survival, with occurrence of septicemia, and with the level of serum interleukin-6. It did not correlate well with the level of plasma endotoxin or with the type of organism that was grown in blood cultures (gram-positive or gram-negative). We propose that the Baltimore Sepsis Scale would be an accurate and easy scale to use for the measurement of interventions that are aimed at improving the septic state.
Kinetics of activation of the respiratory burst oxidase in a fully soluble system from human neutrophils. (1988)

In a fully soluble system from resting human neutrophils, activation of the respiratory burst oxidase under defined conditions was found to follow first-order kinetics. The manner in which this first-order activation process varied with the concentrations of the individual components in the activating system suggested the following. 1) The respiratory burst oxidase occurs in two forms that can be distinguished by their Km values for NADPH. The low-affinity form contains one component (M) from the membrane and two components (S and C alpha) from the cytosol, while the high-affinity form contains an extra cytosolic component (C beta). 2) The active forms of the oxidase are generated in the following reactions: (formula; see text) where S is a stabilizing component and where M.S is an activated form of M.S that is capable of binding C alpha and C beta to produce the active oxidase species M.S.C alpha (the low-affinity form) and M.S.C alpha C beta (the high-affinity form). 3) SDS activates the oxidase by mediating the conversion of M.S to M.S.
Synthesis and Evaluation of Antiparasitic Activities of New 4-[5-(4-Phenoxyphenyl)-2H-pyrazol-3-yl]morpholine Derivatives (2007)

A series of new 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine derivatives, prepared by two synthetic routes, were in vitro assayed against three Trypanosoma strains, Leishmania donovani, and Plasmodium falciparum K1. Seven out of 17 compounds showed moderate to very good activity against blood stage T. b. rhodesiense, with 10 and 17 exhibiting highest potency (IC50 of 1.0 and 1.1 microM, respectively). Interestingly, the beta-diketone precursors 1-3 had good antitrypanosomal activity toward the insect stage, with IC50 values of 1.0-3.4 microM. Among different compounds with moderate activity against T. cruzi, compound 17 showed the lowest IC50 value of 9.5 microM; thus, the series seemed to act selectively toward the different Trypanosoma parasites. Eight compounds were moderately active against L. donovani, with 2, 3, and 12 being the most promising ones (IC50 values of 2.3-5.2 microM), whereas compound 14 was the only derivative with good activity against P. falciparum (IC50 of 3.7 microM).
Osmium tetraoxide cis hydroxylation of unsaturated substrates (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleOsmium tetraoxide cis hydroxylation of unsaturated substratesMartin SchroederCite this: Chem. Rev. 1980, 80, 2, 187–213Publication Date (Print):April 1, 1980Publication History Published online1 May 2002Published inissue 1 April 1980https://pubs.acs.org/doi/10.1021/cr60324a003https://doi.org/10.1021/cr60324a003research-articleACS PublicationsRequest reuse permissionsArticle Views4348Altmetric-Citations521LEARN 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
Selection on the Human Bitter Taste Gene, TAS2R16, inEurasian Populations (2011)

Bitter taste is one of the most important senses alerting humans to noxious foods. In gatherer communities, sensitivity to bitterness is presumably advantageous because of various noxious plants. TAS2R16 is the gene coding the taste receptor molecules for some of the most common toxins in plants. A previous study of this gene indicated selection has increased the frequency of a derived allele in this gene that arose before the human expansion out of Africa. We have applied a different methodology for detecting selection, the Long Range Haplotype (LRH) analysis, to TAS2R16 in a larger sampling of populations from around the world. The haplotype with the derived alleles at both the functional polymorphism and a polymorphism in the regulatory region of TAS2R16 showed evidence for recent positive selection in most of the Eurasian populations, though the highest selection signal occurs in Mbuti Pygmies, an African hunter-gatherer group. In Eurasia, only populations of Mesopotamia and the southeast coast of China have no signals of selection. The evidence of recent selection found in most Eurasian populations differs from the geographic pattern seen in the earlier study of selection. One can speculate that the difference may result from a gathering lifestyle extending into the most recent 10,000 yrs and the need to recognize newly encountered bitter natural toxins as populations expanded into new environments and the biota changes with the ending of the most recent ice age. Alternatively, the promoter region variant may be a marker for altered function beyond what the derived amino acid allele conferred.
Ambulatory Blood Pressure and Cardiovascular Outcome in Relation to Perceived Sleep Deprivation (2007)

