gebhart/patrepeval huggingface dataset:
Sporozoite induced immunity in man against an ethiopian strain of Plasmodium falciparum (1974)

Journal Article Sporozoite induced immunity in man against an ethiopian strain of Plasmodium falciparum Get access Karl H. Rieckmann, Karl H. Rieckmann Laboratory for Tropical Diseases, Rush-Presbyterian-St. Luke's Medical Center, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Paul E. Carson, Paul E. Carson Laboratory for Tropical Diseases, Rush-Presbyterian-St. Luke's Medical Center, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard L. Beaudoin, Richard L. Beaudoin Division of Experimental Parasitology, Naval Medical Research Institute, Bethesda, Maryland, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Joseph S. Cassells, Joseph S. Cassells Division of Experimental Parasitology, Naval Medical Research Institute, Bethesda, Maryland, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Kenneth W. Sell Kenneth W. Sell Division of Experimental Parasitology, Naval Medical Research Institute, Bethesda, Maryland, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Transactions of The Royal Society of Tropical Medicine and Hygiene, Volume 68, Issue 3, 1974, Pages 258–259, https://doi.org/10.1016/0035-9203(74)90129-1 Published: 01 January 1974
Z/EG, a double reporter mouse line that expresses enhanced green fluorescent protein upon cre-mediated excision (2000)

The Cre/loxP system has become an important tool in designing postintegrational switch mechanisms for transgenes in mice. The power and spectrum of application of this system depends on transgenic mouse lines that provide Cre recombinase activity with a defined cell type-, tissue-, or developmental stage-specificity. We have developed a novel mouse line that acts as a Cre reporter. The mice, designated Z/EG (lacZ/EGFP), express lacZ throughout embryonic development and adult stages. Cre excision, however, removes the lacZ gene, which activates expression of the second reporter, enhanced green fluorescent protein. We have found that the double-reporter Z/EG line is able to indicate the occurrence of Cre excision from early embryonic to adult lineages. The advantage of the Z/EG line is that Cre-mediated excision can be monitored in live samples and that live cells with Cre-mediated excision can be isolated using a single-step FACS. It will be a valuable reagent for the increasing number of investigators taking advantage of the powerful tools provided by the Cre/loxP site-specific recombinase system.
Enhancement of the Prolactin Response to d-Fenfluramine in Drug-Naive Schizophrenic Patients (1996)

Central serotonergic tone may be raised in acute, drug-naive schizophrenia and may be associated with the presence of affective symptomatology.
Regulation of Chemotactic and Proadhesive Responses to Chemoattractant Receptors by RGS (Regulator of G-protein Signaling) Family Members (1998)

Serpentine Galphai-linked receptors support rapid adhesion and directed migration of leukocytes and other cell types. The intracellular mechanisms mediating and regulating chemoattractant-directed adhesion and locomotion are only now beginning to be explored. RGS (for regulator of G-protein signaling) proteins are a recently described family that regulate Galphai-stimulated pathways by acting as GTPase-activating proteins. Little is known about the GTPase activity of the Galphai proteins involved in adhesion and chemotaxis, or the significance of their regulation to these responses. Using transiently transfected lymphoid cells as a model system, we show that expression of RGS1, RGS3, and RGS4 inhibits chemoattractant-induced migration. In contrast, RGS2, a regulator of Galphaq activity, had no effect on cell migration to any chemoattractant. RGS1, RGS3, and RGS4 also reduced rapid chemoattractant-triggered adhesion, although the proadhesive response appears quantitatively less sensitive to RGS action than chemotaxis. The results suggest that the duration of the Galphai signal may be a particularly important parameter in the chemotactic responses of leukocytes, and demonstrate the potential for RGS family members to regulate cellular adhesive and migratory behaviors.
Photosensitization of nonlinear scattering and photoacoustic emission from single-walled carbon nanotubes (2008)

