gebhart/patrepeval huggingface dataset:
Monoclonal antibodies provide protection against ocular Pseudomonas aeruginosa infection. (1988)

A panel of well characterized monoclonal antibodies (MAbs) directed against outer membrane proteins H2, or F (porin) of Pseudomonas aeruginosa were examined to determine whether they exhibited any protective effect against subsequent ocular challenge with the bacteria topically applied to the scarified corneal surface. Mice were observed macroscopically following bacterial challenge and the degree of ocular disease graded on a scale of 0 to 4 (0, normal, fully protected cornea; 4, corneal perforation or phthisis, not protected). Mice treated intravenously with either MAb MA1-6 (anti-H2) or MA2-10 (anti-F), or a combination of these two MAbs and MAb MA4-4 (anti-F), two hours before corneal challenge with the viable bacteria, exhibited significantly less corneal disease than mice either not treated with the MAbs, treated with MA4-4 alone or treated with MAb MA1-3 (anti-I). The latter MAb is directed against an outer membrane epitope that is not surface exposed. Light and transmission electron microscopic histopathology also was employed and provided confirmatory evidence to support the macroscopic analyses.
Basic pharmacology relevant to drug abuse assessment: tramadol as example (2008)

Tramadol is a centrally acting analgesic in widespread use throughout the world. Although there is extensive preclinical, clinical, post-marketing and epidemiological data indicating relatively low--but not zero--abuse/dependence, questions continue to arise about its abuse potential and appropriate regulatory classification. This article considers these questions from the point of view of the basic pharmacology of tramadol. There is nothing unique about tramadol in this regard, but its multimodal mechanism of action, pharmacologically active enantiomers, and active metabolite make it a particularly instructive and relevant example.
Agrobacterium tumefaciens transfers single-stranded transferred DNA (T-DNA) into the plant cell nucleus. (1994)

Transferred DNA (T-DNA) is transferred as a single-stranded derivative from Agrobacterium to the plant cell nucleus. This conclusion is drawn from experiments exploiting the different properties of single- and double-stranded DNA to perform extrachromosomal homologous recombination in plant cells. After transfer from Agrobacterium to plant cells, T-DNA molecules recombined much more efficiently if the homologous sequences were of opposite polarity than if they were of the same polarity. This observation reflects the properties of single-stranded DNA; single-stranded DNA molecules of opposite polarity can anneal directly, whereas single-stranded DNA molecules of the same polarity first have to become double stranded to anneal. Judging from the relative amounts of single- to double-stranded T-DNA derivatives undergoing recombination, we infer that the T-DNA derivatives enter the plant nucleus in their single-stranded form.
Graphical I/O devices for medical users (1992)

The paper considers the basic requirements and the desirable features for a "pointing- based" graphical interaction in the medical practice. A set of tasks that can be improved by al- lowing the physician to handle (ID, 2D, and 3D) graphics are discussed. An experimental evaluation of human-factors in graphical interactions is described: medical subjects compared a mouse and a touch screen, by earring on activities composed by sequences of point selections. Results show that a touch screen is not only an efficient and friendly "menu-based" interaction device, but it can also be used by physicians for "pointing- based" graphical interactions.
Epitaxial film growths of artificial (Bi-O)/(Sr-Ca-Cu-O) layered structures (1989)

Epitaxial film growth of artificial (Bi-O)/(Sr-Ca-Cu-O) layered structures on MgO substrates was carried out using reactive-oxygen-gas dual ion beam sputtering and shuttering technique. A 12 Å Sr-Ca-Cu-O buffer layer seems suitable for perfect epitaxial film growth. Single-phase films having periodicities of 12, 15, and 18 Å (which correspond to bulk 24, 30, and 36 Å phases in Bi oxide superconductors) were selectively grown by adjusting the thickness of a Sr-Ca-Cu-O layer sandwiched by Bi-O bi-planes. A high Tc phase film with a total thickness of about 300 Å showed an onset Tc of 110 K and a zero resistivity temperature of 45 K without post-deposition annealing. The shuttering technique seems to enable the layer-by-layer film growth, and it is very effective for the formation of smooth and perfect epitaxial structures.
A Utility-Based Double Auction Mechanism for Efficient Grid Resource Allocation (2008)

