gebhart/patrepeval huggingface dataset:
MntR modulates expression of the PerR regulon and superoxide resistance in Staphylococcus aureus through control of manganese uptake (2002)

The Staphylococcus aureus DtxR-like protein, MntR, controls expression of the mntABC and mntH genes, which encode putative manganese transporters. Mutation of mntABC produced a growth defect in metal-depleted medium and increased sensitivity to intracellularly generated superoxide radicals. These phenotypes resulted from diminished uptake of manganese and were rescued by the addition of excess Mn(II). Resistance to superoxide was incompletely rescued by Mn(II) for STE035 (mntA mntH), and the strain had reduced virulence in a murine abscess model of infection. Expression of mntABC was repressed by Mn(II) in an MntR-dependent manner, which contrasts with the expression of mntH that was not repressed in elevated Mn(II) and was decreased in an mntR mutant. This demonstrates that MntR acts as a negative and positive regulator of these loci respectively. PerR, the peroxide resistance regulon repressor, acts with MntR to control the expression of mntABC and manganese uptake. The expression of the PerR-regulated genes, katA (catalase), ftn (ferritin) and fur (ferric uptake regulator), was diminished in STE031 (mntR) when grown in excess Mn(II). Therefore, the control of Mn(II)-regulated members of the PerR regulon and the Fur protein is modulated by MntR through its control of Mn(II) uptake. The co-ordinated regulation of metal ion homeostasis and oxidative stress resistance via the regulators MntR, PerR and Fur of S. aureus is discussed.
Metabonomics: Its Potential as a Tool in Toxicology for Safety Assessment and Data Integration (2004)

The functional genomic techniques of transcriptomics and proteomics promise unparalleled global information during the drug development process. However, if these technologies are used in isolation the large multivariate data sets produced are often difficult to interpret, and have the potential of missing key metabolic events (e.g. as a result of experimental noise in the system). To better understand the significance of these megavariate data the temporal changes in phenotype must be described. High resolution 1H NMR spectroscopy used in conjunction with pattern recognition provides one such tool for defining the dynamic phenotype of a cell, organ or organism in terms of a metabolic phenotype. In this review the benefits of this metabonomics/metabolomics approach to problems in toxicology will be discussed. One of the major benefits of this approach is its high throughput nature and cost effectiveness on a per sample basis. Using such a method the consortium for metabonomic toxicology (COMET) are currently investigating approximately 150 model liver and kidney toxins. This investigation will allow the generation of expert systems where liver and kidney toxicity can be predicted for model drug compounds, providing a new research tool in the field of drug metabolism. The review will also include how metabonomics may be used to investigate co-responses with transcripts and proteins involved in metabolism and stress responses, such as during drug induced fatty liver disease. By using data integration to combine metabolite analysis and gene expression profiling key perturbed metabolic pathways can be identified and used as a tool to investigate drug function.
Direct Analysis of Semivolatile Organic Compounds in Air by Atmospheric Pressure Chemical Ionization Mass Spectrometry (2001)

Atmospheric pressure chemical ionization is employed for direct air analysis, without ion source modification, by using the sheath gas as the sample transport agent. A simple modification of the sheath gas inlet line allows introduction of gaseous samples into a commercial atmospheric pressure chemical ionization source. Optimization and testing of this novel air sampling method are described and detection of semivolatile compounds is shown. The analytical performance of the technique is established with methyl salicylate, including a limit of quantification of 100 pptr, a limit of detection of 50 pptr, a linear response from 100 pptr to 20 ppb, and rise and fall times of 12 and 20 s, respectively. Using reagent ion monitoring, it is shown that the protonated methanol dimer is the principal CI reagent ion leading to protonated dimethyl methylphosphonate, while the monomer is mainly responsible for protonating methyl salicylate. Since the formation of the CI reagent (methanol clusters) can be controlled by simple variation of experimental parameters, the selectivity of the method can be easily adjusted to suit the targeted analyte. Performance is found to be independent of the choice of air or nitrogen as the sheath gas (and thus as the sample matrix) and this, together with the sensitivity and speed of the technique, make it promising for field studies.
A new hierarchical routing protocol for dynamic multihop wireless networks (2002)

