gebhart/patrepeval huggingface dataset:
Mixed Messages (2005)

In previous studies, mechanical support of medically refractory hearts with a left ventricular assist device (LVAD) has induced regression of many morphological and functional abnormalities characteristic of failing human hearts. To identify transcriptional adaptations in failing and LVAD-supported hearts, we performed a comprehensive transcription analysis using the Affymetrix microarray platform and 199 human myocardial samples from nonfailing, failing, and LVAD-supported human hearts. We also used a novel analytical strategy that defines patterns of interest based on multiple intergroup comparisons. Although over 3088 transcripts exhibited significantly altered abundance in heart failure, most of these did not exhibit a consistent response to LVAD support based on our analysis. Of those 238 with a consistent response to LVAD support, more than 75% exhibited persistence or exacerbation of HF-associated transcriptional abnormalities whereas only 11%, 5%, and 2% exhibited partial recovery, normalization, and overcorrection responses, respectively. Even among genes implicated by previous reports of LVAD-associated myocardial improvements, partial or complete normalization of transcription did not predominate. The magnitude of differences in transcript abundance between nonfailing and failing hearts, and between failing an LVAD-supported hearts, tended to be low with changes greater than or equal to 2-fold infrequently observed. Our results indicate that morphological or functional myocardial improvements may occur without widespread normalization of pathological transcriptional patterns. These observations also suggest that many failure-associated transcriptional changes have only a limited role in regulating cardiac structure and function and may represent epiphenomena and/or nonspecific myocardial plasticity responses. Differences in mRNA localization, translation efficiency, and posttranslational protein modifications or interactions may be more pivotal in regulating myocardial structure and function.
Kinetics and Hydrolysis of Fenamiphos, Fipronil, and Trifluralin in Aqueous Buffer Solutions (1999)

Hydrolyses of fenamiphos, fipronil, and trifluralin were studied in aqueous buffer solutions of pH 4.1, 7.1, and 9.1 at different temperatures, 5, 22 +/- 1, 32 +/- 1, and 50 +/- 1 degrees C. Fenamiphos, fipronil, and trifluralin were found to be more stable in acidic and neutral buffer solutions at temperatures of 5 and 22 +/- 1, and dissipation is rapid at 50 +/- 1 degrees C. In basic buffer and at higher temperature, degradation of fenamiphos was found to be very rapid when compared with fipronil and trifluralin. The rate constants calculated at 32 degrees C for fenamiphos were 2349.4 x 10(-)(8) (pH 4.1), 225.2 x 10(-)(8) (pH 7.1), and 30476.0 x 10(-)(8) (pH 9.1); for fipronil 1750.0 x 10(-)(8) (pH 4.1), 3103.0 x 10(-)(8) (pH 7.1), and 3883.0 x 10(-)(8) (pH 9.1); and for trifluralin 2331.0 x 10(-)(8) (pH 4.1), 2360.0 x 10(-)(8) (pH 7.1), and 3188.0 x 10(-)(8) (pH 9.1). On the basis of rate constant values, these pesticides appeared to be more susceptible to hydrolysis than synthetic organophosphorus compounds such as chlorpyriphos, diazinon, malathion, and ronnel. DT(50) values calculated at 32 degrees C were 228 (pH 4.1), 5310.24 (pH 7.1), and 37.68 (pH 9.1) h for fenamiphos; 608.6 (pH 4.1), 373.9 (pH 7.1), and 270.2 (pH 9.1) h for fipronil; and 502.1 (pH 4.1), 496.8 (pH 7.1), and 355.7 (pH 9.1) h for trifluralin.
A second European collaborative study on polymerase chain reaction forToxoplasma gondii, involving 15 teams (1998)

In order to investigate the accuracy and practicability of the polymerase chain reaction (PCR) in the antenatal diagnosis of congenital toxoplasmosis, a collaborative study involving 15 European laboratories was performed under the auspices of the Biomed 2 Programme of the European Community. Each team received 12 aliquots (four negative, eight positive) of 'artificial samples' made of amniotic fluid spiked with tachyzoites of the RH strain of Toxoplasma gondii. Each team performed its own PCR protocol (all were different). Nine of the 15 laboratories were able to detect a single parasite, but two of the 15 found all samples negative. Four of the 15 laboratories found one or more control samples to be falsely positive. This study highlights the lack of homogeneity between PCR protocols and performance and underlines the need for an external quality assurance scheme which could provide 'reference' samples that could be used by any laboratory wanting to establish and maintain an accurate diagnostic test based on PCR.
The presence of p53 mutations in human osteosarcomas correlates with high levels of genomic instability (2003)

