gebhart/patrepeval huggingface dataset:
Dependability of complex software systems with component upgrading (2002)

Some very large and complex systems, such as telecommunication systems, must (and typically do) exhibit exceptional dependability. These systems are seldom totally replaced with a new system because of the increased likelihood of a lapse in service. Rather, systems are upgraded incrementally while operational, albeit that this often involves large-scale software changes. It is especially important then to ensure that new or replacement components are ready for online installation before they are incorporated into an operational system. It is often costly and time-consuming to determine the readiness of new components for installation. Even then, the result may be unpredictable. Hence, we have developed effective and economical methods for software component verification that ensure and increase the overall system dependability. We tested our technologies using a telecommunication application, an Internet call-agent. Our experimental results show that our dynamic design analysis approach reduces computational costs and detects more errors than conventional approaches. The more frequently that changes are made, the greater the savings in the time required for model analysis and property prediction.
277. Small Molecule-Regulated Antigen Recognition System for Inducible T Cell Targeting of Cancer Cells (2016)

Redirecting T cells against tumors by introducing chimeric antigen receptors (CAR) has demonstrated promising clinical results in certain cancers. However, the constitutive activity of these receptors limits which antigens can be targeted with this approach and may result in persistent elimination of healthy antigen-expressing cells. Successful CAR-T targeting of CD19+ tumors, for example, produces chronic B cell aplasia and necessitates life-long intravenous immunoglobulin (IVIG) treatment. Daric is an alternative antigen targeting approach that aims to: i) minimize the long-term toxicity of CAR-T treatment; ii) allows targeting of previously inaccessible antigens; and iii) is amenable to multiplex antigen targeting and other advanced targeting designs and strategies. The Daric system separates the antigen recognition and signaling functions of a CAR into two distinct polypeptides that contain the FKPB12 and FRB dimerization domains but lack signaling activity in the absence of a dimerization agent. Addition of the FKBP12-FRB bridging drug rapamycin or a non-immunosuppressive rapamycin analogue AP21967 heterodimerizes the signaling and antigen recognition components and restores signaling competency for antigen-dependent T cell activation. Importantly, the FKB12 and FRB dimerization partners are located extracellularly, minimizing interference with endogenously expressed signaling components and eliminating the requirement for rapamycin/AP21967 cell penetrance. A range of extracellular linkers and transmembrane domains were used to design a variety of CD19-targeting Daric constructs that exhibit minimal basal activity and robust drug-dependent antigen-specific cytolytic activity and cytokine production. The CD19-specific Daric T cells exhibited comparable levels of cytokine release, proliferation and cytolytic activity compared to a CD19-targeting CAR T cells. In vitro, Daric T cells were activated at sub-nanomolar to nanomolar concentrations of rapamycin or AP21967. No differences in cellular phenotype, expansion or functional responsiveness of Daric T cells compared to CAR T cells were observed. As expected, rapamycin was immunosuppressive to CAR T cell functionality, however Daric T cells continued to produce high level of cytokines even in the presence of rapamycin. These results highlight the potential of the Daric system to target highly expressed antigens and minimize the off-tumor on-target toxicity associated with traditional CAR designs.
Characteristics of human protoporphyrinogen oxidase in controls and variegate porphyrias. (1997)

Protoporphyrinogen oxidase (E.C.1.3.3.4) (PPO) catalyzes the penultimate step in the heme biosynthetic pathway. Deficiency in activity of this enzyme results in the human genetic disease variegate porphyria. Herein we detail the cloning, expression, purification and characterization of the normal and variegate porphyria forms of human PPO. The cDNA sequence for human ppo is approximately 1.8 kb in length and codes for a protein of 477 amino acids. This protein, which does not contain a typical cleavable mitochondrial targeting sequence, is approximately 51 kDa and contains a putative dinucleotide binding motif near the amino terminus. The active enzyme is a homodimer and contains an FAD. Attachment of a six his amino terminal tag allows for the rapid and efficient purification of approximately 10 mg of enzyme from one liter of E. coli culture. Three variegate porphyria mutant PPO enzymes were expressed and characterized. These mutations, R59W, R168C and A433P, result in decreased enzyme activity by causing a decrease in kcat without a significant change in Km for the substrate protoporphyrinogen IX. Purified R59W lacks the FAD cofactor which may be explained by the fact that this mutation resides within the dinucleotide binding motif of PPO.
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence (1997)

We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
Focal Adhesion Kinase Silencing Augments Docetaxel-Mediated Apoptosis in Ovarian Cancer Cells (2005)

