gebhart/patrepeval huggingface dataset:
Scheduling Lot Switching Operations for Cluster Tools (2013)

A cluster tool that consists of several processing modules, a transport robot, and loadlocks is widely used for wafer processing in the semiconductor industry. The cluster tool repeats an identical operational sequence for processing wafers in a lot, and such a cyclic operation sequence is determined by the wafer flow pattern and process times of a wafer lot. When a wafer lot changes, the tool operation sequence should be switched accordingly. Switching from a cyclic tool operation sequence to another is subject to deadlocks and unnecessary task delays to avoid scheduling complexity. Hence, it is necessary to have a scheduling method for such frequent lot switchings that prevents a deadlock and reduces the switching time. In this paper, we first develop a Petri net model for lot switching operations and then utilize a mixed integer programming model for an optimal schedule. However, since its practical value is limited, we develop effective heuristic methods for lot switching in single-armed and dual-armed cluster tools. The scheduling strategies adapt prevalent cyclic tool scheduling rules, such as backward and swap sequences. By computational experiments, we prove the efficiency and effectiveness of the proposed scheduling rules.
Association of monoamine oxidase (MAO) activity with alcoholism and alcoholic subtypes (1993)

A familial/genetic study of platelet monoamine oxidase (MAO) activity in alcoholics was carried out. MAO activities were determined using phenylethylamine (PEA) as substrate at Km concentration (1.2 microM) and at saturating concentration (12.0 microM). Complex segregation analysis of familial data indicated a single major gene mode of transmission of activity at both substrate concentrations. In addition, the present sample size (13 families, 108 members) proved sufficient to allow correlation analysis of enzyme activity with affection status and clinical subtypes of affecteds. MAO activity was significantly correlated with alcoholism at both Km and saturating substrate concentrations and a significant correlation between low MAO activity and Cloninger Type II alcoholism was seen at Km substrate concentration. These results confirm a hierarchical cosegregation of platelet MAO activity and alcoholism suggesting that MAO activity warrants continued status as a marker in alcoholism.
The Neuromodulation of the Intestinal Immune System and Its Relevance in Inflammatory Bowel Disease (2015)

One of the main tasks of the immune system is to discriminate and appropriately react to "danger" or "non-danger" signals. This is crucial in the gastrointestinal tract, where the immune system is confronted with a myriad of food antigens and symbiotic microflora that are in constant contact with the mucosa, in addition to any potential pathogens. This large number of antigens and commensal microflora, which are essential for providing vital nutrients, must be tolerated by the intestinal immune system to prevent aberrant inflammation. Hence, the balance between immune activation versus tolerance should be tightly regulated to maintain intestinal homeostasis and to prevent immune activation indiscriminately against all luminal antigens. Loss of this delicate equilibrium can lead to chronic activation of the intestinal immune response resulting in intestinal disorders, such as inflammatory bowel diseases (IBD). In order to maintain homeostasis, the immune system has evolved diverse regulatory strategies including additional non-immunological actors able to control the immune response. Accumulating evidence strongly indicates a bidirectional link between the two systems in which the brain modulates the immune response via the detection of circulating cytokines and via direct afferent input from sensory fibers and from enteric neurons. In the current review, we will highlight the most recent findings regarding the cross-talk between the nervous system and the mucosal immune system and will discuss the potential use of these neuronal circuits and neuromediators as novel therapeutic tools to reestablish immune tolerance and treat intestinal chronic inflammation.
Inhibition of vacuolar H(+)-ATPase by disulfide bond formation between cysteine 254 and cysteine 532 in subunit A. (1994)

