gebhart/patrepeval huggingface dataset:
Physical map of the chromosome of Neisseria gonorrhoeae FA1090 with locations of genetic markers, including opa and pil genes (1991)

A physical map of the chromosome of Neisseria gonorrhoeae FA1090 has been constructed. Digestion of strain FA1090 DNA with NheI, SpeI, BglII, or PacI resulted in a limited number of fragments that were resolved by contour-clamped homogeneous electric field electrophoresis. The estimated genome size was 2,219 kb. To construct the map, probes corresponding to single-copy chromosomal sequences were used in Southern blots of digested DNA separated on pulsed-field gels, to determine how the fragments from different digests overlapped. Some of the probes represented identified gonococcal genes, whereas others were anonymous cloned fragments of strain FA1090 DNA. By using this approach, a macrorestriction map of the strain FA1090 chromosome was assembled, and the locations of various genetic markers on the map were determined. Once the map was completed, the repeated gene families encoding Opa and pilin proteins were mapped. The 11 opa loci of strain FA1090 were distributed over approximately 60% of the chromosome. The pil loci were more clustered and were located in two regions separated by approximately one-fourth of the chromosome.
Critical Contribution of Nuclear Factor Erythroid 2-related Factor 2 (NRF2) to Electrophile-induced Interleukin-11 Production (2016)

Nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor that plays a crucial role in protection of cells from electrophile-induced toxicity through up-regulating phase II detoxifying enzymes and phase III transporters. We previously reported that oxidative stress induces up-regulation of interleukin-11 (IL-11), a member of the IL-6 family that ameliorates acetaminophen-induced liver toxicity. However, a role for IL-11 in protection of cells from electrophile-induced toxicity remains unclear. Here we show that an environmental electrophile, 1,2-naphthoquinone (1,2-NQ), but not 15d-prostaglandin J<sub>2</sub> (PGJ<sub>2</sub>) or tert-butylhydroxyquinone (tBHQ), induced IL-11 production. Consistent with a crucial role for prolonged ERK activation in H<sub>2</sub>O<sub>2</sub>-induced IL-11 production, 1,2-NQ, but not 15d-PGJ<sub>2</sub> or tBHQ, elicited prolonged ERK activation. Conversely, inhibition of the ERK pathway by a MEK inhibitor completely blocked 1,2-NQ-induced IL-11 production at both protein and mRNA levels, further substantiating an intimate cross-talk between ERK activation and 1,2-NQ-induced IL-11 production. Promoter analysis of the Il11 gene revealed that two AP-1 sites were essential for 1,2-NQ-induced promoter activities. Among various members of the AP-1 family, Fra-1 was up-regulated by 1,2-NQ, and its up-regulation was blocked by a MEK inhibitor. Although NRF2 was not required for H<sub>2</sub>O<sub>2</sub>-induced IL11 up-regulation, NRF2 was essential for 1,2-NQ-induced IL11 up-regulation by increasing Fra-1 proteins possibly through promoting mRNA translation of FOSL1 Finally, intraperitoneal administration of 1,2-NQ induced body weight loss in wild-type mice, which was further exacerbated in Il11ra1<sup>-/-</sup> mice compared with Il11ra1<sup>+/-</sup> mice. Together, both Fra-1 and NRF2 play crucial roles in IL-11 production that protects cells from 1,2-NQ intestinal toxicity.
Vesicular monoamine transporters: Structure‐function, pharmacology, and medicinal chemistry (2010)

