gebhart/patrepeval huggingface dataset:
Virus Maturation Targets the Protein Capsid to Concerted Disassembly and Unfolding (2000)

Many animal viruses undergo post-assembly proteolytic cleavage that is required for infectivity. The role of maturation cleavage on Flock House virus was evaluated by comparing wild type (wt) and cleavage-defective mutant (D75N) Flock House virus virus-like particles. A concerted dissociation and unfolding of the mature wt particle was observed under treatment by urea, whereas the cleavage-defective mutant dissociated to folded subunits as determined by steady-state and dynamic fluorescence spectroscopy, circular dichroism, and nuclear magnetic resonance. The folded D75N alpha subunit could reassemble into capsids, whereas the yield of reassembly from unfolded cleaved wt subunits was very low. Overall, our results demonstrate that the maturation/cleavage process targets the particle for an "off pathway" disassembly, because dissociation is coupled to unfolding. The increased motions in the cleaved capsid, revealed by fluorescence and NMR, and the concerted nature of dissociation/unfolding may be crucial to make the mature particle infectious.
Phenylimidazoles as Potent and Selective Inhibitors of Coagulation Factor XIa with in Vivo Antithrombotic Activity (2014)

Novel inhibitors of FXIa containing an (S)-2-phenyl-1-(4-phenyl-1H-imidazol-2-yl)ethanamine core have been optimized to provide compound 16b, a potent, reversible inhibitor of FXIa (Ki = 0.3 nM) having in vivo antithrombotic efficacy in the rabbit AV-shunt thrombosis model (ID50 = 0.6 mg/kg + 1 mg kg(-1) h(-1)). Initial analog selection was informed by molecular modeling using compounds 11a and 11h overlaid onto the X-ray crystal structure of tetrahydroquinoline 3 complexed to FXIa. Further optimization was achieved by specific modifications derived from careful analysis of the X-ray crystal structure of the FXIa/11h complex. Compound 16b was well tolerated and enabled extensive pharmacologic evaluation of the FXIa mechanism up to the ID90 for thrombus inhibition.
Stable, Highly Efficient and Temperature Resistant Organic Light-Emitting Devices (2007)

Highly efficient small molecule-based organic light-emitting devices (OLED) that use electrically doped charge injection layers are presented. These structures exhibit low power consumption, long lifetime and high stability when operated at ambient temperature. It is also shown that their performances do not change significantly even when devices are stored at 90 °C for 80 days or 110 °C for 24 h. Such OLED structures thus fulfill the most severe requirements for mobile display applications.
Bile Acids Regulate Cardiovascular Function (2011)

Research over the last decade has uncovered roles for bile acids (BAs) that extend beyond their traditional functions in regulating lipid digestion and cholesterol metabolism. BAs are now recognized as signaling molecules that interact with both plasma membrane and nuclear receptors. Emerging evidence indicates that by interacting with these receptors, BAs regulate their own synthesis, glucose and energy homeostasis, and other important physiological events. Herein, we provide a comprehensive review of the actions of BAs on cardiovascular function. In the heart and the systemic circulation, BAs interact with plasma membrane G-protein-coupled receptors, for example, TGR5 and muscarinic receptors, and nuclear receptors, for example, the farnesoid (FXR) and pregnane (PXR) xenobiotic receptors. BA receptors are expressed in cardiovascular tissue, however, the mechanisms underlying BA-mediated regulation of cardiovascular function remain poorly understood. BAs reduce heart rate by regulating channel conductance and calcium dynamics in sino-atrial and ventricular cardiomyocytes and regulate vascular tone via both endothelium-dependent and -independent mechanisms. End-stage liver disease, obstructive jaundice, and intrahepatic cholestasis of pregnancy are prominent conditions in which elevated serum BAs alter vascular dynamics. This review focuses on BAs as newly recognized signaling molecules that modulate cardiovascular function.
Anti–TGF-β1 Antibody Therapy in Patients with Diabetic Nephropathy (2016)

