gebhart/patrepeval huggingface dataset:
Efficiency of Advanced Ground Transportation Technologies (2002)

This paper presents thermodynamic analyses of ten different scenarios for using natural gas to power motor vehicles. Specifically, it presents a comparison between different types of automotive vehicles using fuels made from natural gas feedstock. In comparing the various fuel-vehicle options, a complete well-to-wheel fuel cycle is considered. This approach starts with the well at which the feedstock is first extracted from the ground and ends with the power finally delivered to the wheels of the vehicle. This all-inclusive comparison is essential in order to accurately and fairly compare the transportation options. This study indicates that at the present time hybrid-electric vehicles, particularly those using diesel components, can achieve the highest efficiency among available technologies using natural gas as the primary energy source. Hydrogen spark ignition, all-electric battery-powered, and methanol fuel cell vehicles rank lowest in well-to-wheel efficiency because of their poor fuel production efficiencies.
Self-cleaving catalytic RNA. (1993)

We describe the structures and catalytic properties of several naturally occurring self-cleaving RNA motifs that give 2', 3' cyclic phosphate products. The hammerhead and hairpin motifs are derived from plant pathogenic RNAs and the delta motif is part of the human hepatitis delta element. A fourth motif from Neurospora is less well characterized. By assembling the self-cleaving RNAs from more than one oligoribonucleotide, the cleavage reaction can be examined under a variety of conditions and catalytic turnover can be demonstrated. Mutagenesis and chemical methods to introduce modified nucleotides allowed the structural requirements to be deduced. The role of divalent cations in the catalytic mechanism is discussed.
Horizontal Underbalanced Drilling of Gas Wells with Coiled Tubing Challenges and Experiences (1997)

Abstract Coiled tubing drilling technology is gaining popularity and momentum as a significant and reliable method of drilling horizontal underbalanced wells, and is quickly moving into new frontiers. To this point, most efforts in the Western Canadian Basin have been focused towards sweet oil reservoirs in the 900 – 1300 metre (3000 – 4300 feet) true vertical depth range, however there is an ever-increasing interest in gas-producing formations. Figure 1 shows a composite vertical section of the horizontal or directional underbalanced wells drilled with coiled tubing in Canada, and also highlights the aforementioned trend towards oil over gas. Significant design challenges on both conventional and coiled tubing drilling operations are imposed when attempting to drill these formations underbalanced. Coiled tubing is an ideal technology for underbalanced drilling due to its absence of drillstring connections resulting in continuous underbalanced capabilities, as well as its suitability for sour well drilling and live well intervention without surface releases of reservoir gas. Through the use of pressure deployment procedures it is possible to complete the drilling operation without need to kill the well, thereby maintaining underbalanced conditions right through to the production phase. The use of coiled tubing also provides the means for continuous wireline communication with downhole steering, logging and pressure recording devices. Coiled tubing drilling rigs currently exist in several different forms and setups, but generally consist of a drilling coil, injector to feed the tubing into or out of the well, BOP system for well control and return fluid path, and a control cab and power unit. The coiled tubing drilling equipment used to drill the case studies presented later in this paper consisted of either 60.3mm or 73.0mm (2.375 or 2.875 inch) coiled tubing and injector with a hydraulic power unit with control cabin and accumulator. A coiled tubing hybrid mast unit and substructure complete with V-door, catwalk and pipe racks was used. Pumping equipment included a fluid pumper capable of liquid rates of 0.10-1.5 m3/min (0.6 – 10 barrels per minute), nitrogen pumper capable of 10-120 m3/min (350 – 4250 standard cubic feet per minute), and a nitrogen bulk storage unit of 50,000 m3 (1.8 million standard cubic feet) capacity. When drilling sour gas formations, a chemical injection pump for corrosion inhibition may be used.
Epithelial activity of hexokinase and glucose-6-phosphate dehydrogenase in cultured bovine lenses recovering from pharmaceutical-induced optical damage. (2003)