Enhancement of laser-induced nonlinear scattering has been observed from an aqueous suspension of single-walled carbon nanotubes (SWCNTs) doped with near-infrared dye chromophores. The underlying mechanism involves cavitation triggered by optical heating and bubble pulsation, which are further enhanced by the dye adsorbed on SWCNT surfaces, resulting in the scattering enhancement and a modification of the accompanying photoacoustic waveform. These photosensitizing effects suggest potential feasibility of dye-doped nanotubes as optically switchable nanoemitters of ultrasound for biomedical applications such as ultrasonic therapy and imaging.
Correlation of projection radiographs in radiation therapy using open curve segments and points (1992)

A method for determining differences in patient position between projection radiographs such as those routinely used in radiation therapy has been developed. Determination of a transformation relating two radiographs permits registration of simulation and portal images and the transfer of information between them. The algorithm is based on spatially registering segments of open curves or points seen on both images, and does not require identification of corresponding curve endpoints. The method as implemented is both fast and accurate. After user definition of the curves or points to be registered, the optimal transformation is calculated in approximately 1 s. Calculational experiments indicate that corresponding points on open curves are registered to better than 2 mm, even when random errors (FWHM 1 mm) in digitization are included. Experiments on the registration of clinical portal and simulation images (pixel size = 0.5 by 0.5 mm) indicate an accuracy on the order of 2 mm or less in translation and 2 deg or less in rotation. Analysis of portal and simulation radiographs of the brain, thorax, and pelvis indicates this algorithm to be robust and clinically applicable. The rapid and accurate registration of portal and simulation images is potentially important in the application of real time portal imaging devices in radiation therapy.
A Quantitative Comparison of Mechanical Blood Damage Parameters in Rotary Ventricular Assist Devices: Shear Stress, Exposure Time and Hemolysis Index (2012)

Ventricular assist devices (VADs) have already helped many patients with heart failure but have the potential to assist more patients if current problems with blood damage (hemolysis, platelet activation, thrombosis and emboli, and destruction of the von Willebrand factor (vWf)) can be eliminated. A step towards this goal is better understanding of the relationships between shear stress, exposure time, and blood damage and, from there, the development of numerical models for the different types of blood damage to enable the design of improved VADs. In this study, computational fluid dynamics (CFD) was used to calculate the hemodynamics in three clinical VADs and two investigational VADs and the shear stress, residence time, and hemolysis were investigated. A new scalar transport model for hemolysis was developed. The results were compared with in vitro measurements of the pressure head in each VAD and the hemolysis index in two VADs. A comparative analysis of the blood damage related fluid dynamic parameters and hemolysis index was performed among the VADs. Compared to the centrifugal VADs, the axial VADs had: higher mean scalar shear stress (sss); a wider range of sss, with larger maxima and larger percentage volumes at both low and high sss; and longer residence times at very high sss. The hemolysis predictions were in agreement with the experiments and showed that the axial VADs had a higher hemolysis index. The increased hemolysis in axial VADs compared to centrifugal VADs is a direct result of their higher shear stresses and longer residence times. Since platelet activation and destruction of the vWf also require high shear stresses, the flow conditions inside axial VADs are likely to result in more of these types of blood damage compared with centrifugal VADs.
Design rule spaces: a new form of architecture insight (2014)

In this paper, we investigate software architecture as a set of overlapping design rule spaces, formed by one or more structural or evolutionary relationships and clustered using our design rule hierarchy algorithm. Considering evolutionary coupling as a special type of relationship, we investigated (1) whether design rule spaces can reveal structural relations among error-prone files; (2) whether design rule spaces can reveal structural problems contributing to error-proneness.We studied three large-scale open source projects and found that error-prone files can be captured by just a few design rule sub-spaces. Supported by our tool, Titan, we are able to flexibly visualize design rule spaces formed by different types of relationships, including evolutionary dependencies. This way, we are not only able to visualize which error-prone files belong to which design rule spaces, but also to visualize the structural problems that give insight into why these files are error prone. Design rule spaces provide valuable direction on which parts of the architecture are problematic, and on why, when, and how to refactor.
312. Developing Qualified Activity and Potency Assays for Gene Therapy and DNA Vaccine Products (2004)