Vesicular monoamine transporters (VMAT) are responsible for the uptake of cytosolic monoamines into synaptic vesicles in monoaminergic neurons. Two closely related VMATs with distinct pharmacological properties and tissue distributions have been characterized. VMAT1 is preferentially expressed in neuroendocrine cells and VMAT2 is primarily expressed in the CNS. The neurotoxicity and addictive properties of various psychostimulants have been attributed, at least partly, to their interference with VMAT2 functions. The quantitative assessment of the VMAT2 density by PET scanning has been clinically useful for early diagnosis and monitoring of the progression of Parkinson's and Alzheimer's diseases and drug addiction. The classical VMAT2 inhibitor, tetrabenazine, has long been used for the treatment of chorea associated with Huntington's disease in the United Kingdom, Canada, and Australia, and recently approved in the United States. The VMAT2 imaging may also be useful for exploiting the onset of diabetes mellitus, as VMAT2 is also expressed in the β-cells of the pancreas. VMAT1 gene SLC18A1 is a locus with strong evidence of linkage with schizophrenia and, thus, the polymorphic forms of the VMAT1 gene may confer susceptibility to schizophrenia. This review summarizes the current understanding of the structure-function relationships of VMAT2, and the role of VMAT2 on addiction and psychostimulant-induced neurotoxicity, and the therapeutic and diagnostic applications of specific VMAT2 ligands. The evidence for the linkage of VMAT1 gene with schizophrenia and bipolar disorder I is also discussed.
Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes (2010)

The EC23S857 assay has a lower limit of detection for E. coli cells than the uidA405 and rodA984 assays due to its multi-copy gene target and therefore provides greater analytical sensitivity in monitoring for these faecal pollution indicators in environmental waters by qPCR methods.
Dominant Expression of the Inhibitory FcγRIIB Prevents Antigen Presentation by Murine Plasmacytoid Dendritic Cells (2009)

Plasmacytoid dendritic cells (pDCs) are key regulators of the innate immune response, yet their direct role as APCs in the adaptive immune response is unclear. We found that unlike conventional DCs, immune complex (IC) exposed murine pDCs neither up-regulated costimulatory molecules nor activated Ag-specific CD4(+) and CD8(+) T cells. The inability of murine pDCs to promote T cell activation was due to inefficient proteolytic processing of internalized ICs. This defect in the IC processing capacity of pDCs results from a lack of activating FcgammaR expression (FcgammaRI, III, IV) and the dominant expression of the inhibitory receptor FcgammaRIIB. Consistent with this idea, transgenic expression of the activating human FcgammaRIIA gene, not present in the mouse genome, recapitulated the human situation and rescued IC antigenic presentation capacity by murine pDCs. The selective expression of FcgammaRIIB by murine pDCs was not strain dependent and was maintained even following stimulation with TLR ligands and inflammatory cytokines. The unexpected difference between the mouse and human in the expression of activating/inhibitory FcgammaRs has implications for the role of pDCs in Ab-modulated autoimmunity and anti-viral immunity.
CD47 (2008)

CD47, originally named integrin-associated protein, is a receptor for thrombospondin-1. A number of important roles for CD47 have been defined in regulating the migration, proliferation, and survival of vascular cells, and in regulation of innate and adaptive immunity. The recent discovery that thrombospondin-1 acts via CD47 to inhibit nitric oxide signaling throughout the vascular system has given new importance and perhaps a unifying mechanism of action to these enigmatic proteins. Here we trace the development of this exciting new paradigm for CD47 function in vascular physiology.
A Proposed Bus Arbitration Scheme for Multimedia Workstations (1993)

The integration of video and audio into computers requires the support of continuous streams at the hardware level. This paper proposes a bus bandwidth management and access arbitration scheme for a multimedia workstation. It is assumed that a multimedia workstation consists of several specialized processing modules which are linked by a packet-switched bus. Using the proposed scheme, the bus can support a mix of real-time continuous media streams and random transactions while fulfilling special requirements corresponding to each traffic type. Specifically, the bus provides very fast response to random transactions and serves continuous media streams in such a way that no piece of data falls behind its deadline. Furthermore, the performance with respect to continuous media traffic is maintained independent of time variations of randomm traffic. Practical implementation guidelines are provided. Finally, the performance of the proposed scheme is compared with other possible approaches.
Role of Polymorphic Human Cytochrome P450 Enzymes in Estrone Oxidation (2006)