These results show that lens optical quality can recover despite a severe reduction in epithelial HK and G6PD activity, indicating that the optical function of the lens may not be directly related to epithelial metabolic activity. The ScanTox In Vitro Assay System provides an objective measure of lens optical quality, enabling a direct comparison of optical damage and recovery to lens biochemical changes.
Response to Oligosaccharide-Protein Conjugate Vaccine againstHemophilus influenzaeb in Two Patients with IgG2Deficiency Unresponsive to Capsular Polysaccharide Vaccine (1986)

In healthy persons IgG antibodies to polysaccharides are predominantly of the IgG2 subclass.1 2 3 Selective deficiency of this subclass is associated with inability to produce antibodies to bacterial capsular polysaccharides, which confer protective immunity to encapsulated bacteria. However, the basis of the relation between antibody responses to capsular polysaccharide and the IgG2 subclass has not been defined. Some insight into that mechanism is offered by the present study of two children with selective IgG2 deficiency and a documented lack of antibody response to immunization with the capsular polysaccharide vaccine of Hemophilus influenzae b. Both patients were subsequently immunized . . .
Graph cut based image segmentation with connectivity priors (2008)

Graph cut is a popular technique for interactive image segmentation. However, it has certain shortcomings. In particular, graph cut has problems with segmenting thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem, we propose to impose an additional connectivity prior, which is a very natural assumption about objects. We formulate several versions of the connectivity constraint and show that the corresponding optimization problems are all NP-hard. For some of these versions we propose two optimization algorithms: (i) a practical heuristic technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition which provides a lower bound on the problem. We use the second technique to verify that for some practical examples DijkstraGC is able to find the global minimum.
Integrin and cytoskeletal regulation of growth factor signaling to the MAP kinase pathway (1999)

Integrin-mediated anchorage of NIH3T3 fibroblasts to the extracellular matrix component fibronectin permits efficient growth factor signaling to the p42 and p44 forms of mitogen-activated protein kinase (MAPK). Since integrins bridge the extracellular matrix to focal adhesion sites and to the actin cytoskeleton, we analyzed the role of these integrin-associated structures in efficient growth factor activation of p42 and p44-MAPKs. Use of specific reagents that disrupt actin stress fiber and focal adhesion formation demonstrated that upon readhesion of NIH3T3 cells to fibronectin, cells that were poorly spread and lacked prominent focal adhesions but that formed cortical actin structures, efficiently signaled to p42 and p44-MAPKs upon EGF stimulation. In contrast, failure to form the cortical actin structures, despite attachment to fibronectin, precluded effective EGF signaling to p42 and p44-MAPKs. Actin cytoskeletal changes induced by expression of dominant-negative and constitutively active forms of Rho GTPases did not alter EGF activation of MAPK in adherent cells. However, active Cdc42, but not active Rac1 or RhoA, partially rescued EGF signaling to p44-MAPK in cells maintained in suspension. These data indicate that a limited degree of adhesion-mediated cytoskeletal organization and focal adhesion complex formation are required for efficient EGF activation of p42 and p44-MAPKs. Our studies exclude a major role for the GTPases RhoA and Rac1 in the formation of cytoskeletal structures relevant for signaling, but indicate that structures regulated by Cdc42 enhance the ability of suspension cells to activate MAPK in response to growth factors.
A Discrete Three-amino Acid Segment (LVI) at the C-terminal End of Kinase-impaired ErbB3 Is Required for Transactivation of ErbB2 (1999)

ErbB3 is unique among other members of the receptor tyrosine kinase family of growth factor receptors in that its kinase domain is enzymatically impaired. This renders it incapable of transducing a signal in response to ligand binding. However, in conjunction with ErbB2, ErbB3 is a potent mediator of signaling by the growth factor heregulin. Heregulin binding to ErbB3 induces formation of a heterodimeric complex with ErbB2, and this results in transactivation of the ErbB2 kinase. Although interaction between the extracellular domains of these receptors is an essential part of this process, it was not clear whether interaction between the cytoplasmic domains is also necessary for transactivation. By examining the abilities of a series of cytoplasmic domain mutants of ErbB3 to activate ErbB2, we have found a discrete sequence of three amino acid residues (LVI), located at the carboxyl-terminal end of the impaired ErbB3 kinase region, that is obligatory for transactivation. We conclude that formation of a functional ErbB2-ErbB3 signaling complex requires the presence of a specific structural feature within the ErbB3 cytoplasmic domain and suggest that ErbB2 transactivation results from a physical interaction between the cytoplasmic domains of these receptors.
Keratoconjunctivitis Sicca Associated With Meibomian Secretion Polar Lipid Abnormality (1998)

