gebhart/patrepeval huggingface dataset:
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline (2019)

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.
A chromogenic substrate culture plate for early identification of Vibrio vulnificus and isolation of other marine Vibrios. (2007)

Vibrio vulnificus infection can result in necrotizing fasciitis and sepsis, which have short latentcy periods and high mortality rates. Thus, an easy and quick detection method is needed to improve the outcome. To distinguish V. vulnificus from other pathogens that cause necrotizing fasciitis, we developed a selective isolation culture agar plate (Chromochecker Vibrio Agar-1; CVA-1) for use in environmental monitoring and in the clinical setting. One hundred four strains of V. vulnificus, already identified biochemically, showed typical colony form and color when grown on CVA-1. Thirty-six of 51 marine bacteria samples suspected to be V. vulnificus on CVA-1 were subsequently identified as V. vulnificus by a biochemical identification system. Of 8 bacteria known to cause necrotizing fasciitis, only V. vulnificus grew on CVA-1. In addition, growth on CVA-1 allowed ready differentiation of Vibrio species. CVA-1 can be used to distinguish pathogenic Vibrios according to colony form and chromatic differences.
Dramatically enhanced polarization in (001), (101), and (111) BiFeO3 thin films due to epitiaxial-induced transitions (2004)

Dramatically enhanced polarization has been found for (001), (101), and (111) films, relative to that of BiFeO3 crystals. The easy axis of spontaneous polarization lies close to (111), for the various oriented films. BiFeO3 films grown on (111) have a rhombohedral structure, identical to that of single crystals; whereas films grown on (101) or (001) are monoclinically distorted from the rhombohedral structure, due to the epitaxial constraint.
Breast cancer-induced angiogenesis: multiple mechanisms and the role of the microenvironment (2003)

Growth and progression of breast cancers are accompanied by increased neovascularization (angiogenesis). A variety of factors, including hypoxia and genetic changes in the tumor cells, contribute to increased production of angiogenic factors. Furthermore, cells within the activated tumor stroma also contribute to the increase in production of vascular endothelial growth factor and other angiogenic factors, including basic fibroblast growth factor and platelet-derived growth factor. The contribution of the microenvironment to tumor-induced angiogenesis is underscored by findings that breast tumors implanted into different tissue sites show marked differences in the extent and nature of the angiogenic response. These findings have important implications for designing anti-angiogenic therapies.
Synthesis and characterization of a water-soluble poly(p-phenylenevinylene) derivative (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of a water-soluble poly(p-phenylenevinylene) derivativeSongqing Shi and Fred WudlCite this: Macromolecules 1990, 23, 8, 2119–2124Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ma00210a004https://doi.org/10.1021/ma00210a004research-articleACS PublicationsRequest reuse permissionsArticle Views712Altmetric-Citations141LEARN 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
Ketorolac Versus DHE and Metoclopramide in the Treatment of Migraine Headaches (1991)

Ketorolac IM was compared to DHE and metoclopramide IV in migraine patients whose regular abortive medication had failed and who presented to a headache clinic for acute treatment. Pain scale ratings and ratings of ability to function were recorded before and after injection. Ketorolac provided moderate relief in headache in six of nine patients compared to eight of nine given DHE and metoclopramide. The average improvement in patients receiving DHE and metoclopramide was greater in pain (p = .031) and disability scores (p = .057), than in those patients given ketorolac.
Seamless texture mapping algorithm for image-based three-dimensional reconstruction (2016)

Texture information plays an important role in rendering true objects, especially with the wide application of image-based three-dimensional (3-D) reconstruction and 3-D laser scanning. This paper proposes a seamless texture mapping algorithm to achieve a high-quality visual effect for 3-D reconstruction. At first, a series of image sets is produced by analyzing the visibility of triangular facets, the image sets are clustered and segmented into a number of optimal reference texture patches. Second, the generated texture patches are sequenced to create a rough texture map, then a weighting process is adopted to reduce the color discrepancies between adjacent patches. Finally, a multiresolution decomposition and fusion technique is used to generate the transition section and eliminate the boundary effect. Experiments show that the proposed algorithm is effective and practical for obtaining high-quality 3-D texture mapping for 3-D reconstruction. Compared with traditional methods, it maintains the texture clarity while eliminating the color seams, in addition, it also supports 3-D texture mapping for big data application.
Salvaguardias y antidumping en la liberalizacion comercial de America Latina : combatiendo el fuego con fuego (2005)