In Grid Computing, harnessing the power of idle resources in a distributed environment is one of the important features. However, to fully benefit from this computing model, an appropriated resource allocation method needs to be carefully chosen and deployed. A number of studies have been done on this area and one of the promising approaches is to adopt a marketing scheme called the auction model, which has been drawing much attention during past several years. In this paper, we propose a new utility-aware resource allocation protocol to make external scheduling decision in Grid. Users and service providers specify one or more weight values, and then, an auctioneer uses these values for calculating both userspsila and service providerspsila utility values which reflect preference upon the matched members in the different group. Then, we map the scheduling problem with these utility values into the problem in a weighted bipartite graph, and propose a new matching algorithm based on the existing SMP (Stable Marriage Problem) matching algorithm. Finally, the performance of this auctionpsilas awarding technique is evaluated.
Second and Third Virial Coefficients of Polystyrene with Benzyl Ends near the ϑ Point (2005)

Second and third virial coefficients (A2 and A3, respectively) for cyclohexane solutions of linear polystyrene (benzyl-PS) samples, synthesized with benzyllithium (n-butyllithium/tetramethylethylenediamine/toluene ligand complex) as an initiator, were determined as functions of temperature and weight-average molecular weight Mw ranging from 710 to 7650. At the ϑ temperature (34.5 °C), where A2 = 0 for sufficiently high Mw, A2 decreased with lowering Mw, in contrast to the sharp increase reported for low molecular weight polystyrene with a butyl group (butyl-PS) at one of the chain ends. This molecular weight dependence of negative A2 for benzyl-PS was explained, without consideration of end effects, by the recent theory of Yamakawa and Yoshizaki for the helical wormlike chain with three-segment interactions, while the upswing of positive A2 for butyl-PS was ascribed primarily to the butyl end effect that surpasses the ternary cluster effect. The A3 values for both benzyl- and butyl-PS were positive and increased with decreasing Mw, showing significant end effects. The end effect in the former was larger than that in the latter, indicating that the three-segment interaction among a chain-end unit and two middle units for benzyl-PS is larger than that for butyl-PS.
An investigation of the electron tunneling leakage current through ultrathin oxides/high-k gate stacks at inversion conditions (2003)

An efficient yet accurate model is used for investigating tunneling of minority carriers from the inversion layer of ultrathin MOSFET structures. The model is derived from the concept of the quasibound states lifetimes, which are calculated using a transfer matrix method based on Airy functions. Comparison with experimental data is provided. Performance of high-k materials is discussed and an investigation of their scalability for future CMOS technology nodes is carried out.
Flexible IO and integration for scientific codes through the adaptable IO system (ADIOS) (2008)

Scientific codes are all subject to variation in performance depending on the runtime platform and/or configuration, the output writing API employed, and the file system for output. Since changing the IO routines to match the optimal or desired configuration for a given system can be costly in terms of human time and machine resources, the Adaptable IO System provides an API nearly as simple as POSIX IO that also provides developers with the flexibility of selection the optimal IO routines for a given platform, without recompilation. As a side effect, we also gain the ability to transparently integrate more tightly with workflow systems like Kepler and Pegasus and visualization systems like Visit with no runtime impact. We achieve this through our library of highly tuned IO routines and other transport methods selected and configured in an XML file read only at startup. ADIOS-based IO has demonstrated high levels of performance and scalability. For example, we have achieved 20 GB/sec write performance using GTC on the Jaguar Cray XT4 system at Oak Ridge National Labs (about 50\% of peak performance). We can change GTC output among MPI-IO synchronous, MPI-IO collective, POSIX IO, no IO (for baseline testing), asynchronous IO using the Georgia Tech DataTap system, and Visit directly for in situ visualization with no changes to the source code. We designed this initial version of ADIOS based on the data requirements of 7 major scientific codes (GTC, Chimera, GTS, XGC1, XGC0, FLASH, and S3D) and have successfully adapted all of them to use ADIOS for all of their IO needs.
Maximal Proliferation of Cytotoxic T Lymphocytes Requires Reverse Signaling through Fas Ligand (1998)