TGF-<i>β</i> has been implicated as a major pathogenic factor in diabetic nephropathy. This randomized, double-blind, phase 2 study assessed whether modulating TGF-<i>β</i>1 activity with a TGF-<i>β</i>1-specific, humanized, neutralizing monoclonal antibody (TGF-<i>β</i>1 mAb) is safe and more effective than placebo in slowing renal function loss in patients with diabetic nephropathy on chronic stable renin-angiotensin system inhibitor treatment. We randomized 416 patients aged ≥25 years with type 1 or type 2 diabetes, a serum creatinine (SCr) level of 1.3-3.3 mg/dl for women and 1.5-3.5 mg/dl for men (or eGFR of 20-60 ml/min per 1.73 m<sup>2</sup>), and a 24-hour urine protein-to-creatinine ratio ≥800 mg/g to TGF-<i>β</i>1 mAb (2-, 10-, or 50-mg monthly subcutaneous dosing for 12 months) or placebo. We assessed a change in SCr from baseline to 12 months as the primary efficacy variable. Although the Data Monitoring Committee did not identify safety issues, we terminated the trial 4 months early for futility on the basis of their recommendation. The placebo group had a mean±SD change in SCr from baseline to end of treatment of 0.33±0.67 mg/dl. Least squares mean percentage change in SCr from baseline to end of treatment did not differ between placebo (14%; 95% confidence interval [95% CI], 9.7% to 18.2%) and TGF-<i>β</i>1 mAb treatments (20% [95% CI, 15.3% to 24.3%], 19% [95% CI, 14.2% to 23.0%], and 19% [95% CI, 14.0% to 23.3%] for 2-, 10-, and 50-mg doses, respectively). Thus, TGF-<i>β</i>1 mAb added to renin-angiotensin system inhibitors did not slow progression of diabetic nephropathy.
The Failing Heart — An Engine Out of Fuel (2007)

Abnormalities of cardiac energy metabolism make an important contribution to chronic heart failure. This review summarizes the main events in cardiac energy metabolism, discusses abnormalities in these metabolic processes in heart failure, and looks to future treatments of heart failure that entail correction of the metabolic defects.
Histone Hyperacetylation Is Associated with Amelioration of Experimental Colitis in Mice (2006)

Inhibitors of histone deacetylases (HDAC) are being studied for their antiproliferative effects in preclinical cancer trials. Recent studies suggest an anti-inflammatory role for this class of compounds. Because inflammatory bowel disease is associated with an increased risk of malignancies, agents with antiproliferative and anti-inflammatory properties would be of therapeutic interest. HDAC inhibitors from various classes were selected and evaluated for their in vitro capacity to suppress cytokine production and to induce apoptosis and histone acetylation. Valproic acid (VPA) and suberyolanilide hydroxamic acid (SAHA) were chosen for further studies in dextran sulfate sodium- and trinitrobenzene sulfonic acid-induced colitis in mice. In vitro, inhibition of HDAC resulted in a dose-dependent suppression of cytokine synthesis and apoptosis induction requiring higher concentrations of HDAC inhibitors for apoptosis induction compared with cytokine inhibition. Oral administration of either VPA or SAHA reduced disease severity in dextran sulfate sodium-induced colitis. The macroscopic and histologic reduction of disease severity was associated with a marked suppression of colonic proinflammatory cytokines. In parallel to the beneficial effect observed, a dose-dependent increase in histone 3 acetylation at the site of inflammation was shown under VPA treatment. Furthermore, SAHA as well as VPA treatment resulted in amelioration of trinitrobenzene sulfonic acid-induced colitis, which was associated with an increase of apoptosis of lamina propria lymphocytes. Inhibitors of HDAC reveal strong protective effects in different models of experimental colitis by inducing apoptosis and suppressing proinflammatory cytokines, thereby representing a promising class of compounds for clinical studies in human inflammatory bowel disease.
Small fiber diameter fibro‐porous meshes: Tissue response sensitivity to fiber spacing (2005)

The purpose of this research was to determine if fiber spacing for small fiber diameter fibro-porous meshes affected tissue response in vivo. Disk-shaped polyurethane meshes, with mean fiber diameters of 7.6 microm and fiber spacing between 6 and 68 microm, were implanted in rat subcutaneous dorsum for 5-week intervals and then prepared for light microscopy and morphological analysis. Results showed that implants with 12- to 68-microm spacing had no histologically apparent fibrous capsule around the perimeter, a result different from that for 6-microm spacing samples that had a capsule around a mean of 34.2% of the perimeter. For the 12- to 68-microm spacing range, a mean of 21.0% of individual fibers within the meshes were encapsulated. Qualitatively, it appeared that larger fibers were encapsulated more frequently than smaller ones. When nodeless or baggy meshes were implanted, cells tended to cluster three or more fibers into groups and then encapsulate each group. Over the 6- to 68-microm spacing range, cell nuclei volume fraction within the meshes increased from the 6- to the 29-microm spacing (p = 0.000) and then decreased from the 29- to the 68-microm spacing (p = 0.015). There was a trend of an increase in local vessel volume fraction with spacing over the 6- to 68-microm range, though the relationship was weak. The results indicate that the reason for the lack of encapsulation of small-fiber fibro-porous meshes is not exclusively a pore boundary explanation, as is proposed for small-pore porous meshes.
[In vitro study of combination rhOPG-Fc and alendronate on inhibition osteoclast]. (2005)

rhOPG-Fc can decrease the number of osteoclasts and inhibit their function. The combination of both rhOPG-Fc and ALN shows the significant inhibition effect on mature osteoclasts.
Development of a Dehalogenase-Based Protein Fusion Tag Capable of Rapid, Selective and Covalent Attachment to Customizable Ligands (2012)

