gebhart/patrepeval huggingface dataset:
REPRESSION OF SPRUCE BEETLE (COLEOPTERA) ATTRACTION BY METHYLCYCLOHEXENONE IN IDAHO (1974)

Abstract Attraction of the spruce beetle, Dendroctonus rufipennis (Kirby), to beetle-infested logs was reduced 99% by addition of 3-methyl-2-cyclohexen-1-one (MCH), the natural antiaggregative pheromone of the Douglas-fir beetle, D . pseudotsugae Hopkins. The synthetic attractant frontalin and α-pinene attracted few spruce beetles and its nominal attraction was nearly nullified by addition of MCH. Male spruce beetles responded to the natural and synthetic attractants in greater numbers than females. When MCH was added to these treatments, females predominated among the few beetles caught. The clerid Thanasimus undatulus Say was strongly attracted to treatments containing frontalin, whether or not MCH was added, but MCH alone was not attractive to this predator. Among 13 other species of scolytids caught, the most abundant were Scierus annectens Leconte and Hylastes nigrinus (Mann.). Two relatively rare species, Scierus pubescens Sw. and Xylechinus montanus Blkm., were attracted in unusual numbers to natural spruce beetle attractant. Intensive study is recommended of the possible use of MCH to prevent increase of spruce beetle populations.
Rearranged immunoglobulin heavy chain variable region (VH) pseudogene that deletes the second complementarity-determining region. (1984)

We have cloned two rearranged heavy chain variable region (VH) genes from the IgG-producing human cell line CESS. The VH gene, which is linked to the mu chain constant region (C mu) gene, has two deletions at residues 45-62 and 82A-90, the former of which corresponds closely to the second complementarity-determining region (CDR2). These results could indicate that translocation of CDR2 occurred and could give support to the argument that reassortment of the V mini-genes is involved in the generation of hypervariability during evolution. However, the rearranged pseudogene could have also arisen by fortuitous deletion. The other VH gene of CESS is an expressed form and is probably linked to the C gamma gene. The diversity region (D) segments used in these rearranged V genes are less than 38% homologous to known human germline D segments, indicating the presence of more unknown germline D segments.
Optimizing Fracturing Fluids From Flowback Water (2009)

Abstract As mature fields produce larger quantities of water, operators and service companies find themselves challenged with disposing flowback and produced water to reduce costs, handling the logistics of getting enough water to hydraulically fracture the well, as well as complying with stricter governmental regulations. As produced water is recycled and used in fracturing applications, each cycle of re-used water returns with a more complex chemical make up than before. Therefore, the usable lifetime of the recycled water is shortened or requires expensive cleaning or dilution with fresh water to make it a viable solvent base for fracturing fluids. This paper describes the process to properly design fracturing fluids using flowback and produced water. The importance of flowback water analysis is highlighted for optimizing fluid performance downhole. Recent developments in proper selection of fluid additives and viscosifiers for slickwater and crosslinked fluids are discussed. We will describe in detail how the salinity, biological activity, and scaling tendency of these waters can impact fluid performance. Other factors, including organics and suspended solids will be included in the discussion. Laboratory examples will be shown to demonstrate the importance of following a systematic approach. Ultimately, this paper focuses on how to optimize well performance using recycled waters in stimulation applications.
Video Collaborative Annotation Forum: Establishing Ground-Truth Labels on Large Multimedia Datasets (2003)

We developed a new version of The VideoAnnEx, a.k.a. IBM MPEG-7 Annotation Tool, for collaborative multimedia annotation task in a distributed environment. The VideoAnnEx assists authors in the task of annotating video sequences with MPEG-7 metadata. Each shot in the video sequence can be annotated with static scene descriptions, key object descriptions, event descriptions, and other lexicon sets. The annotated descriptions are associated with each video shot or regions in the keyframes, and are stored as MPEG-7 XML file. We proposed a forum to collaboratively annotate semantic labels to the NIST TRECVID 2003 development set. From April to July 2003, 111 researchers from 23 institutes worked together to associate 198K of ground-truth labels (433K after hierarchy propagation) to 62.2 hours of videos. This large set of valuable ground-truth data is publicly available to the research community, especially for multimedia indexing and retrieval, semantic understanding, and supervised machine learning fields. 1.
A Crystalline Imine-Linked 3-D Porous Covalent Organic Framework (2009)

