gebhart/patrepeval huggingface dataset:
Vehicle evaporative and exhaust emissions as influenced by benzene content of gasoline. Final report (1986)

To better define the effect of fuel composition on benzene emissions from current production vehicles, the evaporative and exhaust emissions from five current model vehicles equipped with representative emission control systems were studied. Fuels consisting of two aromatic levels and four benzene concentrations were tested in the above vehicles. Benzene and regulated emissions were measured in each test segment. Benzene content and the detailed hydrocarbon (HC) compositions of the fuels were also measured. In addition to the evaporative and exhaust emissions, engine-out and tailpipe-out emissions were measured simultaneously as a means of assessing the on-board catalyst conversion efficiency of benzene. Conclusions are as follows: Head space, evaporative and exhaust emission results reported as benzene, wt % in HC, increase linearly with increasing fuel benzene. Measurable benzene evaporative emissions occurred with benzene-free fuel due to desorption of benzene captured by the canister from previous test fuels. Benzene exhaust emissions occurred with benzene-free fuel due to production of benzene from precursors in the combustion process. Total vehicular benzene emission rates increased about 4 mg/mile for an increase of 1 vol % fuel benzene. Exhaust benzene emission rates increased by about 4 mg/mile for 15 vol % fuel aromatic differential. Vehicular sources ofmore » benzene emissions averaged about 70% exhaust, 20% evaporative, and 10% refueling for 1.5 vol % benzene fuel. Catalyst conversion efficiency results showed benzene conversion ranged from 74 to 95% and HC conversion ranged from 82 to 91% over the five vehicles. The evaporative benzene carry-over study showed that evaporative benzene emissions are directly affected by the composition of prior test fuels for as many as three prior tests.« less
Exoenzyme S of Pseudomonas aeruginosa ADP-ribosylates the intermediate filament protein vimentin (1989)

Exoenzyme S, which had been thought to be unselective, catalyzes the ADP-ribosylation of only a subset of cellular proteins. The intermediate filament protein vimentin is one of the more abundant substrates. Disassembled vimentin, and proteolytic fragments of vimentin that cannot form filaments, is more readily ADP-ribosylated than is filamentous vimentin.
Generalizing the Nonlocal-Means to Super-Resolution Reconstruction (2008)

Super-resolution reconstruction proposes a fusion of several low-quality images into one higher quality result with better optical resolution. Classic super-resolution techniques strongly rely on the availability of accurate motion estimation for this fusion task. When the motion is estimated inaccurately, as often happens for nonglobal motion fields, annoying artifacts appear in the super-resolved outcome. Encouraged by recent developments on the video denoising problem, where state-of-the-art algorithms are formed with no explicit motion estimation, we seek a super-resolution algorithm of similar nature that will allow processing sequences with general motion patterns. In this paper, we base our solution on the Nonlocal-Means (NLM) algorithm. We show how this denoising method is generalized to become a relatively simple super-resolution algorithm with no explicit motion estimation. Results on several test movies show that the proposed method is very successful in providing super-resolution on general sequences.
Analytical Validation of a Hybrid Capture–Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA (2018)

Genomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a noninvasive method for detecting genomic biomarkers to guide clinical decision making for cancer patients. We developed a hybrid capture-based next-generation sequencing assay for genomic profiling of circulating tumor DNA from blood (FoundationACT). High-sequencing coverage and molecular barcode-based error detection enabled accurate detection of genomic alterations, including short variants (base substitutions, short insertions/deletions) and genomic re-arrangements at low allele frequencies (AFs), and copy number amplifications. Analytical validation was performed on 2666 reference alterations. The assay achieved >99% overall sensitivity (95% CI, 99.1%-99.4%) for short variants at AF >0.5%, >95% sensitivity (95% CI, 94.2%-95.7%) for AF 0.25% to 0.5%, and 70% sensitivity (95% CI, 68.2%-71.5%) for AF 0.125% to 0.25%. No false positives were detected in 62 samples from healthy volunteers. Genomic alterations detected by FoundationACT demonstrated high concordance with orthogonal assays run on the same clinical cfDNA samples. In 860 routine clinical FoundationACT cases, genomic alterations were detected in cfDNA at comparable frequencies to tissue; for the subset of cases with temporally matched tissue and blood samples, 75% of genomic alterations and 83% of short variant mutations detected in tissue were also detected in cfDNA. On the basis of analytical validation results, FoundationACT has been approved for use in our Clinical Laboratory Improvement Amendments-certified/College of American Pathologists-accredited/New York State-approved laboratory.
A prospective seroepidemiologic study on dengue in children four to nine years of age in Yogyakarta, Indonesia I. studies in 1995-1996. (1999)