This book is a report on success-success in trade liberalization and in the removal of trade barriers so as to integrate Latin American economies into the international economy. More particularly, this book is about how several Latin American governments created and managed safeguards and antidumping mechanisms as part of this liberalization. The core of this book is a set of studies describing how seven Latin American countries-Argentina, Brazil, Chile, Colombia, Costa Rica, Mexico, and Peru-have used these trade instruments. Each country study was conducted by analysts from that country. Many of the analysts were high government officials during their country's liberalization, so they have hands-on experience with the construction and the management of these instruments.
Migration Phenotype of Brain-Cancer Cells Predicts Patient Outcomes (2016)

Glioblastoma multiforme is a heterogeneous and infiltrative cancer with dismal prognosis. Studying the migratory behavior of tumor-derived cell populations can be informative, but it places a high premium on the precision of in vitro methods and the relevance of in vivo conditions. In particular, the analysis of 2D cell migration may not reflect invasion into 3D extracellular matrices in vivo. Here, we describe a method that allows time-resolved studies of primary cell migration with single-cell resolution on a fibrillar surface that closely mimics in vivo 3D migration. We used this platform to screen 14 patient-derived glioblastoma samples. We observed that the migratory phenotype of a subset of cells in response to platelet-derived growth factor was highly predictive of tumor location and recurrence in the clinic. Therefore, migratory phenotypic classifiers analyzed at the single-cell level in a patient-specific way can provide high diagnostic and prognostic value for invasive cancers.
Opiate (Enkephalin) Receptors of Neuroblastoma Cells: Occurrence in Clusters on the Cell Surface (1979)

A bioactive, fluorescent derivative of enkephalin, Tyr-D-Ala-Gly-Phe-Leu-Lys-rhodamine, was used to determine the distribution of opiate receptors in living neuroblastoma cells. The receptors appeared in clusters on the cell surface, and no internalization was detected. No specific fluorescence or clusters were observed in the presence of [D-Ala2, Leu5]enkephalin or at 4 degrees C, and the clusters were much reduced under ionic conditions (that is, with 100 millimolars sodium) that specifically decrease the binding of opiate agonists.
Synthesis of Jasmine Ketolactone (1984)

The synthesis of jasmine ketolactone 3, a minor component of Italian jasmine oil, via the intramolecular Michael reaction is described.
Image clustering using semantic tolerance relation model (2007)

Because the nature of the concepts regarding images in many domains are imprecise and can be overlapped, and also there is the gap between the ability of machine computation and the high level concepts of human perception, in this paper, we define the tolerance degree between semantic categories, and present a method of semantic-based image presentation using the tolerance relation model. We apply the proposed method to construct a tolerance relation-based semantic clustering algorithm of images. The decision rules, for the semantic categorization based on the concepts of nature vs. man-made, human vs. non-human, and the both of them, are given. The performance evaluations of the proposed methods are executed.
(Invited) Polyacetylene: A Typical Semiconducting and Metallic Polymer (1983)

This paper presents an introductory review of polyacetylene, a typical semiconducting and metallic organic polymer. The electrical conductivity of polyacetylene can be tailored by appropriate “chemical and/or electrochemical doping” with electron accepting or electon donating reagents, spanning the range of insulators (10 -12 S/cm) and metals (10 3 S/cm). Some of the potential applications of the doped polyacetylene are described.
Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition (2020)

Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.
Water–fat separation and parameter mapping in cardiac MRI via deep learning with a convolutional neural network (2019)

1 Technical Efficacy Stage: 1 J. Magn. Reson. Imaging 2019;50:655-665.
Colloidal Dispersion Gels CDG in Dina Cretáceos Field: From Pilot Design to Field Implementation and Performance (2013)

