gebhart/patrepeval huggingface dataset:
AEROSOL SAMPLING SYSTEM FOR COLLECTION OF CAPSTONE DEPLETED URANIUM PARTICLES IN A HIGH-ENERGY ENVIRONMENT (2009)

The Capstone Depleted Uranium (DU) Aerosol Study was undertaken to obtain aerosol samples resulting from a large-caliber DU penetrator striking an Abrams or Bradley test vehicle. The sampling strategy was designed to (1) optimize the performance of the samplers and maintain their integrity in the extreme environment created during perforation of an armored vehicle by a DU penetrator, (2) collect aerosols as a function of time post perforation, and (3) obtain size-classified samples for analysis of chemical composition, particle morphology, and solubility in lung fluid. This paper describes the experimental setup and sampling methodologies used to achieve these objectives. Custom-designed arrays of sampling heads were secured to the inside of the target in locations approximating the breathing zones of the crew locations in the test vehicles. Each array was designed to support nine filter cassettes and nine cascade impactors mounted with quick-disconnect fittings. Shielding and sampler placement strategies were used to minimize sampler loss caused by the penetrator impact and the resulting fragments of eroded penetrator and perforated armor. A cyclone train was used to collect larger quantities of DU aerosol for measurement of chemical composition and solubility. A moving filter sample was used to obtain semicontinuous samples for DU concentration determination. Control for the air samplers was provided by five remotely located valve control and pressure monitoring units located inside and around the test vehicle. These units were connected to a computer interface chassis and controlled using a customized LabVIEW engineering computer control program. The aerosol sampling arrays and control systems for the Capstone study provided the needed aerosol samples for physicochemical analysis, and the resultant data were used for risk assessment of exposure to DU aerosol.
Object matching using deformable templates (1996)

We propose a general object localization and retrieval scheme based on object shape using deformable templates. Prior knowledge of an object shape is described by a prototype template which consists of the representative contour/edges, and a set of probabilistic deformation transformations on the template. A Bayesian scheme, which is based on this prior knowledge and the edge information in the input image, is employed to find a match between the deformed template and objects in the image. Computational efficiency is achieved via a coarse-to-fine implementation of the matching algorithm. Our method has been applied to retrieve objects with a variety of shapes from images with complex background. The proposed scheme is invariant to location, rotation, and moderate scale changes of the template.
Ribosome‐inactivating proteins from plants: more than RNA N‐glycosidases? (2001)

Many plants contain proteins that are capable of inactivating ribosomes and accordingly are called ribosome-inactivating proteins or RIPs. These typical plant proteins receive a lot of attention in biological and biomedical research because of their unique biological activities toward animal and human cells. In addition, evidence is accumulating that some RIPs play a role in plant defense and hence can be exploited in plant protection. To understand the mode of action of RIPs and to optimize their medical and therapeutical applications and their use as antiviral compounds in plant protection, intensive efforts have been made to unravel the enzymatic activities of RIPs and provide a structural basis for these activities. Though marked progress has been made during the last decade, the enzymatic activity of RIPs has become a controversial issue because of the concept that RIPs possess, in addition to their classical RNA N-glycosidase and polynucleotide:adenosine glycosidase activity, other unrelated enzymatic activities. Moreover, the presumed novel enzymatic activities, especially those related to diverse nuclease activities, are believed to play an important role in various biological activities of RIPs. However, both the novel enzymatic activities and their presumed involvement in the biological activities of RIPs have been questioned because there is evidence that the activities observed are due to contaminating enzymes. We offer a critical review of the pros and cons of the putative novel enzymatic activities of RIPs. Based on the available data, it is suggested that there is little conclusive evidence in support of the presumed activities and that in the past too little attention has been given to the purity of the RIP preparation. The antiviral activity and mode of action of RIPs in plants are discussed in view of their classical and presumed novel enzymatic activities.
Prostate‐specific membrane antigen (PSMA) protein expression in normal and neoplastic tissues and its sensitivity and specificity in prostate adenocarcinoma: an immunohistochemical study using mutiple tumour tissue microarray technique (2007)