A prospective study on dengue (DEN) viruses was initiated in October 1995 in Gondokusuman kecamatan, Yogyakarta, Indonesia. This report presents data from the first year of the study. The studied cohort included all children 4-9 years of age living in the kecamatan. Blood samples for serology were collected from 1,837 children in October 1995 and again in October 1996. Blood samples for virus isolation and serology were collected from cohort children who were seen in municipal health clinics with febrile syndromes or admitted to hospitals with a provisional diagnosis of dengue hemorrhagic fever. Dengue serotype antibody prevalence and 1995-1996 infection rates were calculated using a single dilution (1:60) 70% plaque reduction endpoint neutralization test. Prevalence of dengue antibody at the beginning of the study was DEN 1 = 12%, DEN 2 = 16%, DEN 3 = 2%, DEN 4 = 4%, and two or more dengue infections = 22%. Total dengue antibody prevalence increased from 38% in 4-year-old children to 69% in 9-year-old children. During the observation period, primary dengue infection rates were DEN 1 = 4.8%, DEN 2 = 7.7%, DEN 3 = 4.2%, and DEN 4 = 3.4%, while two or more dengue infections occurred in 6.7% of the study population. The secondary dengue infection rate was 19.0%. From febrile cases, all four dengue viruses were isolated with DEN 3 predominating. Seven children were hospitalized, including one fatal case with a hospital diagnosis of dengue shock syndrome. Based upon presence of antibody in the initial cohort bleeding and the serologic response both weeks and several months following illness, all had secondary dengue infections. Neutralizing antibody patterns in the initial cohort bleeding and in late convalescent serum samples permitted recognition of dengue infection sequence in five patients: DEN 2-DEN 1 (3), DEN 2-DEN 4 (1), DEN 1-DEN 3 (1), and none in the sequence DEN 1-DEN 2. In the total cohort 6.5% of the observed secondary infections were of the sequence DEN 2-DEN 1, while 4.9% were DEN 1-DEN 2, a highly pathogenic sequence in previous studies. Reduced pathogenic expression of secondary DEN 2 with enhanced pathogenic expression of secondary DEN 1 infections was an unexpected finding. Further studies will be required to understand the respective contributions to pathogenicity of antibody from initial dengue infections versus the biological attributes of the second infecting dengue viruses.
Controlling β-Sheet Assembly in Genetically Engineered Silk by Enzymatic Phosphorylation/Dephosphorylation (2000)

Enzymatic phosphorylation and dephosphorylation reactions were used to modify a genetically engineered variant of spider dragline silk. The approximately 25 kDa protein was phosphorylated with cyclic AMP-dependent kinase and dephosphorylated with calf intestinal alkaline phosphatase. Phosphorylation inhibited beta-sheet assembly of the protein and enhanced solubility to about 5 mg/mL in water, compared to about 20% of this level upon enzymatic dephosphorylation. The cyclability of the phosphorylation-dephosphorylation system was confirmed by MALDI with a model peptide. Kinetic studies conducted with [gamma-(32)P]ATP illustrate that the phosphorylation reaction proceeds over 6 h. Secondary structure of the phosphorylated and dephosphorylated proteins was determined by CD and FTIR. The results illustrate that an enzymatic phosphorylation event can be used to control the solution structure of a protein like silk, which has a tendency to prematurely precipitate due to the formation of beta-sheets.
Human Mesenchymal Stem Cells as an in Vitro Model for Human Adipogenesis (2003)

hMSCs are renewable sources of noncommitted precursors that are able to differentiate into mature adipocytes under the proper hormonal and pharmacological stimuli. Thus, hMSCs represent a new model for the study of human adipogenesis.
Biomimetic Nanocarrier for Direct Cytosolic Drug Delivery (2009)

