gebhart/patrepeval huggingface dataset:
Constructing interoperable components in distributed systems (2003)

The separation of architecture definition language (ADL) and interface definition language (IDL) is widely accepted in the distributed system community. It separates issues of hierarchical composition and configuration from those of services, communication and synchronisation and thus eases reconfiguration without changing the interfaces and implementation and allows the change of services within well-defined configuration constraints. Our approach towards distributed system definition draws on the Darwin project's notion of distributed system architecture definition and on Eiffel's notion of design-by-contract. We extend contracts to deal with synchronisation and coordination at a higher level, explicitly targeting both large-scale loosely-coupled distributed components and tightly coupled parallel or multithreaded objects. In this paper we present a Java binding of the resulting contract extensions. We incorporate annotations into Java programs adding Eiffel-style assertions and other contractual constraints. Java component code and constraints are then associated to architectural diagrams in a visual programming environment. The paper illustrates the language features in a case study of a lift control system. Based on the case study, the component-based design approach is illustrated and the internal synchronisation of method execution is explained.
DHCP Options and BOOTP Vendor Extensions (1997)

The Dynamic Host Configuration Protocol (DHCP) [1] provides a framework for passing configuration information to hosts on a TCP/IP network.Configuration parameters and other control information are carried in tagged data items that are stored in the 'options' field of the DHCP message.The data items themselves are also called "options."This document specifies the current set of DHCP options.Future options will be specified in separate RFCs.The current list of valid options is also available in ftp://ftp.isi.edu/innotes/iana/assignments[22].All of the vendor information extensions defined in RFC 1497 [2] may be used as DHCP options.The definitions given in RFC 1497 are included in this document, which supersedes RFC 1497.All of the DHCP options defined in this document, except for those specific to DHCP as defined in section 9, may be used as BOOTP vendor information extensions.
Nematic liquid crystal alignment on chemical patterns (2007)

Patterned Self‐Assembled Monolayers (SAMs) promoting both homeotropic and planar degenerate alignment of 6CB and 9CB in their nematic phase were created using microcontact printing of functionalized organothiols on gold films. The effects of a range of different pattern geometries and sizes were investigated, including stripes, circles and checkerboards. Evanescent wave ellipsometry was used to study the orientation of the liquid crystal (LC) on these patterned surfaces during the isotropic‐nematic phase transition. Pretransitional growth of a homeotropic layer was observed on 1 µm homeotropic aligning stripes, followed by a homeotropic monodomain state prior to the bulk phase transition. Accompanying Monte Carlo simulations of LCs aligned on nanoscale‐patterned surfaces were also performed. These simulations also showed the presence of the homeotropic monodomain state prior to the transition.
Targeting the STAT Pathway in Head and Neck Cancer: Recent Advances and Future Prospects (2004)

Head and neck cancer, the sixth most common type of cancer worldwide, is associated with a dismal prognosis that has minimally improved during the last few decades. Future advances in the treatment and prognosis of this fatal disease largely rely upon a better understanding of the molecular events that underlie tumor development and progression, allowing specific targeting of the involved molecules and pathways. In this context, recent efforts have revolved around a family of transcription factors known as STATs (signal transducers and activators of transcription). STAT proteins comprise a family of latent cytoplasmic transcription factors that become transiently activated in response to extracellular signals, leading to regulation of diverse physiological responses. There is compelling evidence that persistent activation of specific STAT molecules, especially Stat3 and Stat5, possesses oncogenic properties in a number of human cancers, including head and neck cancer. The presence of constitutively activated STAT molecules in cancer cells is mainly attributed to the dysregulation of upstream activating pathways and the aberration of negative regulatory mechanisms. The end result is induction of specific target genes that stimulate cell proliferation, prevent apoptosis, promote angiogenesis and facilitate tumor immune evasion. Therefore, targeting and disruption of oncogenic STAT signaling may theoretically be accomplished through various approaches, involving direct (e.g. interference with the various facets of STAT expression, activation or function) and indirect strategies (e.g. inhibition of upstream signaling events and enhancement or restoration of negative regulatory mechanisms). The availability of multiple potential targets for interruption of aberrant STAT signaling in cancer and the thus-far promising results have generated optimism for the clinical applicability of STAT targeting in head and neck cancer, which is the focus of this review.
Laser Desorption and Ejection of Biomolecules From the Condensed Phase into the Gas Phase (1994)