The p53 gene is a critical tumor suppressor that is inactivated in a majority of cancers. The central role of p53 in response to stresses such as DNA damage, hypoxia, and oncogene activation underlies this high frequency of negative selection during tumorigenic transformation. Mutations in p53 disrupt checkpoint responses to DNA damage and result in the potential for destabilization of the genome. Consistent with this, p53 mutant cells have been shown to accumulate genomic alterations in cell culture, mouse models, and some human tumors. The relationship between p53 mutation and genomic instability in human osteosarcoma is addressed in this report. Similar to some other primary human tumors, the mutation of p53 correlates significantly with the presence of high levels of genomic instability in osteosarcomas. Surprisingly, osteosarcomas harboring an amplification of the HDM2 oncogene, which inhibits the tumor-suppressive properties of p53, do not display high levels of genomic instability. These results demonstrate that the inactivation of p53 in osteosarcomas directly by mutation versus indirectly by HDM2 amplification may have different cellular consequences with respect to the stability of the genome.
Effects of agitation level on the adsorption, desorption, and activities on cotton fabrics of full length and core domains of EGV (Humicola insolens) and CenA (Cellulomonas fimi) (2000)

The activities (at pH 7 and 50 degrees C) of purified EGV (Humicola insolens) and CenA (Cellulomonas fimi) were determined on cotton fabrics at high and low levels of mechanical agitation. Similar activity measurements were also made by using the core domains of these cellulases. Activity experiments suggested that the presence of cellulose binding domains (CBDs) is not essential for cellulase performance in the textile processes, where high levels of mechanical agitation are applied. The binding reversibilities of these cellulases and their cores were studied by dilution of the treatment liquor after equilibrium adsorption. EGV showed low percentage of adsorption under both levels of agitation. It was observed that the adsorption/desorption processes of cellulases are enhanced by higher mechanical agitation levels and that the binding of cellulase with CBD of family I (EGV) is more reversible than that of CBD of the cellulase of family II (CenA).
Rationale of Treatment in Graves Ophthalmopathy (2001)

Graves ophthalmopathy is a chronic and multisystem disorder caused by an autoimmune process, characterized by the presence of antibodies that stimulate a general fibroblastic reaction (thyroid gland and lower extremities), and involves orbital fat tissue and muscles. The clinical findings and therapy for the treatment of the exophthalmos, such as changes in extrinsic eye motility, diplopia, optic nerve involvement, and lid retraction, were analyzed, and the various types of surgical treatment currently available for Graves ophthalmopathy were evaluated. The aim was to choose the best option to treat each case. The surgical techniques were transpalpebral decompression by removal of intraorbital fat, three-wall osseous expansion, and zygomatic osteotomy. Adjunctive procedures were lengthening of the levator muscle of the upper eyelid, lengthening of the retractor of the lower eyelid (if necessary), and surgery of the extrinsic muscles to correct diplopia. All these techniques were useful in treating the disease, which is characterized by chronic evolution and, at times, a "malignant" outcome. A total of 39 orbits were treated using different techniques of decompression and secondary adjunctive procedures. Results were analyzed after a minimum 6-month follow-up. It was evident that surgery greatly reduced the degree of exophthalmos and improved eye motility, diplopia, and visual acuity. Close cooperation among a team of specialists, including an endocrinologist, ophthalmologist, neuroradiologist, surgeon, anesthesiologist, and radiotherapist, is essential to manage and to quantify the postoperative results of this complex disorder. The authors' experience and application of different surgical strategies, as based on clinical data and histopathological classification, are presented.
Enzyme-Labeling of Antibodies and Their Fragments for Enzyme Immunoassay and Immunohistochemical Staining (1983)

Abstract The use of an enzyme as a label has a number of advantages over the use of other labels in both immunohistochemistry and immunoassay. Immunofluorescence techniques are not suitable for ultrastructural research on cells, and ferritin-labeled antibodies allow only electronmicroscopic studies. By contrast, enzyme-labeled antibodies permit localization of cellular antigens in relation to tissue structures under light microscope and also demonstration of cellular antigens at an ultrastructural level by electronmicroscopy. Antibody or antibody fragments labeled with enzymes of small molecular weight can more readily permeate cells of tissue sections than ferritin-labeled antibodies. The color of tissue sections prepared by immunoenzymatic techniques is stable for years, while immunofluorescence of tissue sections decreases rapidly when exposed to light. Radioisotope-labeled reagents decay with time; there are health hazards due to radio isotopes; and disposal of radioactive waste is becoming increasingly difficult. By contrast, enzyme-labeled antigens and antibodies are stable for months or even years and there are no problems either of health hazards or of waste disposal with appropriate choice of enzymes and substrates. Under favourable conditions, enzyme immunoassays may be even more sensitive than radioimmunoassays (1). Enzyme-labeled antigens and antibodies have found increasing use during the past decade, reinforced by improvements in enzyme-labeling methods.
System for quantitative three-dimensional echocardiography of the left ventricle based on a magnetic-field position and orientation sensing system (1998)