Estrogen and its metabolites are believed to play important roles in breast cancer. The influence of genetic polymorphisms in the enzymes responsible for formation and disposition of estrogen on breast cancer risk may shed light on the importance of estrogen metabolites in this disease. However, for such studies to be valid, it is important to correctly identify the enzymes involved in estrogen bioactivation. Therefore, we assessed the human cytochrome P450-dependent oxidation of estrone using substrate concentrations that more closely approximate the maximum expected concentrations in breast tissue. The in vitro metabolism of estrone by recombinant human cytochrome P450 enzymes and human liver microsomes was studied. The formation of estrone metabolites (2-hydroxyestrone, 4-hydroxyestrone, and 16alpha-hydroxyestrone) was monitored by high-performance liquid chromatography. 2-Hydroxyestrone formation was catalyzed predominantly by CYP1A2, CYP1A1, and CYP1B1 enzymes; 4-hydroxyestrone formation was catalyzed predominantly by CYP1B1, CYP1A2, and CYP1A1 enzymes; and 16alpha-hydroxyestrone formation was catalyzed predominantly by CYP2C19, CYP1A1, and CYP3A5. This study confirms the important role of members of the CYP1 family in the 2-hydroxylation and 4-hydroxylation of estrone, but the enzymes identified as responsible for the 16alpha-hydroxylation of estrone are different from those previously identified. The relative importance of these enzymes in vivo would depend on the specific tissue expression of the enzymes. These enzymes are all known to be genetically variant in the human population, and additional studies to assess the role CYP1A2, CYP2C19, and CYP3A5 in breast cancer risk are indicated.
A Fast Virtual Machine Storage Migration Technique Using Data Deduplication (2012)

Abstract—In this paper, we proposed a fast virtual machine (VM) storage migration technique. Virtual machine storage migration can migrate entire VM states to other hosts, includ-ing VM disk images. It is widely used for cross-data-center load management. However, VM disk images generally have large file sizes (typically 1-30GB). Thus, storage migration was time-consuming. To address this problem, we introduce the deduplication technique into traditional VM storage migration. We focused on the fact that it is possible to return VMs from the new VM hosts. For example, a VM first migrates from host A to host B. Next, the VM returns from host B to host A. There will then be additional reusable disk pages in host A. Consequently, to expedite the operation, we only return to host A the disk pages that have been updated while in host B. We implement this idea to a QEMU/KVM (kernel virtual machine). To track the reusable disk pages, we developed a DBT (Dirty Block Tracking) mechanism and a new diff format to store the tracking result. In this paper, we discuss the design and implementation of our prototype. Our technique successfully reduced the transfer time for storage migration from 10 minutes to about 10 seconds in some practical workloads.
Mutational analysis of the BRAF, RAS and EGFR genes in human adrenocortical carcinomas (2009)

The serine/threonine kinase B-Raf plays a key role in the Ras/Raf/MEK/ERK pathway that relays extracellular signals for cell proliferation and survival. Several types of human malignancies harbor activating BRAF mutations, most frequently a V600E substitution. The epidermal growth factor receptor (EGFR), a transmembrane tyrosine kinase (TK) receptor that mediates proliferation and survival signaling, is expressed in a wide variety of normal and neoplastic tissues. EGFR inhibitors have produced objective responses in patients with non-small cell lung carcinomas harboring activating EGFR TK domain somatic mutations. We evaluated the presence of mutations in BRAF (exons 11 and 15), KRAS (exons 1 and 2), NRAS (exons 1 and 2), and EGFR (exons 18-21) in adrenal carcinomas (35 tumor specimens and two cell lines) by DNA sequencing. BRAF mutations were found in two carcinomas (5.7%). Four carcinomas (11.4%) carried EGFR TK domain mutations. One specimen carried a KRAS mutation, and another carried two NRAS mutations. No mutations were found in the two adrenocortical cell lines. BRAF- and EGFR-mutant tumor specimens exhibited stronger immunostaining for the phosphorylated forms of the MEK and ERK kinases than their wild-type counterparts. EGFR-mutant carcinomas exhibited increased phosphorylation of EGFR (Tyr 992) compared with wild-type carcinomas. We conclude that BRAF, RAS, and EGFR mutations occur in a subset of human adrenocortical carcinomas. Inhibitors of the Ras/Raf/MEK/ERK and EGFR pathways represent candidate targeted therapies for future clinical trials in carefully selected patients with adrenocortical carcinomas harboring respective activating mutations.
Photosynthetic responses of forest understory tree species to long-term exposure to elevated carbon dioxide concentration at the Duke Forest FACE experiment (2007)

