gebhart/patrepeval huggingface dataset:
The sigma factor RpoS is required for stress tolerance and environmental fitness of Pseudomonas fluorescens Pf-5 (2005)

Many micro-organisms exist in natural habitats that are subject to severe or dramatically fluctuating environmental conditions. Such is the case for bacteria inhabiting plant surfaces, where they are exposed to UV irradiation, oxygen radicals, and large fluctuations in temperature and moisture. This study focuses on the role of RpoS, a central regulator of stationary-phase gene expression in bacterial cells, in stress response and environmental fitness of Pseudomonas fluorescens Pf-5. Strain Pf-5 is a rhizosphere-inhabiting bacterium that suppresses plant diseases caused by several plant-pathogenic fungi and oomycetes. Previous studies demonstrated that rpoS was required for osmotic and oxidative stress resistance of Pf-5. The results of this study demonstrate a role for rpoS in tolerance of Pf-5 to freezing, starvation, UV irradiation and desiccation stress. In field studies, an rpoS mutant was compromised in rhizosphere colonization of plants in dry soil, whereas similar rhizosphere populations were established by Pf-5 and an rpoS mutant in well-irrigated soils. RpoS is a key determinant in stress response and environmental fitness of the rhizosphere bacterium P. fluorescens Pf-5.
Context-aware network security (2009)

The rapid growth in malicious Internet activity, due to the rise of threats like automated worms, viruses, and botnets, has driven the development of tools designed to protect host and network resources. One approach that has gained significant popularity is the use of network based security systems. These systems are deployed on the network to detect, characterize and mitigate both new and existing threats. Unfortunately, these systems are developed and deployed in production networks as generic systems and little thought has been paid to customization. Even when it is possible to customize these devices, the approaches for customization are largely manual or ad hoc. Our observation of the production networks suggest that these networks have significant diversity in end-host characteristics, threat landscape, and traffic behavior -- a collection of features that we call the security context of a network. The scale and diversity in security context of production networks make manual or ad hoc customization of security systems difficult. Our thesis is that automated adaptation to the security context can be used to significantly improve the performance and accuracy of network-based security systems. In order to evaluate our thesis, we explore a system from three broad categories of network-based security systems: known threat detection, new threat detection, and reputation-based mitigation. For known threat detection, we examine a signature-based intrusion detection system and show that the system performance improves significantly if it is aware of the signature set and the traffic characteristics of the network. Second, we explore a large collection of honeypots (or honeynet) that are used to detect new threats. We show that operating system and application configurations in the network impact honeynet accuracy and adapting to the surrounding network provides a significantly better view of the network threats. Last, we apply our context-aware approach to a reputation-based system for spam blacklist generation and show how traffic characteristics on the network can be used to significantly improve its accuracy. We conclude with the lessons learned from our experiences adapting to network security context and the future directions for adapting network-based security systems to the security context.
Very low voltage operational amplifiers using floating gate MOS transistor (2002)

A threshold voltage tunable operational amplifier (op-amp) structure that can be operated with a very low power supply is presented. The use of floating gate MOS transistors as the basic op-amp circuit elements makes it possible to obtain a very low voltage op-amp because of the threshold voltage adjustability of the floating gate transistors. Good matching can also be achieved by tuning the threshold voltages. A two-step threshold voltage tuning scheme is presented. Due to the long term charge retention property of the floating gate transistors, threshold voltage tuning does not have to be done frequently, and near continuous-time operation of the op-amp can be achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
In Vitro and In Vivo Activities of T-705 against Arenavirus and Bunyavirus Infections (2007)

