gebhart/patrepeval huggingface dataset:
Distributed intelligent network management for the SDI ground network (2002)

The authors describe an integrated solution to distributed intelligent network management for the Strategic Defense System (SDS) terrestrial network which emphasizes the partitioning of the problem between rule-based, constraint-based, and algorithmic techniques. Problems in current approaches to network management for the SDS are described which show how this new approach leads to an efficient implementation in a C-based environment via the Harris-developed constraint propagation expert system shell and the C language integrated production system shell. The advantages of constraint-based distributed problem solving are presented. The authors describe how a model of battle management and the evolving battle situation can be used to perform proactive as well as reactive definition of routes, and other network functions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Signal transduction events mediated by the BDNF receptor gp 145trkB in primary hippocampal pyramidal cell culture (1993)

The trkB gene encodes a tyrosine kinase receptor, gp145trkB, for brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NT-4). To understand the role of gp145trkB in the nervous system, we have investigated its expression in embryonic rat hippocampal pyramidal cell cultures and examined the effects of BDNF on signal transduction in the primary neurons. The expression of trkB transcripts was established by PCR analysis and in situ hybridization. In addition to gp145trkB, the pyramidal neuronal cultures expressed transcripts specific for the NT-3 receptor gp145trkC, but not for the high-affinity NGF receptor gp140trk or for p75LNGFR, a low-affinity receptor for all known members of the NGF family of neurotrophins including the gp145trkB ligands, BDNF and NT-4. The presence of gp145trkB receptors in the primary neuronal cultures was confirmed by immunocytochemical analysis in which > 90% of the cells stained with affinity-purified polyclonal antibodies to gp145trkB. Immunoblots using this antibody revealed a single approximately 140 kDa protein in both adult hippocampus and pyramidal cultures. Addition of recombinant BDNF to these cultures induced the tyrosine phosphorylation of gp145trkB, as determined by antiphosphotyrosine staining of gp145trkB immunoprecipitates. Moreover, BDNF treatment activated the microtubule-associated protein (MAP) kinases, as determined by an increase in MAP2 phosphorylation in vitro. Both the 41 and 44 kDa forms of MAP kinase were activated by BDNF. BDNF also increased c-fos expression in over 90% of the cells. These results indicate that gp145trkB does not require p75LNGFR to form a functional receptor for BDNF in hippocampal pyramidal neurons.
Scheduling a Single Machine to Minimize the Number of Late Jobs (1983)

Suppose &lt;i&gt;n&lt;/i&gt; jobs, each with a specified release date, due date and processing time, are to be scheduled for processing by a single machine, with the objective of minimizing the number of jobs that are not completed by their due dates. Three results, in the form of two algorithms and one NP-completeness proof, are presented. Our first result is to show that if release dates and due dates are "compatible," i. e. similarly ordered, an optimal schedule can be found in O(&lt;i&gt;n log n&lt;/i&gt;) time by a procedure that is a natural generalization of that of Moore for the case in which all release dates are equal. This result improves on an O(&lt;i&gt;n squared&lt;/i&gt;) solution to this problem by Kise, Ibaraki and Mine. For our second result, no particular relationship is assumed between the release dates and the due dates and the schedule is allowed to be preemptive. We show that a schedule minimizing the weighted number of late jobs can be found in O(&lt;i&gt;n cubed W cubed&lt;/i&gt;) time where &lt;i&gt;W&lt;/i&gt; is the sum of the integer weights assigned to the jobs. If the jobs are unweighted, then in effect &lt;i&gt;W&lt;/i&gt; = &lt;i&gt;n&lt;/i&gt; and the time bound reduces to O(&lt;i&gt;n&lt;/i&gt; to the 6th power), thereby yielding a polynomial-bounded algorithm for a problem for which no such solution procedure was previously known. For our third result, we suppose that all release dates are equal and that each job has a deadline in addition to its due date. We show that it is an NP-hard problem to minimize the number of late jobs (with respect to due dates) while observing all deadlines. This result resolves an open question suggested by a result of J. Sidney
Translational coregulation of 5′TOP mRNAs by TIA-1 and TIAR (2011)