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML ...Read More
Targeted gene insertion to enhance protein production from cell lines (2007)

Critical to large-scale recombinant protein production is the generation and
characterization of clonal cell lines that exhibit sustained, high level,
expression of the recombinant gene of interest. High expression, as well as
good cell growth and viability, are primary requirements for producer cell
lines, yet generation of cell lines that fit these criteria represents a significant bottleneck in bioprocess. The >1 year timeline commonly experienced
for isolation of a final producer clone represents a costly component of
protein therapeutic development – at least in terms of time to market. In
addition to the time cost are the physical resources required to screen
hundreds or thousands of clones in order to identify those few that exhibit
the desired growth and protein expression properties. This need for largescale clonal screening is a consequence of the limitations of traditional
methods used for generation of recombinant producer cell lines.
Elimination of Cocaine and Metabolites in Plasma, Saliva, and Urine Following Repeated Oral Administration to Human Volunteers (2000)

Chronic administration of lipophilic drugs can result in accumulation and prolonged elimination during abstinence. It has been suggested that cocaine and/or metabolites can be detected in saliva and urine for an extended period following long-term, high-dose administration. The effects of chronic oral cocaine administration in healthy volunteer subjects with a history of cocaine abuse were investigated. Subjects were housed on a closed clinical ward and were administered oral cocaine in up to 16 daily sessions. In each session, volunteers received five equal doses of oral cocaine with 1 h between doses. Across sessions, cocaine was administered in ascending doses from an initial dose of 100 mg (500 mg/day) up to 400 mg (2 g/day), increasing by 25 mg/dose/session (125 mg/session). Participation in the study was terminated if cardiovascular safety parameters were exceeded. Plasma and saliva specimens were collected periodically during the dosing sessions and during the one-week withdrawal phase at the end of the study. All urine specimens were collected throughout the entire study. Specimens were analyzed for cocaine and metabolites by solid-phase extraction followed by gas chromatographic-mass spectrometric analysis in the SIM mode. The limit of detection for each analyte was approximately 1 ng/mL. The analytes measured included benzoylecgonine (BZE), ecgonine methyl ester, cocaine, benzoylnorecgonine, norcocaine, m- and p-hydroxycocaine, and m- and p-hydroxybenzoylecgonine. Noncompartmental analysis was employed for the determination of plasma and saliva pharmacokinetic parameters. Urinary elimination half-lives for cocaine and metabolites were determined by constructing ARE (amount remaining to be excreted) plots. Two phases of urinary elimination of cocaine and metabolites were observed. An initial elimination phase was observed during withdrawal that was similar to the elimination pattern observed after acute dosing. The mean (N = 6) plasma, saliva, and urine cocaine elimination half-lives were 1.5 +/- 0.1 h, 1.2 +/- 0.2 h, and 4.1 +/- 0.9 h, respectively. For three subjects, the mean cocaine urinary elimination half-life for the terminal phase was 19.0 +/- 4.2 h. There was some difficulty in determining if a terminal elimination phase for cocaine was present for the remaining three subjects because of interference by high concentrations of BZE. A terminal elimination phase was also observed for cocaine metabolites with half-life estimates ranging from 14.6 to 52.4 h. These terminal elimination half-lives greatly exceeded previous estimates from studies of acute cocaine administration. These data suggest that cocaine accumulates in the body with chronic use resulting in a prolonged terminal elimination phase for cocaine and metabolites.
Anomalous High Ionic Conductivity of Nanoporous β-Li3PS4 (2013)