There is a need for the development of effective antivirals for the treatment of severe viral diseases caused by members of the virus families Bunyaviridae and Arenaviridae. The pyrazine derivative T-705 (6-fluoro-3-hydroxy-2-pyrazinecarboxamide) has demonstrated remarkable antiviral activity against influenza virus and, to a lesser degree, against some other RNA viruses (Y. Furuta, K. Takahashi, Y. Fukuda, M. Kuno, T. Kamiyama, K. Kozaki, N. Nomura, H. Egawa, S. Minami, Y. Watanabe, H. Narita, and K. Shiraki, Antimicrob. Agents Chemother., 46:977-981, 2002). Here, we report that T-705 is highly active against a panel of bunyaviruses (La Crosse, Punta Toro, Rift Valley fever, and sandfly fever viruses) and arenaviruses (Junin, Pichinde, and Tacaribe viruses) by cytopathic effect and virus yield reduction cell-based assays. The 50% effective concentrations for T-705 ranged from 5 to 30 microg/ml and 0.7 to 1.2 microg/ml against the bunyaviruses and arenaviruses examined, respectively. We also demonstrate that orally administered T-705 is efficacious in treating Punta Toro virus in the mouse and hamster infection models, as well as Pichinde virus infection in hamsters. When administered twice daily for 5 to 6 days, beginning 4 h pre- or 24 h post-Punta Toro virus challenge, a 30-mg/kg of body weight/day dose provided complete protection from death and limited viral burden and liver disease. A dose of 50 mg/kg/day was found to be optimal for treating Pichinde infection and limiting viral replication and disease severity. In general, T-705 was found to be more active than ribavirin in cell-based assays and in vivo, as reflected by substantially greater therapeutic indexes. Our results suggest that T-705 may be a viable alternative for the treatment of life-threatening bunyaviral and arenaviral infections.
Formation of heme-iron complexes with nitric oxide (NO) and peroxynitrite (ONOO-) after ultraviolet radiation as a protective mechanism in rat skin. (2009)

Ultraviolet C (UVC)-irradiated microvessels isolated from rat skin release free nitrogen radicals, i.e. nitric oxide (NO), peroxynitrite (ONOO-) and nitrosocompounds formed from L-arginine. During UVC radiation of microvessels, heme (Fe3+) is released from hemoglobin and reacts with NO to form nitrosyl-heme (Fe2+-NO). The hydroxyl radical (OH*) produced is attached to heme-iron (Fe3+) to form hematin. ONOO- then binds to Fe(OH) and the complex Fe[(OH)ONOO-]2- is formed. Thus, in cases of increased oxidative stress, the free heme can act as an endogenous scavenger of OH* and ONOO-. Furthermore, Fe-NO and Fe[(OH)ONOO-]2- can act as NO donor and as antioxidant in redox cyclic iron-centered heme reactions, respectively. The scavenging-antioxidant properties of heme complexes, which allow it to protect the cells from the cytotoxic effects of the oxygen and/or nitrogen free radicals, were verified by estimating the changes in membrane fluidity of microvessels after UVC radiation. The present study indicates that UVC radiation of the skin acts as a potent stimulator for the formation of Fe-NO and Fe[(OH)ONOO-]2- in microvasculature with cytoprotective effects.
Rapidly solidified aluminum-transition metal alloys for aerospace applications (1988)

Rapid solidification and consolidation P/M technologies have facilitated the development of a family of Al-Fe-V-Si alloys exhibiting a combination of good room temperature ductility and fracture toughness with excellent elevated-temperature strength. Also obtained are high moduli and excellent thermal stability and corrosion resistance, with sufficiently high fabricability to allow economic production of sheet, extrusion, and forging feedstocks applicable to a wide range of aerospace applications; these applications encompass aircraft primary structures, gas turbine compressors, and missile airframes. 10 references.
Mouse CD1-Autoreactive T Cells Have Diverse Patterns of Reactivity to CD1+ Targets (1998)