Purpose: Development of targeted gene transfer technologies is essential for in vivo gene therapy. Adenoviral vectors are capable of gene transfer into a wide variety of cell types but often elicit severe immune-inflammatory responses. A serious adverse event due to systemic inflammatory response syndrome was recently reported after infusion of an adenoviral vector into the liver. To minimize toxicity to the liver, gene transfer and expression should be localized to limited liver segments. In the present study, we examined the feasibility of physical targeting to the selected liver segments using catheterization techniques. Methods: Procedure 1: A vascular clamp was placed across the portal vein (PV) between the upper and the lower segments of the liver in Wistar rats. An adenoviral vector carrying the LacZ gene, AxCALacZ, was infused through the proximal PV. The clamp was removed 5 min later. Procedure 2: Isolated hepatic perfusion technique was applied in addition to clamping as procedure 1. Both PV and the hepatic inferior vena cava (IVC) were cannulated, while the other vasculatures were all clamped. The adenovirus vector was injected through the PV catheter and unbound vector particles were washed out with PBS. The outflow solution from the circulation was collected to the IVC catheter. Results: The beta-gal activity was significantly higher in the proximal segments compared to the distal segments in both procedures. Moderate beta-gal activity was also detected in the spleen in procedure 1, while the activity was hardly detectable in procedure 2. The levels of inflammatory cytokines were reduced by isolated hepatic perfusion. Conclusion: Isolated hepatic perfusion with clamping of specific portal vein branches is useful for adenoviral-mediated local gene delivery to selected liver segments and could be applied to treatment of focal liver diseases such as liver metastases of cancer.
TNF-α promotes LPA1- and LPA3-mediated recruitment of leukocytes in vivo through CXCR2 ligand chemokines (2011)

Lysophosphatidic acid (LPA) is a bioactive lysophospholipid present in low concentrations in serum and biological fluids but in high concentrations at sites of inflammation. LPA evokes a variety of cellular responses via binding to and activation of its specific G protein-coupled receptors (GPCR), namely LPA(1-6). Even though LPA is a chemoattractant for inflammatory cells in vitro, such a role for LPA in vivo remains largely unexplored. In the present study, we used the murine air pouch model to study LPA-mediated leukocyte recruitment in vivo using selective LPA receptor agonist/antagonist and LPA(3)-deficient mice. We report that 1) LPA injection into the air pouch induced leukocyte recruitment and that both LPA(1) and LPA(3) were involved in this process; 2) LPA stimulated the release of the pro-inflammatory chemokines keratinocyte-derived chemokine (KC) and interferon-inducible protein-10 (IP-10) in the air pouch; 3) tumor necrosis factor-α (TNF-α) injected into the air pouch prior to LPA strongly potentiated LPA-mediated secretion of cytokines/chemokines, including KC, IL-6, and IP-10, which preceded the enhanced leukocyte influx; and 4) blocking CXCR2 significantly reduced leukocyte infiltration. We suggest that LPA, via LPA(1) and LPA(3) receptors, may play a significant role in inducing and/or sustaining the massive infiltration of leukocytes during inflammation.
Dual Signaling of the Fas Receptor: Initiation of Both Apoptotic and Necrotic Cell Death Pathways (1998)

Murine L929 fibrosarcoma cells were transfected with the human Fas (APO-1/CD95) receptor, and the role of various caspases in Fas-mediated cell death was assessed. Proteolytic activation of procaspase-3 and -7 was shown by Western analysis. Acetyl-Tyr-Val-Ala-Asp-chloromethylketone and benzyloxycarbonyl-Asp(OMe)-Glu(OMe)-Val-Asp(OMe)-fluoromethylketone++ +, tetrapeptide inhibitors of caspase-1- and caspase-3-like proteases, respectively, failed to block Fas-induced apoptosis. Unexpectedly, the broad-spectrum caspase inhibitors benzyloxycarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone and benzyloxycarbonyl-Asp(OMe)-fluoromethylketone rendered the cells even more sensitive to Fas-mediated cell death, as measured after 18 h incubation. However, when the process was followed microscopically, it became clear that anti-Fas-induced apoptosis of Fas-transfected L929 cells was blocked during the first 3 h, and subsequently the cells died by necrosis. As in tumor necrosis factor (TNF)-induced necrosis, Fas treatment led to accumulation of reactive oxygen radicals, and Fas-mediated necrosis was inhibited by the oxygen radical scavenger butylated hydroxyanisole. However, in contrast to TNF, anti-Fas did not activate the nuclear factor kappaB under these necrotic conditions. These results demonstrate the existence of two different pathways originating from the Fas receptor, one rapidly leading to apoptosis, and, if this apoptotic pathway is blocked by caspase inhibitors, a second directing the cells to necrosis and involving oxygen radical production.
A 40-Mpixel/s bit block transfer graphics processor (1989)