Abstract Dina Cretaceous Field is located in the Upper Magdalena Valley (UMV) Basin, Colombia. Dina Field operated by ECOPETROL S.A. (discovered, 1969) started peripheral water in 1985. Based on high water cuts (96%) and recovery factors of 32%, comprehensive enhanced oil recovery (EOR), screening evaluation began late 2009, identified Colloidal Dispersion Gel (CDG) as an optimum EOR method for the field. This paper summarizes Dina CDG project from the laboratory to the field evaluation. Laboratory studies include basic fluid/fluid evaluation, static adsorption, CDG formulations, slimtube, and coreflood tests. Pilot area selection was based on a comprehensive reservoir and injection/production data analysis, water management, well integrity, among other factors. Pilot design was based on detailed numerical simulations using sector and full field models. CDG pilot design also considered water handling limitations and potential injectivity constraints due to the narrow margin of maximum injection and reservoir pressures, combined with low reservoir permeability (50 to 200 mD). Peripheral CDG pilot included one injector and three producers. CDG injection began in June 2011 and as of September 2012, approximately 437,000 bbl of CDG have been injected (5% of pilot PV). CDG injection strategy considered a fix polymer concentration of 400 ppm and a variable polymer/crosslinker ratio ranging from 40:1 to 80:1; to control maximum injection pressure. Field results showed an important increase in oil recoveries (oil productivity up to 300%) and reduction of water cut decrease (10%). After 16 months, no polymer had been produced in offset producers. Main operating challenges experienced during the pilot project included; the improvement in water quality and its impact on CDG injectivity which will also be described. This study provides guidance to successfully design, implement, and evaluate CDG pilot projects and other potential chemical EOR technologies in waterflooded reservoirs. Lessons learned during pilot testing contributed to defining pilot expansion strategies supported by an integrated decision-risk management approach.
Over 20% of patients with chronic lymphocytic leukemia carry stereotyped receptors: pathogenetic implications and clinical correlations (2006)

The chronic lymphocytic leukemia (CLL) immunoglobulin repertoire is biased and characterized by the existence of subsets of cases with closely homologous ("stereotyped") complementarity-determining region 3 (CDR3) sequences. In the present series, 201 (21.9%) of 916 patients with CLL expressed IGHV genes that belonged to 1 of 48 different subsets of sequences with stereotyped heavy chain (H) CDR3. Twenty-six subsets comprised 3 or more sequences and were considered "confirmed." The remaining subsets comprised pairs of sequences and were considered "potential"; public database CLL sequences were found to be members of 9 of 22 "potential" subsets, thereby allowing us to consider them also "confirmed." The chance of belonging to a subset exceeded 35% for unmutated or selected IGHV genes (eg, IGHV1-69/3-21/4-39). Comparison to non-CLL public database sequences showed that HCDR3 restriction is "CLL-related." CLL cases with selected stereotyped immunoglobulins (IGs) were also found to share unique biologic and clinical features. In particular, cases expressing stereotyped IGHV4-39/IGKV1-39-1D-39 and IGHV4-34/IGKV2-30 were always IgG-switched. In addition, IGHV4-34/IGKV2-30 patients were younger and followed a strikingly indolent disease, contrasting other patients (eg, those expressing IGHV3-21/IGLV3-21) who experienced an aggressive disease, regardless of IGHV mutations. These findings suggest that a particular antigen-binding site can be critical in determining the clinical features and outcome for at least some CLL patients.
Outer-Ring Stereochemical Modulation of Cytotoxicity in Cephalostatins<sup>1</sup> (1999)

[structure: see text] 20- and 25'-epimers of cephalostatin 7, prepared by directed unsymmetrical pyrazine synthesis, address outer-ring topographical and stability questions and intimate an oxacarbenium ion rationale for the role in bioactivity of the spiroketal (E/F, E'/F') rings of this class of antitumor agents.
Emerging strategies for the identification of protein–metabolite interactions (2019)

Interactions between biological molecules enable life. The significance of a cell-wide understanding of molecular complexes is thus obvious. In comparison to protein-protein interactions, protein-metabolite interactions remain under-studied. However, this has been gradually changing due to technological progress. Here, we focus on the interactions between ligands and receptors, the triggers of signalling events. While the number of small molecules with proven or proposed signalling roles is rapidly growing, most of their protein receptors remain unknown. Conversely, there are numerous signalling proteins with predicted ligand-binding domains for which the identities of the metabolite counterparts remain elusive. Here, we discuss the current biochemical strategies for identifying protein-metabolite interactions and how they can be used to characterize known metabolite regulators and identify novel ones.
Angiotensin converting enzyme inhibitors and cardiovascular remodelling (1994)

