gebhart/patrepeval huggingface dataset:
Enhancing the performance of Hopfield Neural Network applied to the Economic Dispatch Problem (2006)

This paper introduces some modifications to the conventional Hopfield Neural Network (HNN) to enhance its performance. A comprehensive study of the effect of the HNN parameters on the solution quality of the Economic Dispatch Problem (EDP), as a case study, is done. By investigating the describing curves, the best values for the HNN parameters are tuned. To further improve the solution quality, an adaptive correction factor is proposed and introduced to the EDP solution obtained by HNN. To investigate the effect of the modifications on the solution quality of the EDP, two case studies are selected and solved. Comparisons of results are then made with others to prove the validity and effectiveness of the proposed modifications.
Nuclear translocation of AMPK-α1 potentiates striatal neurodegeneration in Huntington’s disease (2011)

Adenosine monophosphate-activated protein kinase (AMPK) is a major energy sensor that maintains cellular energy homeostasis. Huntington's disease (HD) is a neurodegenerative disorder caused by the expansion of CAG repeats in the huntingtin (Htt) gene. In this paper, we report that activation of the α1 isoform of AMPK (AMPK-α1) occurred in striatal neurons of humans and mice with HD. Overactivation of AMPK in the striatum caused brain atrophy, facilitated neuronal loss, and increased formation of Htt aggregates in a transgenic mouse model (R6/2) of HD. Such nuclear accumulation of AMPK-α1 was activity dependent. Prevention of nuclear translocation or inactivation of AMPK-α1 ameliorated cell death and down-regulation of Bcl2 caused by mutant Htt (mHtt). Conversely, enhanced expression of Bcl2 protected striatal cells from the toxicity evoked by mHtt and AMPK overactivation. These data demonstrate that aberrant activation of AMPK-α1 in the nuclei of striatal cells represents a new toxic pathway induced by mHtt.
Optimal stochastic scheduling in multiclass parallel queues (1999)

In this paper we consider the problem of scheduling different classes of customers on multiple distributed servers to minimize an objective function based on per-class mean response times. This problem arises in a wide range of distributed systems, networks and applications. Within the context of our model, we observe that the optimal sequencing strategy at each of the servers is a simple static priority policy. Using this observation, we argue that the globally optimal scheduling problem reduces to finding an optimal routing matrix under this sequencing policy. We formulate the latter problem as a nonlinear programming problem and show that any interior local minimum is a global minimum, which significantly simplifies the solution of the optimization problem. In the case of Poisson arrivals, we provide an optimal scheduling strategy that also tends to minimize a function of the per-class response time variances. Applying our analysis to various static instances of the general problem leads us to rederive many results, yielding simple approximation algorithms whose guarantees match the best known results.
<title>A comparison of fitness function evaluation schedules for multi-objective univariate marginal distribution optimization of mixed analog-digital signal circuits</title> (2008)

An increasing complexity of mixed analog-digital signal circuits requires optimization at higher hierarchical level. However, evolutionary optimization of mixed analog-digital signal circuits at the system level results in huge computational costs. A key to manage these computational complexities of evolutionary circuit design is an application of flexible fitness functions evaluation schedules. In this paper we compare the static, dynamic, and co-evolution fitness function evaluation schedules for multi-objective optimization of mixed analog-digital signal circuits at the system level on the base of the univariate marginal distribution algorithm. Experiments for our symmetry recognition circuit benchmark chosen indicate that the dynamic fitness function schedule is a good compromise between computational costs and optimization efficiency.
A criterion for an energy vortex in a sound field (1987)

Measurements with intensity meters have shown that energy vortices exist in certain sound fields. In these vortices, sound energy flows around closed paths, in the steady state. Vortices occur in some sound fields (e.g., that of a point source near a reflecting edge), but not in others (e.g., that of a plane rigid piston in a plane rigid baffle). It is shown that in a two-dimensional or axisymmetric sound field, a necessary and sufficient condition for a vortex to exist is the presence of an isolated maximum or minimum in the stream function. Two examples are given for a vortex in (a) a duct of square cross section, and (b) the field of two monopole sources, one of which just extinguishes the other. Some relations for the interaction between two monopole sources are also given.
SPIN, a substrate in the MAP kinase pathway in mouse oocytes (1998)