A new crystalline porous three-dimensional covalent organic framework, termed COF-300, has been synthesized and structurally characterized. Tetrahedral tetra-(4-anilyl)-methane and linear terephthaldehyde building blocks were condensed to form imine linkages in a material whose X-ray crystal structure shows five independent diamond frameworks. Despite the interpenetration, the structure has pores of 7.2 A diameter. Thus, COF-300 shows thermal stability up to 490 degrees C and permanent porosity with a surface area of 1360 m(2) g(-1).
A family of thermostable fungal cellulases created by structure-guided recombination (2009)

SCHEMA structure-guided recombination of 3 fungal class II cellobiohydrolases (CBH II cellulases) has yielded a collection of highly thermostable CBH II chimeras. Twenty-three of 48 genes sampled from the 6,561 possible chimeric sequences were secreted by the Saccharomyces cerevisiae heterologous host in catalytically active form. Five of these chimeras have half-lives of thermal inactivation at 63 degrees C that are greater than the most stable parent, CBH II enzyme from the thermophilic fungus Humicola insolens, which suggests that this chimera collection contains hundreds of highly stable cellulases. Twenty-five new sequences were designed based on mathematical modeling of the thermostabilities for the first set of chimeras. Ten of these sequences were expressed in active form; all 10 retained more activity than H. insolens CBH II after incubation at 63 degrees C. The total of 15 validated thermostable CBH II enzymes have high sequence diversity, differing from their closest natural homologs at up to 63 amino acid positions. Selected purified thermostable chimeras hydrolyzed phosphoric acid swollen cellulose at temperatures 7 to 15 degrees C higher than the parent enzymes. These chimeras also hydrolyzed as much or more cellulose than the parent CBH II enzymes in long-time cellulose hydrolysis assays and had pH/activity profiles as broad, or broader than, the parent enzymes. Generating this group of diverse, thermostable fungal CBH II chimeras is the first step in building an inventory of stable cellulases from which optimized enzyme mixtures for biomass conversion can be formulated.
Tat-Mediated Delivery of Antibodies into Cultured Cells (2003)

Many questions concerning the function of the cytoskeleton can be addressed using functional antibodies either in in vitro assays or in whole cell systems. Ultimately, the function of a component has to be studied within intact cell systems. A problem, which one has to be overcome, is the delivery of the antibody into the cells. The delivery of antibodies can be a particular problem either, if large numbers of cells will be analyzed or if one wants to study adhesive as well as non-adhesive cells. Several approaches to introduce proteins and other components into cells have been published, such as electroporation (), scrape loading (), or delivery via liposomes (). Among these the most widespread are microinjection and electroporation. While microinjection is routinely used for adhesive cells, this method will be very time consuming when large numbers of cells have to be studied. Also, it is not feasible to employ this technique for small cells in suspension. Electroporation, on the other hand, has been employed successfully to introduce various components in to cells in suspension. Chang (,) has also developed an electroporation method for adhesive cells using an oscillating electric field; still a fare number of cells die during this procedure.
Synthesis of the penta-oxazole core of telomestatin in a convergent approach to poly-oxazole macrocycles (2006)

A protocol for the construction of poly-oxazoles with consecutive 2,4'-linkages is described, and has afforded an efficient route to a penta-oxazole which demarcates a route to telomestatin and related macrocyclic poly-oxazole systems.
Inhibition of Quorum Sensing in Serratia marcescens AS-1 by Synthetic Analogs of N -Acylhomoserine Lactone (2007)

