gebhart/patrepeval huggingface dataset:
Treponema-Specific Tests for Serodiagnosis of Syphilis: Comparative Evaluation of Seven Assays (2011)

The diagnosis of syphilis is challenging and often relies on serologic tests to detect treponemal or nontreponemal antibodies. Recently, the Centers for Disease Control and Prevention and the Association of Public Health Laboratories proposed an update to the syphilis serology testing algorithm, in which serum samples are first tested using a treponema-specific test and positive samples are analyzed with a nontreponemal assay. The goal of this study was to compare the performance of seven treponemal assays (BioPlex 2200 syphilis IgG [Bio-Rad, Hercules, CA], fluorescent treponemal antibody [FTA] assay [Zeus Scientific, Raritan, NJ], Treponema pallidum particle agglutination [TP-PA; Fujirebio Diagnostics, Malvern, PA], Trep-Sure enzyme immunoassay [EIA; Phoenix Biotech, Oakville, Ontario, Canada], Trep-Chek EIA [Phoenix Biotech], Trep-ID EIA [Phoenix Biotech], and Treponema ViraBlot IgG [Viramed Biotech AG, Planegg, Germany]) using serum samples (n = 303) submitted to our reference laboratory. In addition to testing with these 7 assays, all samples were tested by a rapid plasma reagin (RPR) assay and a treponemal IgM Western blot assay (Viramed ViraBlot). Compared to the FTA assay as the gold standard, the evaluated treponemal tests demonstrated comparable levels of performance, with percent agreement ranging from 95.4% (95% confidence interval, 92.3 to 97.3) for the Trep-Sure EIA to 98.4% (96.1 to 99.4) for the Trep-ID EIA. Compared to a "consensus of the test panel" (defined as at least 4 of 7 treponemal tests being in agreement), the percent agreement ranged from 95.7% (92.7 to 97.5) for Trep-Sure to 99.3% (97.5 to 99.9) for Trep-ID. These data may assist clinical laboratories that are considering implementing a treponemal test for screening or confirmatory purposes.
Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch (2012)

C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.
Arimoclomol: a potential therapy under development for ALS (2009)

Arimoclomol, an amplifier of heat shock protein expression involved in cellular stress response, has emerged as a potential therapeutic candidate in amyotrophic lateral sclerosis (ALS) in recent years. Treatment with arimoclomol was reported to improve survival and muscle function in a mouse model of motor neuron disease. Several single- and multiple-dose safety studies have been completed in healthy control subjects. A 3-month Phase IIa study in people with ALS demonstrated safety at dosages up to 300 mg/day and another study is currently recruiting participants with familial ALS caused by mutations in the superoxide dismutase gene. We review the rationale for testing arimoclomol in sporadic and familial ALS in the context of available safety and pharmacokinetic data. Published and unpublished literature relative to the drug in the past two decades is discussed. The current review attempts to bring together our existing understanding of the actions of arimoclomol with the disease profile of ALS. The pharmacological profile of arimoclomol and the available preclinical data make it a promising therapeutic possibility in ALS.
Cryptic Epitopes Induce High-Titer Humoral Immune Response in Patients with Cancer (2010)

In search of novel markers for diagnosis, prognosis, and therapy of cancer, screening of rcDNA expression libraries with patient's sera has been established as a valuable tool for identification of cancer-specific Ags. Interestingly, besides the expected humoral responses to annotated proteins, patients with cancer were frequently found to have serum Abs that bind to peptides without homology to known proteins. So far, the nature of these unconventional epitopes and their possible significance in tumor immunology have never been thoroughly investigated. In our study, we specifically analyzed humoral immune response toward such peptides in patients with pancreatic or breast cancer using yeast-displayed cDNA expression libraries derived from tumor tissue. A detailed analysis of the identified peptides revealed that they originated from translation of sequences outside annotated open reading frames and may derive from the use of alternative start codons or from DNA indel mutations. In several cases, the corresponding mRNA templates have a known association with cancer. In a final analysis, we were able to detect one of these tumor Ags in cancer tissue arrays by a selected Fab-Ab. We conclude that cryptic epitopes may elicit specific humoral immune responses in patients with cancer and thus play a role in immunologic surveillance. Due to the high prevalence of immune responses against some of the peptides, they may also be valuable markers for cancer diagnosis, prognosis, or therapy monitoring.
Inhibition of receptor-localized PI3K preserves cardiac β-adrenergic receptor function and ameliorates pressure overload heart failure (2003)