Humans and mice contain significant populations of T cells that are reactive for autologous CD1 molecules. Using a panel of five mouse CD1 (mCD1)-autoreactive T cell hybridomas, we show here that this autoreactivity does not correlate with the level of CD1 expression. In some cases, these autoreactive T cells can distinguish between different cell types that express the same CD1 molecule, suggesting that some factor in addition to CD1 expression is critical for autoreactive T cell stimulation. To determine whether a CD1-bound ligand may be required, we expressed mutant mCD1 molecules that are defective for the putative endosomal localization sequence in the cytoplasmic domain. We demonstrate that mCD1, like its human CD1 homologues, is found in endosomes, and that it colocalizes extensively with the DM molecule. We further demonstrate, by site-directed mutagenesis, that the tyrosine in the cytoplasmic sequence is required for this endosomal localization. A T cell hybrid expressing Vbeta8 and Valpha14, the major TCR expressed by NK1+ T cells, exhibited greatly diminished reactivity to mutant CD1 molecules that do not traffic through endosomes, although the reactivity of other T cell hybrids to this mutant was not greatly affected. Therefore, we propose that at least some of the autoreactive T cells require endosomally derived CD1-bound ligands, and that they are capable of distinguishing between a diverse set of such self-ligands, which might be either autologous lipoglycans or peptides.
Oxidative Cleavage of Cyclic α-Keto Alcohols by Means of Lead Tetraacetate. II (1942)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidative Cleavage of Cyclic α-Keto Alcohols by Means of Lead Tetraacetate. IIErich BaerCite this: J. Am. Chem. Soc. 1942, 64, 6, 1416–1421Publication Date (Print):June 1, 1942Publication History Published online1 May 2002Published inissue 1 June 1942https://pubs.acs.org/doi/10.1021/ja01258a049https://doi.org/10.1021/ja01258a049research-articleACS PublicationsRequest reuse permissionsArticle Views317Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Sustainable and Socially Inclusive Development of Urban Water Provisioning (2015)

Over the years, the nature of drinking water supply and associated practices of consumption and regulation has enormously evolved in the cities of the global south. The existing literature on water provisioning in Indian cities is mostly skewed towards the megacities. The million plus cities, which are the new sites of ‘urbanization’, are less studied. In this context, the article analyzes the current scenario of drinking water provisioning in Patna and attempts to situate the ‘water economies’ in the broader debates on development, state and sustainability. Patna presents a pertinent case of endemic ‘state failure’ supposedly due to an inept state machinery to manage ‘water economies’ which led to unregulated private and community appropriation of groundwater to meet drinking water needs posing critical sustainability challenges at the city level. The article argues that sustainable development of urban centres will depend on how, in the long run, the unregulated exploitation of natural resources (in this case water) is managed through appropriate ‘institutional mechanism’ and how an equitable water provisioning is ensured to the citizens.
Purification and characterization of a dUTPase from Acholeplasma laidlawii B-PG9 (1984)

dUTP was purified 120-fold from extracts of Acholeplasma laidlawii B-PG9 by Blue-Sepharose, Phenyl-Sepharose, hydroxyapatite, and DEAE-Sephacel chromatography techniques. The only substrate for the enzyme was dUTP with an apparent Km of 4.5 microM. The only reaction products were dUMP and PPi. The dUTPase did not exhibit any specific divalent cation requirement, but it was inhibited by EDTA. The enzyme was not inhibited by Pi or p-hydroxymercuribenzoate. The molecular weight of the enzyme was estimated by gel filtration chromatography to be 48,000, and its isoelectric point was 5.3. The enzyme was thermostable at 55 degrees C for 1 h. A. laidlawii dUTPase was distinguishable from KB (human epidermoid carcinoma) dUTPase by differences in electrophoretic migration, isoelectric point, and thermostability. The enzyme is important in preventing dUTP from being incorporated into DNA and may have a significant role in both the synthesis of thymidine- and PPi-dependent phosphorylations.
Inadequate maternal vascular response to placentation in pregnancies complicated by pre‐eclampsia and by small‐for‐gestational age infants (1986)

An examination of the maternal vascular response to placentation shows that physiological changes in the placental bed normally extend from the decidua into the inner myometrium. In pre-eclampsia and in a proportion of pregnancies with small-for-gestational age infants (SGA) the physiological changes are restricted to the decidual segments alone. In addition, complete absence of physiological changes throughout the entire length of some spiral arteries is seen in pre-eclampsia and SGA. This new observation is confirmed in a study of basal plates of placentas from abnormal pregnancies. Intraluminal endovascular trophoblast may be seen in the placental bed spiral arteries in the third trimester in pre-eclampsia and SGA, a feature not seen beyond the second trimester in normal pregnancy. These findings point to a defect in the normal interaction between migratory trophoblast and maternal uterine tissues in pre-eclampsia and in SGA.
Seven Unidentified Reading Frames of Human Mitochondrial DNA Encode Subunits of the Respiratory Chain NADH Dehydrogenase (1986)