We have previously demonstrated that the coated vesicle vacuolar H(+)-ATPase (V-ATPase) can be inactivated by formation of intramolecular disulfide bonds (Feng, Y., and Forgac, M. (1992) J. Biol. Chem. 267, 19769-19772). The disulfide bond responsible for inactivation can be distinguished from other disulfide bonds that form by the fact that formation of the inactivating disulfide bond is blocked by ATP or high ionic strength. By taking advantage of these properties, we selectively labeled the ATPase at the relevant cysteine residues with fluorescein maleimide. After analyzing the proteolytic fragments that contain the labeled cysteine residues, we found that cysteine 254 and cysteine 532 in subunit A of the bovine V-ATPase are the residues that form the disulfide bond resulting in inactivation of the enzyme. Cysteine 254 and cysteine 532 correspond to 2 of the 3 cysteine residues that are conserved in all available V-ATPase A subunit sequences. Cysteine 254 is located in the consensus motif, G(X)4GKT, corresponding to residues 250-257, which is conserved in many nucleotide binding proteins. Cysteine 532 is located in a region not previously shown to be in proximity to the nucleotide binding site. Modification of cysteine 254 by disulfide bond formation with cysteine 532 or thio-disulfide exchange with cystine does not impair binding of 2-azido-[32P]ATP to the A subunit. The inhibition is therefore likely caused by disruption of the catalytic function of the ATPase on formation of the disulfide bond. A possible role in regulating intracellular acidification by reversible sulfhydryl oxidation and reduction is discussed.
The role of an 80 kDa fragment of E-cadherin in the metastatic progression of prostate cancer. (2003)

In this study, we present the first report of serum levels of the 80 kDa fragment of E-cadherin in prostate cancer patients. This fragment is exclusively seen in neoplastic prostate tissue and may represent a useful biomarker of prostate cancer disease progression. This study also demonstrates an association of increased levels of several metalloproteinases with metastatic prostate cancer and could provide a useful correlation between metalloproteinase expression/activity and E-cadherin cleavage and the metastatic progression of prostate cancer.
Conformal piezoelectric energy harvesting and storage from motions of the heart, lung, and diaphragm (2014)

Here, we report advanced materials and devices that enable high-efficiency mechanical-to-electrical energy conversion from the natural contractile and relaxation motions of the heart, lung, and diaphragm, demonstrated in several different animal models, each of which has organs with sizes that approach human scales. A cointegrated collection of such energy-harvesting elements with rectifiers and microbatteries provides an entire flexible system, capable of viable integration with the beating heart via medical sutures and operation with efficiencies of ∼2%. Additional experiments, computational models, and results in multilayer configurations capture the key behaviors, illuminate essential design aspects, and offer sufficient power outputs for operation of pacemakers, with or without battery assist.
Scalable SQL and NoSQL data stores (2011)

In this paper, we examine a number of SQL and socalled "NoSQL" data stores designed to scale simple OLTP-style application loads over many servers. Originally motivated by Web 2.0 applications, these systems are designed to scale to thousands or millions of users doing updates as well as reads, in contrast to traditional DBMSs and data warehouses. We contrast the new systems on their data model, consistency mechanisms, storage mechanisms, durability guarantees, availability, query support, and other dimensions. These systems typically sacrifice some of these dimensions, e.g. database-wide transaction consistency, in order to achieve others, e.g. higher availability and scalability.
Novel Poly(ADP-ribose) Polymerase-1 Inhibitor, AG14361, Restores Sensitivity to Temozolomide in Mismatch Repair-Deficient Cells (2004)

MMR defects are relatively common in sporadic tumors and cancer syndromes. PARP-1 inhibition represents a novel way of selectively targeting such tumors. The underlying mechanism is probably a shift of the cytotoxic locus of temozolomide to N(7)-methylguanine and N(3)-methyladenine, which are repaired by the base excision repair pathway in which PARP-1 actively participates.
<title>Laser ablation as a new tool for material science</title> (1993)