beta-Adrenergic receptor (betaAR) downregulation and desensitization are hallmarks of the failing heart. However, whether abnormalities in betaAR function are mechanistically linked to the cause of heart failure is not known. We hypothesized that downregulation of cardiac betaARs can be prevented through inhibition of PI3K activity within the receptor complex, because PI3K is necessary for betaAR internalization. Here we show that in genetically modified mice, disrupting the recruitment of PI3K to agonist-activated betaARs in vivo prevents receptor downregulation in response to chronic catecholamine administration and ameliorates the development of heart failure with pressure overload. Disruption of PI3K/betaAR colocalization is required to preserve betaAR signaling, since deletion of a single PI3K isoform (PI3Kgamma knockout) is insufficient to prevent the recruitment of other PI3K isoforms and subsequent betaAR downregulation with catecholamine stress. These data demonstrate a specific role for receptor-localized PI3K in the regulation of betaAR turnover and show that abnormalities in betaAR function are associated with the development of heart failure. Thus, a strategy that blocks the membrane translocation of PI3K and leads to the inhibition of betaAR-localized PI3K activity represents a novel therapeutic approach to restore normal betaAR signaling and preserve cardiac function in the pressure overloaded failing heart.
Essential Roles of Sphingosine 1-Phosphate/S1P1 Receptor Axis in the Migration of Neural Stem Cells Toward a Site of Spinal Cord Injury (2006)

Neural stem/progenitor cells (NSPCs) migrate toward a damaged area of the central nervous system (CNS) for the purpose of limiting and/or repairing the damage. Although this migratory property of NSPCs could theoretically be exploited for cell-based therapeutics of CNS diseases, little is known of the mechanisms responsible for migratory responses of NSPCs. Here, we found that sphingosine 1-phosphate (Sph-1-P), a physiological lysophospholipid mediator, had a potent chemoattractant activity for NSPCs, in which, of Sph-1-P receptors, S1P(1) was abundantly expressed. Sph-1-P-induced NSPC migration was inhibited by the pretreatment with pertussis toxin, Y-27632 (a Rho kinase inhibitor), and VPC23019 (a competitive inhibitor of S1P(1) and S1P(3)). Sph-1-P does not act as intracellular mediator or in an autocrine manner, because [(3)H]sphingosine, incorporated into NSPCs, was mainly converted to ceramide and sphingomyeline intracellularly, and the stimulation-dependent formation and extracellular release of Sph-1-P were not observed. Further, Sph-1-P concentration in the spinal cord was significantly increased at 7 days after a contusion injury, due to accumulation of microglia and reactive astrocytes in the injured area. This locally increased Sph-1-P concentration contributed to the migration of in vivo transplanted NSPCs through its receptor S1P(1), given that lentiviral transduction of NSPCs with a short hairpin RNA interference for S1P(1) abolished in vivo NSPC migration toward the injured area. This is the first report to identify a physiological role for a lipid mediator in NSPC migration toward a pathological area of the CNS and further indicates that the Sph-1-P/S1P(1) pathway may have therapeutic potential for CNS injuries.
The Bacterial Communities Associated with Honey Bee (Apis mellifera) Foragers (2014)

The honey bee is a key pollinator species in decline worldwide. As part of a commercial operation, bee colonies are exposed to a variety of agricultural ecosystems throughout the year and a multitude of environmental variables that may affect the microbial balance of individuals and the hive. While many recent studies support the idea of a core microbiota in guts of younger in-hive bees, it is unknown whether this core is present in forager bees or the pollen they carry back to the hive. Additionally, several studies hypothesize that the foregut (crop), a key interface between the pollination environment and hive food stores, contains a set of 13 lactic acid bacteria (LAB) that inoculate collected pollen and act in synergy to preserve pollen stores. Here, we used a combination of 454 based 16S rRNA gene sequencing of the microbial communities of forager guts, crops, and corbicular pollen and crop plate counts to show that (1) despite a very different diet, forager guts contain a core microbiota similar to that found in younger bees, (2) corbicular pollen contains a diverse community dominated by hive-specific, environmental or phyllosphere bacteria that are not prevalent in the gut or crop, and (3) the 13 LAB found in culture-based studies are not specific to the crop but are a small subset of midgut or hindgut specific bacteria identified in many recent 454 amplicon-based studies. The crop is dominated by Lactobacillus kunkeei, and Alpha 2.2 (Acetobacteraceae), highly osmotolerant and acid resistant bacteria found in stored pollen and honey. Crop taxa at low abundance include core hindgut bacteria in transit to their primary niche, and potential pathogens or food spoilage organisms seemingly vectored from the pollination environment. We conclude that the crop microbial environment is influenced by worker task, and may function in both decontamination and inoculation.
Synthesis and Pairing Properties of Decanucleotides from (3′S,5′R)‐2′‐Deoxy‐3′, 5′‐ethanoβ‐D‐ribofuranosyladenine and ‐thymine (1993)

