gebhart/patrepeval huggingface dataset:
Identification, Cloning, Expression, and Characterization of the Extracellular Acarbose-Modifying Glycosyltransferase, AcbD, fromActinoplanessp. Strain SE50 (2001)

An extracellular enzyme activity in the culture supernatant of the acarbose producer Actinoplanes sp. strain SE50 catalyzes the transfer of the acarviosyl moiety of acarbose to malto-oligosaccharides. This acarviosyl transferase (ATase) is encoded by a gene, acbD, in the putative biosynthetic gene cluster for the alpha-glucosidase inhibitor acarbose. The acbD gene was cloned and heterologously produced in Streptomyces lividans TK23. The recombinant protein was analyzed by enzyme assays. The AcbD protein (724 amino acids) displays all of the features of extracellular alpha-glucosidases and/or transglycosylases of the alpha-amylase family and exhibits the highest similarities to several cyclodextrin glucanotransferases (CGTases). However, AcbD had neither alpha-amylase nor CGTase activity. The AcbD protein was purified to homogeneity, and it was identified by partial protein sequencing of tryptic peptides. AcbD had an apparent molecular mass of 76 kDa and an isoelectric point of 5.0 and required Ca(2+) ions for activity. The enzyme displayed maximal activity at 30 degrees C and between pH 6.2 and 6.9. The K(m) values of the ATase for acarbose (donor substrate) and maltose (acceptor substrate) are 0.65 and 0.96 mM, respectively. A wide range of additional donor and acceptor substrates were determined for the enzyme. Acceptors revealed a structural requirement for glucose-analogous structures conserving only the overall stereochemistry, except for the anomeric C atom, and the hydroxyl groups at positions 2, 3, and 4 of D-glucose. We discuss here the function of the enzyme in the extracellular formation of the series of acarbose-homologous compounds produced by Actinoplanes sp. strain SE50.
Antiretroviral Treatment for Adult HIV Infection in 2002 (2002)

Because of increased awareness of the activity and toxicity of current drugs, the threshold for initiation of therapy has shifted to a later time in the course of HIV disease. However, the optimal time to initiate therapy remains imprecisely defined. Availability of new drugs has broadened options for therapy initiation and management of treatment failure, which remains a difficult challenge.
Mirna-Based Therapies: Strategies and Delivery Platforms for Oligonucleotide and Non-Oligonucleotide Agents (2014)

The discovery of miRNAs as important regulatory agents for gene expression has expanded the therapeutic opportunities for oligonucleotides. In contrast to siRNA, miRNA-targeted therapy is able to influence not only a single gene, but entire cellular pathways or processes. It is possible to supplement downregulated or non-functional miRNAs by synthetic oligonucleotides, as well as alleviating effects caused by overexpression of malignant miRNAs through artificial antagonists, either oligonucleotides or small molecules. Chemical oligonucleotide modifications together with an efficient delivery system seem to be mandatory for successful therapeutic application. While miRNA-based therapy benefits from the decades of research spent on other therapeutic oligonucleotides, there are some specific challenges associated with miRNA therapy, mainly caused by the short target sequence. The current status and recent progress of miRNA-targeted therapeutics is described and future challenges and potential applications in treatment of cancer and viral infections are discussed.
United States life tables, 1997. (1999)

The life tables in this report are current life tables for the United States based on age-specific death rates in 1997. Beginning with 1997 mortality data, complete U.S. life tables were constructed using a new methodology that replaces the abridged life table methodology used previously. The methodology is similar to that used in the decennial life tables. Also, life expectancy and other life table values are shown for ages 85 to 100 years for the first time as part of the annual U.S. life tables. Data used to prepare these life tables are 1997 final mortality statistics; July 1, 1997, population estimates; and data from the Medicare program. Presented are complete life tables by age, race, and sex. In 1997 the overall expectation of life at birth was 76.5 years, an increase of 0.4 years compared with life expectancy in 1996. Life expectancy increased from 1996 to 1997 for each of the four race-sex groups for which life expectancy is reported. Life expectancy increased for black males by 1.1 year (from 66.1 to 67.2), for black females by 0.5 year (from 74.2 to 74.7), for white males by 0.4 year (from 73.9 to 74.3), and for white females by 0.2 year (from 79.7 to 79.9).
Comparison of two density gradient centrifugation systems for the enrichment of disseminated tumor cells in blood (2002)