The newly cloned gene Spin encodes a 30-kDa protein, a well-defined abundant molecule found in mouse oocytes and early embryos. This protein SPIN undergoes metaphase-specific phosphorylation and binds to the spindle. To understand the role of SPIN in oocyte meiosis, oocytes were treated with drugs that affect the cell cycle by activating or inactivating specific kinases. The posttranslational modification of SPIN in the treated oocytes was then investigated by one- and two-dimensional gel electrophoresis. Modification of SPIN is inhibited by treatment with 6-dimethylaminopurine (DMAP), suggesting that SPIN is phosphorylated by a serine-threonine kinase. Furthermore, SPIN from cycloheximide-treated oocytes that lack detectable MAP kinase activity is only partially phosphorylated, indicating that SPIN may be phosphorylated by the MOS/MAP kinase pathway. To confirm this observation, SPIN was analyzed in Mos-null mutant mice lacking MAP kinase activity. Normal posttranslational modification of SPIN did not occur in Mos-null mutant oocytes. In addition, there is reduced association of SPIN with the metaphase I spindle in Mos-null mutant oocytes, as determined by immunohistochemical analysis. These findings suggest that SPIN is a substrate in the MOS/ MAP kinase pathway and further that this phosphorylation of SPIN may be essential for its interaction with the spindle.
A comparative study of time dependent quantum mechanical wave packet evolution methods (1992)

We present a detailed comparison of the efficiency and accuracy of the second- and third-order split operator methods, a time dependent modified Cayley method, and the Chebychev polynomial expansion method for solving the time dependent Schrodinger equation in the one-dimensional double well potential energy function. We also examine the efficiency and accuracy of the split operator and modified Cayley methods for the imaginary time propagation.
Antiproton annihilation in light nuclei (1987)

The possibility of antiproton annihilation on a cluster of nucleons is investigated. In the model, the annihilation forms a quark-gluon plasma droplet which on expansion coagulates into mesons and baryons. The energy spectra and multiplicities of mesons as well as kaon and lambda production ratios are computed. The probability of annihilation on a pair of nucleons is about ten percent, but the lower plasma temperature reduces strangeness production.
Polymers of dimethylketene having prevailingly polyacetalic structure (1962)

Abstract By polymerizing dimethylketene in ether solution in the presence of lithium derivatives such as LiC 4 H 9 and LiOC 4 H 9 , a new crystalline polymer has been prepared, to which an essentially polyacetalic structure can be assigned. The I.R. spectra show the characteristic bands of a earbon‐earbon double bond; the results of the chain degradation by acid alcoholysis and hydrogenolysis with LiAlH 4 agree with the presence of acetalie bonds. A clear likeness between the chemical reactivity of acetalic polydimethylketene and that of polyisobutyraldehyde has been found.
Tannic Acid-Mediated Surface Functionalization of Polymeric Nanoparticles (2016)

Polymeric nanoparticles (NPs) are decorated with various types of molecules to control their functions and interactions with specific cells. We previously used polydopamine (pD) to prime-coat poly(lactic-co-glycolic acid) (PLGA) NPs and conjugated functional ligands onto the NPs via the pD coating. In this study, we report tannic acid (TA) as an alternative prime coating that is functionally comparable to pD but does not have drawbacks of pD such as optical properties and interference of ligand characterization. TA forms a stable and optically inert coating on PLGA NPs, which can accommodate albumin, chitosan, and folate-terminated polyethylene glycol to control the cell-NP interactions. Moreover, TA coating allows for surface loading of polycyclic planar aromatic compounds. TA is a promising reactive intermediate for surface functionalization of polymeric NPs.
A new parasitoid (Diptera: Tachinidae) of Acanthocinus princeps (Coleoptera: Cerambycidae) in North America (2000)