A lower change in entropy upon duplex formation and a higher propensity for the triplex formation with complementary natural DNA, together with a higher resistance to degradation by phosphodiesterases are the main characteristics of the novel DNA analogues 1 and 2. The concept of reducing pairing entropy by reducing the conformational flexibility of an oligonucleotide single strand (preorganization) may be useful in “antisense” research.
Finite, Spherical Coordination Networks that Self‐Organize from 36 Small Components (2004)

Simple banana-shaped organic molecules self-organize into finite, spherical coordination networks with a diameter of up to 7 nm (see structure; green Pd, red O, blue N, gray C). These molecular spheres consist of 12 equivalent metal centers and 24 equivalent ligands and have cuboctahedral symmetry. Functional groups (C60 or porphyrin) attached to each ligand are aligned equivalently at the periphery of the sphere.
Fold surface of polyethylene single crystals as assessed by selective degradation. I. Ozone degradation method (1971)

Abstract Ozone has been used as a selective oxidizing agent for degrading polyethylene single crystals at room temperature in order to confirm and extend results on surface structure obtained by use of fuming nitric acid at temperatures above 60°C. The surfaces of the crystals were rendered highly accessible to the ozone gas by preparing the crystalline material in a highly expanded form; the solvent in which the crystals were suspended was removed by sublimation from the solid state. The extent and nature of the reaction were studied by measuring the increase in weight and in density, by direct chemical analyses, and by making use of infrared spectroscopy and gel‐permeation chromatography. It was found that the surfaces of the crystals are attacked at room temperature by ozone, with resulting chain scission, and the broad features of the chemical reaction were established. Some folded chains are found to be as long as the original thickness of the crystal, and once folds have been cut, continuing reaction shortens the chains. In the early stages of the degradation, during which most of the weight increase takes place, the density of the crystals increases, and the magnitude of the increase is that expected from the increase in weight alone, i.e., assuming no increase in effective volume.
A Survey of Chromosomal and Nucleotide Sequence Variation inDrosophila miranda (2003)

There have recently been several studies of the evolution of Y chromosome degeneration and dosage compensation using the neo-sex chromosomes of Drosophila miranda as a model system. To understand these evolutionary processes more fully, it is necessary to document the general pattern of genetic variation in this species. Here we report a survey of chromosomal variation, as well as polymorphism and divergence data, for 12 nuclear genes of D. miranda. These genes exhibit varying levels of DNA sequence polymorphism. Compared to its well-studied sibling species D. pseudoobscura, D. miranda has much less nucleotide sequence variation, and the effective population size of this species is inferred to be several-fold lower. Nevertheless, it harbors a few inversion polymorphisms, one of which involves the neo-X chromosome. There is no convincing evidence for a recent population expansion in D. miranda, in contrast to D. pseudoobscura. The pattern of population subdivision previously observed for the X-linked gene period is not seen for the other loci, suggesting that there is no general population subdivision in D. miranda. However, data on an additional region of period confirm population subdivision for this gene, suggesting that local selection is operating at or near period to promote differentiation between populations.
The Quadtree and Related Hierarchical Data Structures (1984)

A tutorial survey is presented of the quadtree and related hierarchical data structures. They are based on the principle of recursive decomposition. The emphasis is on the representation of data used in applications in image processing, computer graphics, geographic information systems, and robotics. There is a greater emphasis on region data
Trisacryl gelatin microspheres for therapeutic embolization, II: preliminary clinical evaluation in tumors and arteriovenous malformations. (1996)

The microspheres are easy to use and allow precise control of the embolization procedure. Their physical characteristics make them a safe embolic agent.
Checkpoint Signaling, Base Excision Repair, and PARP Promote Survival of Colon Cancer Cells Treated with 5-Fluorodeoxyuridine but Not 5-Fluorouracil (2011)

The fluoropyrimidines 5-fluorouracil (5-FU) and FdUrd (5-fluorodeoxyuridine; floxuridine) are the backbone of chemotherapy regimens for colon cancer and other tumors. Despite their widespread use, it remains unclear how these agents kill tumor cells. Here, we have analyzed the checkpoint and DNA repair pathways that affect colon tumor responses to 5-FU and FdUrd. These studies demonstrate that both FdUrd and 5-FU activate the ATR and ATM checkpoint signaling pathways, indicating that they cause genotoxic damage. Notably, however, depletion of ATM or ATR does not sensitize colon cancer cells to 5-FU, whereas these checkpoint pathways promote the survival of cells treated with FdUrd, suggesting that FdUrd exerts cytotoxicity by disrupting DNA replication and/or inducing DNA damage, whereas 5-FU does not. We also found that disabling the base excision (BER) repair pathway by depleting XRCC1 or APE1 sensitized colon cancer cells to FdUrd but not 5-FU. Consistent with a role for the BER pathway, we show that small molecule poly(ADP-ribose) polymerase 1/2 (PARP) inhibitors, AZD2281 and ABT-888, remarkably sensitized both mismatch repair (MMR)-proficient and -deficient colon cancer cell lines to FdUrd but not to 5-FU. Taken together, these studies demonstrate that the roles of genotoxininduced checkpoint signaling and DNA repair differ significantly for these agents and also suggest a novel approach to colon cancer therapy in which FdUrd is combined with a small molecule PARP inhibitor.
Neuroprotective Effects of MgSO 4 and MgCl 2 in Closed Head Injury: A Comparative Phosphorus NMR Study (1998)