Quorum sensing is a regulatory system for controlling gene expression in response to increasing cell density. N-Acylhomoserine lactone (AHL) is produced by gram-negative bacteria, which use it as a quorum-sensing signal molecule. Serratia marcescens is a gram-negative opportunistic pathogen which is responsible for an increasing number of serious nosocomial infections. S. marcescens AS-1 produces N-hexanoyl homoserine lactone (C(6)-HSL) and N-(3-oxohexanoyl) homoserine lactone and regulates prodigiosin production, swarming motility, and biofilm formation by AHL-mediated quorum sensing. We synthesized a series of N-acyl cyclopentylamides with acyl chain lengths ranging from 4 to 12 and estimated their inhibitory effects on prodigiosin production in AS-1. One of these molecules, N-nonanoyl-cyclopentylamide (C(9)-CPA), had a strong inhibitory effect on prodigiosin production. C(9)-CPA also inhibited the swarming motility and biofilm formation of AS-1. A competition assay revealed that C(9)-CPA was able to inhibit quorum sensing at four times the concentration of exogenous C(6)-HSL and was more effective than the previously reported halogenated furanone. Our results demonstrated that C(9)-CPA was an effective quorum-sensing inhibitor for S. marcescens AS-1.
Programming an FPGA-based Super Computer Using a C-to-VHDL Compiler: DIME-C (2007)

Since their invention in the 1980s, the logic density of FPGAs has increased exponentially with time. This increase of logic density first led to the development of synthesisable HDLs, and is now leading to the development of high-level languages that target FPGAs (FPGA HLLs). There is now a range of C-to-VHDL compilers, FPGA HLLs that use variant of the ANSI C syntax as their input. These languages have many features in common, as well as distinguishing features. The authors present Nallatech's DIME-C compiler, its features and its novelties. The DIME-C compiler has been used to program a 64-node FPGA supercomputer created as part of the FPHCA project [7]. Using DIME-C to program the supercomputer resulted in significant performance increases (up to 11 Ox) and increased productivity. Some conclusions on design methodology are then drawn.
Generation of self-dual threshold functions and lower bounds of the number of threshold functions and a maximum weight (1962)

This paper consists of the following: recursive methods of generating self-dual threshold functions, a class of self-dual threshold functions which have interesting properties, a lower bound of the number of threshold functions, and a lower bound of a maximum weight. Any threshold function can be reduced from a self-dual threshold function by assigning 1 or 0 to some variable. In this paper, discussion is limited to self-dual threshold functions but it does not lose generality.
Whole-transcriptome analysis links trastuzumab sensitivity of breast tumors to both HER2 dependence and immune cell infiltration (2015)

While results thus far demonstrate the clinical benefit of trastuzumab, some patients do not respond to this therapy. To identify a molecular predictor of trastuzumab benefit, we conducted whole-transcriptome analysis of primary HER2+ breast carcinomas obtained from patients treated with trastuzumab-containing therapies and correlated the molecular portrait with treatment benefit. The estimated association between gene expression and relapse-free survival allowed development of a trastuzumab risk model (TRAR), with ERBB2 and ESR1 expression as core elements, able to identify patients with high and low risk of relapse. Application of the TRAR model to 24 HER2+ core biopsies from patients treated with neo-adjuvant trastuzumab indicated that it is predictive of trastuzumab response. Examination of TRAR in available whole-transcriptome datasets indicated that this model stratifies patients according to response to trastuzumab-based neo-adjuvant treatment but not to chemotherapy alone. Pathway analysis revealed that TRAR-low tumors expressed genes of the immune response, with higher numbers of CD8-positive cells detected immunohistochemically compared to TRAR-high tumors. The TRAR model identifies tumors that benefit from trastuzumab-based treatment as those most enriched in CD8-positive immune infiltrating cells and with high ERBB2 and low ESR1 mRNA levels, indicating the requirement for both features in achieving trastuzumab response.
Functional Antagonism of Gonadal Steroids at the 5-Hydroxytryptamine Type 3 Receptor (1998)

