gebhart/patrepeval huggingface dataset:
Living Dangerously: A Survey of Software Download Practices (2010)

Abstract: Client software, such as Windows.exe files, poses security risks but also adds important functionality that cannot yet be replicated with web applications. These risks can be mitigated by running client software inside a sandbox. Virtual machines offer an easily deployed mechanism to create such a sandbox. This motivates two key questions: Are today’s virtual machine mechanisms sufficient to prevent harm from malicious software? Even if they are sufficient, does it matter – is it the case that everyone has moved on to web applications? We address these questions by carrying out a survey of three populations of computer users: two within Microsoft and one drawn from U.S. users of the Amazon Mechanical Turk service. We note three key findings: First, all three populations download and run client software regularly: Over 70 % of respondents in all three popluations download and run client software monthly or more often. Second, use of virtual machines for sandboxing is rare and inconsistently applied: 68 % of respondents in all three populations say they use virtual machines “occasionally ” or less often. Third, of those who gave a reason for not using VMs, 44 % say it is “too hard. ” We conclude that today’s users are exposed to risk from client software and that today’s sandboxing mechanisms are inadequate to protect them. 1.
Efficient XSLT processing in relational database system (2006)

Efficient processing of XQuery, XPath and SQL/XML on XML documents stored and managed in RDBMS has been widely studied. However, much less of such type of work has been done for efficient XSLT processing of XML documents stored and managed by the database. This is partially due to the observation that the rule based template driven XSLT execution model does not fit nicely with the traditional declarative query language processing model which leverages index probing and iterator based pull mode that can be scaled to handle large size data. In this paper, we share our experience of efficient processing of XSLT in Oracle XML DB. We present the technique of processing XSLT efficiently in database by rewriting XSLT stylesheets into highly efficient XQuery through partially evaluating XSLT over the XML documents structural information. Consequently, we can leverage all the work done for efficient XQuery/XPath processing in database to achieve combined optimisations of XSLT with XQuery/XPath and SQL/XML in Oracle XMLDB. This effectively makes XSLT processing scale to large size XML documents using classical declarative query processing techniques in DBMS.
HER2-specific immunoligands engaging NKp30 or NKp80 trigger NK-cell-mediated lysis of tumor cells and enhance antibody-dependent cell-mediated cytotoxicity (2015)

NK cells detect tumors through activating surface receptors, which bind self-antigens that are frequently expressed upon malignant transformation. To increase the recognition of tumor cells, the extracellular domains of ligands of the activating NK cell receptors NKp30, NKp80 and DNAM-1 (i.e. B7-H6, AICL and PVR, respectively) were fused to a single-chain fragment variable (scFv) targeting the human epidermal growth factor receptor 2 (HER2), which is displayed by various solid tumors. The resulting immunoligands, designated B7-H6:HER2-scFv, AICL:HER2-scFv, and PVR:HER2-scFv, respectively, bound HER2 and the addressed NK cell receptor. However, whereas B7-H6:HER2-scFv and AICL:HER2-scFv triggered NK cells to kill HER2-positive breast cancer cells at nanomolar concentrations, PVR:HER2-scFv was not efficacious. Moreover, NK cell cytotoxicity was enhanced synergistically when B7-H6:HER2-scFv or AICL:HER2-scFv were applied in combination with another HER2-specific immunoligand engaging the stimulatory receptor NKG2D. In contrast, no improvements were achieved by combining B7-H6:HER2-scFv with AICL:HER2-scFv. Additionally, B7-H6:HER2-scFv and AICL:HER2-scFv enhanced antibody-dependent cell-mediated cytotoxicity (ADCC) by the therapeutic antibodies trastuzumab and cetuximab synergistically, with B7-H6:HER2-scFv exhibiting a higher efficacy. In summary, antibody-derived proteins engaging NKp30 or NKp80 may represent attractive biologics to further enhance anti-tumor NK cell responses and may provide an innovative approach to sensitize tumor cells for antibody-based immunotherapy.
[Renal angiomyolipoma, histology, diagnostics and therapy]. (2005)

We define diagnosis by means of CT notation in the most of patients. This notation is not typical by any version of angiomyolipoma and we choose therefore surgical revision.
Enzymatic dehalogenation of pentachlorophenol by extracts from Arthrobacter sp. strain ATCC 33790 (1989)

