gebhart/patrepeval huggingface dataset:
TIR‐X and TIR‐NBS proteins: two new families related to disease resistance TIR‐NBS‐LRR proteins encoded in <i>Arabidopsis</i> and other plant genomes (2002)

The Toll/interleukin-1 receptor (TIR) domain is found in one of the two large families of homologues of plant disease resistance proteins (R proteins) in Arabidopsis and other dicotyledonous plants. In addition to these TIR-NBS-LRR (TNL) R proteins, we identified two families of TIR-containing proteins encoded in the Arabidopsis Col-0 genome. The TIR-X (TX) family of proteins lacks both the nucleotide-binding site (NBS) and the leucine rich repeats (LRRs) that are characteristic of the R proteins, while the TIR-NBS (TN) proteins contain much of the NBS, but lack the LRR. In Col-0, the TX family is encoded by 27 genes and three pseudogenes; the TN family is encoded by 20 genes and one pseudogene. Using massively parallel signature sequencing (MPSS), expression was detected at low levels for approximately 85% of the TN-encoding genes. Expression was detected for only approximately 40% of the TX-encoding genes, again at low levels. Physical map data and phylogenetic analysis indicated that multiple genomic duplication events have increased the numbers of TX and TN genes in Arabidopsis. Genes encoding TX, TN and TNL proteins were demonstrated in conifers; TX and TN genes are present in very low numbers in grass genomes. The expression, prevalence, and diversity of TX and TN genes suggests that these genes encode functional proteins rather than resulting from degradation or deletions of TNL genes. These TX and TN proteins could be plant analogues of small TIR-adapter proteins that function in mammalian innate immune responses such as MyD88 and Mal.
<title>Fabrication of a stainless steel microchannel microcombustor using a lamination process</title> (1998)

Microscale chemical devices have potential application as fuel processors to produce high purity hydrogen for PEM fuel cells from hydrocarbon fuels such as methane, methanol, ethanol, or gasoline. The fabrication of a novel stainless steel catalytic microcombustor/reactor suitable for use to high temperatures is described. The device consisted of three parts to accommodate catalyst loading: a laminated reactor body, a laminated combustor, and a solid cover plate. The laminated components were produced using stacks of photochemically machined stainless steel shims. When formed into solid leak-tight components using a diffusion bonding process, the laminated parts were designed to contain a complex series of internal gas-flow microchannels that could not be produced in a solid metal block by other fabrication methods. Included within the reactor body was an array of heat exchanger microchannels 250 microns wide and 5000 microns deep that were designed to extract heat from the catalytic reaction region and pre-heat the reactant gases. Catalytic combustion of hydrogen or hydrocarbon fuel occurred in a separate laminated combustor plate. The laminated combustor/reactor design has potential for use in a variety of chemical processing and heat exchanger applications.
Complications of Radiofrequency Ablation of Hepatic, Pulmonary, and Renal Neoplasms (2010)

Percutaneous thermal ablation has emerged as a viable technique for treatment of numerous solid organ malignancies. As the number of these procedures increases, so do the complications that are seen. Most common complications are generally related to bleeding from the target organ during or after the procedure and from thermal injury to adjacent structures. The nature of these injuries depends on the particular organ being treated, therefore it it best to categorize them this way. We will review the more common complications seen following the ablation of tumors in the liver, kidney, and lung, discuss the clinical presentation associated with each, and suggest precautions to help avoid them in the future. Understanding the potential risks associated with this procedure is critical for treatment planning and fundamental for performing these procedures safely.
Translocation of Hydrophobic Substances into Soil by Burning Organic Litter (1970)

Abstract Unknown hydrophobic substances were vaporized in surface layers of litter and water repellent soil by an imposed heat treatment. The vaporized substances moved downward and condensed in different test soils where they produced a water repellent layer. The thickness of the water repellent layer in the underlying test soil increased as per cent soilt and clay decreased. The thickest and most intensely water repellent layer was produced in a uniform 35‐mesh sand. The effect of texture on water repellency was attributed to large differences in specific surfaces of the soils which ranged from 0.0077 to 55 m 2 /g. The induced water repellency was not directly related to a given amount of organic matter translocated by the heat treatment. Generally, however, the degree of water repellency increased as the amount of translocated organic matter increased in a given test soil.
Blood Lactate and Heat Stress during Training in Rowers (2007)