Lithium-ion-conducting solid electrolytes hold promise for enabling high-energy battery chemistries and circumventing safety issues of conventional lithium batteries. Achieving the combination of high ionic conductivity and a broad electrochemical window in solid electrolytes is a grand challenge for the synthesis of battery materials. Herein we show an enhancement of the room-temperature lithium-ion conductivity by 3 orders of magnitude through the creation of nanostructured Li(3)PS(4). This material has a wide electrochemical window (5 V) and superior chemical stability against lithium metal. The nanoporous structure of Li(3)PS(4) reconciles two vital effects that enhance the ionic conductivity: (1) the reduction of the dimensions to a nanometer-sized framework stabilizes the high-conduction β phase that occurs at elevated temperatures, and (2) the high surface-to-bulk ratio of nanoporous β-Li(3)PS(4) promotes surface conduction. Manipulating the ionic conductivity of solid electrolytes has far-reaching implications for materials design and synthesis in a broad range of applications, including batteries, fuel cells, sensors, photovoltaic systems, and so forth.
Compiler support for scalable and efficient memory systems (2001)

Technological trends require that future scalable microprocessors be decentralized. Applying these trends toward memory systems shows that the size of the cache accessible in a single cycle will decrease in a future generation of chips. Thus, a bank-exposed memory system comprised of small, decentralized cache banks must eventually replace that of a monolithic cache. This paper considers how to effectively use such a memory system for sequential programs. This paper presents Maps, the software technology central to bank-exposed architectures, which are architectures with bank-exposed memory systems. Maps solves the problem of bank disambiguation-that of determining at compile-time which bank a memory reference is accessing. Bank disambiguation is important because it enables the compile-time optimization for data locality, where data can be placed close to the computation that requires it. Two methods for bank disambiguation are presented: equivalence-class unification and modulo unrolling. Experimental results are presented using a compiler for the MIT Raw machine, a bank-exposed architecture that relies on the compiler to 1) manage its memory and 2) orchestrate its instruction level parallelism and communication. Results on Raw using sequential codes demonstrate that using bank disambiguation improves performance, by a factor of 3 to 5 over using ILP alone.
Disruption of the c-JUN-JNK Complex by a Cell-permeable Peptide Containing the c-JUN δ Domain Induces Apoptosis and Affects a Distinct Set of Interleukin-1-induced Inflammatory Genes (2003)

The transcription factor activator protein (AP)-1 plays crucial roles in proliferation, cell death, and the immune response. c-JUN is an important component of AP-1, but only very few c-JUN response genes have been identified to date. Activity of c-JUN is controlled by NH2-terminal phosphorylation (JNP) of its transactivation domain by a family of JUN-NH2-terminal protein kinases (JNK). JNK form a stable complex with c-JUN in vitro and in vivo. We have targeted this interaction by means of a cell-permeable peptide containing the JNK-binding (delta) domain of human c-JUN. This peptide strongly and specifically induced apoptosis in HeLa tumor cells, which was paralleled by inhibition of serum-induced c-JUN phosphorylation and up-regulation of the cell cycle inhibitor p21cip/waf. Application of the c-JUN peptide to interleukin (IL)-1-stimulated human primary fibroblasts resulted in up-regulation of four genes, namely COX-2, MnSOD, I kappa B alpha, and MAIL and down-regulation of 10 genes, namely CCL8, mPGES, SAA1, hIAP-1, hIAP-2, pent(r)axin-3, CXCL10, IL-1 beta, ICAM-1, and CCL2. Only a small group of genes, namely pent(r)axin-3, CXCL10, ICAM-1, and IL-1 beta, was inhibited by both the c-JUN peptide and the JNK inhibitor SP600125. Thereby, and by additional experiments using small interfering RNA to suppress endogenous c-JUN we identify for the first time three distinct groups of inflammatory genes whose IL-1-induced expression depends on c-JUN, on JNK, or on both. These results shed further light on the complexity of c-JUN-JNK-mediated gene regulation and also highlight the potential use of dissecting signaling downstream from JNK to specifically target proliferative diseases or the inflammatory response.
Endocan Is a Novel Chondroitin Sulfate/Dermatan Sulfate Proteoglycan That Promotes Hepatocyte Growth Factor/Scatter Factor Mitogenic Activity (2001)