Arthrobacter sp. strain ATCC 33790 was grown with pentachlorophenol (PCP) as the sole source of carbon and energy. Crude extracts, which were prepared by disruption of the bacteria with a French pressure cell, showed no dehalogenating activity with PCP as the substrate. After sucrose density ultracentrifugation of the crude extract at 145,000 x g, various layers were found in the gradient. One yellow layer showed enzymatic conversion of PCP. One chloride ion was released per molecule of PCP. The product of the enzymatic conversion was tetrachlorohydroquinone. NADPH and oxygen were essential for this reaction. EDTA stimulated the enzymatic activity by 67%. The optimum pH for the enzyme activity was 7.5, and the temperature optimum was 25 degrees C. Enzymatic activity was also detected with 2,4,5-trichlorophenol, 2,3,4-trichlorophenol, 2,4,6-trichlorophenol, and 2,3,4,5-tetrachlorophenol as substrates, whereas 3,4,5-trichlorophenol, 2,4-dichlorophenol, 3,4-dichlorophenol, and 4-chlorophenol did not serve as substrates.
Mechanism of lymphocyte function-associated molecule 3-Ig fusion proteins inhibition of T cell responses. Structure/function analysis in vitro and in human CD2 transgenic mice. (1994)

Soluble ligands specific for cell surface molecules involved in APC-T cell interactions can signal cells and modulate immune responses. Recently, we reported that LFA3TIP, a fusion protein comprised of the first LFA-3 extracellular domain fused to the hinge, CH2, and CH3 regions of a human IgG1 inhibits proliferation of human T cells in vitro. We report herein the cell-based mechanism(s) of LFA3TIP in inhibition by studying the effects of structurally altered LFA3-Ig fusion proteins on proliferation of human PBL in vitro and on responses of mice transgenic for human CD2. We show that LFA3TIP inhibition requires expression of both the LFA-3 and CH2 domains of the fusion protein that bind CD2 and Fc gamma RI or Fc gamma RIII, respectively. LFA3TIP forms an intracellular Fc gamma R/CD2 bridge and directs cytolysis of CD2+ cells by freshly drawn human PBL in vitro as well as the non-C-mediated depletion of peripheral T cells of human CD2 transgenic mice. The cell-based mechanism(s) of LFA3TIP inhibition are discussed.
miRNAs in lung cancer - Studying complex fingerprints in patient's blood cells by microarray experiments (2009)

Our findings support the idea that neoplasia may lead to a deregulation of miRNA expression in blood cells of cancer patients compared to blood cells of healthy individuals. Furthermore, we provide evidence that miRNA patterns can be used to detect human cancers from blood cells.
Extending Pummerer Reaction Chemistry. Application to the Oxidative Cyclization of Indole Derivatives (2004)

The diastereoselective oxidative cyclization of a beta-oxygenated tryptophan derivative is reported. This process, which utilizes a new variant of the Pummerer reaction, may have application in TMC-95A synthesis.
G Protein-Coupled Receptor Rhodopsin: A Prospectus (2003)

Rhodopsin is a retinal photoreceptor protein of bipartite structure consisting of the transmembrane protein opsin and a light-sensitive chromophore 11-cis-retinal, linked to opsin via a protonated Schiff base. Studies on rhodopsin have unveiled many structural and functional features that are common to a large and pharmacologically important group of proteins from the G protein-coupled receptor (GPCR) superfamily, of which rhodopsin is the best-studied member. In this work, we focus on structural features of rhodopsin as revealed by many biochemical and structural investigations. In particular, the high-resolution structure of bovine rhodopsin provides a template for understanding how GPCRs work. We describe the sensitivity and complexity of rhodopsin that lead to its important role in vision.
Current understanding of multi‐species biofilms (2011)