Getting straight to the point: A peptide–phospholipid-based biomimetic nanocarrier was developed that can transport cargo molecules directly into cytosolic compartments through a non-endocytotic uptake mechanism mediated by scavenger receptor class B type I (SR-BI; see schematic illustration). The fluorescent image shows the cytosolic localization of a dye (red) delivered by the nanocarrier to SR-BI-positive cells (nuclei: blue, membranes: cyan). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Genetic programs of epithelial cell plasticity directed by transforming growth factor-β (2001)

Epithelial-mesenchymal transitions (EMTs) are an essential manifestation of epithelial cell plasticity during morphogenesis, wound healing, and tumor progression. Transforming growth factor-beta (TGF-beta) modulates epithelial plasticity in these physiological contexts by inducing EMT. Here we report a transcriptome screen of genetic programs of TGF-beta-induced EMT in human keratinocytes and propose functional roles for extracellular response kinase (ERK) mitogen-activated protein kinase signaling in cell motility and disruption of adherens junctions. We used DNA arrays of 16,580 human cDNAs to identify 728 known genes regulated by TGF-beta within 4 hours after treatment. TGF-beta-stimulated ERK signaling mediated regulation of 80 target genes not previously associated with this pathway. This subset is enriched for genes with defined roles in cell-matrix interactions, cell motility, and endocytosis. ERK-independent genetic programs underlying the onset of EMT involve key pathways and regulators of epithelial dedifferentiation, undifferentiated transitional and mesenchymal progenitor phenotypes, and mediators of cytoskeletal reorganization. The gene expression profiling approach delineates complex context-dependent signaling pathways and transcriptional events that determine epithelial cell plasticity controlled by TGF-beta. Investigation of the identified pathways and genes will advance the understanding of molecular mechanisms that underlie tumor invasiveness and metastasis.
Activation of human factor VII during clotting in vitro (1985)

We have studied factor VII activation by measuring the ratio of factor VII clotting to coupled amidolytic activity (VIIc/VIIam) and cleavage of 125I-factor VII. In purified systems, a low concentration of Xa or a higher concentration of IXa rapidly activated 125I-factor VII, yielding a VIIc/VIIam ratio of 25 and similar gel profiles of heavy and light chain peaks of VIIa. On further incubation, VIIa activity diminished and a third 125I-peak appeared. When normal blood containing added 125I- factor VII was clotted in a glass tube, the VIIc/VIIam ratio rose fivefold, and 20% of the 125I-factor VII was cleaved. Clotting normal plasma in an activated partial thromboplastin time (APTT) system yielded a VIIc/VIIam ratio of 25 and over 90% cleavage of 125I-factor VII. Clotting factor XII-deficient plasma preincubated with antibodies to factor X in an APTT system with added XIa yielded a VIIc/VIIam ratio of 19 and about 60% cleavage, which indicates that IXa, at a concentration achievable in plasma, can effectively activate factor VII. Clotting normal plasma with undiluted tissue factor yielded a VIIc/VIIam ratio of 15 to 20 and 60% cleavage of 125I-factor VII, whereas clotting plasma with diluted tissue factor activated factor VII only minimally. We conclude that both Xa and IXa can function as significant activators of factor VII in in vitro clotting mixtures but believe that only small amounts of factor VII may be activated in vivo during hemostasis.
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of DHNA synthetase fromGeobacillus kaustophilus (2007)

The aerobic Gram-positive bacterium Geobacillus kaustophilus is a bacillus species that was isolated from deep-sea sediment from the Mariana Trench. 1,4-Dihydroxy-2-naphthoate (DHNA) synthetase plays a vital role in the biosynthesis of menaquinone (vitamin K(2)) in this bacterium. DHNA synthetase from Geobacillus kaustophilus was crystallized in the orthorhombic space group C222(1), with unit-cell parameters a = 77.01, b = 130.66, c = 131.69 A. The crystal diffracted to a resolution of 2.2 A. Preliminary studies and molecular-replacement calculations reveal the presence of three monomers in the asymmetric unit.
Record Linkage: Current Practice and Future Directions (2003)