Sleep deprivation induced by cuff inflations during overnight blood pressure (BP) monitoring might interfere with the prognostic significance of nighttime BP. In 2934 initially untreated hypertensive subjects, we assessed the perceived quantity of sleep during overnight BP monitoring. Overall, 58.7%, 27.7%, 9.7%, and 4.0% of subjects reported a sleep duration perceived as usual (group A), <2 hours less than usual (group B), 2 to 4 hours less than usual (group C), and >4 hours less than usual (group D). Daytime BP did not differ across the groups (all Ps not significant). Nighttime BP increased from group A to D (124/75, 126/76, 128/77, and 129/79 mm Hg, respectively; all Ps for trend <0.01). Over a median follow-up period of 7 years there were 356 major cardiovascular events and 176 all-cause deaths. Incidence of total cardiovascular events and deaths was higher in the subjects with a night/day ratio in systolic BP >10% compared with those with a greater day-night BP drop in the group with perceived sleep duration as usual or <2 hours less than usual (both P<0.01), not in the group with duration of sleep >or=2 hours less than usual (all Ps not significant). In a Cox model, the independent prognostic value of nighttime BP for total cardiovascular end points and all-cause mortality disappeared in the subjects with perceived sleep deprivation >or=2 hours. In conclusion, nighttime BP rises and loses its prognostic significance in the hypertensive subjects who perceive a sleep deprivation by >or=2 hours during overnight monitoring.
Modification of a Glassy Carbon Electrode with Diols for the Suppression of Electrode Fouling in Biological Fluids. (1996)

The surface of a glassy carbon (GC) electrode was modified covalently with ethyleneglycol, diethyleneglycol, 1,2-propanediol, and 1,3-propanediol by electrochemical oxidation in order to suppress the electrode fouling originating from non-specific adsorption of serum proteins. Human serum albumin (HSA) was adsorbed significantly on the surface of a bare GC electrode, which was monitored by cyclic voltammetry in the presence of Fe(CN)6(4)-/Fe(CN)6(3)-ions. In contrast, the diol-modified GC electrodes were scarcely fouled in HSA solution and even in human serum. The results were explained reasonably based on the hydrophilic nature of the diol-modified GC surface.
Lower Critical Solution Temperatures of Aqueous Copolymers of N-Isopropylacrylamide and Other N-Substituted Acrylamides (1987)

High polymers of N-isopropyl acrylamide (NIPAAM) exhibit a lower critical solution temperature (LCST) in phosphate buffered saline: above 31°C precipitation occurs, with minimal concentration dependence. Copolymers of NIPAAM with acrylamide (AAM), N-methyl acrylamide (NMAAM) and N-ethyl acrylamide (NEAAM) exhibited LCSTs elevated in proportion to their comonomer content. As expected acrylamide was the most effective at elevating the LCST of the copolymer formed. However, NEAAM was more effective than NMAAM. The reason for this is not clear. In contrast, copolymers of NIPAAM with N-t-butyl acrylamide (NTBAAM) exhibited LCSTs that were lowered as a linear function of the comonomer input ratio. Copolymers with N-n-butyl acrylamide (NNBAAM) displayed similar behavior up to 40% NNBAAM, but then the LCST dropped abruptly fron 17°C to below zero. The use of these copolymers in diagnostics and bioseparations is discussed.
relA -Independent Amino Acid Starvation Response Network of Streptococcus pyogenes (2001)

Streptococcus pyogenes (group A streptococcus [GAS]), a multiple-amino-acid-auxotrophic human pathogen, may face starvation for essential amino acids during various stages of the infection process. Since the response of GAS to such conditions is likely to influence pathogenetic processes, we set out to identify by transcriptional analyses genes and operons that are responsive to amino acid starvation and examined whether functionally meaningful response patterns can be ascertained. We discovered that GAS are capable of mounting a relA-independent amino acid starvation response that involves transcriptional modulation of a wide array of housekeeping genes as well as accessory and dedicated virulence genes. Housekeeping genes that were upregulated during starvation of both wild-type and relA mutant strains included the newly identified T-box members of the aminoacyl-tRNA synthetase genes, the genes for components of the tmRNA-mediated peptide tagging and proteolysis system for abnormal proteins (ssrA, smpB, clpP, and clpC), and the operons for the dnaK and groE groups of molecular chaperones. In addition to upregulation of the genes for oligopeptide permease (opp), intracellular peptidase (pepB), and the two-component regulator covRS reported previously (K. Steiner and H. Malke, Mol. Microbiol. 38:1004-1016, 2000), amino acid starvation stimulated the transcription of the growth phase-associated, virulence-regulatory fas operon, the streptolysin S operon (sag), and the gene for autoinducer-2 production protein (luxS). A prominent feature of operons exhibiting internal transcriptional termination (opp, fas, and sag) was starvation-promoted full-length transcription, a mechanism that improves the efficacy of these systems by increasing the level of coordinate transcription of functionally related genes. Based on these results, a regulatory network with feedback mechanisms is proposed that counteracts the stringent response, links the levels of key rate-limiting enzymes to virulence gene expression, and enables the organism in a dynamic way to take advantage of protein-rich environments provided by its human host. As several of the affected target genes are controlled by more than one regulator, fine modulation may result in accordance with the demands imposed by ecologically different colonization sites upon the adaptive capacity of the pathogen.