Fas ligand (FasL/CD95L) is best known for its role in delivering apoptotic signals through its receptor, Fas (APO-1/CD95). In this study, we present evidence that FasL has a second role as a signaling receptor. Alloantigen-specific proliferation by multiple FasL- murine CTL lines is depressed compared to that of FasL+ CTL lines. FasL- CTLs kill efficiently on a per recovered cell basis and can achieve wild-type levels of proliferation upon stimulation by optimal doses of anti-CD3, suggesting the lack of a costimulatory signal during antigen stimulation. To test this hypothesis directly, soluble FasIgG, a fusion protein of murine Fas and human IgG1, was added to FasL+ CTLs to demonstrate that blocking cell surface Fas-FasL interactions mimics the depression observed for FasL- CTLs. In addition, plate-bound FasIgG in conjunction with suboptimal anti-CD3 stimulation augments proliferative signals in FasL+ but not FasL- CTLs. In contrast to these results with CD8+ T cells, alloantigen-stimulated FasL- CD4+ T cells proliferate vigorously compared to FasL+ cells. These data demonstrate that reverse signaling through FasL is required for CTLs to achieve maximal proliferation and may provide clues to differences in the homeostatic regulation of activated CD4+ and CD8+ T cells during an immune response.
Use of computed radiography for portal imaging (1990)

This paper compares image quality of conventional film based portal images with the quality of portal images based on computed radiography (CR). The paper concludes that portal imaging with CR imaging plates instead of the conventional film provides images which have a significantly higher image quality. CR based portal images permit better visualization of important landmarks.
Standard methods for estimating strength parameters of Apis mellifera colonies (2013)

This paper covers measures of field colony strength, by which we mean population measures of adult bees and brood. There are generally two contexts in which an investigator wishes to measure colony strength: 1. at the beginning of a study as part of manipulations to produce uniform colonies and reduce experimental error and; 2. as response variables during or at the end of an experiment. Moreover, there are two general modes for measuring colony strength: 1. an objective mode which uses empirical measures and; 2. a subjective mode that relies on visual estimates by one or more observers. There is a third emerging mode for measuring colony strength; 3. computer-assisted digital image analysis. A final section deals with parameters that do not directly measure colony strength yet give important indicators of colony state: flight activity at the entrance; comb construction; and two proxy measures of colony fitness: production of queen cells and drone brood. How to conduct different types of experiments are described, including infectious dose, dose effects, course of infection and longevity tests.
Genetic evidence for a role of parC mutations in development of high-level fluoroquinolone resistance in Escherichia coli (1996)

Fifteen strains of Escherichia coli with MICs of ciprofloxacin (CIP) between 0.015 and 256 micrograms/ml were examined for the presence of mutations in the quinolone resistance-determining region of the gyrA gene and in an analogous region of the parC gene. No mutation was found in a susceptible isolate (MIC of CIP, 0.015 microgram/ml). Four moderately resistant strains (MIC of CIP 0.06 to 4 micrograms/ml) carried one gyrA mutation affecting serine 83, but in only one strain was an additional parC mutation (Gly-78 to Asp) detected. All ten highly resistant strains examined (MIC of CIP, > 4 micrograms/ml) carried two gyrA mutations affecting residues serine 83 and aspartate 87, and at least one parC mutation. These parC mutations included alterations of serine 80 to arginine or isoleucine and glutamate 84 to glycine or lysine. The parC+ and two mutant alleles (parCI-80 and parCI-80,G-84) were inserted into the mobilizable vector pBP507. Transfer of a plasmid-coded parC+ allele into parC+ strains did not alter the susceptibilities towards ciprofloxacin or nalidixic acid, while a significant increase in susceptibility was detectable for parC mutants. This increase, however, did not restore wild-type susceptibility, whereas transfer of a plasmid-coded gyrA+ allele alone or in combination with parC+ did. These data are in agreement with the view that topoisomerase IV is a secondary, less sensitive target for quinolone action in Escherichia coli and that the development of high-level fluoroquinolone resistance in E. coli requires at least one parC mutation in addition to the gyrA mutation(s).
[Physical dependence of dihydroetorphine in mice and monkeys (author's transl)]. (1982)