OncoQuick significantly reduced the co-enriched number of MNCs, with a high tumor cell recovery rate. Processing blood from tumor patients with OncoQuick increased the chance of detecting circulating tumor cells.
Expression of a virus-derived cytokine, KSHV vIL-6, in HIV-seronegative Castleman's disease. (1997)

Castleman's disease is a rare B cell lymphoproliferative disorder related to excess interleukin-6 (IL-6)-like activity. Kaposi's sarcoma-associated herpesvirus (KSHV or HHV8), which encodes a functional cytokine (vIL-6), has been found in some patients with Castleman's disease. Lymph nodes from 14 HIV-seronegative Castleman's disease patients were compared to hyperplastic lymph nodes from 25 HIV-seronegative patients as well as Kaposi's sarcoma lesions from 48 patients for KSHV infection and vIL-6, human IL-6, and Epstein-Barr virus EBER expression. While all Kaposi's sarcoma tissues examined were polymerase chain reaction-positive and all control lymph nodes were polymerase chain reaction-negative for KSHV, none had detectable vIL-6 expression. Six of 14 (43%) Castleman's tissues were positive for KSHV by polymerase chain reaction and all 6 had evidence of vIL-6 expression by immunohistochemistry. vIL-6-positive Castleman's disease patients generally had the multicentric plasma cell variant form of the disease and had a rapidly fatal clinical course frequently associated with autoimmune hemolytic anemia and gammopathy. In contrast, 7 (88%) of the 8 vIL-6-negative Castleman's disease patients had localized disease and have remained disease-free after therapy. KSHV vIL-6 expression appears to be limited to hematopoietic cells and is not present in Kaposi's sarcoma spindle cells. These data suggest that Castleman's disease is a syndrome of multiple etiologies involving aberrant IL-6 activity from either endogenous or viral sources.
Histologic evaluation of an Nd:YAG laser-assisted new attachment procedure in humans. (2007)

This report presents histologic results in humans following a laser-assisted new attachment procedure (LANAP) for the treatment of periodontal pockets. Six pairs of single-rooted teeth with moderate to advanced chronic periodontitis associated with subgingival calculus deposits were treated. A bur notch was placed within the pocket at the clinically and radiographically measured apical extent of calculus. All teeth were scaled and root planed with ultrasonic and hand scalers. One of each pair of teeth received treatment of the inner pocket wall with a free-running pulsed neodymium:yttrium-aluminum-garnet (Nd:YAG) laser to remove the pocket epithelium, and the test pockets were lased a second time to seal the pocket. After 3 months, all treated teeth were removed en bloc for histologic processing. LANAP-treated teeth exhibited greater probing depth reductions and clinical probing attachment level gains than the control teeth. All LANAP-treated specimens showed new cementum and new connective tissue attachment in and occasionally coronal to the notch, whereas five of the six control teeth had a long junctional epithelium with no evidence of new attachment or regeneration. There was no evidence of any adverse histologic changes around the LANAP specimens. These cases support the concept that LANAP can be associated with cementum-mediated new connective tissue attachment and apparent periodontal regeneration of diseased root surfaces in humans.
Building high-level features using large scale unsupervised learning (2012)

We consider the problem of building high-level, class-specific feature detectors from only unlabeled data. For example, is it possible to learn a face detector using only unlabeled images using unlabeled images? To answer this, we train a 9-layered locally connected sparse autoencoder with pooling and local contrast normalization on a large dataset of images (the model has 1 billion connections, the dataset has 10 million 200×200 pixel images downloaded from the Internet). We train this network using model parallelism and asynchronous SGD on a cluster with 1,000 machines (16,000 cores) for three days. Contrary to what appears to be a widely-held intuition, our experimental results reveal that it is possible to train a face detector without having to label images as containing a face or not. Control experiments show that this feature detector is robust not only to translation but also to scaling and out-of-plane rotation. We also find that the same network is sensitive to other high-level concepts such as cat faces and human bodies. Starting with these learned features, we trained our network to obtain 15.8% accuracy in recognizing 20,000 object categories from ImageNet, a leap of 70% relative improvement over the previous state-of-the-art.
In vitro activity of N-formimidoyl thienamycin (MK0787) (1980)