Evaporative KCS syndrome (rather than tear insufficiency) in many individuals may be the result of polar lipid abnormalities. We believe that the 2 associated phospholipids identified in the patients with chronic blepharitis act as important structural components in the polar phase of the tear film lipid layer. We suggest that a deficiency in these lipids results in a poorly structured polar phase that in turn affects the nonpolar phase. Ultimately water transmission through the tear film lipid layer increases, thus resulting in evaporative KCS. These results should aid in development of tear film substitutes directed toward specific abnormalities.
Periodontal ligament cellular structures engineered with electrospun poly(DL‐lactide‐co‐glycolide) nanofibrous membrane scaffolds (2008)

Periodontal tissue engineering is expected to overcome the limitations associated with the existing regenerative techniques for the treatment of periodontal defects involving alveolar bone, cementum, and periodontal ligament. Cell-based tissue engineering approaches involve the utilization of in vitro expanded cells with regenerative capacity and their delivery to the appropriate sites via biomaterial scaffolds. The aim of this study was to establish living periodontal ligament cell-containing structures on electrospun poly(DL-lactic-co-glycolic acid) (PLGA) nanofiber membrane scaffolds, assess their viability and characteristics, and engineer multilayered structures amenable to easy handling. Human periodontal ligament (hPDL) cells were expanded in explant culture and then characterized morphologically and immunohistochemically. PLGA nanofiber membranes were prepared by the electrospinning process; mechanical tensile properties were determined, surface topography, nanofiber size, and porosity status were investigated with SEM. Cells were seeded on the membranes at approximately 50,000 cell/cm(2) and cultured for 21 days either in expansion or in osteogenic induction medium. Cell adhesion and viability were demonstrated using SEM and MTT, respectively, and osteogenic differentiation was determined with IHC and immunohistomorphometric evaluation of osteopontin, osteocalcin, and bone sialoprotein marker expression. At days 3, 6, 9, and 12 additional cell/membrane layers were deposited on the existing ones and multilayered hybrid structures were established. Results indicate the feasibility of periodontal ligament cell-containing tissue-like structures engineering with PDL cells and electrospun nanofiber PLGA scaffolds supporting cell adhesion, viability and osteogenic differentiation properties of cells in hybrid structures amenable to macroscopic handling.
Evidence of a Role for Monocytes in Dissemination and Brain Invasion byCryptococcus neoformans (2008)

The pathogenesis of cryptococcosis, including the events leading to the production of meningoencephalitis, is still largely unknown. Evidence of a transcellular passage of Cryptococcus neoformans across the blood-brain barrier (BBB) and subsequent BBB disruption exists, but the paracellular passage of free yeasts and the role of monocytes in yeast dissemination and brain invasion (Trojan horse method) remain uncertain. We used our model of disseminated cryptococcosis, in which crossing of the BBB starts 6 h after intravenous inoculation, to study paracellular passage of the BBB. We prepared bone marrow-derived monocytes (BMDM) infected in vitro with C. neoformans (BMDM yeasts) and free yeasts and measured fungal loads in tissues. (i) Spleen and lung CFU were >2-fold higher in mice treated with BMDM yeasts than in those treated with free yeasts for 1 and 24 h (P < 0.05), while brain CFU were increased (3.9 times) only at 24 h (P < 0.05). (ii) By comparing the kinetics of brain invasion in naïve mice and in mice with preestablished cryptococcosis, we found that CFU were lower in the latter case, except at 6 h, when CFU from mice inoculated with BMDM yeasts were comparable to those measured in naïve mice and 2.5-fold higher than those in mice with preestablished cryptococcosis who were inoculated with free yeasts. (iii) Late phagocyte depletion obtained by clodronate injection reduced disease severity and lowered the fungal burden by 40% in all organs studied. These results provide evidence for Trojan horse crossing of the BBB by C. neoformans, together with mechanisms involving free yeasts, and overall for a role of phagocytes in fungal dissemination.
Folate Conjugation to Polymeric Micelles via Boronic Acid Ester to Deliver Platinum Drugs to Ovarian Cancer Cell Lines (2013)