The routing techniques used in conventional packet radio networks are not suitable for dynamic multihop wireless networks because of their unique architecture. In this paper a new hierarchical multihop routing algorithm is introduced which balances the cost of location-update and path-finding operations by partitioning the terminals and mobile base stations to produce a virtual topology. Based on the virtual topology each network entity stores a fraction of the network topology information and maintains the routing efficiency. Finally, the performance of the hierarchical multihop routing algorithm is investigated through simulations.
矿产资源＋工程、经济与法律的可行性＝矿石储量（一） (2001)

在过去的35年里,对矿产项目业绩的一些评论指出,由于在地质信息和储量估算,选矿和冶金试验,可行性研究的目的与要求,以及项目启动方法等方面存在着缺点.导致采矿工程失败的一些偶然的但可再现的典型事例对于质量保证性和不断地改进方法以及获得质量适宜的充足数据来说,有某种约定是至为紧要的.矿产资源和矿石储量定义的新的国际的与加拿大的方案已采取非传统的姿态,这将损害有效的矿床圈定及储量估算的工业准则、方针、要求,以及项目可行性的抉择.为了有助于减少问题,支持矿山开发和生产决策的每一可行性研究应以适于达到类似于对银行家的竣工目标的目的和方法为依据,作为可获利的项目的良好的商业目标.在资源/储量体系中,储量的使用应限于符合顺利实施该项目所需的技术的、经济的和法律的可行性要求的项目,而且这些级别的定义应该有明确的界限.现时的缺点将限制合格人选提供适宜的职业惯例,履行对资方或客户的职业责任和向投资公众提供适宜信息的能力.我们一定要从为新千年建立新标准的目前机会中获益.
MicroRNAs 221 and 222 Bypass Quiescence and Compromise Cell Survival (2008)

MicroRNAs (miRNA) have tumor suppressive and oncogenic potential in human cancer, but whether and how miRNAs control cell cycle progression is not understood. To address this question, we carried out a comprehensive analysis of miRNA expression during serum stimulation of quiescent human cells. Time course analyses revealed that four miRNAs are up-regulated and >100 miRNAs are down-regulated, as cells progress beyond the G(1)-S phase transition. We analyzed the function of two up-regulated miRNAs (miR-221 and miR-222) that are both predicted to target the cell growth suppressive cyclin-dependent kinase inhibitors p27 and p57. Our results show that miR-221 and miR-222 both directly target the 3' untranslated regions of p27 and p57 mRNAs to reduce reporter gene expression, as well as diminish p27 and p57 protein levels. Functional studies show that miR-221 and miR-222 prevent quiescence when elevated during growth factor deprivation and induce precocious S-phase entry, thereby triggering cell death. Thus, the physiologic up-regulation of miR-221 and miR-222 is tightly linked to a cell cycle checkpoint that ensures cell survival by coordinating competency for initiation of S phase with growth factor signaling pathways that stimulate cell proliferation.
Managing the Transition: Defining Government's Role in the Defense Conversion (1993)

"So goes the popular concept of defense conversion or whatever you call it (diversification, economic adjustment, military transition, defense reinvestment...). The central tenet of conversion asserts that companies which produce goods for the defense market can be guided, with a little effort, toward a successful civilian market. The benefits to the country could be immense. Labor and machinery reserved for defense could be retrained and retooled for civilian use. Rebuilding the infrastructure, developing civilian technologies, and shoring-up the nation's economic competitive edge are all plausible options. However, those grandiose designs of a new civilian economy are not the reasons why conversion is a favorite in Washington. The real motive for conversion is jobs. Defense cutbacks will have a crippling effect on private industry. Everyone knows that the Department of Defense(DoD) is a tremendous stimulant to the economy. Along with the Pentagon, it practices a de facto industrial policy, subsidizing key technologies and investing in basic and applied research and development (R and D). This high-tech research is spunoff, giving the products of civilian firms a competitive boost over foreign products. But as defense funds begin to taper off, bases will close, military personnel dismissed, and defense contractors starved for income, triggering a new wave of unemployment..."--from page 10
THE LINKAGE OF GENES FOR THE HUMAN INTERFERON-INDUCED ANTIVIRAL PROTEIN AND INDOPHENOL OXIDASE-B TRAITS TO CHROMOSOME G-21 (1973)