The in vitro activity of N-formimidoyl thienamycin (MK0787), a stable congener of thienamycin, was determined against 200 species of aerobic and 84 species of anaerobic bacteria. The compound was highly active against resistant gram-negative bacilli, penicillin-resistant Staphylococcus aureus, enterococci, and anaerobic bacteria. The new derivative of thienamycin was more active than the parent compound, probably reflecting the stability of the analog.
Remarkably Active Non-Metallocene Ethylene Polymerization Catalysts (1999)

The bis(tri-tert-butylphosphinimide) complexes (t-Bu3PN)2TiCl2 (1) and (t-Bu3PN)2TiMe2 (2) were prepared and characterized crystallographically. Stoichiometric reactions of 2 with PhNMe2H[B(C6F5)4] in the presence of PMe3 afforded [(t-Bu3PN)2TiMe(PMe3)][B(C6F5)4] (3), while reaction of 2 with B(C6F5)3 affords (t-Bu3PN)2TiMe(μ-Me)B(C6F5)3 (4). Under laboratory conditions these compounds are effective ethylene polymerization catalysts. Under commercially relevant solution polymerization conditions, these catalysts are exceptionally active. Complex 2, when activated with Ph3C[B(C6F5)4], produces high molecular weight polyethylene with a narrow polydispersity at a rate approximately 4 times faster than the constrained geometry catalyst ((C5Me4SiMe2N-t-Bu)TiX2). As such, these catalysts represent the first non-cyclopentadienyl, single-site catalysts competitive with derivatives of metallocenes under commercially relevant polymerization conditions.
The ENACT study: a pan-European survey of acute coronary syndromes (2000)

The ENACT study provides robust data, for the first time, on the relative frequency of unstable angina and acute myocardial infarction across Europe. It provides insight into differences in management across Europe and a reference benchmark of current treatment.
Insulin receptor is phosphorylated in response to treatment of HepG2 cells with insulin-like growth factor I (1990)

1. Binding of insulin and insulin-like growth factor I (IGF-I) to HepG2 cells was analysed with regard to competition by both insulin and IGF-I. At concentrations of insulin that caused maximal phosphorylation of the insulin receptor, virtually no displacement of IGF-I binding was observed. Similarly, at concentrations of IGF-I that caused maximal phosphorylation of the IGF-I receptor, no displacement of insulin binding was observed. 2. When the phosphorylation of both receptors was examined individually by using specific monoclonal antibodies to immunoprecipitate the receptors, phosphorylation of the insulin receptor was found to increase on both serine and tyrosine residues in cells treated with 100 ng of IGF-I/ml. In contrast, no increased phosphorylation of IGF-I receptor was observed in cells treated with 100 ng of insulin/ml. 3. The increase in phosphorylation of insulin receptor in response to IGF-I correlated with the dose-response of IGF-I-stimulated phosphorylation of the IGF-I receptor. 4. The IGF-I-stimulated phosphorylation of the insulin receptor could be blocked by preincubation with a monoclonal antibody that blocks IGF-I binding to the IGF-I receptor.
DNA repair and neurological disease: From molecular understanding to the development of diagnostics and model organisms (2019)