In this study, a novel technique was used for the reversible attachment of folic acid on the surface of polymeric micelles for a tumor-specific drug delivery system. The reversible conjugation is based on the interaction between phenylboronic acid (PBA) and dopamine to form a borate ester. The conjugation is fast and efficient and in vitro experiments via confocal fluorescent microscopy show that the linker is stable in for several hours. Reversible addition-fragmentation chain transfer (RAFT) polymerization was used to synthesize two various sized water-soluble block copolymer of oligoethylene glycol methylether methacylate and methyl acrylic acid (POEGMEMA(35)-b-PMAA(200) and POEGMEMA(26)-b-PMAA(90)). The platinum drug, oxoplatin, was then subsequently attached to the polymer via ester formation leading to platinum loading of 12 wt % as determined by TGA. The platinum-induced amphiphilic block copolymers that consequently led to the formation of micelles of sizes 150 and 20 nm in an aqueous environment with the longer PMAA block forming larger micelles. The small micelles were in addition cross-linked using 1,8-diaminooctane to further stabilize their structure. The targeting ability of folate conjugated polymeric micelles was investigated against two types of tumor cell lines: A549 (-FR) and OVCAR-3 (+FR). The cell line growth inhibitory efficacy of material synthesized was evaluated by using SRB method. The results revealed that folate conjugated micelles showed higher activity in FR + OVCAR-3 cells but not in FR - A549 cells. Similar results were obtained for both small and large micelles without the conjugation of folate. Comparing large and small micelles it can be observed that larger micelles are more efficient, which has been attributed to the lower stability of the smaller micelles. Micelle stabilization via cross-linking could indeed increase the toxicity of the drug carrier.
Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients. (1999)

We have studied the feasibility of detecting tumor-associated aberrant p16 methylation in the circulation of patients with hepatocellular carcinoma (HCC). We extracted DNA from the tumor tissues and peripheral blood plasma or serum of 22 HCC patients. p16 methylation was found in 73% (16 of 22) of HCC tissues using methylation-specific PCR. Among the 16 cases with aberrant methylation in the tumor tissues, similar changes were also detected in the plasma/serum samples of 81% (13 of 16) of the cases. No methylated p16 sequences were detected in the peripheral plasma/serum of the six HCC cases without these changes in the tumor, in 38 patients with chronic hepatitis/cirrhosis, or in 10 healthy control subjects. These results suggest that circulating liver tumor DNA may be detected using tumor-associated DNA methylation changes. Because methylation abnormalities have been found in many other genes and tumor types, this approach may have implications for the noninvasive detection of a wide variety of cancers.
Genome-wide search for genes affecting the risk for alcohol dependence (1998)

Alcohol dependence is a leading cause of morbidity and premature death. Several lines of evidence suggest a substantial genetic component to the risk for alcoholism: sibs of alcoholic probands have a 3-8 fold increased risk of also developing alcoholism, and twin heritability estimates of 50-60% are reported by contemporary studies of twins. We report on the results of a six-center collaborative study to identify susceptibility loci for alcohol dependence. A genome-wide screen examined 291 markers in 987 individuals from 105 families. Two-point and multipoint nonparametric linkage analyses were performed to detect susceptibility loci for alcohol dependence. Multipoint methods provided the strongest suggestions of linkage with susceptibility loci for alcohol dependence on chromosomes 1 and 7, and more modest evidence for a locus on chromosome 2. In addition, there was suggestive evidence for a protective locus on chromosome 4 near the alcohol dehydrogenase genes, for which protective effects have been reported in Asian populations.
Thin collagenous septa in cardiac muscle (1987)