An undescribed species of Bi/laea Robineau-Desvoidy was reared from field-collected larvae of Acanthocinus princeps (Walker) maintained on artificial diet in the laboratory.Billaea is a novel larval parasitoid for 4. princeps with natural parasitism levels of ca.28%.
Identification of confusion and surprise in spoken dialog using prosodic features (2006)

Sensitivity to a user's emotional state offers promise in improving the state of the art in spoken dialog systems.In this work, we attempt to detect the speaker's states of confusion and surprise using prosodic features from his/her utterances.We have collected a corpus of utterances in realistic settings using an experimental methodology aimed at eliciting confusion and surprise from users.Classification experiments have yielded up to a 27.2% improvement over baseline performance using F0 and power features.We achieved the greatest success at classification of emotions that were most successfully elicited.
Evidence for Synergy Between α <sub>2</sub> -Adrenergic and Nonadrenergic Mechanisms in Central Blood Pressure Regulation (2002)

These results demonstrate that a central imidazoline-sensitive, but non--alpha(2)-adrenergic, mechanism can modify BP by itself. This mechanism, which may involve I(1)BS, interacts synergistically with an alpha(2)-adrenergic mechanism to decrease BP.
Characterization of photodynamic therapy responses elicited in A431 cells containing intracellular organelle‐localized photofrin (2010)

Photodynamic therapy (PDT), a photochemotherapeutic regimen used to treat several diseases, including cancer, exerts its effects mainly through induction of cell death. Using human epidermoid carcinoma A431 cells as a model, we previously showed that distinct cell death types could be triggered by protocols that selectively delivered Photofrin (a clinically approved photosensitizer) to different subcellular sites (Hsieh et al. [2003] J Cell Physiol 194: 363-375]. Here, the responses elicited by PDT in A431 cells containing intracellular organelle-localized Photofrin were further characterized. Two prominent cell phenotypes were observed under these conditions: one characterized by perinuclear vacuole (PV) formation 2-8 h after PDT followed by cell recovery or shrinkage within 48 h, and a second characterized by typical apoptotic features appearing within 4 h after PDT. DCFDA-sensitive reactive oxygen species formed proximal to PVs during the response to PDT, covering areas in which both endoplasmic reticulum (ER) and the Golgi complex were located. Biochemical analyses showed that Photofrin-PDT also induced JNK activation and altered the protein secretion profile. A more detailed examination of PV formation revealed that PVs were derived from the ER. The alteration of ER structure induced by PDT was similar to that triggered by thapsigargin, an ER Ca(2+)-ATPase inhibitor that perturbs Ca(2+) homeostasis, suggesting a role for Ca(2+) in the formation of PVs. Microtubule dynamics did not significantly affect PV formation. This study demonstrates that cells in which intracellular organelles are selectively loaded with Photofrin mount a novel response to ER stress induced by PDT.
Morphopathological aspects of healthy nails and nails affected by onychomycosis (2014)

Patients of onychomycosis are common in the dermatology practice. Contemporary morphology creates opportunities to study the functional units of the nail when such infections occur from morphopathological point of view. There were 22 nails biopsies from onychomycosis patients taken for the research of morphopathological changes in the thickened nail plate affected by onychomycosis. Samples of cadaverous' nails were used as a control material. The material was stained with haematoxylin and eosin and immunohistochemical methods. Terminal deoxynucleotidyl transferase dUTP nick end labelling reaction and periodic acid-Schiff reaction were also performed. We found patchy hypertrophy in the granulose layer of the epidermis, with focal acanthosis. In the horn layer, we identified nests of parakeratosis of various sizes, with incorporations of homogenous and eosinophil masses. We found high levels of interleukin 6 and interleukin 10 positive cells in the nail bed and in the bloodstream. Interleukin 1, however, was not a part of any of the functional units of any of the nails. Significant amount of fibres containing human beta defensin-2 were found in the bed and plate of the nail. Therefore one can conclude that as regards the nails affected by onychomycosis, the most effective morphopathogenical processes include cytokine and defensin excretion occurrence in the nail bed.
Crystallographic investigations of alcohol dehydrogenases (1994)