Record linkage is the task of quickly and accurately identifying records corresponding to the same entity from one or more data sources. Record linkage is also known as data cleaning, entity reconciliation or identification and the merge/purge problem. This paper presents the &amp;quot;standard&amp;quot; probabilistic record linkage model and the associated algorithm. Recent work in information retrieval, federated database systems and data mining have proposed alternatives to key components of the standard algorithm. The impact of these alternatives on the standard approach are assessed. The key question is whether and how these new alternatives are better in terms of time, accuracy and degree of automation for a particular record linkage application.
Calcium and Membrane Binding Properties of Bovine Neurocalcin δ Expressed in Escherichia coli (1995)

Neurocalcins are brain-specific proteins that belong to a new subclass of the EF-hand superfamily of calcium binding proteins, defined by the photoreceptor cell-specific protein, recoverin. Recoverin, which regulates the desensitization of photo-excited rhodopsin, is myristoylated and exhibits a calcium-myristoyl switch. Like recoverin, neurocalcins have a signal for N-myristoylation and possess four EF-hands, although the first one lacks some residues critical for calcium binding. In this work, I have examined the calcium and membrane binding properties of recombinant myristoylated and unmyristoylated neurocalcin delta. I show that neurocalcin, like recoverin, binds to biological membranes in a calcium- and myristoyl-dependent manner. Both myristoylated and unmyristoylated proteins bind three calcium ions. However, the unmyristoylated form exhibits a higher affinity for calcium than the myristoylated protein but shows a lower cooperativity in binding calcium. These data support the model for the calcium-myristoyl switch mechanism proposed for recoverin (Zozulya, S., and Stryer, L. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 11569-11573; Dizhoor, A. M., Chen, C. K., Olshevskaya, E., Sinelnikova, V. V., and Hurley, J. B. (1993) Science 259, 829-832). Using point mutations, I have investigated the relative importance of each of the three functional EF hands (EF2, EF3, and EF4) in the calcium and membrane binding properties of neurocalcin. Calcium and membrane binding properties of the mutant-myristoylated proteins suggest that binding of calcium to EF2 is critical in triggering the binding of the protein to membranes.
Transport Pathways for Clearance of Human Alzheimer's Amyloid β-Peptide and Apolipoproteins E and J in the Mouse Central Nervous System (2006)

Amyloid beta-peptide (Abeta) clearance from the central nervous system (CNS) maintains its low levels in brain. In Alzheimer's disease, Abeta accumulates in brain possibly because of its faulty CNS clearance and a deficient efflux across the blood-brain barrier (BBB). By using human-specific enzyme-linked immunosorbent assays, we measured a rapid 30 mins efflux at the BBB and transport via the interstitial fluid (ISF) bulk flow of human-unlabeled Abeta and of Abeta transport proteins, apolipoprotein E (apoE) and apoJ in mice. We show (i) Abeta40 is cleared rapidly across the BBB via low-density lipoprotein receptor-related protein (LRP)1 at a rate of 0.21 pmol/min g ISF or 6-fold faster than via the ISF flow; (ii) Abeta42 is removed across the BBB at a rate 1.9-fold slower compared with Abeta40; (iii) apoE, lipid-poor isoform 3, is cleared slowly via the ISF flow and across the BBB (0.03-0.04 pmol/min g ISF), and after lipidation its transport at the BBB becomes barely detectable within 30 mins; (iv) apoJ is eliminated rapidly across the BBB (0.16 pmol/min g ISF) via LRP2. Clearance rates of unlabeled and corresponding 125I-labeled Abeta and apolipoproteins were almost identical, but could not be measured at low physiologic levels by mass spectrometry. Amyloid beta-peptide 40 binding to apoE3 reduced its efflux rate at the BBB by 5.7-fold, whereas Abeta42 binding to apoJ enhanced Abeta42 BBB clearance rate by 83%. Thus, Abeta, apoE, and apoJ are cleared from brain by different transport pathways, and apoE and apoJ may critically modify Abeta clearance at the BBB.
Repeated restraint stress suppresses neurogenesis and induces biphasic PSA‐NCAM expression in the adult rat dentate gyrus (2003)