Despite its expression by subsets of various types of malignancies, PSMA is still considered to be fairly sensitive and highly specific for PaC.
Infection-associated type IV secretion systems ofBartonellaand their diverse roles in host cell interaction (2008)

Type IV secretion systems (T4SSs) are transporters of Gram-negative bacteria that mediate interbacterial DNA transfer, and translocation of virulence factors into eukaryotic host cells. The a-proteobacterial genus Bartonella comprises arthropod-borne pathogens that colonize endothelial cells and erythrocytes of their mammalian reservoir hosts, thereby causing long-lasting intraerythrocytic infections. The deadly human pathogen Bartonella bacilliformis holds an isolated position in the Bartonella phylogeny as a sole representative of an ancestral lineage. All other species evolved in a separate 'modern' lineage by radial speciation and represent highly host-adapted pathogens of limited virulence potential. Unlike B. bacilliformis, the species of the modern lineage encode at least one of the closely related T4SSs, VirB/VirD4 or Vbh. These VirB-like T4SSs represent major host adaptability factors that contributed to the remarkable evolutionary success of the modern lineage. At the molecular level, the VirB/VirD4 T4SS was shown to translocate several effector proteins into endothelial cells that subvert cellular functions critical for establishing chronic infection. A third T4SS, Trw, is present in a sub-branch of the modern lineage. Trw does not translocate any known effectors, but produces multiple variant pilus subunits critically involved in the invasion of erythrocytes. The T4SSs laterally acquired by the bartonellae have thus adopted highly diverse functions during infection, highlighting their versatility as pathogenicity factors.
Conversion of Mono- and Oligodeoxyribonucleotides to 5'-Triphosphates1 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConversion of Mono- and Oligodeoxyribonucleotides to 5'-Triphosphates1Donald E. Hoard and Donald G. OttCite this: J. Am. Chem. Soc. 1965, 87, 8, 1785–1788Publication Date (Print):April 1, 1965Publication History Published online1 May 2002Published inissue 1 April 1965https://pubs.acs.org/doi/10.1021/ja01086a031https://doi.org/10.1021/ja01086a031research-articleACS PublicationsRequest reuse permissionsArticle Views1517Altmetric-Citations317LEARN 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
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences (2011)

Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it substantially improved the performance of secondary structure predictions. CentroidHomfold, however, forces users to prepare homologous sequences of the target sequence. We have developed a Web application (CentroidHomfold-LAST) that predicts the secondary structure of the target sequence using automatically collected homologous sequences. LAST, which is a fast and sensitive local aligner, and CentroidHomfold are employed in the Web application. Computational experiments with a commonly-used data set indicated that CentroidHomfold-LAST substantially outperformed conventional secondary structure predictions including CentroidFold and RNAfold.
Trends in Child and Adolescent Injury Mortality in Taiwan, 1986-2006 (2010)

Objectives: To describe national trends in injury mortality rates for Taiwanese children aged 0-19 from 1986 to 2006. Methods: Data were obtained from the official Vital Statistics System of the Department of Health, Executive Yuan. Injuries were classified by intent and mechanism using ICD-9 criteria. Mortality rates were age-adjusted for each year's standard population. Simple linear regression was used to determine the trends. Results: From 1986 to 2006, the mortality rate per 100,000 for unintentional injuries at ages 0-19 declined by 63% (from 35.3 to 13.2) and the suicide rate declined by almost half (from 1.9 to 1.0). The homicide rate for ages 0-19 combined declined but the homicide rate for children under age 5 increased. Except for homicide in young children, all age groups showed decreasing trends. The 15-19 age group had the highest total death rate due to injury and accounted for 52% of all injury deaths. Motor vehicle injuries (MVI) were the most common cause of death (accounting for 50% of all injury deaths), followed by drowning (17%), suffocation (7%), fire and flames (4%), falls (4%) and poisoning (2%). Suffocation caused 68% of injury deaths in infants. Conclusions: After 1989, the mortality rates for unintentional injuries and suicide declined, but the homicide rate for young children increased. Laws to prevent violence in the home must be enforced, and drowning prevention programs implemented and incorporated into the Children and Adolescent Safety Implementation Program. Preventive efforts should also target MVI and suicide in the15-19 age group, drowning at all ages, and suffocation and homicide for infants and children under 5 years of age.
Single Component and Selective Competitive Protein Adsorption in a Patchy Polymer Brush: Opposition between Steric Repulsions and Electrostatic Attractions (2011)