The purpose of the present study was to test the hypothesis that large increases in blood lactate concentration ([La] (b)) and/or body temperature may occur during an endurance training on a rowing ergometer and disrupt training. The influence of an increase in air convection on the capacity to perform a prolonged exercise was also explored. Ten trained oarsmen were asked to undergo twice, in control (C) and increased air ventilation (AV) conditions, two 30-min trainings on a rowing ergometer at a work rate corresponding to 2.5 mmol . L (-1) of [La] (b) determined during a previous incremental exercise (P (2.5)). Four subjects did not complete the training session in C despite a steady state in [La] (b) in two of them. In these four subjects, the end of the exercise was associated with the highest measured rectal temperatures (T (re), 39.4 +/- 0.1 degrees C) and rate of perceived exertion (RPE, 17.8 +/- 0.3). Regarding the six other subjects, their heart rate, oxygen uptake, RPE, T (re) and water loss values were lower (p < 0.05) in AV than in C. [La] (b) displayed the same profile in C and AV. This study suggests that i) high body temperature may constitute a significant factor of perceived exertion and disrupt indoor training session, and ii) capacity to perform an endurance training on a rowing ergometer was improved by increasing air convection.
Toughening Polylactide (2008)

Polylactide is a commercially‐produced thermoplastic that is derived from renewable resources and is environmentally degradable. Due to these attributes, polylactide holds tremendous promise as an alternative to the ubiquitous petroleum‐based materials. However, in situations that require a high level of impact strength, the toughness of polylactide in its pristine state is often insufficient. As such, there has been tremendous effort in developing ways to improve this material property deficiency. In this review we summarize these approaches for increasing the toughness of polylactide with an eye toward how the toughening protocols influence the overall mechanical properties of the resultant materials.
Endothelium-derived factors in microalbuminuric and nonmicroalbuminuric essential hypertensives (2000)

Previous evidence has demonstrated a relationship between growth factors and cardiovascular diseases. This study was aimed at evaluating levels of some endothelium-derived growth factors, and their relationship with microalbuminuria (MAU), in essential hypertension. Ninety-nine mild-moderate essential hypertensives (EH) and 25 healthy controls were studied. All patients underwent 24-h blood pressure monitoring, serum endothelin-1 (ET-1), basic fibroblast growth factor (bFGF) and platelet-derived growth factor (PDGF), and 24-h MAU assays. Later, EH were divided into two subsets consisting of microalbuminurics (MAU >11 microg/min) and nonmicroalbuminurics (MAU <11 microg/min). In microalbuminuric EH, circulating ET-1, bFGF, and PDGF were significantly higher than in nonmicroalbuminurics (P < .0001, P < .0001, P < .005, respectively) or in controls. In the group of 99 EH, significant positive correlations of MAU with both ET-1 and bFGF (r = 0.35, P < .001, and r = 0.34, P < .001, respectively) were found. ET-1 and bFGF correlated significantly (r = 0.31, P < .002). Circulating bFGF also correlated significantly with MAU in the microalbuminuric EH subset (r = 0.49, P < .01). Our results show that in microalbuminuric EH circulating levels of certain growth factors are increased. In human essential hypertension these factors are linked with MAU, an early cardiovascular and renal damage marker.
Making software accessible to people with severe memory deficits (2005)

Good interface design must take into account limits on the users’ short-term memory. With conditions such as dementia, the working (short-term) memory can be so impaired as to be virtually non-operative. This present a significant challenge in designing interactive systems for people with this condition. If the difficulties can be overcome, however, such systems offer the possibility of improving the communication abilities of people with dementia, and eventually providing them with satisfying activities that can carry out unaided. We report on a project that has developed a hypermedia based reminiscence aid for older people with dementia, which been designed to be usable by people with short-term memory deficits. The system has proved remarkably effective in supporting the communication of people with dementia.
Disposition of Positively Charged Bowman–Birk Protease Inhibitor Conjugates in Mice: Influence of Protein Conjugate Charge Density and Size on Lung Targeting (1995)