13 independent mouse-human somatic cell hybrid clones derived from beta-propiolactone-inactivated Sendai stimulated cell fusion of human cells with mouse cells were tested for their sensitivities to human and mouse interferon. All of them were protected by mouse interferon and only six of the clones were protected by both human and mouse interferon. Only the six that were protected by human interferon were shown to express the human dimeric form of indophenol oxidase. Complete chromosomal analysis of the clones indicated human chromosome G-21 to be the only human chromosome in common for the six clones which had both phenotypes present. Nine subclones were derived from one of the clones expressing both phenotypes. Eight of the nine subclones were shown to retain both phenotypes, whereas one subclone lost both. Chromosomal analysis of the subclones indicated the loss of chromosome G-21 from the subclone which lost both phenotypes. It is apparent from these findings that the gene(s) for indophenol oxidase (IPO-B) and the gene(s) for the antiviral protein are syntenic and that they are linked to human chromosome G-21.
After dark in the antipodes: pedagogy, place and queer phenomenology (2010)

This paper pursues issues of pedagogy, place and queer phenomenology in the context of what might be meant by the term ‘after‐queer’ or ‘what falls outside queer’ as we currently theorise, practice and locate queer. Inspired by Sara Ahmed’s account of how bodies become oriented by the ways in which they take up time and space, this paper investigates how bodies become oriented within and around the field of a television series that centres Indigenous terms and orientations and thereby, still further, problematises the directions and orientations of desire. The paper explores the narrative and queer and other couplings of an Australian tele‐series, The Circuit. It raises issues of audience, public pedagogy and we refer to guestbook discussion as we strive to foreground a methodology for working with sexuality and race that recognises and disturbs in order to read sexual and racial orientations as mixed and unfixed orientations.
The intracellular domain of mouse Notch: a constitutively activated repressor of myogenesis directed at the basic helix-loop-helix region of MyoD (1994)

We show that Myf-5 and mNotch mRNA are both present in the presomitic mesoderm before muscle cell commitment and before muscle structural gene activation. The failure of presomitic mesoderm to respond to Myf-5 and express myogenic properties implies that there may be a mechanism in presomitic mesoderm to suppress muscle differentiation. Here we show that ectopic expression of the intracellular domain of mNotch (mNotchIC) functions as a constitutively activated repressor of myogenesis both in cultured cells and in frog embryos. Mutagenesis experiments indicate that the target for inactivation by mNotch is the MyoD basic helix-loop-helix domain. mNotchIC contains a nuclear localization signal and localizes to the nucleus. Removal of the nuclear localization signal (NLS) reduces nuclear localization and diminishes the inhibition of myogenesis caused by Myf-5 or MyoD. Additional experiments show that the CDC10/SWI6/ankyrin repeats are also necessary for myogenic inhibition.
The relationship between Precision-Recall and ROC curves (2006)

Receiver Operator Characteristic (ROC) curves are commonly used to present results for binary decision problems in machine learning. However, when dealing with highly skewed datasets, Precision-Recall (PR) curves give a more informative picture of an algorithm's performance. We show that a deep connection exists between ROC space and PR space, such that a curve dominates in ROC space if and only if it dominates in PR space. A corollary is the notion of an achievable PR curve, which has properties much like the convex hull in ROC space; we show an efficient algorithm for computing this curve. Finally, we also note differences in the two types of curves are significant for algorithm design. For example, in PR space it is incorrect to linearly interpolate between points. Furthermore, algorithms that optimize the area under the ROC curve are not guaranteed to optimize the area under the PR curve.
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes (2015)

MetAnnotate is multi-threaded and installable as a local web application or command-line tool on Linux systems. Metannotate is a useful framework for general and/or function-specific taxonomic profiling and comparison of metagenomes.
Propagation of CubeSats in LEO using NORAD Two Line Element Sets: Accuracy and Update Frequency (2013)