The response of cells to changes in their environment often requires coregulation of gene networks, but little is known about how this can occur at the post-transcriptional level. An important example of post-transcriptional coregulation is the selective translational regulation in response to growth conditions of mammalian mRNAs that encode protein biosynthesis factors and contain hallmark 5'-terminal oligopyrimidine tracts (5'TOP). However, the responsible trans-factors and the mechanism by which they coregulate 5'TOP mRNAs have remained elusive. Here we identify stress granule-associated TIA-1 and TIAR proteins as key factors in human 5'TOP mRNA regulation, which upon amino acid starvation assemble onto the 5' end of 5'TOP mRNAs and arrest translation at the initiation step, as evidenced by TIA-1/TIAR-dependent 5'TOP mRNA translation repression, polysome release, and accumulation in stress granules. This requires starvation-mediated activation of the GCN2 (general control nonderepressible 2) kinase and inactivation of the mTOR (mammalian target of rapamycin) signaling pathway. Our findings provide a mechanistic explanation to the long-standing question of how the network of 5'TOP mRNAs are coregulated according to amino acid availability, thereby allowing redirection of limited resources to mount a nutrient deprivation response. This presents a fundamental example of how a group of mRNAs can be translationally coregulated in response to changes in the cellular environment.
Chronic exposure to paclitaxel diminishes phosphoinositide signaling by calpain-mediated neuronal calcium sensor-1 degradation (2007)

Paclitaxel (Taxol) is a well established chemotherapeutic agent for the treatment of solid tumors, but it is limited in its usefulness by the frequent induction of peripheral neuropathy. We found that prolonged exposure of a neuroblastoma cell line and primary rat dorsal root ganglia with therapeutic concentrations of Taxol leads to a reduction in inositol trisphosphate (InsP(3))-mediated Ca(2+) signaling. We also observed a Taxol-specific reduction in neuronal calcium sensor 1 (NCS-1) protein levels, a known modulator of InsP(3) receptor (InsP(3)R) activity. This reduction was also found in peripheral neuronal tissue from Taxol treated animals. We further observed that short hairpin RNA-mediated NCS-1 knockdown had a similar effect on phosphoinositide-mediated Ca(2+) signaling. When NCS-1 protein levels recovered, so did InsP(3)-mediated Ca(2+) signaling. Inhibition of the Ca(2+)-activated protease mu-calpain prevented alterations in phosphoinositide-mediated Ca(2+) signaling and NCS-1 protein levels. We also found that NCS-1 is readily degraded by mu-calpain in vitro and that mu-calpain activity is increased in Taxol but not vehicle-treated cells. From these results, we conclude that prolonged exposure to Taxol activates mu-calpain, which leads to the degradation of NCS-1, which, in turn, attenuates InsP(3)mediated Ca(2+) signaling. These findings provide a previously undescribed approach to understanding and treating Taxol-induced peripheral neuropathy.
Sensitization to Sunflower Pollen: Only an Occupational Allergy? (1994)

Sunflower (Helianthus annuus) pollen sensitization has been reported as an occupational allergy. In this report, the sensitization of the general population living in sunflower-growing areas to Helianthus pollen was studied. Both RAST results in 32 adults with summer symptoms previously diagnosed as allergic to Artemisia pollen, and cross-reactivity studies between H. annuus and other Compositae suggested that H. annuus pollen was the main allergen involved in the hypersensitivity reaction of those patients. Good correlation was found between RAST and SPT to Helianthus and between RAST and conjunctival provocation test to Helianthus. Bronchial challenge tests performed on 8 of the 32 patients confirmed the clinical implication of Helianthus pollen in suspected subjects. Five workers, handling sunflower pollen, who suffered from related symptoms were subjected to the same study, showing lesser wheal areas and lesser specific IgE levels than a non-worker group. Thirteen patients with RAST values ≥ class 2 showed 2 IgE-binding fractions at 34.0 and 42.8 kD in 65% of sera and 3 IgE-binding fractions at pI 4.9, 9.6 and 10.2 in 54% of sera. By means of micropreparative high-resolution chromatography, it was possible to purify a 34-kD major allergen. Analysis performed by RAST inhibition with sera from atopic patients and ELISA inhibition with experimental anti-Helianthus rabbit sera demonstrated a cross-reactivity between Helianthus and other Compositae, but low affinity of specific anti-Helianthus antibodies for heterologous antigens. Taking into account the above-mentioned data, and the high prevalence of Helianthus pollen in the atmosphere during harvesting (in spite of its entomophilous character), Helianthus pollen should be considered as an allergenic source to be investigated in the general population living in sunflower-growing regions suffering from seasonal summer allergy.
TRANCE is a TNF family member that regulates dendritic cell and osteoclast function (1999)