Proteoglycans that modulate the activities of growth factors, chemokines, and coagulation factors regulate in turn the vascular endothelium with respect to processes such as inflammation, hemostasis, and angiogenesis. Endothelial cell-specific molecule-1 is mainly expressed by endothelial cells and regulated by pro-inflammatory cytokines (Lassalle, P., Molet, S., Janin, A., Heyden, J. V., Tavernier, J., Fiers, W., Devos, R., and Tonnel, A. B. (1996) J. Biol. Chem. 271, 20458-20464). We demonstrate that this molecule is secreted as a soluble dermatan sulfate (DS) proteoglycan. This proteoglycan represents the major form either secreted by cell lines or circulating in the human bloodstream. Because this proteoglycan is specifically secreted by endothelial cells, we propose to name it endocan. The glycosaminoglycan component of endocan consists of a single DS chain covalently attached to serine 137. Endocan dose-dependently increased the hepatocyte growth factor/scatter factor (HGF/SF)-mediated proliferation of human embryonic kidney cells, whereas the nonglycanated form of endocan did not. Moreover, DS chains purified from endocan mimicked the endocan-mediated increase of cell proliferation in the presence of HGF/SF. Overall, our results demonstrate that endocan is a novel soluble dermatan sulfate proteoglycan produced by endothelial cells. Endocan regulates HGF/SF-mediated mitogenic activity and may support the function of HGF/SF not only in embryogenesis and tissue repair after injury but also in tumor progression.
High-level expression of a proteolytically sensitive diphtheria toxin fragment in Escherichia coli (1987)

ABM508 is a recombinant fusion protein consisting of the N-terminal 485 amino acids of diphtheria toxin joined to alpha-melanocyte-stimulating hormone. When expressed in Escherichia coli under the control of the tox promoter and signal sequence, ABM508 is severely degraded. When overexpressed from a thermoinducible lambda pR promoter fusion, ABM508 is largely insoluble. We compared the expression of ABM508 (501 amino acids) to a full-length mutant form of the toxin (CRM197; 535 amino acids) and found that CRM197 showed minimal proteolysis. Thus, the removal of the C-terminal 50 amino acids of the toxin destabilizes the protein, making it a target for proteases. Proteolysis of ABM508 could be reduced by removal of the tox signal sequence (thereby directing the protein to the cytoplasm) and growth in lon and htpR mutant strains of E. coli. We also showed that the solubility of tox gene products expressed in E. coli was directly related to the growth temperature of the culture. Thus, a fragment A fusion protein (223 amino acids), ABM508, and CRM197 were found in soluble extracts when expressed at 30 degrees C but could not be released by the same procedures after growth at 42 degrees C. On the basis of these observations, we fused the coding sequences for mature ABM508 to the trc promoter (inducible at 30 degrees C by isopropyl-beta-D-thiogalactoside) and expressed this construct in a lon htpR strain of E. coli. This plasmid made 10 mg of soluble tox protein per liter of culture (7.7% of the total cell protein) or 14 times more than our previous maximal level. Extracts from lon htpR cells harboring this plasmid had high levels of ADP-ribosyltransferase activity, and although proteolysis still occurred, the major tox product corresponded to full-length ABM508.
Comparison of various diagnostic methods for the detection of Mycoplasma bovis (1993)

Mycoplasma bovis, the main causative agent of mycoplasmal mastitis, arthritis and pneumonia in cattle, causes considerable economic losses. Veterinary hygiene measures would be most effective if introduced at an early stage, especially the culling of cows shedding the pathogen for the control of mastitis. It is therefore crucial to ensure that diagnostic methods are available which can perform rapid and specific detection of the agent at acceptable costs. Six different detection methods have been compared and evaluated in terms of performance parameters and suitability for routine diagnosis. Conventional M. bovis isolation and identification from culture is the only technique used for routine diagnosis at present. However, this process is rather laborious and time-consuming, and final results are available only after several days. Enzyme-linked immunosorbent assay (ELISA) techniques can be used to screen for M. bovis antibodies or antigens in clinically-diseased animals. Detection of the agent in subclinical cases was accomplished in pre-incubated samples by an antigen capture ELISA involving a monoclonal antibody. Whole-cell protein patterns generated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis were used to identify and classify field isolates. Nucleic acid hybridizations using probes of defined specificity were conducted both as filter dot blot assay and in solution with ribosomal ribonucleic acid as the target. The latter was found to be potentially suitable for the screening of biological samples, although problems due to high background and reduced specificity remained. Finally, the presence of M. bovis cells in culture supernatant and in milk samples was demonstrated using the polymerase chain reaction. This procedure is potentially superior to all others currently available, due to its high sensitivity, specificity and speed. However, a number of practical problems must be solved prior to full-scale introduction of this technique for routine diagnosis.
Nitric Oxide Donors for Cardiovascular Implant Applications (2012)