Molecular studies on the human mitochondrial genome started well before the introduction of the modern nucleic acid cloning, mapping, and sequencing technologies. The compartmentalized character of this genome, its small size, and the ease of its isolation have made it, since its discovery, an attractive object for studies of gene organization and expression in a simple eukaryotic system. As a result, about 10 years ago, mtDNA was the best characterized portion of the human genome. Its physical structure was well understood, the unique features of its transcription were known, the two rRNAs and most of the tRNAs encoded in mtDNA had been identified and mapped, and the first hints of the extraordinarily compact organization of this genome had been discovered (Attardi et al. 1976); furthermore, evidence was already available about the number of mRNAs and proteins encoded in this genome, and the probable function of some of these proteins (Costantino...
Evaluation of H2 Getter Materials for Use in the TRUPACT-II (1999)

Savannah River Site (SRS) has many waste drums containing Pu-238 that exceed the currently allowed wattage for transportation in the Transuranic Package Transporter-II (TRUPACT-II). By eliminating layers of confinement in waste drums and using getters to remove hydrogen gas, the TRUPACT-II waste loading can be increased significantly, with the potential of reaching the package''s 40-watt thermal limit. The cost savings associated with increasing the waste loading are enormous, and can be measured by reduced numbers of shipments, required processing facilities, and years of effort. To support the decision-making process and provide a good starting point for future development efforts at SRTC, the design requirements for a getter system to be used in the TRUPACT-II were compiled and are discussed in detail in the Appendix.
Online visualization of noisy 3D point clouds: from monocular image sequences to synthetic views (2010)

This paper addresses the generation and visualization of noisy 3D point clouds. The goal is to extract 3D information from image sequences in real-time and to transform the resulting noisy point clouds into a representation with dense surfaces and an intuitive character. Therefore a bridge is built from image sequence analysis to computer graphics. A point cloud is calculated from a single camera by using state of the art algorithms for egomotion estimation and dense 3D reconstruction. Due to inaccuracies in the measurement process and hence of the resulting depth maps, a degree of uncertainty of the 3D data is defined. This additional information can be used to filter the point cloud in space and time. We present an approach to filter and polygonize weighted point clouds and visualize it by mapping image texture on the resulting surface.
Obstacle detection using unsynchronized multi-camera network (2015)

In this paper, we present a simple algorithm for obstacle detection, road surface extraction and tracking using Kalman filter and u-v-disparity images. The proposed approach is based on the use of an unsynchronized camera system and the use of sparse maps instead of dense ones due to the unsynchronization constraint. First, a sparse disparity map is computed from two images then the u-v-disparity images are built from it. Road and obstacles are extracted using a modified Hough transform. Our experimental results on real images show the efficiency of our algorithm.
Interactions between Abscisic Acid and Ethylene Signaling Cascades (2000)

We screened for mutations that either enhanced or suppressed the abscisic acid (ABA)-resistant seed germination phenotype of the Arabidopsis abi1-1 mutant. Alleles of the constitutive ethylene response mutant ctr1 and ethylene-insensitive mutant ein2 were recovered as enhancer and suppressor mutations, respectively. Using these and other ethylene response mutants, we showed that the ethylene signaling cascade defined by the ETR1, CTR1, and EIN2 genes inhibits ABA signaling in seeds. Furthermore, epistasis analysis between ethylene- and ABA-insensitive mutations indicated that endogenous ethylene promotes seed germination by decreasing sensitivity to endogenous ABA. In marked contrast to the situation in seeds, ein2 and etr1-1 roots were resistant to both ABA and ethylene. Our data indicate that ABA inhibition of root growth requires a functional ethylene signaling cascade, although this inhibition is apparently not mediated by an increase in ethylene biosynthesis. These results are discussed in the context of the other hormonal regulations controlling seed germination and root growth.
Quantitative cell dispersion analysis: New test to measure tumor cell aggressiveness (2001)