This work explores the use of "patchy" polymer brushes to control protein adsorption rates on engineered surfaces and to bind targeted species from protein mixtures with high selectivity but without invoking molecular recognition. The brushes of interest contain embedded cationic "patches" composed of isolated adsorbed poly(l-lysine) coils (PLL) that are about 10 nm in diameter and are randomly arranged on a silica substrate. Around these patches is a protein-resistant poly(ethylene glycol) (PEG) brush that is formed from the adsorption of a PLL-g-PEG graft copolymer on the remaining silica surface. Electrostatic attractions between individual cationic patches and the negative regions of approaching proteins may be energetically insufficient to bind proteins. Furthermore, protein-patch attractions are reduced by steric repulsions between proteins and the PEG brush. We show that protein adsorption, gauged by ultimate short-term coverages and by the initial protein adsorption rate, exhibits an adhesion threshold: pure PEG brushes of the architectures employed here and brushes containing sparse loadings of PLL patches do not adsorb protein. Above a critical PLL patch loading or threshold, protein adsorption proceeds, often dramatically. The PLL patch thresholds are specific to the protein of interest, allowing surfaces to be engineered to adhesively discriminate different proteins within a mixture. The separation achieved is remarkably sharp: one protein adsorbs, but the second is completely rejected from the interface. The surfaces in this study, by virtue of their well-controlled and well-characterized patchy nature, distinguish themselves from multicomponent brushes or brushes used to end-tether peptide sequences and nucleotides.
Anti-MET ImmunoPET for Non–Small Cell Lung Cancer Using Novel Fully Human Antibody Fragments (2014)

MET, the receptor of hepatocyte growth factor, plays important roles in tumorigenesis and drug resistance in numerous cancers, including non-small cell lung cancer (NSCLC). As increasing numbers of MET inhibitors are being developed for clinical applications, antibody fragment-based immunopositron emission tomography (immunoPET) has the potential to rapidly quantify in vivo MET expression levels for drug response evaluation and patient stratification for these targeted therapies. Here, fully human single-chain variable fragments (scFvs) isolated from a phage display library were reformatted into bivalent cys-diabodies (scFv-cys dimers) with affinities to MET ranging from 0.7 to 5.1 nmol/L. The candidate with the highest affinity, H2, was radiolabeled with (89)Zr for immunoPET studies targeting NSCLC xenografts: low MET-expressing Hcc827 and the gefitinib-resistant Hcc827-GR6 with 4-fold MET overexpression. ImmunoPET at as early as 4 hours after injection produced high-contrast images, and ex vivo biodistribution analysis at 20 hours after injection showed about 2-fold difference in tracer uptake levels between the parental and resistant tumors (P < 0.01). Further immunoPET studies using a larger fragment, the H2 minibody (scFv-CH3 dimer), produced similar results at later time points. Two of the antibody clones (H2 and H5) showed in vitro growth inhibitory effects on MET-dependent gefitinib-resistant cell lines, whereas no effects were observed on resistant lines lacking MET activation. In conclusion, these fully human antibody fragments inhibit MET-dependent cancer cells and enable rapid immunoPET imaging to assess MET expression levels, showing potential for both therapeutic and diagnostic applications.
The Effects of Hydrogen Addition on Natural Gas Engine Operation (1993)