Direct observation of a wide range of natural microorganisms has revealed the fact that the majority of microbes persist as surface-attached communities surrounded by matrix materials, called biofilms. Biofilms can be formed by a single bacterial strain. However, most natural biofilms are actually formed by multiple bacterial species. Conventional methods for bacterial cleaning, such as applications of antibiotics and/or disinfectants are often ineffective for biofilm populations due to their special physiology and physical matrix barrier. It has been estimated that billions of dollars are spent every year worldwide to deal with damage to equipment, contaminations of products, energy losses, and infections in human beings resulted from microbial biofilms. Microorganisms compete, cooperate, and communicate with each other in multi-species biofilms. Understanding the mechanisms of multi-species biofilm formation will facilitate the development of methods for combating bacterial biofilms in clinical, environmental, industrial, and agricultural areas. The most recent advances in the understanding of multi-species biofilms are summarized and discussed in the review.
Allelic drop-out and preferential amplification in single cells and human blastomeres: implications for preimplantation diagnosis of sex and cystic fibrosis (1995)

Previously the diagnosis of sex and cystic fibrosis status has been studied on single cells using the polymerase chain reaction (PCR). It has been suggested that allelic drop-out (PCR failure of one allele) and/or preferential amplification (hypo-amplification of one allele) may contribute to poor reliability and misdiagnosis, although this remains controversial as some reports suggest that allelic drop-out does not occur. We investigated an improved method of diagnosing sex and cystic fibrosis in single cells using a new technology (fluorescent PCR) to determine the base level of PCR artefacts (allelic drop-out and preferential amplification) which, in combination with improved sensitivity, should improve PCR reliability and accuracy. Fluorescent PCR gives high reliability (∼97%) and accuracy rates (∼97%) in somatic cells for both sex and cystic fibrosis diagnosis and its lower detection threshold allows allelic drop-out and preferential amplification to be easily distinguished. We also achieved high reliability and accuracy in diagnosing cystic fibrosis in human blastomeres. This study confirms earlier reports of both allelic drop-out and preferential amplification in single cell analysis. We demonstrate that both allelic drop-out and preferential amplification occur in somatic cells and suggest these are separate phenomena. Preferential amplification appeared common in single cell PCR while allelic dropout apparently occurred at random in each allele. Preferential amplification was mainly amplification of the larger allele. We suggest that some inaccuracy/misdiagnosis may be due to both preferential amplification as well as allelic drop-out. Other findings were variability in drop-out between PCR and that amplification of signals from human blastomeres may be linked to embryo quality. We suggest that allelic drop-out is dependent on the number of cells within the sample.
Injectables in the treatment of female stress incontinence (1995)

The failure to store urine resulting from bladder outflow incompetence requires a method to increase outflow resistance. Peri- and intraurethral injection is one form of treatment capable of accomplishing this need. The best results are obtained in those women who do not have detrusor abnormalities, who have adequate bladder capacity, who have no anatomic abnormality, and have demonstrable intrinsic sphincteric deficiency of function. The technique is tolerated well by patients and reduces the need for alternative major open surgical procedures.
WS1279, a novel lipopeptide isolated from Streptomyces willmorei. Biological activities. (1993)

WS1279, a new lipopeptide isolated from the fermentation broth of Streptomyces willmorei No. 1279, stimulated the proliferation of mouse bone marrow cells in vitro and accelerated the recovery of granulocyte counts in bone marrow from leukopenia induced by mitomycin C (MMC) in mice. The glycerylcysteine moiety of WS1279 is necessary and the lipid peptide structure is required for manifestation of full stimulating activity in vitro. WS1279 was the most effective on the proliferation of bone marrow cells among the tested immunostimulants in vitro. However, the effect of WS1279 on restoration of reduced granulocyte counts in MMC-induced leukopenia in mice was less than that of FK-565, lipopolysaccharide, picibanil or forphenicinol. WS1279 augmented host resistance to infection with Staphylococcus aureus 47 in normal and immunosuppressed mice.
Heparin inhibition of von Willebrand factor-dependent platelet function in vitro and in vivo. (1991)