Tumor necrosis factor (TNF)-related activation-induced cytokine (TRANCE) is a new member of the TNF family emerging as a key regulator of the immune system and of bone development and homeostasis. TRANCE is expressed on activated T cells and activates mature dendritic cells (DC), suggesting that it plays a role in the T cell-DC interaction during an immune response. Furthermore, TRANCE is expressed on osteoblasts stimulated with vitamin D3, dexamethasone, and parathyroid hormone. TRANCE, when expressed on osteoblasts, induces osteoclastogenesis and osteoclast activation, suggesting that it links known calciotropic hormones to bone resorption. TRANCE mediates its effects via the TRANCE-receptor (TRANCE-R/RANK), whereas its activity can be inhibited by the soluble decoy receptor osteoprotegerin/osteoclast inhibitory factor (OPG/OCIF). OPG can be neutralized by another TNF-family member, the TNF-related apoptosis-inducing ligand (TRAIL), suggesting that TRANCE is part of a complex cytokine network that regulates a diverse set of functions. We will discuss the current literature describing TRANCE and its receptors and its role in controlling DC and osteoclast function.
Minimizing Latency in Fetching Virtual Machine Images Based on Multi-point Collaborative Approach (2013)

Cloud computing centers enable to provision diverse virtual machine (VM) in an elastic and scalable manner. VMs are created by instantiating VM images that encapsulate the required applications or services with their support environment. The multi-gigabyte VM images are hosted in the central image repository, while hosting centers are geographically dispersed. Thus, to fetch a GigaByte sized VM image from a repository over the Internet is time consuming. To address this problem, we first take advantage of high degree of commonality of VM images, and divide the VM images into fine-grain chunks by designing a mixed chunk scheme. And then, based on chunk-level sharing among different images, we propose a novel VM images acquisition scheme based on multi-point collaboration (MPCA), which minimizes latency in fetching VM images. Our experiments show that our proposed scheme can largely reduce request service time. Moreover, it can efficiently decentralize network traffic load, reduce the contention result from additional traffic introduced in the network, especially when traffic load is heavy.
Versatile Linker Chemistry for Synthesis of 3‘-Modified DNA (1997)

A general method is described for the solid phase supported synthesis of DNA containing 3'-terminal phosphodiesters modified with linkers bearing either amino, thiol, or hydroxyl groups. These products are all made from a common intermediate, obtained by the reaction of trimellitic anhydride chloride with aminopropyl CPG. The anhydride-derivatized support was then reacted with three appropriate bifunctional spacers, giving DMT-protected hydroxyl solid supports bearing the masked functionality as an ester, amide, or thioester. DNA synthesis was then performed, followed by ammonia cleavage and deprotection, giving the hydroxyl-, amino-, or thiol-functionalized DNA 3'-phosphate diesters, respectively. Test mononucleotides synthesized with each of the new supports were identical with control mononucleotides made with 5'-immobilized nucleosides and alkylhydroxyl, alkylamino, and alkylthio phosphoramidites. The new supports were then used to prepare several 3'-modified oligonucleotides, which were characterized by gel electrophoresis, HPLC, and MALDI mass spectroscopy. The amino- and thiol-functionalized DNAs were conjugated with chromophores, and purification of these products was facilitated by use of reversed phase cartridges.
Autonomous growth and increased cytotoxicity of natural killer cells expressing membrane-bound interleukin-15 (2014)