We examined the photosynthetic responses of four species of saplings growing in the understory of the Duke Forest FACE experiment during the seventh year of exposure to elevated CO2 concentration ([CO2]). Saplings of these same species were measured in the first year of the Duke Forest FACE experiment and at that time showed only seasonal fluctuations in acclimation of photosynthesis to elevated [CO2]. Based on observations from the Duke Forest FACE experiment, we hypothesized that after seven years of exposure to elevated [CO2] significant photosynthetic down-regulation would be observed in these tree species. To test our hypothesis, photosynthetic CO2-response and light-response curves, along with chlorophyll fluorescence, chlorophyll concentration and foliar N were measured twice during the summer of 2003. Exposure to elevated [CO2] continued to increase photosynthesis in all species measured after seven years of treatment with the greatest photosynthetic increase observed near saturating irradiances. In all species, elevated [CO2] increased electron transport efficiency but did not significantly alter carboxylation efficiency. Quantum yield estimated by light curves, chlorophyll concentration, and foliar nitrogen concentrations were unaffected by elevated [CO2]. Contrary to our hypothesis, there is little evidence of progressive N limitation of leaf-level processes in these understory tree species after seven years of exposure to elevated [CO2] in the Duke Forest FACE experiment.
Electric Conductivity-Tunable Transparent Flexible Nanowire-Filled Polymer Composites: Orientation Control of Nanowires in a Magnetic Field (2011)

Cobalt compound nanowires were dispersed in a transparent nonconductive polymer film by merely stirring, and the film's transparency and electrical conductivity were examined. This composite film is a unique system in which the average length of the nanowires exceeds the film's thickness. Even in such a system, a percolation threshold existed for the electric conductivity in the direction of the film thickness, and the value was 0.18 vol%. The electric conductivity value changed from ∼1 × 10(-12) S/cm to ∼1 × 10(-3) S/cm when the volume fraction exceeded the threshold. The electric conductivity apparently followed the percolation model until the volume fraction of the nanowires was about 0.45 vol %. The visible light transmission and electric conductivity of the composite film of about 1 vol % nanowires were 92% and 5 × 10(-3) S/cm, respectively. Moreover, the electric conductivity in the direction parallel to the film surface did not depend on the amount of the dispersed nanowires, and its value was about 1 × 10(-14) S/cm. Even in a weak magnetic field of about 100 mT, the nanowires were aligned in a vertical and parallel direction to the film surface, and the electric conductivity of each aligned composite film was 2.0 × 10(-2) S/cm and 2.1 × 10(-12) S/cm. The relation between the average wire length and the electric conductivity was examined, and the effect of the magnetic alignment on that relation was also examined.
Palivizumab for immunoprophylaxis of respiratory syncitial virus (RSV) bronchiolitis in high-risk infants and young children: a systematic review and additional economic modelling of subgroup analyses (2011)

This report was funded by the HTA programme of the National Institute for Health Research.
The dual role of the neuroinflammatory response after ischemic stroke: modulatory effects of hypothermia (2010)

Neuroinflammation is a key element in the ischemic cascade after cerebral ischemia that results in cell damage and death in the subacute phase. However, anti-inflammatory drugs do not improve outcome in clinical settings suggesting that the neuroinflammatory response after an ischemic stroke is not entirely detrimental. This review describes the different key players in neuroinflammation and their possible detrimental and protective effects in stroke. Because of its inhibitory influence on several pathways of the ischemic cascade, hypothermia has been introduced as a promising neuroprotective strategy. This review also discusses the influence of hypothermia on the neuroinflammatory response. We conclude that hypothermia exerts both stimulating and inhibiting effects on different aspects of neuroinflammation and hypothesize that these effects are key to neuroprotection.
Targeted Cell Entry of Lentiviral Vectors (2008)