In an era of increased cardiovascular disease burden in the ageing population, there is great demand for devices that come in to contact with the blood such as heart valves, stents, and bypass grafts that offer life saving treatments. Nitric oxide (NO) elution from healthy endothelial tissue that lines the vessels maintains haemostasis throughout the vasculature. Surgical devices that release NO are desirable treatment options and N-diazeniumdiolates and S-nitrosothiols are recognized as preferred donor molecules. There is a keen interest to investigate newer methods by which NO donors can be retained within biomaterials so that their release and kinetic profiles can be optimized. A range of polymeric scaffolds incorporating microparticles and nanomaterials are presenting solutions to current challenges, and have been investigated in a range of clinical applications. This review outlines the application of NO donors for cardiovascular therapy using biomaterials that release NO locally to prevent thrombosis and intimal hyperplasia (IH) and enhance endothelialization in the fabrication of next generation cardiovascular device technology.
Effect of dehydrodidemnin B on human colon carcinoma cell lines. (1997)

Didemnins are cytotoxic agents belonging to a depsipeptide family isolated from marine tunicates. In the present study, a new member, dehydrodidemnin B (DDB), isolated from the mediterranean tunicate Aplidium albicans, was used. The effect of the drug on human colon cultured cell lines was tested using multiple approaches: proliferation studies, long term survival after three hours of exposure to DDB by means of a clonogenic assay and the decrease of the protooncogen, ornithine decarboxylase, activity. A dehydrodidemnin B concentration of 10(-8) M completely inhibited cell growth. The IC50 obtained using the MTT proliferation test, indicated that the most proliferative cell line (CT-2) was the most sensitive to the drug. Using a clonogenic assay a clear dose-response was obtained for the three cell lines used; HT-29 cell line showed the minimum survival after 3 hours of dehydrodidemnin B treatment. A dose-dependent decrease in ornithine decarboxylase activity was also observed in three cell lines assayed. The data presented indicate that the dehydrodidemnin B is a potent cytotoxic agent on rapidly dividing human colon cancer cells.
Fourier Acoustics: Sound Radiation and Nearfield Acoustical Holography (2000)

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Heat Shock Paradox and a New Role of Heat Shock Proteins and their Receptors as Anti-Inflammation Targets (2007)

This article discusses the role of heat shock proteins (Hsps) and their receptors as anti-inflammation targets. Hsps are highly conserved proteins that protect cells against noxious or deleterious stimulus. Intracellular Hsps function as molecular chaperones governing protein assembly, folding, or transport and as anti-apoptotic regulators of cell signalling pathways leading to cell death. In addition, intracellular Hsps have recently been shown to have an anti-inflammatory role in various inflammatory conditions such as infection, ischemia/reperfusion injury, and cardiovascular diseases. However, the heat shock response and the induction of Hsps have paradoxical effects against cell injury. Hsp induction before a pro-inflammatory stimulus is clearly beneficial but Hsp induction after a pro-inflammatory stimulus is cytotoxic. These paradoxical and contradictory effects may result from the different functions of intracellular versus extracellular Hsps. Extracellular Hsps released from cells with compromised integrity may function as danger signals activating innate immunity by interacting with their receptors. Therefore, modulating the levels of intracellular Hsps or the activities of Hsp receptors will be potential drug targets in inflammation.