Accurate measurement of left-ventricular (LV) volume and function are important to monitor disease progression and assess prognosis in patients with heart disease. Existing methods of three-dimensional (3-D) imaging of the heart using ultrasound have shown the potential of this modality, but each suffers from inherent restrictions which limit its applicability to the full range of clinical situations. We have developed a technique for image acquisition using a magnetic-field system to track the 3-D echocardiographic imaging planes and 3-D image analysis software including the piecewise smooth subdivision method for surface reconstruction. The technique offers several advantages over existing methods of 3-D echocardiography. The results of validation using in vitro LV's show that the technique allows accurate measurement of LV volume and anatomically accurate 3-D reconstruction of LV shape and is, therefore, suitable for analysis of regional as well as global function.
Loss of Response to Anti-TNFs: Definition, Epidemiology, and Management (2016)

Tumor necrosis factor-α (TNFα) antagonists have advanced the management of inflammatory bowel diseases patients leading to an improvement of patient's quality of life with the reduction of number of surgeries and hospitalizations. Despite these advances, many patients do not respond to the induction therapy (primary non-response-PNR) or lose response during the treatment (secondary loss of response-LOR). In this paper we will provide an overview of the definition, epidemiology and risk factors for PNR and LOR, as well as discuss the therapeutic options for managing LOR.
Bacterial Iron Transport: Coordination Properties of Pyoverdin PaA, a Peptidic Siderophore of Pseudomonas aeruginosa (1994)

cited By 113
Structure of Hepatitis B Dane Particle DNA and Nature of the Endogenous DNA Polymerase Reaction (1977)

The circular DNA of hepatitis B Dane particles, which serves as the primer/template for an endogenous DNA polymerase, was analyzed by electrophoresis before and after a polymerase reaction and after digestion by restriction endonuclease or single-strand-specific endonuclease S1. The unreacted molecules extracted from the particles were electrophoretically heterogeneous, and treatment with S1 nuclease produced double-stranded linear DNA ranging in length from 1,700 to 2,800 base pairs (bp). After an endogenous DNA polymerase reaction, two discrete species of DNA molecules were found: a circular form and a linear form 3,200 bp long. The reaction resulted in a population of molecules with an elongated and more homogeneous double-stranded region. These results suggest that the circular molecules in Dane particles have single-stranded regions of varying lengths that are made double stranded during the DNA polymerase reaction. The endogenous DNA polymerase was found to initiate apparently at random in a region spanning more than a third of the molecule. Analysis of restriction endonuclease cleavage fragments of the fully elongated DNA revealed that although the molecules were of a uniform length, they were somewhat heterogeneous in sequence. The sum of the sizes of the 10 major endonuclease Hae III-generated fragments, detected by ethidium bromide, was 3,880 bp. Two additional fragments (B and G) detected by autoradiography after an endogenous DNA polymerase reaction with (32)P-labeled deoxynucleoside triphosphates made the total 4,910 bp.
Palladium-Catalyzed Hydroamination of 1,3-Dienes:  A Colorimetric Assay and Enantioselective Additions (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPalladium-Catalyzed Hydroamination of 1,3-Dienes: A Colorimetric Assay and Enantioselective AdditionsOliver Löber, Motoi Kawatsura, and John F. HartwigView Author Information Department of Chemistry, Yale University P.O. Box 208107, New Haven, Connecticut 06520-8107 Cite this: J. Am. Chem. Soc. 2001, 123, 18, 4366–4367Publication Date (Web):April 13, 2001Publication History Received14 December 2000Published online13 April 2001Published inissue 1 May 2001https://pubs.acs.org/doi/10.1021/ja005881ohttps://doi.org/10.1021/ja005881orapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views6829Altmetric-Citations321LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Catalysts,Chemical reactions,Ligands,Organic reactions Get e-Alerts
Biosynthesis of the antitumor antibiotic pactamycin. A methionine-derived ethyl group and a C7N unit (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiosynthesis of the antitumor antibiotic pactamycin. A methionine-derived ethyl group and a C7N unitDwight D. Weller and Kenneth L. Rinehart Jr.Cite this: J. Am. Chem. Soc. 1978, 100, 21, 6757–6760Publication Date (Print):October 1, 1978Publication History Published online1 May 2002Published inissue 1 October 1978https://pubs.acs.org/doi/10.1021/ja00489a039https://doi.org/10.1021/ja00489a039research-articleACS PublicationsRequest reuse permissionsArticle Views236Altmetric-Citations40LEARN 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
Interaction of bioactive hydrophobic peptides with the human multidrug transporter (1994)