The influence of conjugate charge density and size on the targeting of cationic Bowman-Birk inhibitor (BBI) conjugates to the lungs was studied in mice. The biodistribution of BBI, either as the native protein or in the conjugated form (conjugated to a dicationic, tetracationic, or polycationic carrier), indicated that by increasing the charge density of BBI conjugates, the lung accumulation of the conjugates administered intravenously (i.v.) can be increased. The order of lung accumulation in these studies was as follows: polycationic- > tetracationic- > dicationic-conjugated BBI > BBI. The influence of conjugate size on lung accumulation was studied in three experiments. First, the biodistribution of poly(D-lysine) carriers of equal charge density but different molecular weight demonstrated that lung accumulation of polycationic carriers increases with an increase in carrier size. Second, the biodistributions of BBI, tyramine-derivatized poly(D-lysine)3 kDa, and poly(D-lysine)3 kDa conjugated to BBI indicated that an increase in conjugate size alone is not sufficient to promote the lung accumulation of cationic BBI conjugates. Finally, the biodistribution poly(D-lysine) complexed with heparin showed that targeting of a conjugate to the lungs can be abolished by neutralizing the charge on the carrier. Collectively, data in this paper demonstrate that the carrier-mediated targeting of BBI to the lungs is dependent on (a) cationization of BBI, (b) the conjugate positive charge density, and (c) the size of the cationic conjugate if the charge density is maintained. Also, the data show the size of the conjugate alone does not make a significant impact on lung accumulation.
Semiconductor lasers for microsoldering (1991)

The minimal rise in substrate temperature reduces mechanical stress, the rapid melting and cooling of the solder prevents the formation of intermetallic compounds. Recent advances in semiconductor physics have brought about the availability of semiconductor laser diodes capable of delivering CW powers of 1 watt from single diodes and 5-10 watts CW from 'multiple emitter' devices. These power sources emit at a wavelength of 800-900 nm. The semiconductor laser diodes exhibit efficiencies of around 30% and can be powered from a 2 volt source! From work on laser soldering by Lish (1985) and Greenstein (1989) it has been shown that the efficiency of energy absorption increases as the wavelength decreases. Thus in this respect the semiconductor laser is more efficient for soldering than the Nd:YAG laser. Add to this the advantages of compactness, and the future for these devices in automated soldering systems becomes attractive. Fibre optics can be used to transmit their energy.
Evaluating Crude Oils by SARA Analysis (2002)

Abstract The effectiveness of some improved oil recovery schemes can depend on the composition of the target oil. Crude oils can be described compositionally by a number of methods. SARA analysis divides crude oil components according to their polarizability and polarity using a family of related analytical techniques. Problems arise because several of the analytical techniques in use do not produce identical results, although the users of the data rarely distinguish between them, assuming that SARA fraction values generated by any of the common techniques are essentially interchangeable. We examine this assumption for three SARA analysis methods: gravity-driven chromatographic separation, thin layer chromatography (TLC), and high pressure liquid chromatography (HPLC). Results for a suite of six crude oil samples show that a significant volume of volatile material that contains both saturates and aromatics is lost in the TLC analysis. Application of SARA fraction data to assessment of asphaltene stability is demonstrated.
Persistence of Selectable Herpesvirus Saimiri in Various Human Haematopoietic and Epithelial Cell Lines (1991)

Herpesvirus (h.) saimiri, an infectious agent of squirrel monkeys, is capable of persisting in T lymphocytes of various primate species. It has been used as a vector for the functional analysis of regulatory genes in primary human T lymphocytes. As it is not yet known whether other cell types are capable of supporting viral persistence, various human cell lines were investigated using selectable h. saimiri recombinants. The lines chosen represent cells from the epithelium and connective tissue as well as from all haematopoietic lineages, i.e. cells of B and T lymphoid origin as well as myeloid-, fibroblast- and carcinoma-derived cultures converted to Geneticin or hygromycin B resistance, and harbouring episomal DNA of the selectable recombinants. The Burkitt's lymphoma-derived cell line Raji also contained simultaneously persisting episomes of the Epstein-Barr virus. Most of the cell cultures except a pancreatic carcinoma line and foreskin fibroblasts did not produce infectious virus. These observations show that a herpesvirus genome can persist episomally in a broad range of cultured cell types. The variety of infectable cell types and species suggests the presence of a widely distributed and well conserved virus receptor for h. saimiri. Thus the h. saimiri genome could be applied more generally as a vector.
Site-Specific Nick in the T-DNA Border Sequence as a Result of <i>Agrobacterium vir</i> Gene Expression (1987)