The ability of producing physical dependence of dihydroetorphine (DHE) was compared with that of morphine in mice and monkeys.
 In nalorphine-challenged mice the average numbers of jumping of the mice after DHE were less than those after morphine and etorphine (E).
 In 3 monkeys treated chronically with DHE abstinence syndrome failed to occur in nalorphine (5—8 mg/kg，sc) precipitated withdrawal tests during 108 days.
 A low degree of abstinence responses was seen in these monkeys in abrupt withdrawal tests. In contrast to this, severe abstinence syndrome was seen in other 3 morphine-dependent monkeys in both nalorphine precipitated and abrupt withdrawal tests.
 In 2 morphine-dependent monkeys (sc 50 mg/kg daily), their abstinence syndrome was suppressed for ⅟2——2⅟2 h by sc DHE 0.43—1.43 μg/kg, while sc morphine 5— 10 mg/kg could suppress their abstinence syndrome for more than 5 h.
 These data suggest that DHE produces a relatively low physical dependence in animals.
Estrogen‐induced osteogenesis in mice is associated with the appearance of Cbfa1‐expressing bone marrow cells (2001)

Cbfa1 is a transcription factor recognised as being involved in early osteoblast differentiation during embryonic skeletogenesis. To determine whether Cbfa1 plays a similar role in bone formation in the adult, we analysed whether its expression is altered during estrogen-induced osteogenesis, following our recent studies which suggest that this response involves the generation of early osteoblast precursors within bone marrow. To facilitate identification of Cbfa1-expressing cells, these studies were performed in mice heterozygous for a cbfa1 gene deletion (cbfa1(+/-)) using beta-galactosidase (lacZ) as a genetic marker. Cbfa1-expressing cells were identified by lacZ staining of longitudinal sections of the proximal tibial metaphysis. Treatment of cbfa1(+/-) mice with 17beta-estradiol 0.5 mg/week for 24 days led to the appearance of new cancellous bone surfaces. This response was associated with a marked increase in number of Cbfa1-expressing cells within the metaphysis, consisting not only of osteoblasts on bone surfaces but also of cells within the adjacent bone marrow. We subsequently enumerated Cbfa1-expressing cells at earlier time-points following estrogen, in sections co-stained for ALP activity. After 4 days of estrogen treatment, a population of cells appeared within the marrow cavity which expressed Cbfa1, but were negative for ALP. At later time-points, large numbers of Cbfa1 + bone marrow cells were still present, but the majority of these were close to new trabecular bone surfaces at sites which showed high levels of ALP activity. An equivalent distribution of Cbfa1-expressing cells was observed in further studies where Cbfa1 expression was analysed in wild-type mice by immunohistochemistry. We conclude that estrogen-induced osteogenesis is associated with the appearance of a population of Cbfa1-expressing cells within bone marrow, which we hypothesize to represent the osteoblast precursor population responsible for subsequent new bone formation.
Interaction of the Crystalline Bacterial Cell Surface Layer Protein SbsB and the Secondary Cell Wall Polymer of Geobacillus stearothermophilus PV72 Assessed by Real-Time Surface Plasmon Resonance Biosensor Technology (2004)