In both replicating and non-replicating cells, the maintenance of genomic stability is of utmost importance. Dividing cells can repair DNA damage during cell division, tolerate the damage by employing potentially mutagenic DNA polymerases or die via apoptosis. However, the options for accurate DNA repair are more limited in non-replicating neuronal cells. If DNA damage is left unresolved, neuronal cells die causing neurodegenerative disorders. A number of pathogenic variants of DNA repair proteins have been linked to multiple neurological diseases. The current challenge is to harness our knowledge of fundamental properties of DNA repair to improve diagnosis, prognosis and treatment of such debilitating disorders. In this perspective, we will focus on recent efforts in identifying novel DNA repair biomarkers for the diagnosis of neurological disorders and their use in monitoring the patient response to therapy. These efforts are greatly facilitated by the development of model organisms such as zebrafish, which will also be summarised.
Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria (2005)

Gram-positive bacteria with a high G+C content are currently recognized as a distinct phylum, Actinobacteria, on the basis of their branching in 16S rRNA trees. Except for an insert in the 23S rRNA, there are no unique biochemical or molecular characteristics known at present that can distinguish this group from all other bacteria. In this work, three conserved indels (i.e. inserts or deletions) are described in three widely distributed proteins that are distinctive characteristics of the Actinobacteria and are not found in any other groups of bacteria. The identified signatures are a 2 aa deletion in cytochrome-c oxidase subunit 1 (Cox1), a 4 aa insert in CTP synthetase and a 5 aa insert in glutamyl-tRNA synthetase (GluRS). Additionally, the actinobacterial specificity of the large insert in the 23S rRNA was also tested. Using primers designed for conserved regions flanking these signatures, fragments of most of these genes were amplified from 23 actinobacterial species, covering many different families and orders, for which no sequence information was previously available. All the 61 sequenced fragments, except two in GluRS, were found to contain the indicated signatures. The presence of these signatures in various species from 20 families within this phylum provides evidence that they are likely distinctive characteristics of the entire phylum, which were introduced in a common ancestor of this group. The absence of all four of these signatures in Symbiobacterium thermophilum suggests that this species, which is distantly related to other actinobacteria in 16S rRNA and CTP synthetase trees, may not be a part of the phylum Actinobacteria. The identified signatures provide novel molecular means for defining and circumscribing the phylum Actinobacteria. Functional studies on them should prove helpful in understanding novel biochemical and physiological characteristics of this group of bacteria.
MR-Guided Focused Ultrasound Surgery (1992)

Magnetic resonance guided focused ultrasound surgery provides a minimally invasive controlled method for selectively destroying deep-lying tissue. A thermal analysis of focused ultrasound provides an estimate of the time-dependent temperature distribution and thermal dose required for ultrasound surgery. The temperature distribution is estimated by accumulating heat sources, considering the effects of thermal conductivity, heat content, and perfusion. In this study, both gel phantoms and excised in vitro bovine muscle specimens were imaged in a 1.5 T MR system while heated with a 5 cm diameter, 10 cm focal length, 1.1 MHz transducer. During sonication, the thermal effects were observed with T1-weighted pulse sequences. Below a critical temperature, the heat zone appeared as a dark spot that moved with the focal spot. Above a critical thermal dose, the in vitro tissue was irreversibly altered and the focal lesion was observed on both the MR image and the specimen slice.
The Covalent Binding Reaction of Complement Component C3 (1998)

The covalent binding of C3 to target molecules on the surfaces of pathogens is crucial in most complement-mediated activities. When C3 is activated, the acyl group is transferred from the sulfhydryl of the internal thioester to the hydroxyl group of the acceptor molecule; consequently, C3 is bound to the acceptor surface by an ester bond. It has been determined that the binding reaction of the B isotype of human C4 uses a two-step mechanism. Upon activation, a His residue first attacks the internal thioester to form an acyl-imidazole bond. The freed thiolate anion of the Cys residue of the thioester then acts as a base to catalyze the transfer of the acyl group from the imidazole to the hydroxyl group of the acceptor molecule. In this article, we present results which indicate that this two-step reaction mechanism also occurs in C3.
Surfactant Proteins in Innate Host Defense of the Lung (2005)

