gebhart/patrepeval huggingface dataset:
Progressive epithelial to mesenchymal transitions in ARCaPE prostate cancer cells during xenograft tumor formation and metastasis (2009)

Results from this study demonstrate that through interaction with the host tumor microenvironment, cancer cells acquire cellular plasticity. During xenograft tumor formation and metastasis, a single clone of cancer cells could yield a heterogeneous population, with a substantial number of tumor cells adopting mesenchymal stroma-like phenotypes.
LadR, a new PadR-related transcriptional regulator fromListeria monocytogenes, negatively regulates the expression of the multidrug efflux pump MdrL (2005)

The Listeria monocytogenes genome encodes putative multidrug efflux transporters but only the MdrL transporter has been partially characterized in the wild-type LO28 strain. Here, we show in the LO28 strain, that the expression of MdrL is repressed at the transcriptional level, under standard growth conditions, by the product of a new gene ladR (lmo1408), and the expression of MdrL is induced in the presence of rhodamine. Phylogenetic analysis in related firmicutes shows that LadR, conserved in all sequenced Listeria genomes, forms an independent group from the large and diverse PadR transcriptional regulator family (PF03551). This is the first report of a bacterial multidrug transporter controlled by a member of the PadR family.
Increased phospho-AKT (Ser(473)) expression in bronchial dysplasia: implications for lung cancer prevention studies. (2003)

AKT, a downstream mediator of phosphatidylinositol 3'-kinase, is activated in non-small cell lung cancer (NSCLC), but we have not yet defined the stage of malignant transformation at which AKT is activated in the bronchial epithelium. We performed immunohistochemical analysis of activated AKT [phosphorylated (p)-AKT Ser(473)] in tissue specimens of normal bronchial epithelium, bronchial hyperplasia and squamous metaplasia ("reactive" epithelium), bronchial dysplasia, and NSCLC. Among NSCLC specimens, immunohistochemical findings were correlated with patient demographics, tumor stage, histology, and survival. We observed p-AKT expression in 12 of 44 (27.3%) normal bronchial biopsy specimens, 4 of 9 (44.4%) reactive epithelium specimens, 22 of 25 (88%) dysplastic specimens, and 25 of 76 (33%) NSCLC specimens. Among patients with resected early-stage or locally advanced NSCLC, p-AKT expression had no effect on tumor stage, histology, or survival. Of the histological groups examined, bronchial dysplasia specimens expressed p-AKT most frequently, supporting AKT activation as an early event in lung cancer progression. Given its role as a mediator of malignant transformation, p-AKT should be investigated as a potential target in future lung cancer prevention studies.
The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer-promoter interaction (1999)

The scs and scs' elements were proposed to function as chromatin domain boundaries for the 87A7 heat shock locus in Drosophila melanogaster. Here we report the identification and characterization of SBP (scs binding protein), a component of the scs nucleoprotein complex. SBP binds specifically to a 24-bp region of scs in vitro and is associated with scs in vivo. Multiple copies of an oligonucleotide containing the SBP recognition sequence are capable of blocking enhancer-promoter interactions in transgene assays. Mutations in the oligonucleotide that disrupt SBP binding in vitro also eliminate enhancer-blocking activity in vivo. We show that SBP is encoded by the zeste-white 5 gene and that mutations in zeste-white 5 reduce the enhancer-blocking activity of the multimerized oligonucleotides.
Scalable rule management for data centers (2013)

Cloud operators increasingly need more and more fine-grained rules to better control individual network flows for various traffic management policies. In this paper, we explore automated rule management in the context of a system called vCRIB (a virtual Cloud Rule Informa-tion Base), which provides the abstraction of a central-ized rule repository. The challenge in our approach is the design of algorithms that automatically off-load rule processing to overcome resource constraints on hypervi-sors and/or switches, while minimizing redirection traf-fic overhead and responding to system dynamics. vCRIB contains novel algorithms for finding feasible rule place-ments and adapting traffic overhead induced by rule placement in the face of traffic changes and VM migra-tion. We demonstrate that vCRIB can find feasible rule placements with less than 10 % traffic overhead even in cases where the traffic-optimal rule placement may be in-feasible with respect to hypervisor CPU or memory con-straints. 1
A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. (1979)

A new approach for evaluating homologous sequences among related DNAs is presented. Conventional filter hybridization techniques are employed at 35 degrees C in a range of formamide concentrations in order to perform annealings at effective temperatures as low as Tm -50 degrees C which permits the detection of regions of homology with as much as 33% base mismatch. Under such nonstringent conditions, high levels of specific annealing can be obtained at plateau levels. In combination with the Southern "blotting" technique (1975), this approach can be used to perform biochemical heteroduplex melting experiments. The homology among the genomes of the murine polyoma virus (Py), the simian virus 40 (SV40), and the human papovavirus BK was evaluated using this new methodology.
Respiratory syncytial virus heterogeneity during an epidemic: analysis by limited nucleotide sequencing (SH gene) and restriction mapping (N gene) (1991)