Regional alterations in left ventricular function are generally present in patients who sustain an acute myocardial infarction. Segmental wall motion abnormalities in left ventricular systolic function can be identified in the hyperacute period and generally persist in patients with myocardial infarction. Through the process of infarct expansion, the infarcted territory may thin and lengthen in the short term following a myocardial infarction. Some infarct survivors are also prone to further progressive alterations in the shape and size of the left ventricle, a process that has been termed "postinfarction ventricular remodelling". Although a component of left ventricular remodelling appears to represent an adaptive process serving to preserve stroke volume and cardiac output following myocardial injury, the enlargement process may have undesirable long term effects on global left ventricular function and on clinical prognosis. Fortunately, recent experimental and clinical evidence shows that ventricular remodelling and its deleterious consequences may be preventable.
Block copolymers of L-Lactide, D-lactide and E-caprolactone (1991)

The synthesis of poly-L-lactide, PLLA, prepared by ring-opening polymerization of L-lactide using aluminum isopropoxide as an initiator proceeds with a living character. This allowed us to synthesize copolymers composed of L- and D-lactide blocks. In a similar way block copolymers were synthesized using ε-caprolactone as a first and L-lactide as a second monomer.
Performance Comparison of Gateway Discovery Algorithms in Ad Hoc Networks with Mobile Nodes (2006)

Abstract — The connection of ad-hoc networks to the Internet is typically established via gateways. To start an Internet con-nection, gateways have to be discovered by the mobile nodes within the ad-hoc cluster. This paper presents a new gateway discovery algorithm based on HELLO messages of the AODV protocol and compares the performance of the new algorithm with standard proactive and reactive algorithms. NS-2 simulator is used to investigate the algorithms on the basis of the discovery time and the handover delay. Our results show good performance of the new HELLO message based algorithm in both terms. I.
Stability of miRNA in Human Urine Supports its Biomarker Potential (2013)

Aim: miRNAs are showing utility as biomarkers in urologic disease, however, a rigorous evaluation of their stability in urine is lacking. Here, we evaluate the stability of miRNAs in urine under clinically relevant storage procedures. Materials & methods: Eight healthy individuals provided clean catch urine samples that were stored at room temperature or at 4°C for 5 days, or subjected to ten freeze–thaw cycles at -80°C. For each condition, two miRNAs, miR-16 and miR-21, were quantitated by quantitative real-time PCR. Results: All conditions demonstrated a surprising degree of stability of miRNAs in the urine: by the end of ten freeze–thaw cycles, 23–37% of the initial amount remained; over the 5-day period of storage at room temperature, 35% of the initial amount remained; and at 4°C, 42–56% of the initial amount remained. Both miRNAs also showed degradation at approximately the same rate. Conclusion: miRNAs are relatively stable in urine under a variety of storage conditions, which supports their utility as urinary biomarkers.
Syntax and discontinuity based error concealment for compressed video in a packet environment (2002)

This paper addresses the problem of error resilience of compressed video. The errors considered are lost packets which are generally caused by network congestion in a packet switched network. We propose distributing the bits from a single slice among several packets so that the loss of a packet will result in only one or a few errors in any one slice. The loss of the packet is expected to be detected by the depacketizer and the bits thus lost are treated as erasures. We proceed to generate candidates for corrupted slices and test their syntactical integrity and their spatial smoothness. The smoothest candidate for a slice which is syntatically correct is chosen as the corrected slice. The scheme need not add overhead to the bitstream, bits will insert delay. A parameter of our scheme is the number of bits from a single slice inserted into one packet (M). Results of delay simulations over the parameter M are given. Complexity is also simulated over the parameter M. The improvement in performance objectively and subjectively is shown.
Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria (2012)

These observations suggest complex evolutionary dynamics and still unexplored interactions to achieve copper homeostasis, challenging some of the molecular transport mechanism proposed for these systems.