The intravenous administration of heparin to patients before open heart surgery reduced ristocetin cofactor activity by 58% (P less than 0.01, t test), and this impairment of von Willebrand factor-dependent platelet function was closely related to plasma heparin levels (r2 = 0.9), but not to plasma von Willebrand factor (vWF) levels. We hypothesized that heparin may inhibit vWF-dependent platelet hemostatic functions by directly binding vWF in solution and interfering with vWF-GpIb binding. Using the in vitro techniques of ristocetin-induced platelet agglutination, fluorescent flow cytometric measurement of vWF-platelet binding, and conventional radioligand binding assays we observed that heparin inhibited both vWF-dependent platelet function and vWF-platelet binding in a parallel and dose-dependent manner. Heparin also inhibited platelet agglutination induced by bovine vWF and inhibited the binding of human asialo-vWF to platelets in ristocetin-free systems. The inhibitory potency of heparin was not dependent upon its affinity for antithrombin III, but was molecular weight dependent: homogeneous preparations of lower molecular weight were less inhibitory. Heparin impairment of vWF function may explain why some hemorrhagic complications of heparin therapy are not predictable based on techniques for monitoring the conventional anticoagulant effects of heparin.
Inhibition of Gastric Acid Secretion by Peptide YY Is Independent of Gastric Somatostatin Release in the Rat (1988)

The purpose of this study was to determine whether the inhibitory action of peptide YY (PYY) on gastric acid secretion is attributable to the release of gastric somatostatin in rats. Two groups of rats (six rats/group) were anesthetized with urethane and prepared with gastric fistulas and jugular catheters. Pentagastrin (18 micrograms/kg-h) was given intravenously for 150 min to stimulate gastric acid secretion. Intravenous PYY (130 micrograms/kg-h) inhibited pentagastrin-stimulated gastric acid secretion significantly (P less than 0.05). Administration of iv PYY resulted in a 41% reduction (P less than 0.05) in pentagastrin-stimulated gastric acid secretion. In another group of anesthetized rats, administration of PYY (10(-7), 10(-8) M) failed to stimulate a release of somatostatin from the isolated-perfused rat stomach. Our findings indicate that PYY can inhibit gastric acid secretion independently of release of gastric somatostatin in the rat.
Polarization birefringence measurements for characterizing the myocardium, including healthy, infarcted, and stem-cell-regenerated tissues (2010)

Myocardial infarction leads to structural remodeling of the myocardium, in particular to the loss of cardiomyocytes due to necrosis and an increase in collagen with scar formation. Stem cell regenerative treatments have been shown to alter this remodeling process, resulting in improved cardiac function. As healthy myocardial tissue is highly fibrous and anisotropic, it exhibits optical linear birefringence due to the different refractive indices parallel and perpendicular to the fibers. Accordingly, changes in myocardial structure associated with infarction and treatment-induced remodeling will alter the anisotropy exhibited by the tissue. Polarization-based linear birefringence is measured on the myocardium of adult rat hearts after myocardial infarction and compared with hearts that had received mesenchymal stem cell treatment. Both point measurement and imaging data show a decrease in birefringence in the region of infarction, with a partial rebound back toward the healthy values following regenerative treatment with stem cells. These results demonstrate the ability of optical polarimetry to characterize the micro-organizational state of the myocardium via its measured anisotropy, and the potential of this approach for monitoring regenerative treatments of myocardial infarction.
Delivering MPEG-4 Based Audio-Visual Services (2000)

Delivering MPEG-4 Based Audio-Visual Services investigates the different aspects of end-to-end multimedia services; content creation, server and service provider, network, and the end-user terminal. Part I provides a comprehensive introduction to digital video communications, MPEG standards, and technologies, and deals with system level issues including standardization and interoperability, user interaction, and the design of a distributed video server. Part II investigates the systems in the context of object-based multimedia services and presents a design for an object-based audio-visual terminal, some of these features having been adopted by the MPEG-4 Systems specification. The book goes on to study the requirements for a file format to represent object-based audio-visual content and the design of one such format. The design introduces new concepts such as direct streaming that are essential for scalable servers.
Interactions Between Trichoderma harzianum Strain T22 and Maize Inbred Line Mo17 and Effects of These Interactions on Diseases Caused by Pythium ultimum and Colletotrichum graminicola (2004)