The genes encoding the small hydrophobic (SH) proteins of a series of respiratory syncytial (RS) virus strains were amplified using the polymerase chain reaction, cloned and sequenced. Analysis of the SH gene sequences from 12 RS virus strains isolated between 1956 and 1989 confirmed the homogeneity of the two subgroups. A and B, previously defined serologically. Although there is only 76% deduced amino acid sequence identity of SH proteins between subgroups, there was little variation in deduced amino acid sequences within the subgroups; nucleotide homologies within the subgroups ranged between 93% and 99%. Forty-two isolates of RS virus from a single epidemic season (autumn/winter 1989) were also examined to determine their relatedness. For these isolates regions of both the SH and nucleocapsid protein genes of each isolate were amplified and these regions were further analysed by direct nucleotide sequencing or restriction mapping. It was possible to discriminate at least six different lineages (or substrains) of RS virus circulating at the same time and in the same locality.
Diadenosine polyphosphates in the central nervous system (1997)

Adenine dinucleotides are a family of compounds consisting of two molecules of adenosine linked by a phosphate chain which can vary in length from 2 to 6. These naturally occurring compounds are present and stored in the CNS and are released to the synaptic cleft after stimulation. Diadenosine polyphosphates can interact with purine receptors mainly P2 and dinucleotide receptors. The second subtype of purinoceptors is specific for adenine dinucleotides, which mediate Ca2+ entry from the extracellular space in a process modulated by protein kinases A, C and protein phosphatases. This dinucleotide receptor is not sensitive to P1- and P2-purinergic antagonists. Nevertheless, diinosine pentaphosphate, Ip5I, is a potent antagonist of the dinucleotide receptor. The topographical distribution of these dinucleotides, studied by autoradiography, demonstrates a higher concentration in the cerebellum, olfactory bulb, facial nuclei and superior olive. This distribution suggests the involvement of adenine dinucleotides in motor, sensory and behavioural processes. © 1997 John Wiley & Sons, Ltd.
Plasmid marker rescue transformation in Bacillus subtilis (1983)

We constructed an 18-megadalton plasmid (pBD221) carrying resistance determinants for kanamycin, chloramphenicol, and erythromycin, as well as the hisH determinant from the Bacillus licheniformis chromosome. This plasmid has a copy number of about one and can be stably maintained in Bacillus subtilis. Linear fragments of pBD221 DNA were used to transform competent cultures carrying mutant variants of the same plasmid. Rescue transformation did not proceed by recircularization and replication of the donor DNA. Rescue transformation exhibited first-order dependence on DNA concentration, and the concentration dependence curve was virtually identical to the curve obtained with chromosomal DNA. The donor DNA molecular weight dependence of plasmid marker rescue transformation obtained by using restriction fragments was not distinguishable from previously published data obtained by using fractionated sheared chromosomal DNA. Plasmid rescue transformation, like chromosomal transformation, was dependent on the recE, recA, recB, and recD gene products. Plasmid rescue transformation, like chromosomal transformation, proceeded with few exchanges. Linkage data obtained with the plasmid rescue system fit a quantitative model based on studies with chromosomal transformation. We conclude that plasmid marker rescue transformation probably proceeds by a mechanism similar to the mechanism used during the formation of chromosomal transformants and hence may be considered an appropriate general model for the study of transformational recombination.
A VLIW architecture for a trace scheduling compiler (1988)

A VLIW (very long instruction word) architecture machine called the TRACE has been built along with its companion Trace Scheduling compacting compiler. This machine has three hardware configurations, capable of executing 7, 14, or 28 operations simultaneously. The 'seven-wide' achieves a performance improvement of a factor of five or six for a wide range of scientific code, compared to machines of higher cost and fast chip implementation technology (such as the VAX 8700). The TRACE extends some basic reduced-instruction-set computer (RISC) precepts: the architecture is load/store, the microarchitecture is exposed to the compiler, there is no microcode, and there is almost no hardware devoted to synchronization, arbitration, or interlocking of any kind (the compiler has sole responsibility for run-time resource usage). The authors discuss the design of this machine and present some initial performance results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improving the Electrical Conductivity of Carbon Nanotube Networks: A First-Principles Study (2011)

We address the issue of the low electrical conductivity observed in carbon nanotube networks using first-principles calculations of the structure, stability, and ballistic transport of different nanotube junctions. We first study covalent linkers, using the nitrene-pyrazine case as a model for conductance-preserving [2 + 1] cycloadditions, and discuss the reasons for their poor performance. We then characterize the role of transition-metal adsorbates in improving mechanical coupling and electrical tunneling between the tubes. We show that the strong hybridization between the transition-metal d orbitals with the π orbitals of the nanotube can provide an excellent electrical bridge for nanotube-nanotube junctions. This effect is maximized in the case of nitrogen-doped nanotubes, thanks to the strong mechanical coupling between the tubes mediated by a single transition metal adatom. Our results suggest effective strategies to optimize the performance of carbon nanotube networks.
Groupware comes to the Internet (1999)