Docetaxel induces FAK cleavage, mediated through activation of caspase-3, in taxane-sensitive ovarian cancer cells but not in taxane-resistant cells. The absence of FAK degradation may contribute to cell survival in taxane-resistant cells. FAK silencing promotes the in vitro efficacy of docetaxel in both taxane-sensitive and taxane-resistant cell lines and may serve as a novel therapeutic approach.
Synthesis and Antimicrobial Evaluation of Some Heterocyclic Chalcone Derivatives (2011)

Some new heterocyclic compounds containing isoxazole, pyrazole and oxadiazole ring systems were prepared from various chalcones. The synthesized compounds have been characterized by elemental analysis and spectral methods. These compounds were screened for their antimicrobial activities.
Properties of Photogenerated Tryptophan and Tyrosyl Radicals in Structurally Characterized Proteins Containing Rhenium(I) Tricarbonyl Diimines (2001)

Aromatic amino acid radicals are key intermediates in nucleic acid biosynthesis, DNA repair, dioxygen reduction by cytochrome oxidase, water oxidation by PSII, as well as other biological procesess. In our work on electron tunneling in proteins, we have developed laser flash/quench methods that potentially could facilitate the study of such highly reactive radicals. To test our methods, we are investigating two structurally characterized proteins, [Re(CO)_3(L)(H83)]^+AzM^(2+) and [Re(CO)_3(L)(H107)]^+AzM^(2+) (L ) 1,10-phenanthroline (phen) or 4,7-Me_2phen; Az ) Pseudomonas aeruginosa azurin; M ) Cu or Zn). Of special interest is that calculations and experiments on the H107 protein show that Cu^+ oxidation via electron transfer (ET) through an intervening tyrosine (Cu^+ → Y108^(./) → Re(2+)) is over 2 orders of magnitude faster than optimized (Cu^+ → Re^(2+)) electron tunneling.
Crystallization and thermal properties of PLLA comb polymer (2008)

Abstract Poly( L ‐lactide) (PLLA) on poly(2‐hydroxyethyl methacrylate) (PHEMA) backbone was prepared by a combination of atom transfer radical polymerization (ATRP) and ring‐opening polymerization (ROP). The structure of the comb polymer was analyzed by wide angle X‐ray diffraction (WAXD), small angle X‐ray scattering (SAXS), and differential scanning calorimetry (DSC). WAXD result indicates that the comb polymer has α crystalline modification with a 10 3 helical conformation. Lamellar parameters of the crystalline structure were obtained by one‐dimension correlation function (1DCF) calculated from SAXS results. The calculations show that the thickness of crystalline layer is controlled by annealing temperature and comb structure. DSC was applied to study kinetics of the crystallization and melting behavior. Two melting peaks on melting curves of the comb polymer at different crystallization temperature were detected, and the peak at higher temperature is attributed to the melt‐recrystallization. The equilibrium melting temperature is found to be influenced by the comb structure. In this article the effects of the comb structure on Avrami exponent, equilibrium melting point and melting peak of the comb polymer were discussed. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 589–598, 2008
An Adaptive Recommendation System in Social Media (2012)

In a broader sense, news recommendation essentially is to select relevant news by their themes. Identification of topical patterns is critical in this task. Common strategies in the previous studies rely on news entities to extract topic patterns. In such a way, news is recommended solely based on the author's point of view. In this article, we argue that, in social media, the performance of recommendation can be immensely enhanced if user interaction is better utilized. It overcomes the bias of traditional news recommendation by suggesting relevant information with a balanced perspective of authors and readers. This is achieved by identifying and using the topic patterns of the original news posting and its comments, one of the most useful records of user behaviors in social media. In particular, to capture the dynamic concerns of users, hidden topic patterns are extracted by utilizing both textual and structural information of comments. To do so, we model the relationship among comments and that relative to the original posting using an undirected a cyclic graph, where each node is a word, each edge is a structural link between words. Experiments indicate that our proposed solution provides an effective news recommendation service in social media.
Denoising of Array-Based DNA Copy Number Data Using The Dual-tree Complex Wavelet Transform (2007)

Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable detection of local one-copy-level variations. Characterization of these DNA copy number changes is important for both the basic understanding of cancer and its diagnosis. In order to develop effective methods to identify aberration regions from array CGH data, many recent research works focus on both smoothing-based and segmentation-based data processing. In this paper, we propose to use the dual-tree complex wavelet transform to smooth the array CGH data. We demonstrate the effectiveness of our approach through theoretic and experimental exploration of a set of array CGH data, including both synthetic data and real data. The comparison results show that our method outperforms the previous approaches.
Inflammatory cytokines and cytokine antagonists in whole blood cultures of patients with systemic juvenile chronic arthritis (1998)