A man-machine-interface-oriented graphics processor featuring data transfer speed of over 40 picture/s and character-front bit-mapped speed of over 15000 characters/s in a 1024*768-pixel-resolution color-CRT (cathode-ray-tube) system is discussed. The high-speed operation was attained by a memory interleaving scheme. The detailed timing for the high-speed scheme and its compactness are shown, using an actually fabricated application board. The chip layout was accomplished with a standard-cell-based approach with 1.0- mu m CMOS process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Truffles - Secure File Sharing with Minimal System Administrator Intervention (1993)

The Truffles file system supports file sharing between arbitrary users at arbitrary sites connected by a network. Truffles is an interesting example of a service of the future that will automatically allow users to collaborate with other users anywhere in the world in ways not currently possible. These services, and Truffles in particular, have the potential of greatly increasing the workload of system administrators, if the services are not designed properly. This paper describes how Truffles approaches solving its problems without unduly burdening system administrators. INTRODUCTION As improvements in hardware and software make new services available, users naturally want to take advantage of them. Frequently, however, a new service means a new burden for system administrators. Beyond the inevitable costs of installing and maintaining the service, however, some services may require more frequent ongoing attention. In particular, a class of services of the future will make resources...
Copolymers of Starch and Polyacrylonitrile. Influence of Granule Swelling on Copolymer Composition under Various Reaction Conditions (1970)

Abstract Molecular weights and grafting frequencies of graft copolymers prepared with ferrous ammonium sulfate-hydrogen peroxide initiation showed a dependence on granule swelling similar to that found with ceric ammonium nitrate (increased swelling of starch granules decreased the number of grafted polyacrylonitrile chains and increased their average molecular weight). As with unswollen starch, the composition of the copolymer prepared from swollen starch was not influenced by granule size. Molecular weights of polyacrylonitrile branches grafted to swollen and unswollen starch were independent of reaction time; however, grafting frequencies with swollen and unswollen starch tended to converge toward a common value with increased reaction time and increased dilution. Data suggest that the influence of granule swelling on copolymer composition is due to a faster termination rate for growing polyacrylonitrile chains in unswollen starch.
Differing substrate specificities of members of the DYRK family of arginine‐directed protein kinases (2001)

The mammalian DYRK (dual specificity tyrosine phosphorylated and regulated kinase) family of protein kinases comprises a number of related, but poorly understood enzymes. DYRK1A is nuclear while DYRKs 2 and 3 are cytoplasmic. We recently showed that DYRK2 phosphorylates the translation initiation factor eIF2B at Ser539 in its epsilon-subunit and thereby "primes" its phosphorylation by glycogen synthase kinase-3. Here we have used peptides based on the sequence around Ser539 to help define the specificity of DYRK2/3 in comparison with DYRK1A. These kinases require an arginine N-terminal to the target residue for efficient substrate phosphorylation. This cannot be replaced even by lysine. A peptide with arginine at -2 is phosphorylated much less well by all three kinases than one with arginine at -3. Replacement of the +1 proline by alanine almost completely eliminates substrate phosphorylation, but valine here does allow phosphorylation especially by DYRK2. This study reveals both similarities and differences in the specificities of these arginine-dependent protein kinases.
52. A synthesis of dihydroindole, dihydrothionaphthen, and dihydrobenzofuran (1941)

G. M. Bennett and M. M. Hafez, J. Chem. Soc., 1941, 287 DOI: 10.1039/JR9410000287
Stable, Long‐Term Bacterial Production of Soluble, Dimeric, Disulfide‐Bonded Protein Pharmaceuticals without Antibiotic Selection (2000)