Light and electron microscopy were used to study the structure and distribution of thin collagenous septa (sheets) in dog and rabbit cardiac muscle to determine whether they, like thick collagenous septa, could affect electrical impulse propagation. Generally, thin septa (0.2-0.5 micron) ensheathed myocytes or groups of myocytes for short distances and thicker septa partially or completely ensheathed groups of myocytes for long distances (up to several mm); together, thin, and thick septa divided the myocardial mass into myocyte cords (funicles) of 10-30 micron diameter. Septal architecture varied not only between regions and within regions at different ages but also within single bundles, precluding the assumption that the architecture found in one bundle can be applied to another. Electron microscopy demonstrated that thick septa consisted of many tightly packed collagen fibrils, often with distinct layers running at different angles; thin septa consisting largely of circumferential collagen fibrils. Thin septa in dog ventricular papillary muscle generally contained few and widely spaced collagen fibrils, whereas thin septa in dog atrial Bachmann's bundle contained tightly packed collagen fibrils. In either site, thin septa were rarely breached by nexuses and thus marked sites where lateral intercellular electrical coupling was unlikely. Serial 7 micron cross sections of dog Bachmann's bundle stained by a modification of the picrosirius red technique showed that thin septa sometimes persisted uninterrupted over several myocyte lengths. The results provide evidence that thin septa comprised of tightly packed collagen fibrils may significantly modify impulse propagation transverse to the longitudinal axis of the myocytes.
Organic Light Emitters Gain Longevity (1996)

For much of the past decade, researchers have been promising to put thin films of light-emitting plastics and other organic materials on display: large, flexible, inexpensive, and efficient screens to be used for everything from lightweight backlights for computer displays to TVs that you can hang flat on the wall or roll up and put in your pocket. Yet, many of these promises have fallen flat as well. Organic lights have tended to burn out after just days or weeks of operation. Recently, however, researchers have been crafting films without as many burnout-causing defects and building devices with additional film layers to enhance light emission. As a result, the future prospects for their devices are beginning to shine.
Layer Thinning and Etching of Mechanically Exfoliated MoS2 Nanosheets by Thermal Annealing in Air (2013)

A simple thermal annealing method for layer thinning and etching of mechanically exfoliated MoS2 nanosheets in air is reported. Using this method, single-layer (1L) MoS2 nanosheets are achieved after the thinning of MoS2 nanosheets from double-layer (2L) to quadri-layer (4L) at 330 °C. The as-prepared 1L MoS2 nanosheet shows comparable optical and electrical properties with the mechanically exfoliated, pristine one. In addition, for the first time, the MoS2 mesh with high-density of triangular pits is also fabricated at 330 °C, which might arise from the anisotropic etching of the active MoS2 edge sites. As a result of thermal annealing in air, the thinning of MoS2 nanosheet is possible due to its oxidation to form MoO3 . Importantly, the MoO3 fragments on the top of thinned MoS2 layer induces the hole injection, resulting in the p-type channel in fabricated field-effect transistors.
The prophylactic and therapeutic activity of a broadly active ribonucleoside analog in a murine model of intranasal venezuelan equine encephalitis virus infection (2019)

The New World alphaviruses Venezuelan, Eastern, and Western equine encephalitis viruses (VEEV, EEEV and WEEV, respectively) commonly cause a febrile disease that can progress to meningoencephalitis, resulting in significant morbidity and mortality. To address the need for a therapeutic agent for the treatment of Alphavirus infections, we identified and pursued preclinical characterization of a ribonucleoside analog EIDD-1931 (β-D-N<sup>4</sup>-hydroxycytidine, NHC), which has shown broad activity against alphaviruses in vitro and has a very high genetic barrier for development of resistance. To be truly effective as a therapeutic agent for VEEV infection a drug must penetrate the blood brain barrier and arrest virus replication in the brain. High plasma levels of EIDD-1931 are rapidly achieved in mice after oral dosing. Once in the plasma EIDD-1931 is efficiently distributed into organs, including brain, where it is rapidly converted to its active 5'-triphosphate. EIDD-1931 showed a good safety profile in mice after 7-day repeated dosing with up to 1000 mg/kg/day doses. In mouse model studies, EIDD-1931 was 90-100% effective in protecting mice against lethal intranasal infection when therapeutic treatment was started as late as 24 h post-infection, and partial protection was achieved when treatment was delayed for 48 h post-infection. These results support further preclinical development of EIDD-1931 as a potential anti-alphavirus drug.