The T-DNA transfer process of Agrobacterium tumefaciens is activated by the induction of the expression of the Ti plasmid virulence (vir) loci by plant signal molecules such as acetosyringone. The vir gene products act in trans to mobilize the T-DNA element from the bacterial Ti plasmid. The T-DNA is bounded by 25-base pair direct repeat sequences, which are the only sequences on the element essential for transfer. Thus, specific reactions must occur at the border sites to generate a transferable T-DNA copy. The T-DNA border sequences were shown in this study to be specifically nicked after vir gene activation. Border nicks were detected on the bottom strand just after the third or fourth base (+/- one or two nucleotides) of the 25-base pair transferpromoting sequence. Naturally occurring and base-substituted derivatives of the 25-base pair sequences are effective substrates for acetosyringone-induced border cleavage, whereas derivatives carrying only the first 15 or last 19 base pairs of the 25-base pair sequence are not. Site-specific border cleavages occur within 12 hours after acetosyringone induction and probably represent an early step in the T-DNA transfer process.
A SIP-based architecture model for contextual coalition access control for ubiquitous computing (2005)

A significant deterrent to the ability to connect in a spontaneous manner in cross-enterprise collaborative applications is the difficulty in users from different domains being able to access resources or services located and owned by other entities. Coalition access control encompasses control mechanisms dealing with access between users of two or more different security domains. In this paper we present an approach to add contextual information to the distributed role based access control (dRBAC) model to support spontaneous coalition. The dRBAC model is a relatively new approach for coalition access control based on a delegation model but has been targeted towards pre-arranged delegations among distributed enterprises. A delegation architecture is presented that leverages SIP communication sessions to discover delegation security managers that can automatically exchange roles and delegations based on location and communication session contexts.
Study of Oxidation of TiSi<sub>2</sub> Thin Film by XPS (1984)

Titanium was deposited on a single-silicon wafer and made to form TiS 2 by thermal annealing in vacuum. Samples were then oxidized at temperatures from 100 to 1000°C for 60 min in air. When the oxidized TiS 2 was studied by X-ray photoelectron spectroscopy (XPS) in conjunction with argon-ion sputtering, SiO 2 was found to be dominant in the oxide products at various oxidation temperatures. Full-width at half maximum (FWHM) and Si/Ti atomic ratio analyses led to the conclusion that various Ti oxides exist in oxidized TiSi 2 , but that the intermediate Ti-silicides (TiSi and Ti 5 Si 3 ) do not. The growth of a Ti-free layer of SiO 2 at 1000°C was also observed. SEM micrographs showed that no surface morphologies varied before or after oxidation in air at temperatures from 100 to 800°C. Above 1000°C, however, the TiSi 2 film was thermally grooved at its grain boundaries, and the grain sizes were increased. Analytic electron-microscope photographs showed that the crystalline grains consisted of TiSi 2 , but that the grain boundaries lay within the Ti-free zone.
Droplet Structure in a Water-in-CO<sub>2</sub> Microemulsion (1996)

High-pressure small-angle neutron-scattering measurements show that a dichain hydrocarbon−fluorocarbon surfactant ((C7H15)(C7F15)CHSO4-Na+) stabilizes spherical droplets, with mean water core radius around 25 Å, in a water-in-CO2 microemulsion (temperature = 25 °C, pressure = 500 bar). At lower pressures droplet clustering is observed. Our structural work on this system builds on initial phase stability studies by Johnston et al. (Langmuir 1994, 10, 3536).
Characterizing junction-to-case thermal resistance and its impact on end-use applications (2012)