&lt;div class="htmlview paragraph"&gt;An experimental investigation was carried out to assess the effect on engine operation of the addition of 20% hydrogen by volume to natural gas. Blends of hydrogen and natural gas are referred to as hythane in this report. Three groups of testing were conducted. All the tests were conducted at light loads similar to those in urban driving. The first group of tests were conducted using a 2.0 liter Nissan four cylinder engine to measure the increase in flame front propagation rate when fueled with hythane as compared to pure methane (simulating natural gas). The second group of tests were conducted with a 1.6 liter Toyota four cylinder engine to measure the changes in emissions and thermal efficiency comparing hythane operation to pure methane operation. The third group of tests were conducted with a 1.6 liter Toyota four cylinder engine operating on pure methane to measure changes in emissions and thermal efficiency with and without a pre-chamber installed in the normally hemispherical combustion chamber. The second and third group of tests were conducted to ascertain the relative benefits of modifying the fuel as opposed to modifying the engine configuration.&lt;/div&gt;
Genetic risk, ethnic variations and pharmacogenetic biomarkers in AMD and polypoidal choroidal vasculopathy (2013)

In recent years, there has been increasing evidence of ethnic differences in the epidemiology, risk factors, clinical presentation and manifestation of age-related macular degeneration (AMD). Although phenotypically very similar to AMD, polypoidal choroidal vasculopathy has a very different natural history, treatment response to anti-VEGF agents and photodynamic therapy and marked ethnic differences in disease prevalence. Despite these differences, there is supporting evidence, particularly from a genetics perspective, that links these two disease entities. In this review, the authors compare and contrast AMD and polypoidal choroidal vasculopathy with particular reference to ethnic variation, genetic disease risk assessment and potential for pharmacogenetic interventions. With advances in massively parallel next-generation sequencing and decreased cost of such technologies, investigators will be able to more thoroughly assess rare variants and their contribution to disease susceptibility.
Absence of an Essential Role for Thymic Stromal Lymphopoietin Receptor in Murine B-Cell Development (2004)

The murine cytokine thymic stromal lymphopoietin (TSLP) supports the development of B220+ IgM+ immature B cells and induces thymocyte proliferation in vitro. Human TSLP, by contrast, activates CD11c+ dendritic cells, but not B or T cells. Recent studies have demonstrated that the receptor for TSLP consists of a heterodimer of the interleukin 7 (IL-7) alpha chain and a novel protein that resembles the hematopoietic cytokine receptor common gamma chain. We examined signal transduction by the gamma-like chains using chimeric receptor proteins. The cytoplasmic domain of the human, but not of the murine, gamma-like chain, activates Jak2 and Stat5 and supports the proliferation of hematopoietic cell lines. In order to assess the role of the murine gamma-like chain in vivo, we generated gamma-like chain-deficient mice. Receptor-deficient mice are unresponsive to TSLP but exhibit no obvious phenotypic defects. In particular, hematopoietic cell development appeared normal. B-cell development, including the IgM+ compartment, was unaffected by loss of the TSLP pathway, as were T lymphopoiesis and lymphocyte proliferation in vitro. Cytokine receptors that utilize the common gamma chain signal through the lymphocyte-specific kinase Jak3. Mice deficient in Jak3 exhibit a SCID phenotype but harbor a residual B220+ splenic lymphocyte population. We demonstrate here that this residual lymphocyte population is lost in mice lacking both the gamma-like chain and Jak3.
The Structure of the Trimer of Human 4-1BB Ligand Is Unique among Members of the Tumor Necrosis Factor Superfamily (2009)