Information on the orbital characteristics of satellites and other earth-orbiting objects is made available to the public in the form of two-line element sets (TLEs), published by the North American Aerospace Defense Command (NORAD). TLEs are typically not used alone for applications that require reliable and accurate position determination because TLEs are not accompanied by any indicators of accuracy or consistency. In this paper, we analyze the characteristics of TLE updates for CubeSats in low-Earth orbit (LEO) with respect to both update frequency and accuracy. We use both catalogued TLE data from July 2011 to July 2012 alone in a Monte Carlo analysis as well as compare TLE-only propagation with “truth” on-orbit GPS data from The Aerospace Corporation’s recent satellite mission, the PicoSatellite Solar Cell Testbed 2 (PSSCT-2), which launched in 20 July 2011 and operated until 8 December 2011. In addition to calculating the error statistics between the PSSCT-2 GPS positions and TLE propagated positions using the unusually frequent TLE updates available over the 213.5 minute period of time that GPS data is available, we also calculate error statistics as a function of less frequent TLE updates as well as calculate error statistics using a Monte Carlo simulation for TLE updates. From the latter we find that a CubeSat-class mission operating in a low orbit (under 350 km) using TLE propagation may be able to resolve position determination errors to as low as: in-track with mean = 0.177 km and standard deviation = 0.619 km; cross-track with mean = 0.108 km and standard deviation 0.619 km; and radial with mean = -0.068 km and standard deviation = 0.274 km, for a total mean = 0.832 km and standard deviation = 0.444 km.
The immunoprotective Anaplasma marginale major surface protein 2 is encoded by a polymorphic multigene family (1994)

An Anaplasma marginale Florida msp-2 gene was cloned and expressed in Escherichia coli. Pulsed-field gel electrophoresis and Southern blot analysis revealed the presence of multiple msp-2 gene copies that were widely distributed throughout the chromosomes of all three strains examined. Genomic polymorphism among copies was greatest in the 5' end of msp-2 but also occurred in 3' regions. The presence of gene-copy-specific epitopes was indicated by the reactivity of the cloned msp-2 copy with some, but not all, monoclonal antibodies that bound native MSP-2. Multiple antigenically distinct MSP-2 molecules were expressed within strains and were coexpressed by individual A. marginale organisms. These results suggest that expression of polymorphic msp-2 gene copies is responsible for the significant percentages of A. marginale organisms within strains that do not react with individual anti-MSP-2 monoclonal antibodies. Sequence analysis revealed highly significant MSP-2 homology with two rickettsial surface proteins, A. marginale MSP-4 and Cowdria ruminantium MAP-1. Immunization with MSP-4 has been shown to induce protective immunity in a manner similar to that of immunization with MSP-2. These findings support the hypothesis that A. marginale surface proteins are targets of protective immune responses but are antigenically polymorphic.
Pulmonary and Hepatic Gene Expression following Cecal Ligation and Puncture: Monophosphoryl Lipid A Prophylaxis Attenuates Sepsis-Induced Cytokine and Chemokine Expression and Neutrophil Infiltration (1998)

Polymicrobial sepsis induced by cecal ligation and puncture (CLP) reproduces many of the pathophysiologic features of septic shock. In this study, we demonstrate that mRNA for a broad range of pro- and anti-inflammatory cytokine and chemokine genes are temporally regulated after CLP in the lung and liver. We also assessed whether prophylactic administration of monophosphoryl lipid A (MPL), a nontoxic derivative of lipopolysaccharide (LPS) that induces endotoxin tolerance and attenuates the sepsis syndrome in mice after CLP, would alter tissue-specific gene expression post-CLP. Levels of pulmonary interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-alpha), granulocyte colony-stimulating factor (G-CSF), IL-1 receptor antagonist (IL-1ra), and IL-10 mRNA, as well as hepatic IL-1beta, IL-6, gamma interferon (IFN-gamma), G-CSF, inducible nitric oxide synthase, and IL-10 mRNA, were reduced in MPL-pretreated mice after CLP compared to control mice. Chemokine mRNA expression was also profoundly mitigated in MPL-pretreated mice after CLP. Specifically, levels of pulmonary and hepatic macrophage inflammatory protein 1alpha (MIP-1alpha), MIP-1beta, MIP-2, and monocyte chemoattractant protein-1 (MCP-1) mRNA, as well as hepatic IFN-gamma-inducible protein 10 and KC mRNA, were attenuated in MPL-pretreated mice after CLP. Attenuated levels of IL-6, TNF-alpha, MCP-1, MIP-1alpha, and MIP-2 in serum also were observed in MPL-pretreated mice after CLP. Diminished pulmonary chemokine mRNA production was associated with reduced neutrophil margination and pulmonary myeloperoxidase activity. These data suggest that prophylactic administration of MPL mitigates the sepsis syndrome by reducing chemokine production and the recruitment of inflammatory cells into tissues, thereby attenuating the production of proinflammatory cytokines.
Laminar/Turbulent Plasma Jets Generated at Reduced Pressure (2008)