In the present study, we investigated the kinetics and the activation thresholds for the production of a number of pro-inflammatory cytokines and cytokine antagonists in Escherichia coli lipopolysaccharide (LPS) or phytohaemagglutinin (PHA) stimulated whole blood cultures of 13 patients with systemic juvenile chronic arthritis (SJCA) and 10 healthy children. In unstimulated cultures, the levels of interleukin (IL)-1beta, IL-6 and tumour necrosis factor alpha (TNF-alpha) were undetectable in both groups, suggesting that there was no spontaneous production of these cytokines by circulating leucocytes. The activation thresholds for the production of these cytokines, as well as the capacity for production, did not differ significantly between patients and controls. The level of interleukin-1 receptor antagonist (IL-1ra) in plasma of the patients was significantly elevated, while the in vitro production of IL-1ra was essentially normal and it did not correlate with plasma levels of IL-1ra. Supernatant levels of soluble TNF-alpha receptor (sTNF-R) I and II were both significantly elevated and correlated with the global activity score. In contrast, the supernatant levels of IL-10 were reduced in both PHA- and LPS-driven cultures. Although IL-10 levels did not correlate with laboratory or clinical indices of disease activity, the results suggest that reduced IL-10 production may play a pathogenetic role in SJCA.
Toward autonomous driving: the CMU Navlab. I. Perception (1991)

The Navlab project, which seeks to build an autonomous robot that can operate in a realistic environment with bad weather, bad lighting, and bad or changing roads, is discussed. The perception techniques developed for the Navlab include road-following techniques using color classification and neural nets. These are discussed with reference to three road-following systems, SCARF, YARF, and ALVINN. Three-dimensional perception using three types of terrain representation (obstacle maps, terrain feature maps, and high-resolution maps) is examined. It is noted that perception continues to be an obstacle in developing autonomous vehicles. This work is part of the Defense Advanced Research Project Agency. Strategic Computing Initiative.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tape Casting as a Multi Purpose Shaping Technology for Different Applications in Energy Issues (2012)

Tape casting is widely used in industrial scale for production of multilayer ceramic capacitors or substrates for different applications. In 2009, it was successfully introduced as standard shaping technology for 3 (BSCF) are shown. The entire scope from the preparation of the used powders, the different manufacturing steps and their optimization potential up to the final tape-cast product will be discussed. The influence of the use of pore forming agents, heat treatment or other parameters during processing will be described in detail. Finally, the option of sequential tape casting of different materials for graded structures as a future step in shaping technology will be presented for different applications.
Monoclonal Antibody Conjugates of Doxorubicin Prepared with Branched Peptide Linkers:  Inhibition of Aggregation by Methoxytriethyleneglycol Chains (2002)

High mole ratio BR96 immunoconjugates were synthesized using branched peptide-doxorubicin linkers designed to liberate doxorubicin following antigen-specific internalization into lysosomes. However, these immunoconjugates are highly prone to noncovalent, dimeric aggregation. We hypothesize that this is due to (1) the hydrophobic nature of the peptides, (2) the loss of positive charge upon amide formation at the 3'-amino group of doxorubicin, and (3) the proximity of the peptide hydrophobic residues to form efficient intermolecular stacking interactions. By introducing a hydrophilic methoxytriethylene glycol chain onto the doxorubicin portion of the branched peptide linkers, aggregation has been eliminated or greatly reduced in the immunoconjugate products. The methoxytriethylene glycol chain was linked to the doxorubicin moiety of the linker via a hydrazone bond that is stable at pH 7 but hydrolyzes rapidly at pH 5 to release free drug. BR96 immunoconjugates synthesized from methoxytriethylene glycol-modified branched peptide-doxorubicin linkers are highly potent and immunospecific in vitro. The data suggest that the methoxytriethylene glycol chain hydrolyzes as designed upon antigen-specific internalization into tumor lysosomes in vitro, where enzymatic degradation of the peptide linker releases free doxorubicin.
Adenovirus Early Region 3 (E3) Immunomodulatory Genes Decrease the Incidence of Autoimmune Diabetes in NOD Mice (2001)