The recent rapid advances in the field of laser ablation have led to an important new tool for both material synthesis and material processing. Experiments in our laboratory have served as examples of both types of contributions from this new technique. The kinetic differences of growth between standard solid state synthesis and in situ growth by laser ablation have allowed the substitution of Ce, Tb and Th for Y in Y<SUB>1</SUB>Ba<SUB>2</SUB>Cu<SUB>3</SUB>O<SUB>7</SUB> for the first time. The effects of substitution for Y on the material Tc is discussed within the framework of the existing models for the Pr system. We suggest that localization of the holes by trapping may provide a suitable mechanism to account for the observed properties of the Pr and Ce substituted compounds. As an example of new material processing, polytetrafluoroethylene (PTFE) films were deposited by the laser ablation of a bulk PTFE target using the 4<SUP>th</SUP> harmonic, at 266 nm, of a Nd-YAG laser. The films are found to be stoichiometric with bulk- like optical properties. We propose a model which suggests that UV absorption onsets the pyrolitic decomposition of PTFE leading to monomer as the main ablation product. The monomer, ejected from the target at high velocity, subsequently re-polymerizes on the substrate.
Comparison of K‐ras point mutation distributions in intraductal papillary‐mucinous tumors and ductal adenocarcinoma of the pancreas (2004)

Intraductal papillary-mucinous tumors (IPMT) consist of cells with varying histologic degrees of severity and exhibit multiple tumor loci; however, whether or not these lesions exhibit the same genetic changes has not been clarified. To investigate this point, we analyzed K-ras mutations in multiple IPMT lesions from each patient enrolled in our study and compared our findings to those for patients with ductal adenocarcinoma of the pancreas (DC). Twenty IPMT specimens and 7 DC specimens were resected, microdissected and analyzed for the presence of K-ras mutations. The mutated genes were then sequenced using a genetic analyzer. K-ras mutations were observed in 80% of IPMT and 100% of DC patients. More than 2 types of K-ras mutation were observed in the main tumors of 43.8% of IPMT and 0% of DC patients. K-ras mutations in peritumoral and separated lesions were observed in 66.7% and 62.5% of IPMT patients, respectively. At least one identical mutation between the main tumor and the peritumoral or separated lesions was recognized in all of the IPMT patients with those lesions. Different mutations from those in the main tumor were observed in 40% of IPMT patients with separated lesions. The survival curve of IPMT-carcinoma patients with more than 2 types of K-ras mutation in the main tumor was better than that with one type of K-ras mutation. IPMT patients exhibit a remarkably genetic heterogeneity in main tumor and have good prognosis.
Disposition and Analgesic Effects of Systemic Morphine, Morphine‐6‐glucuronide and Normorphine in Rat (1996)

Morphine, morphine-6-glucuronide and normorphine were administered to male Sprague-Dawley-rats. Analgesic effect was estimated with the hot plate and spinal nociceptive reflex depression. After intraperitoneal administration the molar potency ratio of morphine-6-glucuronide/morphine was 1.7 estimated by the paw lick latency on the hot plate utilizing a linked pharmacokinetic-pharmacodynamic model. The potency ratio of morphine-6-glucuronide/morphine utilizing the spinal nociceptive reflex depression after intravenous administration was estimated to be within the earlier reported range of 1-4 after systemic administration of the drugs. In contrast to what is seen in man virtually no morphine-6-glucuronide was formed in Sprague-Dawley rats after administration of morphine, much lower levels of morphine-3-glucuronide were also seen. The molar AUC ratio of morphine-3-glucuronide/morphine was 1.8 +/- 0.5 and the corresponding ratio for normorphine/morphine was 0.2 +/- 0.06. After intraperitoneal administration of morphine, morphine-6-glucuronide and normorphine mean systemic clearance values of 413 +/- 95, 50 +/- 11 and 187 +/- 54 ml.min.kg-1 respectively were observed. Varea was 9.0 +/- 2.1, 0.8 +/- 0.2 and 4.9 +/- 1.4 L.kg-1 respectively. The slow absorption of morphine-6-glucuronide was illustrated by the mean Tmax-value of the 16 min. as compared with 9 min. for morphine and 10 min. for normorphine. It was possible to fit pharmacokinetic and pharmacodynamic data of behavioural analgesic effect of both morphine and morphine-6-glucuronide to a parametric model linking the sigmoid Emax model to standard pharmacokinetic equations.
Overexpression of Caspase-1 in adenocarcinoma of pancreas and chronic pancreatitis (2003)