Surfactant proteins A and D (SP-A and SP-D) are members of the collectin family of host defense proteins that are expressed in epithelial cells lining the lung. SP-A and SP-D interact with surfactant lipids in complex ways to determine the structure of tubular myelin, and the ratio of surfactant subfractions that, in turn, influences surfactant uptake and metabolism, respectively. SP-A and SP-D play critical roles in host defense of the lung against diverse viral, fungal, and bacterial pathogens. The collectins bind to the surfaces of microbes via carbohydrate-dependent interaction, aggregating, opsonizing, and enhancing clearance of the organisms by alveolar macrophages in the lung. Pulmonary surfactant proteins A and D play dual roles in pulmonary homeostasis, determining the structure of alveolar lipids and mediating the innate host defense system of the lung.
Platelet Consumption by Arterial Prostheses (1977)

The thrombogenic mechanism of arterial grafts has been studied by determining the relative utilization of platelets, fibrinogen and plasminogen by human arterial prostheses, and by direct examination of arterial grafts in a baboon model. Forty-one survival and turnover measurements of (51)Crplatelets, (131)I-fibrinogen and (125)I-plasminogen in ten patients with aortofemoral knitted Dacron prostheses demonstrated platelet consumption after graft placement (platelet survival 4.2 days +/- 0.5 and turnover 68,000 plat/ul/day +/-10,000 compared with 8.2 days +/- 0.3 and 35,000 plat/ul/day +/- 5,000 respectively for control subjects with stable vascular disease, p < 0.01). In vitro platelet function test results were normal. Platelet consumption was interrupted by dipyridamole or a combination of dipyridamole and acetylsalicylic acid, and platelet survival normalized spontaneously during nine months postoperatively. No significantly increased consumption of fibrinogen or plasminogen was found in these patients with arterial grafts. Placement of impervious knitted Dacron velour aortic grafts in baboons reproduced platelet consumption that progressively normalized over six weeks postoperatively. Platelet survival measurements correlated directly with endothelial cell coverage of the graft luminal surface in these animals implying that endothelialization of the graft surface was also occurring postoperatively in patients.
Theory of DNA Sequencing Using Free-Solution Electrophoresis of Protein-DNA Complexes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheory of DNA Sequencing Using Free-Solution Electrophoresis of Protein-DNA ComplexesPascal. Mayer, Gary W. Slater, and Guy. DrouinCite this: Anal. Chem. 1994, 66, 10, 1777–1780Publication Date (Print):May 15, 1994Publication History Published online1 May 2002Published inissue 15 May 1994https://pubs.acs.org/doi/10.1021/ac00082a029https://doi.org/10.1021/ac00082a029research-articleACS PublicationsRequest reuse permissionsArticle Views358Altmetric-Citations83LEARN 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
Coexpression of platelet-derived growth factor (PDGF) and PDGF-receptor genes by primary human astrocytomas may contribute to their development and maintenance. (1990)

The present studies investigated the expression of the two PDGF genes (c-sis/PDGF-2 and PDGF-1) and the PDGF-receptor b gene (PDGF-R) in 34 primary human astrocytomas. Northern blot analysis demonstrated the coexpression of the c-sis/PDGF-2 protooncogene and the PDGF-R gene in all astrocytomas examined. The majority of the tumors also expressed the PDGF-1 gene. There was no correlation between the expression of the two PDGF genes. Nonmalignant human brain tissue expressed the PDGF-R and PDGF-1 genes but not the c-sis/PDGF-2 protooncogene. In situ hybridization of astrocytoma tissue localized the expression of the c-sis and PDGF-R mRNA's in tumor cells. Capillary endothelial cells also expressed c-sis mRNA. In contrast, nonmalignant human brain tissue expressed only PDGF-R mRNA but not c-sis/PDGF-2 mRNA. The coexpression of a potent mitogenic growth factor protooncogene (c-sis) and its receptor gene in astrocytoma tumor cells suggests the presence of an autocrine mechanism that may contribute to the development and maintenance of astrocytomas. The expression of c-sis mRNA in tumor cells but not in nonmalignant brain cells may serve as an additional diagnostic criterion for the detection of astrocytomas in small tissue specimen using in situ hybridization for the detection of c-sis mRNA and/or immunostaining for the recognition of its protein product.