Steroid hormone action involves binding to cognate intracellular receptors that, in turn, bind to respective response elements and thus modulate gene expression. The present study shows that the gonadal steroids, 17beta-estradiol and progesterone, may also act as functional antagonists at the 5-hydroxytryptamine type 3 (5-HT3) receptor in whole-cell voltage-clamp recordings of HEK 293 cells stably expressing the 5-HT3 receptor. Functional antagonistic properties at this ligand-gated ion channel could also be shown for 17alpha-estradiol, 17alpha-ethinyl-17beta-estradiol, mestranol, R 5020, testosterone, and allopregnanolone but not for pregnenolone sulfate and cholesterol. An antagonism at the 5-HT3 receptor could further be observed with the aromatic alcohol 4-dodecylphenol but not with phenol or ethanol. Thus, the modulation of 5-HT3 receptor function by steroids or alcohols is dependent on their respective molecule structure. The antagonistic action of steroids at the 5-HT3 receptor is not mediated via the serotonin binding site because the steroids did not alter the binding affinity of [3H]GR65630 to the 5-HT3 receptor, and kinetic experiments revealed a quite different response pattern to 17beta-estradiol when compared with the competitive antagonist metoclopramide. BSA-conjugated gonadal steroids labeled with fluorescein isothiocyanate bound to membranes of HEK 293 cells expressing the 5-HT3 receptor in contrast to native HEK 293 cells. However, there was no dose-dependent displacement of the binding of gonadal steroids to membranes of cells expressing the 5-HT3 receptor in binding experiments or fluorescence studies. Thus, gonadal steroids probably interact allosterically with the 5-HT3 receptor at the receptor-membrane interface. The functional antagonism of gonadal steroids at the 5-HT3 receptor may play a role for the development and course of nausea during pregnancy and of psychiatric disorders.
A Tile-Expansion Router (1987)

A router based on a tile-expansion algorithm and corner stitching data structure is presented. This program finds connections with a minimum number of jogs and it ensures that a possible solution will be found. Using a working tree, it allows an exhaustive and recursive search along all available areas for routing. The connections are made going back through the working tree until the starting terminal is reached. There are two Manhattan layers that the user can choose for each direction to implement connections; the router can be used to wire hierarchical blocks using a chip planning methodology. The program has been successfully tested on examples concerning different classes of problems.
A herpes simplex virus mutant in which glycoprotein D sequences are replaced by beta-galactosidase sequences binds to but is unable to penetrate into cells (1988)

Herpes simplex virus (HSV) glycoprotein gD is a major component of the virion envelope and is thought to play an important role in the initial stages of viral infection and stimulates the production of high titers of neutralizing antibodies. We assumed that gD plays an essential role in virus replication, and so to complement viruses with mutations in the gD gene we constructed a cell line, denoted VD60, which is capable of expressing high levels of gD after infection with HSV. A recombinant virus, designated F-gD beta, in which sequences encoding gD and a nonessential glycoprotein, gI, were replaced by Escherichia coli beta-galactosidase sequences, was selected on the basis that it produced blue plaques on VD60 cell monolayers under agarose overlays containing 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal). F-gD beta was able to replicate normally on complementing VD60 cells. However, F-gD beta was unable to form plaques on noncomplementing Vero cells. Virions lacking gD were produced in normal amounts by Vero cells infected with F-gD beta, and the virus particles were distributed throughout the cytoplasm and on the cell surface, suggesting that gD is not essential for HSV envelopment and egress. Virions lacking gD were able to bind to cells, but were unable to initiate synthesis of viral early polypeptides. Plaque production of F-gD beta particles lacking gD was enhanced by polyethylene glycol treatment, suggesting that gD is essential for penetration of HSV into cells. Other HSV glycoproteins have been implicated in the entry of virus into cells, and thus this process appears to involve multiple interactions at the cell surface.
Na/K-ATPase Tethers Phospholipase C and IP3 Receptor into a Calcium-regulatory Complex (2005)