Overexpression of Caspase-1 is a frequent event in pancreatic disorders and its differential expression patterns may reflect two functions of the protease. One is its participation in the apoptotic pathway in atrophic acinar cells and tumor-surrounding pancreatitis tissue, the other is its possible role in proliferative processes in pancreatic cancer cells and hyperplastic duct cells and dedifferentiating acinar cells in chronic pancreatitis.
ReDAC -- Dynamic Reconfiguration of Distributed Component-Based Applications with Cyclic Dependencies (2008)

This paper introduces ReDAC, a new algorithm for dynamic reconfiguration of multi-threaded applications. In order to achieve high reliability and availability, distributed component software has to support dynamic reconfiguration. Typical examples include the application of hot-fixes to deal with security vulnerabilities. ReDAC can be implemented on top of the modern component-platforms Java and .NET. We extend the statical term component, denoting a unit of deployment, to runtime by defining a capsule (runtime component instance) to be a set of interconnected objects. This allows us to apply dynamic updates at the level of components during runtime without stopping whole applications. Using system-wide unique identifiers for threads (logical thread IDs), we can detect and also bring capsules into a reconfigurable state by selectively blocking threads, relying on data structures maintained by additional logic integrated into the capsules using aspect-oriented programming. An important contribution of this paper is that ReDAC supports the dynamic reconfiguration of distributed multi-threaded and re-entrant components with cyclic call dependencies.
[Research advances in new treatment of heart failure]. (2007)

The treatments for heart failure were developed rapidly in recent years ; new therapeutic techniques such as cytokine therapy, gene therapy and pacemaker therapy have been developed respectively. This paper reviews the mechanisms, therapeutic effect and limitation of these new techniques, and the future work in this research field is also discussed.
Synthesis and Properties of Novel Water-Soluble Conducting Polyaniline Copolymers (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and Properties of Novel Water-Soluble Conducting Polyaniline CopolymersMy T. Nguyen, Paul Kasai, James L. Miller, and Arthur F. DiazCite this: Macromolecules 1994, 27, 13, 3625–3631Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/ma00091a026https://doi.org/10.1021/ma00091a026research-articleACS PublicationsRequest reuse permissionsArticle Views1023Altmetric-Citations161LEARN 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
Risk factors for human disease emergence (2001)

A comprehensive literature review identifies 1415 species of infectious organism known to be pathogenic to humans, including 217 viruses and prions, 538 bacteria and rickettsia, 307 fungi, 66 protozoa and 287 helminths. Out of these, 868 (61%) are zoonotic, that is, they can be transmitted between humans and animals, and 175 pathogenic species are associated with diseases considered to be 'emerging'. We test the hypothesis that zoonotic pathogens are more likely to be associated with emerging diseases than non-emerging ones. Out of the emerging pathogens, 132 (75%) are zoonotic, and overall, zoonotic pathogens are twice as likely to be associated with emerging diseases than non-zoonotic pathogens. However, the result varies among taxa, with protozoa and viruses particularly likely to emerge, and helminths particularly unlikely to do so, irrespective of their zoonotic status. No association between transmission route and emergence was found. This study represents the first quantitative analysis identifying risk factors for human disease emergence.
Superresolution restoration of an image sequence: adaptive filtering approach (1999)

This paper presents a new method based on adaptive filtering theory for superresolution restoration of continuous image sequences. The proposed methodology suggests least squares (LS) estimators which adapt in time, based on adaptive filters, least mean squares (LMS) or recursive least squares (RLS). The adaptation enables the treatment of linear space and time-variant blurring and arbitrary motion, both of them assumed known. The proposed new approach is shown to be of relatively low computational requirements. Simulations demonstrating the superresolution restoration algorithms are presented.
Therapeutic cancer vaccines: Using unique antigens (2004)