Chronic restraint stress has been shown to induce structural remodelling throughout the interconnected dentate gyrus-CA3 fields. To find out how this stressor affects the rate of adult hippocampal neurogenesis, we subjected rats to acute or chronic restraint stress and assessed the proliferation, survival and differentiation of newly born cells in the dentate gyrus. We also examined polysialylated neural cell adhesion molecule expression, a molecule normally expressed in immature neurons and important for morphological plasticity. The results show that acute restraint stress did not change either the proliferation of dentate gyrus precursor cells or the expression of polysialylated neural cell adhesion molecule, whereas 3 weeks of chronic restraint stress suppressed proliferation by 24% and increased polysialylated neural cell adhesion molecule expression by 40%. The study was extended for an additional 3 weeks to trace the survival and development of the cells born after the initial 3 weeks of restraint. Rats subjected to 6 weeks of daily restraint stress exhibited suppressed cell proliferation and attenuated survival of the recently born cells after the extended time course, resulting in a 47% reduction of granule cell neurogenesis. Furthermore, 6 weeks of chronic stress significantly reduced the total number of granule cells by 13% and the granule cell layer volume by 5%. Expression of polysialylated neural cell adhesion molecule followed a biphasic time course, displaying a significant up-regulation after 3 weeks of daily restraint stress that was lost after 6 weeks of stress. These studies may help us understand the basis for hippocampal shrinkage and raise questions about the ultimate reversibility of the effects of chronic stress.
A method for determining the driving currents for focused stimulation in the cochlea (1995)

A pseudo-inverse technique has been applied to a lumped-element model of the first turn of an implanted cochlea of a guinea pig. The method calculates the currents necessary to focus or distribute stimuli in desired patterns across the location of the family of auditory nerve cells in the implanted ear. Studies in animals are being undertaken to validate the technique.
On multi-column foreign key discovery (2010)

A foreign/primary key relationship between relational tables is one of the most important constraints in a database. From a data analysis perspective, discovering foreign keys is a crucial step in understanding and working with the data. Nevertheless, more often than not, foreign key constraints are not specified in the data, for various reasons; e.g., some associations are not known to designers but are inherent in the data, while others become invalid due to data inconsistencies. This work proposes a robust algorithm for discovering single-column and multi-column foreign keys. Previous work concentrated mostly on discovering single-column foreign keys using a variety of rules, like inclusion dependencies, column names, and minimum/maximum values. We first propose a general rule, termed Randomness , that subsumes a variety of other rules. We then develop efficient approximation algorithms for evaluating randomness, using only two passes over the data. Finally, we validate our approach via extensive experiments using real and synthetic datasets.
Duodenal Ulcer and Eradication ofHelicobacter pyloriin a Developing Country An 18-Month Follow-up Study (1992)

Forty-eight patients with endoscopically proven duodenal ulcer (DU) and Helicobacter pylori infection detected by 14C-urea breath test (BT) were assigned to 5 days of treatment with furazolidone, metronidazole, and amoxicillin in addition to eventual classical anti-ulcer agents if necessary. Clinical evaluation and BT were repeated at 2, 6, and 18 months after therapy to determine H. pylori eradication or reinfection. Endoscopy was also repeated at 6 and 18 months after treatment to detect DU relapse. In 29 (60%) patients H. pylori had been eradicated at 2 months after therapy, and in 19 (40%) infection persisted. After successful eradication, 6 of 29 (20.7%) were reinfected. All 24 patients who were negative at the 18-month evaluation were asymptomatic, free of anti-ulcer drugs, and with healed ulcers, whereas among the 19 positive patients followed up, 11 (57%) continued to be symptomatic and still using anti-ulcer agents (p less than 0.010), and 10 (53%) showed active ulcers at endoscopy (p less than 0.010). H. pylori eradication is clearly followed by long-term remission of DU. Reinfection may be an additional problem in treating DU patients in developing countries.