We have shown that the caveolar Na/K-ATPase transmits ouabain signals via multiple signalplexes. To obtain the information on the composition of such complexes, we separated the Na/K-ATPase from the outer medulla of rat kidney into two different fractions by detergent treatment and density gradient centrifugation. Analysis of the light fraction indicated that both PLC-gamma1 and IP3 receptors (isoforms 2 and 3, IP3R2 and IP3R3) were coenriched with the Na/K-ATPase, caveolin-1 and Src. GST pulldown assays revealed that the central loop of the Na/K-ATPase alpha1 subunit interacts with PLC-gamma1, whereas the N-terminus binds IP3R2 and IP3R3, suggesting that the signaling Na/K-ATPase may tether PLC-gamma1 and IP3 receptors together to form a Ca(2+)-regulatory complex. This notion is supported by the following findings. First, both PLC-gamma1 and IP3R2 coimmunoprecipitated with the Na/K-ATPase and ouabain increased this interaction in a dose- and time-dependent manner in LLC-PK1 cells. Depletion of cholesterol abolished the effects of ouabain on this interaction. Second, ouabain induced phosphorylation of PLC-gamma1 at Tyr(783) and activated PLC-gamma1 in a Src-dependent manner, resulting in increased hydrolysis of PIP2. It also stimulated Src-dependent tyrosine phosphorylation of the IP3R2. Finally, ouabain induced Ca(2+) release from the intracellular stores via the activation of IP3 receptors in LLC-PK1 cells. This effect required the ouabain-induced activation of PLC-gamma1. Inhibition of Src or depletion of cholesterol also abolished the effect of ouabain on intracellular Ca(2+).
Next-Generation Cancer Vaccine Approaches: Integrating Lessons Learned From Current Successes With Promising Biotechnologic Advances (2013)

With the recent approval of sipuleucel-T for metastatic castration-resistant prostate cancer and ipilimumab for metastatic melanoma, there is increasing excitement in the field of cancer immunotherapy. A large number of clinical trials are currently testing various vaccine vectors in a diverse array of cancer types. Which of these strategies will ultimately prove successful has yet to be determined. However, a better understanding of the complex interplay of tumor-specific T cells and the challenges faced at the tumor microenvironment, advances in biotechnology, and lessons learned from prior successes and failures will likely lead to approvals of other therapeutic cancer vaccines.
Structure and expression of the human and mouse T4 genes. (1987)

The T4 molecule may serve as a T-cell receptor recognizing molecules on the surface of specific target cells and also serves as the receptor for the human immunodeficiency virus. To define the mechanisms of interaction of T4 with the surface of antigen-presenting cells as well as with human immunodeficiency virus, we have further analyzed the sequence, structure, and expression of the human and mouse T4 genes. T4 consists of an extracellular segment comprised of a leader sequence followed by four tandem variable-joining (VJ)-like domains, a transmembrane domain, and a cytoplasmic segment. The structural domains of the T4 protein deduced from amino acid sequence are precisely reflected in the intron-exon organization of the gene. Analysis of the expression of the T4 gene indicates that T4 RNA is expressed not only in T lymphocytes, but in B cells, macrophages, and granulocytes. T4 is also expressed in a developmentally regulated manner in specific regions of the brain. It is, therefore, possible that T4 plays a more general role in mediating cell recognition events that are not restricted to the cellular immune response.
99mTc-Labeled Small Peptides as Diagnostic Radiopharmaceuticals (1999)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT99mTc-Labeled Small Peptides as Diagnostic RadiopharmaceuticalsShuang Liu and D. Scott EdwardsView Author Information DuPont Pharmaceuticals Company, Medical Imaging Division, 331 Treble Cove Road, North Billerica, Massachusetts 01862 Cite this: Chem. Rev. 1999, 99, 9, 2235–2268Publication Date (Web):July 28, 1999Publication History Received21 December 1998Revised14 May 1999Published online28 July 1999Published inissue 8 September 1999https://doi.org/10.1021/cr980436lCopyright © 1999 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2605Altmetric-Citations403LEARN 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 InReddit Read OnlinePDF (781 KB) Get e-AlertsSUBJECTS:Nuclear medicine,Peptides and proteins,Pharmaceuticals,Receptors,Technetium Get e-Alerts
Velocity-Strength Relationship of Concrete by Impact-Echo Method (2003)

First Name is required invalid characters Last Name is required invalid characters Email Address is required Invalid Email Address Invalid Email Address