A decade ago, it seemed rational that our rapidly increasing knowledge of the molecular identities of tumor antigens and a deeper understanding of basic immunology would point the way to an effective therapeutic cancer vaccine. Significant progress has been made, but we do not yet have a cancer vaccine that can reliably and consistently induce tumor destruction or improve patient survival. Random mutations in cancer cells generate unique antigens in each individual, and this may be important in terms of generating a therapeutic immune response. Autologous heat shock protein-peptide complexes produced from each patient's tumor is a logical personalized approach that may obviate the need to identify the unique antigens contained in the individual vaccine. Heat shock proteins elicit adaptive and innate immune responses and have been tested in a variety of animal models and different human cancers. Activity has been seen in several animal studies. Early-phase human studies have also suggested some activity in certain cancers. Large, randomized phase 3 studies are ongoing, and these will effectively answer the question of efficacy regarding this approach to therapeutic vaccination. There are sufficient data to support the notion that cancer vaccines can induce anti-tumor immune responses in humans with cancer. How best to translate this increase in immune responsiveness to consistently and reproducibly induce objective cancer regression or increased survival remains unclear at this time.
Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units (2001)

Multizinc finger peptides are likely to reach increased prominence in the search for the "ideal" designer transcription factor for in vivo applications such as gene therapy. However, for these treatments to be effective and safe, the peptides must bind with high affinity and, more importantly, with great specificity. Our previous research has shown that zinc finger arrays can be made to bind 18 bp of DNA with picomolar affinity, but also has suggested that arrays of fingers also may bind tightly to related sequences. This work addresses the question of zinc finger DNA binding specificity. We show that by changing the way in which zinc finger arrays are constructed--by linking three two-finger domains rather than two three-finger units--far greater target specificity can be achieved through increased discrimination against mutated or closely related sequences. These new peptides have the added capability of being able to span two short gaps of unbound DNA, although still binding with picomolar affinity to their target sites. We believe that this new method of constructing zinc finger arrays will offer greater efficacy in the fields of gene therapy and in the production of transgenic organisms than previously reported zinc finger arrays.
Hypoxia-inducible Mammalian Gene Expression Analyzed in Vivo at a TATA-driven Promoter and at an Initiator-driven Promoter (1998)

We have analyzed protein-DNA interactions in vivo at transcriptional control elements for two hypoxia-inducible genes in mouse hepatoma cells. The promoter for the phosphoglycerate kinase 1 (PGK1) gene contains an initiator element, but no TATA sequence, whereas the promoter for the glucose transporter 1 (Glut1) gene contains a TATA element but no initiator sequence. Our findings reveal hypoxia-inducible, Arnt-dependent occupancy of DNA recognition sites for hypoxia-inducible factor 1 (HIF-1) upstream of both target genes. The conserved recognition motif among the five recognition sites is 5'-CGTG-3'. The PGK1 promoter exhibits constitutive occupancy of a binding site for an unknown protein(s); however, we detect no protein-DNA interaction at the initiator element, in either uninduced or induced cells. The Glut1 promoter also exhibits constitutive protein binding; in addition, the TATA element exhibits partial occupancy in uninduced cells and increased occupancy under hypoxic conditions. We find no evidence for hypoxia-induced changes in chromatin structure of either gene. Time-course analyses of the Glut1 gene reveal a temporal relationship between occupancy of HIF-1 sites and TATA element occupancy. Our findings suggest that the promoters for both hypoxia-responsive genes constitutively maintain an accessible chromatin configuration and that HIF-1 facilitates transcription by recruiting and/or stabilizing a transcription factor(s), such as TFIID, at both promoters.
Synthesis and Hybridisation Properties of Phosphonamidate Ester Modified Nucleic Acid (2001)

The replacement of the two backbone oxygen atoms of the phosphodiester linkage of DNA with carbon and nitrogen in the form of a phosphonamidate ester linkage, in both possible regioisomeric forms, is described. An alkylation reaction with the 3′-C-P-N-5′ methyl phosphoamidate regioisomer yielded the corresponding N-methylated analogues. For each example separation into individual phosphonamidate ester diastereoisomers was performed prior to incorporation into oligonucleotides. The effect upon duplex stability for DNA oligonucleotides containing each of these modifications with complimentary RNA is reported.