Our fundamental understanding of proteins and their biological significance has been enhanced by genetic fusion tags, as they provide a convenient method for introducing unique properties to proteins so that they can be examinedin isolation. Commonly used tags satisfy many of the requirements for applications relating to the detection and isolation of proteins from complex samples. However, their utility at low concentration becomes compromised if the binding affinity for a detection or capture reagent is not adequate to produce a stable interaction. Here, we describe HaloTag® (HT7), a genetic fusion tag based on a modified haloalkane dehalogenase designed and engineered to overcome the limitation of affinity tags by forming a high affinity, covalent attachment to a binding ligand. HT7 and its ligand have additional desirable features. The tag is relatively small, monomeric, and structurally compatible with fusion partners, while the ligand is specific, chemically simple, and amenable to modular synthetic design. Taken together, the design features and molecular evolution of HT7 have resulted in a superior alternative to common tags for the overexpression, detection, and isolation of target proteins.
The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV‐B light, drought and cold stress responses (2007)

The tolerance responses of plants to many abiotic stresses are conjectured to be controlled by complex gene networks. In the frame of the AtGenExpress project a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray in order to understand these regulatory networks in detail. In contrast to earlier studies, we subjected, side-by-side and in a high-resolution kinetic series, Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols. Here we describe the technical performance of the experiments. We also present a general overview of environmental abiotic stress-induced gene expression patterns and the results of a model bioinformatics analysis of gene expression in response to UV-B light, drought and cold stress. Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses. In addition, there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses. In summary, the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress.
Tumor-selective modification of cellular microenvironment in vivo: effect of glucose infusion on the pH in normal and malignant rat tissues. (1982)

The pH distributions in transplanted neural (TV1A, BT1A) and hepatic (HV1A3) tumors and in brain and kidney of BDIX rats were analyzed as a function of serum glucose concentration (SGC), tumor size, and tissue architecture. Tissue damage during pH measurements in vivo could be minimized by the use of pH microelectrodes with tip diameters of less than or equal to 10 micrometers. In normoglycemic rats, the pH in TV1A tumors was only slightly lower than in brain or kidney. However, at 6 hr after the induction of hyperglycemia by continuous i.v. infusion of glucose, the average pH in TV1A tumors had fallen to 6.7 at an SGC of 27 mM and to 6.1 at an SGC of 50 mM. A similar glucose-mediated pH reduction was observed in BT1A and HV1A3 tumors. No significant increase in tissue acidity occurred in brain and kidney. The pH in tumors had reached its minimum at 2 hr after the onset of high-dose glucose infusion (SGC, 50 mM) and could be maintained at this level in hyperglycemic rats for at least 48 hr. In hyperglycemic hosts, an increased retention of acidic metabolites in the tumor tissue with decreasing vascular density was reflected by a tumor size (age)-dependent pH reduction and a higher degree of intratumoral pH variation. In partially necrotic tumors, pH values as low as 5.2 were recorded. Oral administration of NaHCO3 to tumor-bearing rats had no effect on the average pH in TV1A tumors.
Enrichment of Clinical Study Populations (2010)