Natural killer (NK) cell survival and, hence, cytotoxicity requires cytokine support. We determined whether expression of interleukin-15 (IL-15) in a nonsecretory, membrane-bound form could sustain NK cell growth. We linked the human IL15 gene to that encoding CD8α transmembrane domain (mbIL15). After retroviral transduction, human NK cells expressed mbIL15 on the cell surface; IL-15 secretion was negligible. Survival of mbIL15-NK cells without interleukin-2 (IL-2) after 7-day culture was vastly superior to that of mock-transduced NK cells (P < .001, n = 15) and of NK cells expressing nonmembrane-bound IL-15 (P = .025, n = 9); viable mbIL15-NK cells were detectable for up to 2 months. In immunodeficient mice, mbIL15-NK cells expanded without IL-2 and were detectable in all tissues examined (except brain) in much higher numbers than mock-transduced NK cells (P < .001). Expansion further increased with IL-2. The primary mechanism of mbIL15 stimulation was autocrine; it activated IL-15 signaling and antiapoptotic signaling. NK cells expressing mbIL15 had higher cytotoxicity against leukemia, lymphoma, and solid tumor cells in vitro and against leukemia and sarcoma cells in xenograft models. Thus, mbIL15 confers independent growth to NK cells and enhances their antitumor capacity. Infusion of mbIL15-NK cells would allow NK cell therapy without the potential adverse effects of cytokine administration.
Regulation of collagen biosynthesis by ascorbic acid: a review. (1986)

L-ascorbic acid is an essential cofactor for lysyl hydroxylase and prolyl hydroxylase, enzymes essential for collagen biosynthesis. In addition, L-ascorbic acid preferentially stimulates collagen synthesis in a manner which appears unrelated to the effect of L-ascorbic acid on hydroxylation reactions. This reaction is stereospecific and unrelated to intracellular degradation of collagen. The effect apparently occurs at a transcriptional or translational level, since L-ascorbic acid preferentially stimulates collagen-specific mRNA. In addition, it stimulates lysyl hydroxylase activity but inhibits prolyl hydroxylase activity in human skin fibroblasts in culture.
Nanoscale Growth and Patterning of Inorganic Oxides Using DNA Nanostructure Templates (2013)

We describe a method to form custom-shaped inorganic oxide nanostructures by using DNA nanostructure templates. We show that a DNA nanostructure can modulate the rate of chemical vapor deposition of SiO2 and TiO2 with nanometer-scale spatial resolution. The resulting oxide nanostructure inherits its shape from the DNA template. This method generates both positive-tone and negative-tone patterns on a wide range of substrates and is compatible with conventional silicon nanofabrication processes. Our result opens the door to the use of DNA nanostructures as general-purpose templates for high-resolution nanofabrication.
Construction of a Combinatorial IgE Library from an Allergic Patient (1996)

To characterize human IgE antibodies with specificity for a major allergen at the molecular level, we have constructed an IgE combinatorial library from a grass pollen allergic patient. cDNAs coding for IgE heavy chain fragments and for light chains were reverse-transcribed and polymerase chain reaction-amplified from RNA of peripheral blood lymphocytes and randomly combined in plasmid pComb3H to yield a combinatorial library of 5 x 10(7) primary clones. IgE Fabs with specificity for Phl p 5, a major timothy grass pollen allergen, were isolated by panning. Sequence analysis showed that the 4 of the Fabs used the same heavy chain fragments which had combined with different kappa light chains. Soluble recombinant IgE Fabs were purified by affinity chromatography to Phl p 5 and, like natural IgE antibodies, cross-reacted with group 5 allergens from different grass species. The described approach should facilitate studies on the molecular interaction between IgE antibodies and allergens and encourages the consideration of specific IgE Fabs that are capable of interfering with allergen-IgE binding as potential therapeutic tools.
The Photochemistry of Stilbenoid Compounds and Their Role in Materials Technology (1992)