The structures of horse liver alcohol dehydrogenase class I in its apoenzyme form and in different ternary complexes have been determined at high resolution. The complex with NAD+ and the substrate analogue pentafluorobenzyl alcohol gives a detailed picture of the interactions in an enzyme-substrate complex. The alcohol is bound to the zinc and positioned so that the hydrogen atom can be directly transferred to the C4 atom of the nicotinamide ring. The structure of cod liver alcohol dehydrogenase with hybrid properties (functionally of class I but structurally overall closer to class III) has been determined by molecular replacement methods to 3 A resolution. Yeast alcohol dehydrogenase has been crystallized, and native data have been collected to 3 A resolution.
Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms (2016)

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes.
Abstract P5-03-13: Detection of tumor initiating cells (TIC) among the peripherally circulating epithelial tumor cells from patients with breast cancer (2012)

Abstract Background: The detection of tumor cells circulating in the peripheral blood of patients with breast cancer is a sign that cells have been able to leave the primary tumor and survive in the circulation. However, in order to form metastases they require additional properties such as the ability to adhere, self renew and grow. Here we present data that a variable fraction among the circulating tumor cells detected by the maintrac® approach express mRNA of the stem cell gene nanog and of the adhesion molecule vimentin and are capable of forming tumor spheres a property ascribed to TIC. Patients and methods: Between 10 to 50 circulating epithelial antigen positive cells detected by the maintrac® approach were selected randomly from each of 20 patients with breast cancer before and after surgery and isolated using automated capillary aspiration and deposited individually onto slides for expression profiling. In addition, the circulating tumor cells were cultured without isolation among the white blood cells from 5 patients with breast cancer in different stages of disease using culture methods favoring growth of epithelial cells. Results: Although no EpCAM mRNA positive cells expressing stem cell genes or the adhesion molecule vimentin were detected before surgery, 10 to 20% of the cells were found to be positive for mRNA of these genes after surgery. Most surprisingly, it was possible to grow tumor spheres (Fig 1) from these circulating cells without previous isolation in all patients in a fraction comprising between 1% of the epithelial antigen positive cells in patients with newly diagnosed tumor up to 10% in a patient with advanced breast cancer. Conclusion: We here show, that among the peripherally circulating tumor cells a variable fraction is able to express stem cell and adhesion properties and can be grown into tumor spheres, a property ascribed to cells capable of initiating tumors and metastases. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-03-13.
Enzymatic formation of capsaicinoid from vanillylamine and iso-type fatty acids by cell-free extracts of Capsicum annuum var. annuum cv. Karayatsubusa. (1980)

Cell-free extracts of placenta of Capsicum annuum var. annuum cv. Karayatsubusa catalyzed the formation of capsaicinoid from vanillylamine and 7-methylocatnoyl CoA (iso-C-9:0-CoA), 8-methylnonanoyl CoA (iso-C-10:0-CoA), 8-methyl-6-nonenoyl CoA (iso-C-10:1-CoA), or 9-methyldecanoyl CoA (iso-C-11:0-CoA). Iso-type fatty acid-activating reaction required CoA, ATP and Mg++ as cofactors. Among acyl-CoAs examined, iso-C-9:0-CoA was used most effectively as acyl donor for capsaicinoid formation. 5-methylhexanoyl CoA (iso-C-7:0-CoA), 6-methylheptanoyl CoA (iso-C-8:0-CoA), 10-methylundecanoyl CoA (iso-C-12:0-CoA) and decanoyl CoA (n-C-10:0-CoA) were not used as acyl donor. When equivalent amounts of iso-C-9:0-CoA, iso-C-10:0-CoA, iso-C-10:1-COA, and iso-C-11:0-CoA were added together as acyl donors, nordihydrocapsaicin was the major product, occupying more than 60% of the total capsaicinoid formed. The optimum pH for capsaicinoid formation was around 9.0, when iso-C-10:0-CoA was used as acyl donor.
Regulation of Membrane‐Type Matrix Metalloproteinase‐1 Expression by Growth Factors and Phorbol 12‐Myristate 13‐Acetate (1996)