Early experiences with Web-based groupware point to new collaboration opportunities within and between organizations. We report the results of a study of more than 100 organizations that have used Web-based groupware to understand better how they are using it and what advantages and disadvantages they have experienced. We then use these data to develop a framework for analyzing and assessing the fit of groupware systems to organizational needs. We close with a discussion of the evolution and future of groupware.
Ionic liquids promote PCR amplification of DNA (2012)

A bicyclic imidazolium ionic liquid (4d), [b-4C-im][Br], was found to be highly effective not only for promoting PCR of GC-rich DNA by minimizing non-specific amplification, but also for facilitating PCR of normal-GC DNA under mild conditions.
Arthroscopic multiple osteochondral transplantation to the chondral defect in the knee associated with anterior cruciate ligament disruption (1993)

Treatment of a chondral lesion in the knee, associated with anterior cruciate ligament disruption, is known to be difficult and controversial. This article presents an arthroscopic technique for transplantation of multiple osteochondral fragments, harvested from the same knee, to this chondral lesion. A 3-year follow-up shows excellent results with good cartilage repair confirmed by second-look arthroscopy.
Obesity alters the expression profile of clock genes in peripheral blood mononuclear cells. Preliminary results (2011)

Differences were observed in the expression profile variation of clock genes between the obese and non-obese groups. This study reveals the differences in clock gene expression profiles between obese and non-obese subjects, with evidence for two distinct chronotypes, and suggests a contribution of these chronotypes to fat accumulation in humans.
Haplotype-based variant detection from short-read sequencing (2012)

The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods. Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes.
The C-type lectin SIGN-R1 mediates uptake of the capsular polysaccharide ofStreptococcus pneumoniaein the marginal zone of mouse spleen (2003)

SIGN-R1, a recently discovered C-type lectin expressed at high levels on macrophages within the marginal zone of the spleen, mediates the uptake of dextran polysaccharides by these phagocytes. We now find that encapsulated Streptococcus pneumoniae are rapidly cleared by these macrophages from the bloodstream, and that capture also takes place when different cell lines express SIGN-R1 after transfection. To assess the role of the capsular polysaccharide of S. pneumoniae (CPS) in the interaction of SIGN-R1 with pneumococci, we first studied binding and uptake of serotype 14 CPS in transfected cells. Binding was observed and was of a much higher avidity (3000-fold) for CPS 14 than dextran. The CPSs from four different serotypes were also cleared by marginal zone macrophages in vivo. To establish a role for SIGN-R1 in this uptake, we selectively down-regulated expression of the lectin by pretreatment of the mice with SIGN-R1 antibodies, including a newly generated hamster monoclonal called 22D1. For several days after this transient knockout, the marginal zone macrophages were unable to take up either CPSs or dextrans. Therefore, marginal zone macrophages in mice have a receptor that interacts with capsular pneumococcal polysaccharides, setting the stage for further studies of the functional consequences of this interaction.
Initiation and Regulation of Complement during Hemolytic Transfusion Reactions (2012)

Hemolytic transfusion reactions represent one of the most common causes of transfusion-related mortality. Although many factors influence hemolytic transfusion reactions, complement activation represents one of the most common features associated with fatality. In this paper we will focus on the role of complement in initiating and regulating hemolytic transfusion reactions and will discuss potential strategies aimed at mitigating or favorably modulating complement during incompatible red blood cell transfusions.
Low Rayleigh scattering P/sub 2/O/sub 5/-F-SiO/sub 2/ glasses (1992)

The Rayleigh scattering and infrared absorption losses of P/sub 2/O/sub 5/-F-doped silica glass, which is a candidate material for ultra-low-loss optical fiber, were investigated experimentally. The Rayleigh scattering loss of 8.5 wt.% P/sub 2/O/sub 5/ and 0.3 wt.% F-doped SiO/sub 2/ glass is found to be 0.8 times that of pure silica glass. It is also found that the infrared absorption property of P/sub 2/O/sub 5/-F-SiO/sub 2/ glass is almost the same as that of pure silica glass. The minimum loss for the proposed composition is estimated to be 0.11 dB/km at 1.55 mu m wavelength, and 0.21 dB/km at 1.3 mu m wavelength.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Jurkat T 세포에서 Ginsenoside - Rg1 이 p561ck Kinase 활성과 세포증식에 미치는 영향 (1995)