Numerous biopharmaceuticals and other recombinant biotechnology products are made in prokaryotic hosts. However, bacterial production of native, biologically active eukaryotic proteins is rarely possible for disulfide-bonded and/or multisubunit proteins. We previously described the production of soluble, native disulfide-bonded dimeric proteins in the Escherichia coli cytoplasm (Miele et al., 1990; Mantile et al., 1993). Native, biologically active proteins with up to six disulfide bonds have been produced with our expression system (Garces et al., 1997). However, plasmid instability during induction limited its usefulness. We now report the stable, high-level expression of soluble, disulfide-bonded human uteroglobin without antibiotic selection. We designed a new vector containing a multifunctional stabilization region that confers complete plasmid stability and increased protein yields without copy number increases. Recombinant expression remains fully inducible after long-term continuous culture in nonselective liquid medium (at least 260 generations). This system may significantly expand the applications of bacterial expression to recombinant production of soluble, bioactive proteins for biochemical studies and biopharmaceutical/industrial purposes. As a result of the very broad activity spectrum of the stabilization region we selected, its use could be extended to bacterial hosts other than enterobacteria.
Yaa autoimmune phenotypes are conferred by overexpression of TLR7 (2008)

The Y-linked autoimmune accelerating (Yaa) locus drives the transition to fatal lupus nephritis when combined with B6.Sle1 in our C57BL/6J (B6)-congenic model of systemic autoimmunity. We and others recently demonstrated that the translocation of a cluster of X-linked genes onto the Y chromosome is the genetic lesion underlying Yaa (Subramanian, S. et al., Proc. Natl. Acad. Sci. USA 2006. 103: 9970-9975; Pisitkun, P. et al., Science 2006. 312: 1669-1672). In male mice carrying Yaa, the transcription of several genes within the translocated segment is increased roughly twofold. Although the translocated X chromosome segment in Yaa may contain as many as 16 genes, the major candidate gene for causation of the Yaa-associated autoimmune phenotypes has been TLR7. To confirm the role of TLR7 in Yaa-mediated autoimmune phenotypes, we introgressed a targeted disruption of TLR7 (TLR7(-)) onto B6.Sle1Yaa to produce B6.Sle1YaaTLR7(-) and examined evidence of disease at 6 and 9 months of age. Our results demonstrate that the up-regulation of TLR7 in the B6.Sle1Yaa strain is responsible for splenomegaly, glomerular nephritis and the majority of the cellular abnormalities of B, T and myeloid cells. The up-regulation of TLR7 was also responsible for driving the infiltration and activation of leukocytes in the kidney, in which activated T cells were a primary component. However, the resolution of TLR7 up-regulation did not eliminate the enhanced humoral autoimmunity observed in B6.SleYaa, suggesting that additional elements in the translocation may contribute to the disease phenotype.
The Chinese hamster ovary glycosylation mutants LEC11 and LEC12 express two novel GDP-fucose:N-acetylglucosaminide 3-alpha-L-fucosyltransferase enzymes. (1984)

Evidence is presented that the GDP-fucose:N-acetyl-glucosaminide 3-alpha-L-fucosyltransferase activities of two Chinese hamster ovary glycosylation mutants, LEC11 and LEC12, are structurally distinct enzymes. The alpha(1,3)fucosyltransferase in LEC12 cell extracts binds to GDP-hexanolamine-Sepharose and is unaffected by 3 mM N-ethylmaleimide. In contrast, the alpha(1,3)fucosyltransferase activity in LEC11 cells does not bind readily to GDP-hexanolamine-Sepharose and is completely inhibited by 1 mM N-ethylmaleimide. The LEC11 and LEC12 alpha(1,3)fucosyltransferases also differ in the degree to which they are stimulated by divalent cations as well as in their abilities to fucosylate a variety of exogenous substrates. Of particular interest is the finding that the LEC11 alpha(1,3)fucosyltransferase adds fucose to certain sialylated glycoproteins, whereas the LEC12 enzyme is essentially unable to fucosylate these acceptors, although it is very active with their desialylated derivatives. The combined evidence shows that the LEC11 and LEC12 alpha(1,3)fucosyltransferase enzymes are different molecules and presumably, therefore, the products of distinct genes. In addition, neither of the enzymes appears identical to any of the previously described alpha(1,3)fucosyltransferase activities from other sources.