Abstract Stilbenes and compounds containing stilbene units in their structures form the material basis for numerous research projects in photophysics and photochemistry. Moreover, because these compounds are easy to synthesize and are thermally and chemically stable, they are taking on an increasingly prominent role in the area of materials science investigations into optical, electrical, and optoelectronic properties. In accordance with the interdisciplinary nature of such studies, this article aims to provide a bridge extending from molecular theory and photophysical measurements, through preparative applications, to material effects and their potential technical applications.
Crystallographic refinement of ricin to 2.5 Å (1991)

The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR). The last model (9) has an R factor of 21.6% and RMS deviations from standard bond lengths and angles of 0.021 A and 4.67 degrees, respectively. Refinement required several peptide segments in the original model to be adjusted translationally along the electron density. A wide range of lesser changes were also made. The RMS deviation of backbone atoms between the original and model 9 was 1.89 A. Molecular dynamics proved to be a very powerful refinement tool. However, tests showed that it could not replace human intervention in making adjustments such as local translations of the peptide chain. The R factor is not a completely satisfactory indicator of refinement progress; difference Fouriers, when observed carefully, may be a better monitor.
Key words for use in RFCs to Indicate Requirement Levels (1997)

In many standards track documents several words are used to signify the requirements in the specification. These words are often capitalized. This document defines these words as they should be interpreted in IETF documents. Authors who follow these guidelines should incorporate this phrase near the beginning of their document:
Depudecin induces morphological reversion of transformed fibroblasts via the inhibition of histone deacetylase (1998)

Depudecin is a fungal metabolite that reverts the rounded phenotype of NIH 3T3 fibroblasts transformed with v-ras and v-src oncogenes to the flattened phenotype of the nontransformed parental cells. The mechanism of detransformation induced by this agent had not been determined. Here, we demonstrate that depudecin inhibits histone deacetylase (HDAC) activity effectively both in vivo and in vitro. Depudecin induces similar morphological reversion in v-ras transformed NIH 3T3 cells as do other naturally occurring HDAC inhibitors such as trichostatin A or trapoxin. It competitively inhibits the binding of [3H]trapoxin in vitro and the nuclear binding of a trapoxin-coumarin fluorophore in vivo, suggesting that depudecin shares a nuclear binding protein and site on that protein with trapoxin. Furthermore, depudecin induces hyperacetylation of histones in a dose-dependent manner and at concentrations comparable with that required for detransformation. An in vitro histone deacetylase assay, using purified recombinant HDAC1, reveals that depudecin inhibits 50% of the enzyme activity at a concentration of 4.7 microM. These results demonstrate that depudecin is a novel HDAC inhibitor and suggest that its ability to induce morphological reversion of transformed cells is the result of its HDAC inhibitory activity.
An Apical PDZ Protein Anchors the Cystic Fibrosis Transmembrane Conductance Regulator to the Cytoskeleton (1998)

The function of the cystic fibrosis transmembrane conductance regulator (CFTR) as a Cl- channel in the apical membrane of epithelial cells is extensively documented. However, less is known about the molecular determinants of CFTR residence in the apical membrane, basal regulation of its Cl- channel activity, and its reported effects on the function of other transporters. These aspects of CFTR function likely require specific interactions between CFTR and unknown proteins in the apical compartment of epithelial cells. Here we report that CFTR interacts with the recently discovered protein, EBP50 (ERM-binding phosphoprotein 50). EBP50 is concentrated at the apical membrane in human airway epithelial cells, in vivo, and CFTR and EBP50 associate in in vitro binding assays. The CFTR-EBP50 interaction requires the COOH-terminal DTRL sequence of CFTR and utilizes either PDZ1 or PDZ2 of EBP50, although binding to PDZ1 is of greater affinity. Through formation of a complex, the interaction between CFTR and EBP50 may influence the stability and/or regulation of CFTR Cl- channel function in the cell membrane and provides a potential mechanism through which CFTR can affect the activity of other apical membrane proteins.