ABSTRACT Seed treatment with Trichoderma harzianum strain T22, which results in colonization of plant roots but little or no colonization of shoots or leaves, had substantial effects on growth of and disease expression in maize inbred line Mo17. Shoots and roots of 10-day-old seedlings grown in a sandy loam field soil were larger (roots were nearly twice as long) in the presence of T22 than in its absence. Both main and secondary roots were increased in size and area and the root hair area was greater with T22. However, root hair area per unit of root length was greater in control plants. Increased growth probably was due to direct stimulation of plant growth in addition to effects from biological control of deleterious microflora. Seedlings of Mo17 grown in autoclaved or mefenoxamtreated sandy loam field soil were larger than those produced in untreated soil. However, seedlings grown in the presence of T22, either in treated or untreated soil, were larger than those produced in its absence. Infestation of soil with Pythium ultimum had little effect upon growth of Mo17. The presence of T22 increased protein levels and activities of beta-1,3 glucanase, exochitinase, and endochitinase in both roots and shoots, even though T22 colonized roots well but colonized shoots hardly at all. With some enzymes, the combination of T22 plus P. ultimum gave the greatest activity. Plants grown from T22-treated seed had reduced symptoms of anthracnose following inoculation of leaves with Colletotrichum graminicola, which indicates that root colonization by T22 induces systemic resistance in maize.
Graphene‐Based Electrochemical Sensors (2013)

Graphene, one kind of emerging carbon nanomaterial, has attracted increasing attention recently. Due to its fascinating physical and electrochemical properties, graphene as a promising electrode material has been widely used in electrochemical sensing applications. In this review, different approaches for the fabrication of graphene and the preparation of graphene-modified electrodes for electrochemical sensors are introduced. Moreover, recent research results on different graphene-based materials as an electrochemical platform for the detection of various biomolecules and chemicals are reviewed and compared. More electrochemical studies on this novel material should show up in the near future.
The TAO of MEKK (1998)

Cloning and characterization of MEKK1 in 1993 revealed that in addition to Raf there were other pathways activated by extracellular stimuli that were responsible for ERK activation. Since then, three additional MEKK family members have been cloned adding even further diversity to the regulation of MAPK pathways. The MEKK family members are regulated by a diverse array of extracellular stimuli ranging from growth factors to DNA damaging stimuli and so are important for the cell to sense exposure to various environmental stimuli. One important aspect of MEKK biology is that they can potentially serve in more than one pathway. Regulation of MEKK family members often involves LMWG proteins, phosphorylation and subcellular localization. With regard to at least MEKK1, serine/threonine kinases such as NIK, GLK and HPK1 appear also to be important for regulation. Of the MEKK family members, the biological role of MEKK1 is best characterized and studies have shown that MEKK1 is important in mediating survival vs. apoptosis, possibly via its ability to regulate transcription factors, the expression of death receptors and their ligands. The biological roles of MEKK2, 3 and 4 are under investigation and undoubtedly homologous deletion of these MEKK family members will be invaluable at determining the biological functions of these MEKKs. At present, the MEKK family members are characterized as localized sensors that control cell responses at the level of gene expression, metabolism and the cytoskeleton
Phenotypic correction of dwarfism by constitutive expression of growth hormone (1996)

GH is normally secreted in a pulsatile fashion. When GH is deficient, dwarfism is the result in both rodents and humans. An adenoviral vector containing the rat GH complementary DNA was used to induce constitutive GH expression in hepatocytes of GH-deficient lit/lit mice. Elevated serum GH increased circulating insulin-like growth factor I concentrations, corrected the growth deficiency, and normalized body composition. The results indicate that correction of the dwarf phenotype can be achieved by constitutive expression of GH at an ectopic site by gene transfer.
Optimized DNA “Nanosuitcases” for Encapsulation and Conditional Release of siRNA (2016)

We set out to design, synthesize, and optimize a DNA-minimal cage capable of encapsulating oligonucleotide drugs to facilitate their delivery. Through rational design and optimization using in vitro assays, we have assembled the first DNA “nanosuitcase” that can encapsulate a siRNA construct and release it upon recognition of an oligonucleotide trigger. The latter may be a mRNA or a microRNA (miRNA) which offers potential for dual or synergistic therapy. This construct assembles in near 100% yield, releases its cargo on demand, and can sustain biological conditions. Moreover, we find that the DNA scaffold is able to protect its cargo against site-specific cleavage and nuclease degradation. Release of the cargo is performed with fixed cells using a FRET-enabled construct imaged by confocal microscopy and reveals that the DNA cage remains responsive at the molecular level in a complex cellular environment. We foresee this construct will be able to address challenges in drug delivery, more specifically in nontoxic delivery and targeted release.