The interaction between S-layer protein SbsB and the secondary cell wall polymer (SCWP) of Geobacillus stearothermophilus PV72/p2 was investigated by real-time surface plasmon resonance biosensor technology. The SCWP is an acidic polysaccharide that contains N-acetylglucosamine, N-acetylmannosamine, and pyruvic acid. For interaction studies, recombinant SbsB (rSbsB) and two truncated forms consisting of either the S-layer-like homology (SLH) domain (3SLH) or the residual part of SbsB were used. Independent of the setup, the data showed that the SLH domain was exclusively responsible for SCWP binding. The interaction was found to be highly specific, since neither the peptidoglycan nor SCWPs from other organisms nor other polysaccharides were recognized. Data analysis from that setup in which 3SLH was immobilized on a sensor chip and SCWP represented the soluble analyte was done in accordance with a model that describes binding of a bivalent analyte to a fixed ligand in terms of an overall affinity for all binding sites. The measured data revealed the presence of at least two binding sites on a single SCWP molecule with a distance of about 14 nm and an overall Kd of 7.7 x 10(-7) M. Analysis of data from the inverted setup in which the SCWP was immobilized on a sensor chip was done in accordance with an extension of the heterogeneous-ligand model, which indicated the existence of three binding sites with low (Kd = 2.6 x 10(-5) M), medium (Kd = 6.1 x 10(-8) M), and high (Kd = 6.7 x 10(-11) M) affinities. Since in this setup 3SLH was the soluble analyte and the presence of small amounts of oligomers in even monomeric protein solutions cannot be excluded, the high-affinity binding site may result from avidity effects caused by binding of at least dimeric 3SLH. Solution competition assays performed with both setups confirmed the specificity of the protein-carbohydrate interaction investigated.
Factor Xa interacts with two sites on monocytes with different functional activities (1992)

Studies were performed to elucidate the functional significance of factor Xa interactions at the monocyte membrane in the presence and absence of factor Va, with respect to prothrombin and factor IX cleavage. Factor Xa-catalyzed prothrombin activation at the monocyte surface was absolutely dependent on the addition of factor Va, indicating that thrombin was generated solely by a membrane-bound complex of factors Va and Xa. In contrast, in the absence of added factor Va, factor Xa bound to monocytes catalyzed the cleavage of factor IX to the nonenzymatic intermediate factor IX alpha through a reaction that was dependent on both monocyte and factor Xa concentration. At limiting factor Xa concentration, added factor Va inhibited the factor Xa-catalyzed cleavage of factor IX, suggesting that a monocyte-bound complex of factors Va and Xa did not recognize factor IX as a substrate. These combined data suggest that factor Xa interacts with the monocyte through two sites which can be distinguished by their requirement for added factor Va and their expression of different functional activities. Both functional sites could be distinguished also by their differential susceptibility to inhibition by a monoclonal antibody directed against the light chain of factor Va (alpha-HFV1). At the monocyte surface, the factor Va/Xa-catalyzed activation of prothrombin was maximally inhibited with 0.25 mumol/L alpha-HFV1, whereas 1.0 mumol/L alpha-HFV1 was required to effect 50% inhibition of the factor Xa-catalyzed cleavage of factor IX. The ability of factor Va to modulate factor Xa substrate specificity was investigated further. Factor Xa bound to thrombin-activated platelets either through platelet-released factor Va or added factor Va did not cleave factor IX. Consistent with this result, a plasma concentration of factor IX had no effect on thrombin generation catalyzed by a platelet-bound complex of factors Va and Xa. In marked contrast, factor Xa bound to phospholipid vesicles either independently or in complex with factor Va catalyzed factor IX cleavage with equal efficiency. These combined data indicate that factor Va bound to cell surfaces modulates factor Xa substrate specificity, whereas no discriminatory effect is conferred by factor Va bound to phospholipid vesicles. Thus, by providing two distinct sites at its membrane surface, the monocyte modulates factor Xa binding and the functional activity expressed by the bound enzyme, depending on the availability of factor Va.