Laminar DC plasma jets are attractive for precisely controlled plasma-material processing. The design of a novel nontransferred plasma torch enabled the switching between turbulent and laminar plasma flows by simply changing the plasma generation parameters. Images of the plasma flows generated at different conditions are presented.
The BlueWand as interface for ubiquitous and wearable computing environments (2003)

The achievements of modem electronics more and more enmesh our daily life with various wirelessly communicating gadgets. Some of them are carried around e.g. cell-phones, personal digital assistants, or portable music players. Others are absorbed into the environment, e.g. access control systems, vehicle electronics, remotely controlled home appliances and consumer electronics. Typically, each such device is handled by a dedicated keypad. And sometimes, miniaturization has pushed the keys' size already beyond the limit of easy usage. This paper presents the BlueWand as a control means for such ubiquitous and wearable computing environments. The BlueWand is a small pen-like device that can be used to control other Bluetooth enabled devices by hand-movements. Based on a 6-axis accelerometer and gyroscope system it is able to detect its orientation and movement in space and to transmit this data via Bluetooth to any device that can interpret these movements and execute associated commands. The BlueWand is especially suited for scenarios that require only a limited set of commands or where the controlled devices themselves are an unnatural place for the human-computer interface. Thus the BlueWand facilitates a true wireless experience.
Serum Elastin-Derived Peptides in Age-Related Macular Degeneration (2005)

The cause of this association between S-EDPs and AMD is unknown, but it suggests that systemic elastin degradation may increase the risk of conversion from early ARM to neovascular AMD. Further studies are needed to confirm whether the serum level of S-EDPs is a useful predictor of conversion from early ARM to neovascular AMD.
Parkin Suppresses Unfolded Protein Stress-induced Cell Death through Its E3 Ubiquitin-protein Ligase Activity (2000)

Autosomal recessive juvenile parkinsonism (AR-JP) is caused by mutations in the parkin gene. Parkin protein is characterized by a ubiquitin-like domain at its NH(2)-terminus and two RING finger motifs and an IBR (in between RING fingers) at its COOH terminus (RING-IBR-RING). Here, we show that Parkin is a RING-type E3 ubiquitin-protein ligase which binds to E2 ubiquitin-conjugating enzymes, including UbcH7 and UbcH8, through its RING-IBR-RING motif. Moreover, we found that unfolded protein stress induces up-regulation of both the mRNA and protein level of Parkin. Furthermore, overexpression of Parkin, but not a set of mutants without the E3 activity, specifically suppressed unfolded protein stress-induced cell death. These findings demonstrate that Parkin is an E3 enzyme and suggest that it is involved in the ubiquitination pathway for misfolded proteins derived from endoplasmic reticulum and contributes to protection from neurotoxicity induced by unfolded protein stresses.
Evaluation of the Proteasome Inhibitor MLN9708 in Preclinical Models of Human Cancer (2010)

The proteasome was validated as an oncology target following the clinical success of VELCADE (bortezomib) for injection for the treatment of multiple myeloma and recurring mantle cell lymphoma. Consequently, several groups are pursuing the development of additional small-molecule proteasome inhibitors for both hematologic and solid tumor indications. Here, we describe MLN9708, a selective, orally bioavailable, second-generation proteasome inhibitor that is in phase I clinical development. MLN9708 has a shorter proteasome dissociation half-life and improved pharmacokinetics, pharmacodynamics, and antitumor activity compared with bortezomib. MLN9708 has a larger blood volume distribution at steady state, and analysis of 20S proteasome inhibition and markers of the unfolded protein response confirmed that MLN9708 has greater pharmacodynamic effects in tissues than bortezomib. MLN9708 showed activity in both solid tumor and hematologic preclinical xenograft models, and we found a correlation between greater pharmacodynamic responses and improved antitumor activity. Moreover, antitumor activity was shown via multiple dosing routes, including oral gavage. Taken together, these data support the clinical development of MLN9708 for both hematologic and solid tumor indications.