In this report we demonstrate that various biologically active hydrophobic peptide derivatives, e.g., proteinase inhibitors, chemoattractants, ionophores, enkephalins, and immunosuppressants, stimulate a membrane ATPase activity associated with the human multidrug transporter (MDR1). The stimulation of the MDR1-ATPase by these agents does not correlate with their known biochemical or pharmacological activities but rather with their hydrophobicity. The peptides that show high-affinity interaction with the MDR1-ATPase also interfere strongly with fluorescent dye extrusion catalyzed by the multidrug transporter in intact cells and some have been shown to reverse drug resistance in cultured cells. These data suggest that several hydrophobic peptides behave as substrates of the multidrug transporter and may be used to modulate the chemotherapy resistance of tumor cells.
Evaluation of the in vitro antioxidant activity in extracts of Uncaria tomentosa (Willd.) DC. (1997)

Different extracts of U. tomentosa were tested in vitro for their antioxidant activity utilizing tert -butyl-hydroperoxide-initiated chemiluminescence in rat liver homogenates. Methanol fractions of both stem-bark and roots were capable of exerting antioxidant activity by this technique. The presence of different concentrations of bark and root methanol extracts also prevented TBARS production and free radical-mediated DNA-sugar damage. © 1997 John Wiley & Sons, Ltd.
Exploiting hardware performance counters with flow and context sensitive profiling (1997)

A program profile attributes run-time costs to portions of a program's execution. Most profiling systems suffer from two major deficiencies: first, they only apportion simple metrics, such as execution frequency or elapsed time to static, syntactic units, such as procedures or statements; second, they aggressively reduce the volume of information collected and reported, although aggregation can hide striking differences in program behavior.This paper addresses both concerns by exploiting the hardware counters available in most modern processors and by incorporating two concepts from data flow analysis--flow and context sensitivity--to report more context for measurements. This paper extends our previous work on efficient path profiling to flow sensitive profiling, which associates hardware performance metrics with a path through a procedure. In addition, it describes a data structure, the calling context tree, that efficiently captures calling contexts for procedure-level measurements.Our measurements show that the SPEC95 benchmarks execute a small number (3--28) of hot paths that account for 9--98% of their L1 data cache misses. Moreover, these hot paths are concentrated in a few routines, which have complex dynamic behavior.
Kinetic Effects on the Convective Plasma Diffusion and the Heat Transport (1979)

Cross field heat and particle transport due to the thermally excited convective cell mode is investigated both by theoretical work and by particle simulations. It is shown that there is a parameter range where the heat diffusion coefficient D H is considerably less than the particle diffusion coefficient D P . This results from the fact that high energy particles in a velocity distribution diffuse much more slowly than the low energy particles because the fluctuating electric fields are averaged over their finite Larmor radii. The magnetic field scaling of D H / D P is also discussed. The results imply that ions in a thermonuclear reactor should be less affected by turbulence than are electrons as appears to be the case.
Topoisomerase I-DNA Complex Stability Induced by Camptothecins and Its Role in Drug Activity&# (2004)

The mechanism of cytotoxicity of the camptothecin family of antitumor drugs is thought to be the consequence of a collision between moving replication forks and camptothecin-stabilized cleavable DNA-topoisomerase I complexes. One property of camptothecin analogs relevant to their potent antitumor activity is the slow reversal of the cleavable complexes formed with these drugs. The persistence of cleavable complexes with time may be an essential property for increasing the likelihood of a collision between the replication fork and a cleavable complex, giving rise to lethal DNA lesions. In this paper, we examined a number of camptothecin analogs forming cleavable complexes with distinctly different stabilities. Absolute reaction rate analysis was carried out for each derivative. Our results indicate that the stability of the cleavable complex is dominated by the activation entropy (DeltaS++) of the reversal process. We measured the relative lipophilicity of the CPT analogs by reverse-phase HPLC, but the DeltaS++ of complex reversal is not directly related to the lipophilicity of the CPT analog being used. We suggest that solvent ordering around the 7- through 10-position of the CPT ring may be responsible for reversal rate's dependence on DeltaS++. We demonstrate that the cleavable complex stability conferred by each camptothecin analog is directly correlated with the induction of apoptosis and cytotoxicity to tumor cells.
Peripheral signals in the control of satiety and hunger (2003)

A better understanding of these systems and how they relate to body adiposity will prove to have important clinical applications. The available data suggest that interventions directed at multiple targets in the energy homeostasis system may be necessary to achieve and maintain weight loss.