Tumor progression requires the dispersion of epithelial cells from neoplastic clusters and cell invasion of adjacent stromal connective tissue. Aiming at demonstrating the precise relationships between cell dispersion and cell invasion, related respectively to expression of E-cadherin/catenin complex and matrix metalloproteinases (MMPs), we developed an original in vitro model of cell dispersion analysis. Our study reports the validation of this model that allowed us to analyze and quantify the cell cohesion level by means of time-lapse videomicroscopy and computer analysis based on the observation of spatial and temporal cell distribution. Our model was able to distinguish 2 groups among different human bronchial and mammary epithelial cells previously characterized for the expression of E-cadherin/catenin complex and MMPs and their invasive capacity in the Boyden chamber assay. The first group (16HBE14o(-), MCF-7, T47D) that expressed membranous E-cadherin and beta-catenin, and was negative for MMP-2 expression and non-invasive, displayed a highly cohesive pattern corresponding to a cluster spatial distribution. The second group (Beas2B, BZR, BZR-T33, MDA-MB-231, MDA-MB-435, BT549 and HS578T) that was invasive and showed lack of expression of E-cadherin and a cytoplasmic redistribution of beta-catenin, displayed a dispersed pattern corresponding to a random spatial distribution. Downregulation of E-cadherin by a blocking antibody induced a more random distribution. Conversely, expression of E-cadherin by cDNA transfection induced a cluster distribution. Moreover, tumor cell lines that co-expressed MT1-MMP and MMP-2 (Beas2B, BZR, BZR-T33, MDA-MB-435, BT549 and HS578T) showed a more dispersed pattern than tumor cell lines that did not express MMP-2 (MDA-MB-231). In conclusion, we demonstrated that the spatial group behavior of cell lines, i.e., their cohesion/dispersion ability, reflects their invasive properties. Thus, this model of cell dispersion analysis may represent a new test to measure tumor cell aggressiveness.
<title>Mapping of thermal injury in biologic tissues using quantitative pathologic techniques</title> (1999)

Qualitative and quantitative pathologic techniques can be used for (1) mapping of thermal injury, (2) comparisons lesion sizes and configurations for different instruments or heating sources and (3) comparisons of treatment effects. Concentric zones of thermal damage form around a single volume heat source. The boundaries between some of these zones are distinct and measurable. Depending on the energy deposition, heating times and tissue type, the zones can include the following beginning at the hotter center and progressing to the cooler periphery: (1) tissue ablation, (2) carbonization, (3) tissue water vaporization, (4) structural protein denaturation (thermal coagulation), (5) vital enzyme protein denaturation, (6) cell membrane disruption, (7) hemorrhage, hemostasis and hyperhemia, (8) tissue necrosis and (9) wound organization and healing.
AlGaAs/GaAs visible distributed feedback laser operating at 770 nm (1987)

A visible-light AlGaAs/GaAs DFB laser with practical characteristics oscillating at 770 nm has been fabricated by using two-step liquid phase epitaxy for the first time. Threshold current of 90 mA measured at room temperature is satisfactorily low for its simple oxide stripe structure. The same DFB mode oscillation without mode hopping has been maintained in a considerably wide range of temperature. The results show a possibility of realising a high-performance DFB laser in the visible-wavaelength region.
Electroless Deposition of Electrodes in Solid‐Oxide Fuel Cells (1994)

LPI
Impact of green revaluation variables on agriculture productivity in Pakistan. (2013)

This paper attempts to analyze the impact of different inputs factors on agriculture productivity in Pakistan for the period 1980-2010. Time series econometric technique has been used for the analysis. Johansen cointegration and vector error correction methods were used to determine the long run and short run relationship in the model, and Granger causality test was used to determine the direction of relationship. The results indicate that, even though all the green revaluation variables except fertilizers are positively related to agriculture productivity in Pakistan, the impact of these variables is not that significant