The early three (E3) region of the adenovirus (Ad) encodes a number of immunomodulatory proteins that interfere with class I major histocompatibility-mediated antigen presentation and confer resistance to cytokine-induced apoptosis in cells infected by the virus. Transgenic expression of Ad E3 genes under the rat insulin II promoter (RIP-E3) in beta-cells in nonobese diabetic (NOD) mice decreases the incidence and delays the onset of autoimmune diabetes. The immune effector cells of RIP-E3/NOD mice maintain the ability to infiltrate the islets and transfer diabetes into NOD-scid recipients, although at a significantly reduced rate compared with wild-type littermates. The islets of RIP-E3/ NOD mice can be destroyed by adoptive transfer of splenocytes from wild-type NOD mice; however, the time to onset of hyperglycemia is delayed significantly, and 40% of these recipients were not diabetic at the end of the experiment. These findings suggest that expression of E3 genes in beta-cells affects both the activation of immune effector cells and the intrinsic resistance of beta-cells to autoimmune destruction.
Automated instrumentation for comprehensive two-dimensional high-performance liquid chromatography/capillary zone electrophoresis (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAutomated instrumentation for comprehensive two-dimensional high-performance liquid chromatography/capillary zone electrophoresisMichelle M. Bushey and James W. JorgensonCite this: Anal. Chem. 1990, 62, 10, 978–984Publication Date (Print):May 15, 1990Publication History Published online1 May 2002Published inissue 15 May 1990https://pubs.acs.org/doi/10.1021/ac00209a002https://doi.org/10.1021/ac00209a002research-articleACS PublicationsRequest reuse permissionsArticle Views517Altmetric-Citations176LEARN 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
Disulfiram Implant: A Double‐Blind Placebo Controlled Follow‐Up on Treatment Outcome (1991)

Seventy-six alcohol-dependent patients participated in a study of the clinical effect of implanted disulfiram (DS). The patients were randomized to a DS group (n = 40), receiving a subcutaneous abdominal implantation of 10 x 100 mg DS tablets and a placebo group (PL group) receiving an implantation of 9 x 100 mg calcium phosphate tablets together with one calcium phosphate tablet containing 1 mg DS. Both groups believed they were receiving DS. At admission there was no significant difference between the DS and PL groups with regard to demographic characteristics, psychosocial adjustment, drinking variables, medical disorders, or laboratory results. After a study period of approximately 300 days, 63 patients (33 DS; 30 PL) were assessed using a battery of tests. There was no significant difference between the groups with regard to reduction in average alcohol consumption, number of days to the first alcohol intake after implantation, or level of psychosocial function. Nevertheless, both groups reduced their ethanol consumption significantly, probably due to the psychological deterrent effect. The DS implant did result in a significantly higher incidence of wound complications. This study does not support the idea that a 1-g DS implant has any significant clinical effect different from the implant containing only 1 mg DS (placebo).
In Vitro Synthesis of Polypeptides of Moderately Large Size by Poly(A)‐Containing Messenger RNA from Postmortem Human Brain and Mouse Brain (1983)

Studies were undertaken to optimize the conditions for isolation and in vitro translation of poly(A)-containing mRNA from human postmortem brain. The comparison of several methods for preparation of mRNA from frozen mouse brain indicated that although the yield of mRNA was increased using polysomes prepared in the presence of ribonucleoside vanadyl complexes and subsequently extracted with guanidinium thiocyanate, the translation products were indistinguishable from those synthesized by total cellular RNA directly extracted from tissue with guanidinium thiocyanate. The oligo d(T)-cellulose-purified poly(A)-containing mRNA preparations were translated in vitro in a rabbit reticulocyte lysate in the presence of L-[35S]methionine. Messenger RNA from frozen mouse brain stimulated protein synthesis from 9- to 20-fold over endogenous mRNA. Over 450 polypeptides were reproducibly synthesized and separated by two-dimensional polyacrylamide gel electrophoresis (PAGE); size classes up to 130,000 daltons were present. Direct extraction of RNA from frozen human cerebral cortex and cerebellum with guanidinium thiocyanate followed by oligo d(T)-cellulose chromatography yielded 1.8 micrograms/g and 2.0 micrograms/g, respectively, of poly(A)-containing mRNA; this represents a two- to fourfold increase over our earlier results. In the rabbit reticulocyte translation system human brain mRNA stimulated protein synthesis nearly threefold over endogenous mRNA. Compared with earlier studies, the number of newly synthesized polypeptides was increased by 30%. Over 300 species were separated by two-dimensional PAGE, and size classes up to 130,000 daltons were present, as compared to 70,000 in an earlier report. The polypeptides synthesized by human cerebral cortex and cerebellum were indistinguishable. However, several appeared to be uniquely human when compared with the products synthesized by mouse brain mRNA. The method described for the preparation of postmortem human brain mRNA eliminates the need to prepare polysomes, which are recovered in variable and low yield from the postmortem human brain. The procedure appears applicable to studies on the synthesis of moderately large human brain polypeptides and for investigations of brain protein polymorphism when relatively large numbers of products are required for analysis.