We studied the effects of ginsenoside-Rg_1 (G-Rg_1) extracted from Panax ginseng C.A. Meyer on p56^lck kinase and cell proliferation in Jurkat T cells. p56^lck was maximally activated within 5 min after the treatment of 16.7 ㎍/㎖ of G-Rg_1 increasing the activity by 1.2∼2 times relative to untreated control, thereafter its activity was gradually decreased to the level of untreated control. The action of EGTA on the kinase was altered by the addition of G-Rg_1, accompanying the band shift of p56^lck to p60^lck. In addition, G-Rg_1 promoted cell proliferation in a concentration-dependent manner. These results suggest that G-Rg_1 may be involved in T cell receptor-CD3 (TCR) signaling via the activation of p56^lck and the change of cellular calcium concentration.
One- and Two-Photon Absorption in CdS Nanodots and Wires: The Role of Dimensionality in the One- and Two-Photon Luminescence Excitation Spectrum (2014)

We investigate the spectral dependence of the linear and two-photon absorption of wurtzite CdS nanoparticles (dots and rods) by means of quantitative one- and two-photon photoluminescence excitation spectroscopy and effective mass theory modeling. Absolute two-photon absorption cross sections free from spectrally varying beam related uncertainties are obtained by means of a new reference dye-based method. The two-photon spectrum features of rods strongly differ from those of dots, due to the distinct energy structure of quasi-one-dimensional systems. The transversal confinement is found to dominate the energy of the absorption maxima while the longitudinal one dominates their absorption intensity. This suggests two-photon transition energy and intensity can be controlled independently in nanorods. For both geometries we observe a sizable spectral shift between the first one- and two-photon absorption maxima, which we conclude is inherent to the small rates of near-bandgap two-photon transitions rather than to the particular geometry of the absorber. The provided understanding of the spectral dependence of the two-photon absorption of CdS dots and rods is of strong interest for the design of nanocrystals with optimized two-photon absorption properties for bioimaging and phototherapy applications.
Transcriptional regulation of Bacillus subtilis glucose starvation-inducible genes: control of gsiA by the ComP-ComA signal transduction system (1992)

The Bacillus subtilis glucose starvation-inducible transcription units, gsiA and gsiB, were characterized by DNA sequencing, transcriptional mapping, mutational analysis, and expression in response to changes in environmental conditions. The gsiA operon was shown to consist of two genes, gsiAA and gsiAB, predicted to encode 44.9- and 4.8-kDa polypeptides, respectively. The gsiB locus contains a single cistron which encodes a protein of unusual structure; most of its amino acids are arranged in five highly conserved, tandemly repeated units of 20 amino acids. The 5' ends of gsiA and gsiB mRNAs were located by primer extension analysis; their locations suggest that both are transcribed by RNA polymerase containing sigma A. Expression of both gsiA and gsiB was induced by starvation for glucose or phosphate or by addition of decoyinine, but only gsiA was induced by exhaustion of nutrient broth or by amino acid starvation. Regulation of gsiA expression was shown to be dependent upon the two-component signal transduction system ComP-ComA, which also controls expression of genetic competence genes. Mutations in mecA bypassed the dependency of gsiA expression on ComA. Disruption of gsiA relieved glucose repression of sporulation but did not otherwise interfere with sporulation, development of competence, motility, or glucose starvation survival. We propose that gsiA and gsiB are members of an adaptive pathway of genes whose products are involved in responses to nutrient deprivation other than sporulation.
HHV8-encoded vMIP-I Selectively Engages Chemokine Receptor CCR8 (1999)

Uncertainty regarding viral chemokine function is mirrored by an incomplete knowledge of host chemokine receptor usage by the virally encoded proteins. One such molecule is vMIP-I, a C-C type chemokine of undefined function and binding specificity, encoded by the Kaposi's sarcoma herpesvirus HHV-8. We report here that vMIP-I binds to and induces cytosolic [Ca(2+)] signals in human T cells selectively through CCR8, a CC chemokine receptor associated with Th2 lymphocytes. Furthermore, using a panel of 65 different human, viral, and rodent chemokines, we have established a comprehensive ligand binding "fingerprint" for CCR8. The receptor exhibits marked "high" affinity (K(d) < 15 nM) only for four chemokines, three of them of viral origin: vMIP-I, vMIP-II, vMCC-I, and human I-309. A previously unreported second class of lower affinity ligands includes MCP-3 and possibly two other viral chemokines. vMIP-I and I-309 appear to act as CCR8 agonists: binding to and inducing cytosolic [Ca(2+)] elevation through the receptor. By contrast, vMIP-II and vMCC-I act as potent antagonists: binding without inducing signaling, and blocking the effects of I-309 and vMIP-I. These results suggest a ligand hierarchy for CCR8, identifying vMIP-I as a selective viral chemokine agonist. CCR8 may thus engage a specific subset of chemokines with the potential to regulate each other during viral infection and immune regulation.