Previous studies have shown that free magnesium levels decline after traumatic brain injury and that magnesium salt administration improves posttraumatic outcome. These earlier studies, however, have been limited to models of injury that do not produce a significant degree of diffuse axonal injury and have used either MgSO4 or MgCl2 as the magnesium salt. The present study compares the neuroprotective efficacy of MgSO4 and MgCl2 in a severe model of diffuse axonal injury in rats using phosphorus nuclear magnetic resonance spectroscopy and the rotarod test to monitor effects on metabolism and neurologic outcome, respectively. Both MgSO4 and MgCl2 given as a bolus of 100 micromoles/kg at 30 min after severe, closed head injury significantly improved brain intracellular free magnesium concentration and neurologic outcome. These findings suggest that both salts penetrate the blood-brain barrier after brain trauma, enter injured tissue, and subsequently improve neurologic outcome.
Definitions for sepsis and organ failure (1992)

Department of Internal Medicine, Rush-Presbyterian-St. Luke's Medical Center, Rush University, 1753 West Congress Parkway, Chicago IL 60612.
Ro 32-3555, an orally active collagenase selective inhibitor, prevents structural damage in the STR/ORT mouse model of osteoarthritis (1998)

Ro 32-3555, a collagenase selective inhibitor, inhibits both the cartilage and bone changes in this mouse model of OA, and thus shows great potential as a treatment of OA in humans.
Influence of Life Stress on Depression: Moderation by a Polymorphism in the 5-HTT Gene (2003)

In a prospective-longitudinal study of a representative birth cohort, we tested why stressful experiences lead to depression in some people but not in others. A functional polymorphism in the promoter region of the serotonin transporter (5-HT T) gene was found to moderate the influence of stressful life events on depression. Individuals with one or two copies of the short allele of the 5-HT T promoter polymorphism exhibited more depressive symptoms, diagnosable depression, and suicidality in relation to stressful life events than individuals homozygous for the long allele. This epidemiological study thus provides evidence of a gene-by-environment interaction, in which an individual's response to environmental insults is moderated by his or her genetic makeup.
Fluorescence Studies of Ionomers (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorescence Studies of IonomersHerbert MorawetzCite this: Acc. Chem. Res. 1994, 27, 6, 174–178Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/ar00042a004https://doi.org/10.1021/ar00042a004research-articleACS PublicationsRequest reuse permissionsArticle Views103Altmetric-Citations5LEARN 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
Assembly of Nanoparticles into Hollow Spheres Using Block Copolypeptides (2002)

Various modes are being explored for the construction of functional materials out of nanoparticles. Despite these efforts, the assembly of nanoparticles remains challenging with respect to the requirement of multiple component organization on varying dimensions and length scales. We report here a room-temperature, wet chemical-based synthesis route in which silica and gold nanoparticles (∼10 nm) are cooperatively assembled with lysine−cysteine diblock copolypeptides into robust hollow spheres (diameter ∼ microns). The walls of the hollow spheres are composed of two distinct layers of silica and gold nanoparticles, and the hollow center is created without the use of a sacrificial core, emulsion phase, or hollow preformed substrate. Block copolypeptides designed with specific recognition sites for nanoparticles of various compositions provide a versatile approach for the hierarchical organization of nanoparticles into multidimensional composite arrays.
Absorbed dose calculations in Haversian canals for several beta-emitting radionuclides. (1993)

A mathematical model of a Haversian canal was used to calculate absorbed dose factors for 90Sr, 90Y, 45Ca, 89Sr, 32P, 131I and 153Sm. The regions of interest considered in this study were the blood canal, the wall or bone surface and the bone matrix. The source regions were the blood canal and the bone surface. Absorbed dose calculations were performed with the EGS4-PRESTA Monte Carlo transport code. Dose factors were calculated for Haversian canals of 5-microns to 50-microns radius. These data are also tabulated so that dose factors can be evaluated for other radii. An example is given in which these data are used along with a biokinetic model of a radioactive material in bone to assess doses from diagnostic and radiotherapy procedures.