Binding of the 4-1BB ligand (4-1BBL) to its receptor, 4-1BB, provides the T lymphocyte with co-stimulatory signals for survival, proliferation, and differentiation. Importantly, the 4-1BB-4-1BBL pathway is a well known target for anti-cancer immunotherapy. Here we present the 2.3-A crystal structure of the extracellular domain of human 4-1BBL. The ectodomain forms a homotrimer with an extended, three-bladed propeller structure that differs from trimers formed by other members of the tumor necrosis factor (TNF) superfamily. Based on the 4-1BBL structure, we modeled its complex with 4-1BB, which was consistent with images obtained by electron microscopy, and verified the binding site by site-directed mutagenesis. This structural information will facilitate the development of immunotherapeutics targeting 4-1BB.
Comparison of Biodegradable Conduits within Aged Rat Sciatic Nerve Defects (2007)

The results showed differences in myelination; Neurotubes promoted the highest degree of myelination (p < 0.001) as compared with all groups. The authors found no improvement in function of the repaired nerve as measured by percentage of autotomy, the sciatic function index, and gastrocnemius muscle weight. No group was able to recover function in this aged model.
A Study of the Relationship between Cornea Permeability and Eye Irritation Using Membrane-Interaction QSAR Analysis (2005)

A methodology termed membrane-interaction QSAR (MI-QSAR) analysis has been used to develop QSAR models to predict drug permeability coefficients across cornea and its component layers (epithelium, stroma, and endothelium). From a training set of 25 structurally diverse drugs, significant QSAR models are constructed and compared for the permeability of the cornea, epithelium, and stroma plus endothelium. Cornea permeability is found to depend on the measured distribution coefficient of the drug, the cohesive energy of the drug, the total potential energy of the drug-membrane "complex," and three other energy refinement descriptor terms. The endothelium may be a more important barrier in cornea permeation than the stroma. Moreover, an investigation of the correlation between cornea permeation and eye irritation is presented as an example of a cross study on different ADMET properties using MI-QSAR analysis. Thirteen structurally diverse drugs, whose molar-adjusted eye irritation scores (MES) have been measured using the Draize rabbit-eye test, were chosen as an eye irritation comparison set. A poor correlation (R(2) = 0.0232) between the MES measures and the predicted cornea permeability coefficients for the drugs in the eye irritation set suggests there is no significant relationship between eye irritation potency and the cornea permeability.
Identification of mar mutations in herpes simplex virus type 1 glycoprotein B which alter antigenic structure and function in virus penetration (1989)

Analysis of six monoclonal antibody-resistant (mar) mutants in herpes simplex virus type 1 glycoprotein B identified two type-common (II and III) and two type-specific (I and IV) antigenic sites on this molecule. To derive additional information on the location of these sites, mar mutations were mapped and nucleotide alterations were identified by DNA sequencing. Each mutant carried a single amino acid substitution resulting from a G-to-A base transition. Alterations affecting antibody neutralization were identified at residues 473, 594, 305, and 85 for mutants in sites I through IV, respectively. Two clonally distinct site II antibodies each selected mar mutants (Gly to Arg at residue 594) that exhibited a reduction in the rate of entry (roe) into host cells. A site II mar revertant that regained sensitivity to neutralization by site II antibodies also showed normal entry kinetics. DNA sequencing of this virus identified a single base reversion of the site II mar mutation, resulting in restoration of the wild-type sequence (Arg to Gly). This finding demonstrated that the mar and roe phenotypes were the result of a single mutation. To further define structures that contributed to antibody recognition, monoclonal antibodies specific for all four sites were tested for their ability to immune precipitate a panel of linker-insertion mutant glycoprotein B molecules. Individual polypeptides that contained single insertions of 2 to 28 amino acids throughout the external domain were not recognized or were recognized poorly by antibodies specific for sites II and III, whereas no insertion affected antibody recognition of sites I and IV. mar mutations affecting either site II or III were previously shown to cause temperature-sensitive defects in glycoprotein B glycosylation, and variants altered in both these sites were temperature sensitive for virus production. Taken together, the data indicate that antigenic sites II and III are composed of higher-order structures whose integrity is linked with the ability of glycoprotein B to function in virus infectivity.