High power packages require a low junction-to-case thermal resistance (Theta jc) to achieve target junction temperatures. Theta jc is a metric used to compare package-to-package relative thermal performance. It is also used in two-resistor models to predict thermal performance under system level conditions. This study shows that the commonly used Theta jc definition does not correctly track package junction temperatures in actual end-use applications nor does it serve as a reliable metric for comparing package-to-package performance. When spreading resistance in the lid is taken into account, the modified Theta jc definition overcomes some of the shortfalls found with the standard Theta jc calculation. Lastly, a simplified thermal interface resistance model is presented as a more accurate alternative to the one resistor Theta jc and the multi-resistor Delphi models.
Basic science of abdominal aortic aneurysms: emerging therapeutic strategies for an unresolved clinical problem (1996)

Abdominal aortic aneurysms (AAAs) are an increasingly common and potentially lethal condition. Surgical repair of AAA is now yet performed quite safely, yet ruptured AAAs still carry mortality rates of 50% to 70%. Ultrasound screening may help identify unsuspected AAA, thereby allowing elective repair. Because AAAs too small to warrant operation still expand progressively, therapeutic approaches to suppress AAA growth would be welcome. Current concepts indicate that AAAs arise through pathophysiologic process distinct from occlusive atherosclerosis and dominated by degenerative changes in the elastic media. These include marked alterations in elastin and collagen, chronic inflammation, and features of autoimmunity, medial neovascularization, and a decrease in vascular smooth muscle cells. Proteinases associated with mononuclear inflammatory cells, particularly matrix metalloproteinases, likely mediate the degradation of structural proteins in the aortic wall. Experimental studies demonstrate that similar processes occur in an elastase-induced rodent model of AAA, providing a means by which to develop novel therapeutic strategies for this disease. Pharmacologic inhibitors of matrix metalloproteinases act to suppress aortic elastin degradation and limit the growth of experimental AAA in vivo, suggesting at least one approach that may be useful in clinical application. Further developments can be expected to increase knowledge of the pathophysiology underlying aortic aneurysm disease, ultimately providing new therapies for small AAAs based on sound understanding of disease mechanisms.
Mechanisms of Fibrolysis in Chronic Liver Injury (with Special Emphasis on MMPs and TIMPs) (2007)

Regeneration from liver fibrosis is characterized by four essential events: 1. eradication of pathological agents, 2. apoptosis of activated hepatic stellate cells, 3. remodeling of extracellular matrix, and 4. regeneration of parenchyma and liver function. The temporal and spatial regulation of matrix metalloproteinase (MMP) activity and expression of their specific inhibitors, the tissue inhibitors of metalloproteinases (TIMPs), play a pivotal role in matrix remodeling during hepatic fibrogenesis and recovery. According to current knowledge, the main topics and mechanisms in regeneration from hepatic fibrosis with special emphasis on MMPs and TIMPs are presented. MMP and TIMP expression patterns during hepatic fibrogenesis and fibrolysis, specific characteristics like regulation, expression of cell types, gene expression (RNA/protein), and the underlying disease are summarized. Studies presenting a time course for MMP and TIMP expression during recovery from hepatic fibrosis were taken into consideration to point out a synchronizing behavior in the expression pattern.
Trapping and storage of particles in electroactive microwells (2007)

The authors describe electroactive microwells which exploit highly localized electrokinetic effects in order to actively concentrate, confine, store, and reject particles in well defined geometries. In this letter the authors present experimental results demonstrating repeatable trapping and repulsion of polystyrene particles in wells ranging in diameter from 6to20μm in the presence of a superimposed pressure driven flow. A comprehensive finite element model is developed to describe the transport physics involved in the attraction and repulsion processes. Immediate applications include active cell trapping, particle concentration and unlabeled sensing.
Pernicious Papillomavirus Infection (1999)

More than 100 years have passed since an association between sexual behavior and cancer of the cervix was reported. In the ensuing years, the elusive sexually transmitted agent has been intensively sought. It was not long ago that the herpes simplex virus (HSV) was thought to be this agent on the basis of serologic studies, and indeed, HSV remains in the collective consciousness of many physicians as a causative agent of cancer of the cervix, despite the lack of evidence supporting this conclusion. With the advent of recombinant DNA technology and the cloning of oncogenic human papillomaviruses (HPV), it became . . .