Overexpression of membrane-type matrix metalloproteinase (MT-MMP-1) results in the activation of both endogenous and exogenous 72-kDa gelatinase. To understand the effects of MT-MMP-1 on 72-kDa gelatinase activation, we analyzed its expression in human fibroblasts and HT-1080 fibrosarcoma cells. Both cell types expressed the MT-MMP-1 mRNA constitutively at a considerable level and treatment of cells with PMA enhanced the expression about 2-3-fold. Concanavalin A treatment increased MT-MMP-1 mRNA levels in fibroblasts about 4-fold. Induction of MT-MMP-1 by phorbol 12-myristate 13-acetate (PMA) required protein synthesis as shown by cycloheximide inhibition. The induction was also inhibited by dexamethasone. Analysis of MT-MMP-1 mRNA stability using actinomycin D indicated that the half-life was rather long and not affected by PMA, suggesting transcriptional regulation. Only HT-1080 cells had significant 72-kDa gelatinase processing activity after treatment with PMA or concanavalin A, while fibroblasts were virtually negative. Immunoblotting analysis of fibroblast lysates indicated that MT-MMP-1 was present mainly in a 60-kDa form. PMA and concanavalin A caused 2-4-fold increases in its protein levels, while in HT-1080 cells PMA, concanavalin A, or overexpression of MT-MMP-1 did not significantly enhance the level of the 60-kDa protein. Instead, an immunoreactive, proteolytically processed 43-kDa form was observed, and its appearance correlated to 72-kDa gelatinase processing activity. Thus 72-kDa gelatinase activation, while enhanced by MT-MMP-1 expression, needs additional co-operating factors.
Role of Poly [ADP-ribose] Polymerase 1 in Activating the Kirsten ras (KRAS) Gene in Response to Oxidative Stress (2020)

In pancreatic Panc-1 cancer cells, an increase of oxidative stress enhances the level of 7,8-dihydro-8-oxoguanine (8OG) more in the <i>KRAS</i> promoter region containing G4 motifs than in non-G4 motif G-rich genomic regions. We found that H<sub>2</sub>O<sub>2</sub> stimulates the recruitment to the <i>KRAS</i> promoter of poly [ADP-ribose] polymerase 1 (PARP-1), which efficiently binds to local G4 structures. Upon binding to G4 DNA, PARP-1 undergoes auto PARylation and thus becomes negatively charged. In our view this should favor the recruitment to the <i>KRAS</i> promoter of MAZ and hnRNP A1, as these two nuclear factors, because of their isoelectric points >7, are cationic in nature under physiological conditions. This is indeed supported by pulldown assays which showed that PARP-1, MAZ, and hnRNP A1 form a multiprotein complex with an oligonucleotide mimicking the <i>KRAS</i> G4 structure. Our data suggest that an increase of oxidative stress in Panc-1 cells activates a ROS-G4-PARP-1 axis that stimulates the transcription of <i>KRAS</i>. This mechanism is confirmed by the finding that when PARP-1 is silenced by siRNA or auto PARylation is inhibited by Veliparib, the expression of <i>KRAS</i> is downregulated. When Panc-1 cells are treated with H<sub>2</sub>O<sub>2</sub> instead, a strong up-regulation of <i>KRAS</i> transcription is observed.
ChemInform Abstract: Corrosion Inhibition of Cobalt in Some Acid Solutions by Bismuth(III) Chloride. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.