Retargeting of lentiviral vector entry to cell types of interest is a key factor in improving the safety and efficacy of gene transfer. In this study we show that the retargetable envelope glycoproteins of measles virus (MV), namely, the hemagglutinin (H) responsible for receptor recognition and the fusion protein (F), can pseudotype human immunodeficiency virus 1 (HIV-1) vectors when their cytoplasmic tails are truncated. We then pseudotyped HIV-1 vectors with MV glycoproteins displaying on H either the epidermal growth factor or a single-chain antibody directed against CD20, but without the ability to recognize their native receptors. Gene transfer into cells that expressed the targeted receptor was several orders of magnitude more efficient than into cells that did not. High-target versus nontarget cell discrimination was demonstrated in mixed cell populations, where the targeting vector selectively eliminated CD20-positive cells after suicide gene transfer. Remarkably, primary human CD20-positive B lymphocytes were transduced more efficiently by the CD20-targeted vector than by a vector pseudotyped with the vesicular stomatitis virus G (VSV-G) protein. In addition, the CD20-targeted vector was able to transduce even unstimulated primary B cells, whereas VSV-G pseudotyped vectors were unable to do so. Because MV enters cells through direct fusion at the cell membrane, this novel targeting system should be widely applicable.
Artificial intelligence: a modern approach (1995)

The long-anticipated revision of this #1 selling book offers the most comprehensive, state of the art introduction to the theory and practice of artificial intelligence for modern applications. Intelligent Agents. Solving Problems by Searching. Informed Search Methods. Game Playing. Agents that Reason Logically. First-order Logic. Building a Knowledge Base. Inference in First-Order Logic. Logical Reasoning Systems. Practical Planning. Planning and Acting. Uncertainty. Probabilistic Reasoning Systems. Making Simple Decisions. Making Complex Decisions. Learning from Observations. Learning with Neural Networks. Reinforcement Learning. Knowledge in Learning. Agents that Communicate. Practical Communication in English. Perception. Robotics. For computer professionals, linguists, and cognitive scientists interested in artificial intelligence.
Hydrogen production and deuterium-proton exchange reactions catalyzed by Desulfovibrio nickel(II)-substituted rubredoxins (1988)

The nickel tetrahedral sulfur-coordinated core formed upon metal replacement of the native iron in Desulfovibrio sp. rubredoxins is shown to mimic the reactivity pattern of nickel-containing hydrogenases with respect to hydrogen production, deuterium-proton exchange, and inhibition by carbon monoxide.
Temperature data and specific absorption rates in pelvic tumours: predictive factors and correlations (2001)

The system BSD 2000 has been in clinical use for regional hyperthermia for more than 10 years. Several technical details of this hyperthermia system, as well as the results of clinical studies employing this system have been investigated. The intention of this paper is to investigate the correlation between technical efficiency or feasibility of hyperthermia with the BSD 2000, in terms of power densities and temperatures depending upon parameters such as tumour histology, tumour location, patient age, patient sex, and patient cross section. The possible conclusions of predictive factors derived from the above correlations were closely scrutinized. Data acquired from 772 treatment sessions of 190 patients with pelvic tumours, mainly sarcomas and carcinomas of the rectum, cervix, prostate and anus, have been evaluated. For every session, index temperatures T90 (temperature attained at 90% of tumour related measurement points), cumulative minutes for T90 > Tref, tumour related power density (SAR: specific absorption rate, in W/kg) and the effective perfusion Weff (in ml/100 g min) were calculated. Temperatures were measured either invasively or endoluminally. The statistics software SPSS was employed subsequently for univariate, as well as multivariate analyses. The results exhibit that index temperatures mainly depend on the power density SAR and the hyperthermia induced effective perfusion. The total power P (in 100 W) and, complementarily, the relative power density absolute value(SAR) (= SAR/P) seem to have lesser influence. Clear differences between the tumour entities were established regarding their index temperatures and temperature distributions. SAR, Weff and P were correlated with several anatomical, biological and clinical factors. Sessions rendering low index temperatures and SAR values also revealed decreased individual tolerance to the treatment. This clearly displays that power-induced side effects define the limits of the efficiency of regional hyperthermia. Equivalent relationships and correlations are derived from intratumoural and endoluminal thermometry. Individual limitations of regional hyperthermia caused by anatomical, biological and clinical factors are liable to be difficult to overcome with the rather restricted potentials of the BSD 2000 system to control the SAR distribution.