Those who conduct clinical trials "enrich" study populations in a variety of ways in order to identify a population of patients in whom a drug effect, if present, is more likely to be demonstrable. The principal ways to do this are as follows: (i) practical enrichment, i.e., generally seeking to reduce noise (variability of measurement) and heterogeneity (by avoiding the enrollment of patients with other diseases and individuals in whom the disease disappears spontaneously), (ii) prognostic enrichment, i.e., finding patients who are likely to have the event of interest when enrolling for risk-reduction studies, and (iii) predictive enrichment, i.e., finding the individuals who are more likely to respond. Enrichment fits well into the growing interest in "individualization" of therapy but creates some tension with another trend, namely, the desire for "real-world studies" with less restrictive entry criteria and other requirements.
A New, Titanium-Mediated Approach to Pyrroles: First Synthesis of Lukianol A and Lamellarin O Dimethyl Ether (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA New, Titanium-Mediated Approach to Pyrroles: First Synthesis of Lukianol A and Lamellarin O Dimethyl EtherAlois Fuerstner, Holger Weintritt, and Achim HuppertsCite this: J. Org. Chem. 1995, 60, 20, 6637–6641Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/jo00125a068https://doi.org/10.1021/jo00125a068research-articleACS PublicationsRequest reuse permissionsArticle Views1257Altmetric-Citations179LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Total synthesis and evaluation of (.+-.)-N-(tert-butoxycarbonyl)-CBI, (.+-.)-CBI-CDPI1, and (.+-.)-CBI-CDPI2: CC-1065 functional agents incorporating the equivalent 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) left-hand subunit (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis and evaluation of (.+-.)-N-(tert-butoxycarbonyl)-CBI, (.+-.)-CBI-CDPI1, and (.+-.)-CBI-CDPI2: CC-1065 functional agents incorporating the equivalent 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) left-hand subunitDale L. Boger, Takayoshi Ishizaki, Ronald J. Wysocki Jr., Stephen A. Munk, Paul A. Kitos, and Oranart SuntornwatCite this: J. Am. Chem. Soc. 1989, 111, 16, 6461–6463Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://pubs.acs.org/doi/10.1021/ja00198a089https://doi.org/10.1021/ja00198a089research-articleACS PublicationsRequest reuse permissionsArticle Views751Altmetric-Citations150LEARN 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 Get e-Alerts
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing (2016)

Abstract Amplicon sequencing of tags such as 16S and ITS ribosomal RNA is a popular method for investigating microbial populations. In such experiments, sequence errors caused by PCR and sequencing are difficult to distinguish from true biological variation. I describe UNOISE2, an updated version of the UNOISE algorithm for denoising (error-correcting) Illumina amplicon reads and show that it has comparable or better accuracy than DADA2.
Constitutive Bcl-2 expression throughout the hematopoietic compartment affects multiple lineages and enhances progenitor cell survival (1999)

Bcl-2, which can both reduce apoptosis and retard cell cycle entry, is thought to have important roles in hematopoiesis. To evaluate the impact of its ubiquitous overexpression within this system, we targeted expression of the human bcl-2 gene in mice by using the promoter of the vav gene, which is active throughout this compartment but rarely outside it. The vav-bcl-2 transgene was expressed in essentially all nucleated cells of hematopoietic tissues but not notably in nonhematopoietic tissues. Presumably because of enhanced cell survival, the mice displayed increases in myeloid cells as well as a marked elevation in B and T lymphocytes. The spleen was enlarged and the lymphoid follicles expanded. Although total thymic cellularity was normal, T cell development was altered: cells at the very immature and most mature stages were increased, whereas those at the intermediate stage were decreased. Unexpectedly, blood platelets were reduced by half, suggesting that their production from megakaryocytes is regulated by the Bcl-2 family. Colony formation by myeloid progenitor cells in vitro remained cytokine dependent, and the frequency of most progenitor and preprogenitor cells was normal. Macrophage progenitors were less frequent and yielded smaller colonies, however, perhaps reflecting inhibitory effects of Bcl-2 on cell cycling in specific lineages. After irradiation or factor deprivation, Bcl-2 markedly enhanced clonogenic survival of all tested progenitor and preprogenitor cells. Thus, Bcl-2 has multiple effects on the hematopoietic system. These mice should help to further clarify the role of apoptosis in the development and homeostasis of this compartment.
Electronic Chronicles: Empowering Individuals, Groups, and Organizations (2005)

Continuing strides in processing, storage, sensing, and networking technologies are enabling people to capture their activities and experiences as greater volumes of ever-richer media. A big emerging challenge today is the organization, retrieval, and exploitation of such multimedia data surrounding the activities of individuals or enterprises. The field of multimedia electronic chronicles deals with the unified contextual organization, presentation, and analysis of temporal streams of multimedia data captured by individuals, groups, or organizations. The value of electronic chronicles is in converting activity and experience from the past into actionable intelligence in the present. Such multimedia electronic chronicles, with their associated techniques for search and navigation, analysis and reasoning, and prediction and alerting, will have enormous impact on various spheres of life spanning enhancement of personal life, business productivity, entertainment, and government operations. This paper, which serves as a companion to a keynote talk by the first author at ICME 2005, explains the notion of electronic chronicles and outlines the research challenges in this area