gebhart/patrepeval huggingface dataset:
Systemic Effect of Human Growth Hormone after Intramuscular Injection of a Single Dose of a Muscle-Specific Gene Medicine (1998)

A muscle-specific gene medicine is described that provides for long-term secretion of biologically active human growth hormone (hGH) from skeletal muscle into the systemic circulation. The hGH gene medicine is composed of a muscle-specific hGH plasmid expression system complexed with a protective, interactive, non-condensing (PINC) delivery system. The muscle-specific gene expression system, pSK-hGH-GH, was constructed by linking the promoter/enhancer regions of chicken skeletal alpha-actin to hGH gene. C2C12 myoblast transfection with pSK-hGH-GH resulted in the synthesis of hGH in a muscle-specific manner. Direct injection into rat tibialis cranialis muscle of pSK-hGH-GH complexed with a polymeric PINC delivery system, polyvinylpyrrolidone (PVP), produced hGH levels in muscle that were 10- to 15-fold higher compared with plasmid formulated in saline at 14 days post-injection. Intratracheal instillation in rat lung of pSK-hGH-GH did not produce significantly detectable levels of hGH. In hypophysectomized rats, a single intramuscular dose of the pSK-hGH-GH/PVP complex resulted in hGH expression and a subsequent increase in serum levels of rat IGF-I and growth. hGH expression and effects on rat serum IGF-I levels were detectable up to 28 days after injection of formulated plasmid and effects on growth were detectable unto 21 days. Anti-hGH antibodies were detectable in serum at 14 days post-injection, reached a plateau at 21 days, and remained elevated through the study period. Cyclosporin treatment of the pSK-hGH-GH/PVP-injected animals completely inhibited the antibody response and resulted in increased hGH expression.
Two-photon polymerization for biological applications (2017)

Two-photon polymerization (2PP) leverages the two-photon absorption (TPA) of near-infrared (NIR) radiation for additive manufacturing with sub-diffraction limit resolution within the bulk of a photosensitive material. This technology draws heavily on photosensitive polymers from the microelectronics industry, which were not optimized for TPA or for biocompatibility. 2PP with sub 100 nm resolution has been repeatedly demonstrated; however, this level of fabrication resolution comes at the expense of long fabrication times. Manufacturing of medical devices beyond surface texturing would be prohibitively slow using the current state of the art 2PP technology. Current research into TPA-sensitive photopolymers with good biocompatibility and holographic projections using spatial light modulators address current technological limitations by providing materials specifically formulated for biological applications and by making better use of available laser power for applications in which nanoscale resolution is not required.
A Coupled Sharp-Interface Immersed Boundary-Finite-Element Method for Flow-Structure Interaction With Application to Human Phonation (2010)

A new flow-structure interaction method is presented, which couples a sharp-interface immersed boundary method flow solver with a finite-element method based solid dynamics solver. The coupled method provides robust and high-fidelity solution for complex flow-structure interaction (FSI) problems such as those involving three-dimensional flow and viscoelastic solids. The FSI solver is used to simulate flow-induced vibrations of the vocal folds during phonation. Both two- and three-dimensional models have been examined and qualitative, as well as quantitative comparisons, have been made with established results in order to validate the solver. The solver is used to study the onset of phonation in a two-dimensional laryngeal model and the dynamics of the glottal jet in a three-dimensional model and results from these studies are also presented.
Empirical Bayes Estimates for Large-Scale Prediction Problems (2009)

Classical prediction methods such as Fisher's linear discriminant function were designed for small-scale problems, where the number of predictors N is much smaller than the number of observations n. Modern scientific devices often reverse this situation. A microarray analysis, for example, might include n = 100 subjects measured on N = 10,000 genes, each of which is a potential predictor. This paper proposes an empirical Bayes approach to large-scale prediction, where the optimum Bayes prediction rule is estimated employing the data from all the predictors. Microarray examples are used to illustrate the method. The results show a close connection with the shrunken centroids algorithm of Tibshirani et al. (2002), a frequentist regularization approach to large-scale prediction, and also with false discovery rate theory.
A Novel Promiscuous Class of Camelid Single-Domain Antibody Contributes to the Antigen-Binding Repertoire (2010)

It is well established that, in addition to conventional Abs, camelids (such as Camelus dromedarius and Lama glama) possess unique homodimeric H chain Abs (HCAbs) devoid of L chains. The Ag-binding site of these HCAbs consists of a single variable domain, referred to as VHH. It is widely accepted that these VHHs, with distinct framework-2 imprints evolved within the V(H) clan III-family 3, are exclusively present on HCAbs. In this study, we report the finding of a distinct leader signal sequence linked to variable genes displaying a high degree of homology to the clan II, human VH(4) family that contributes to the HCAb Ag-binding diversity. Although the VHH framework-2 imprints are clearly absent, their VH(4)-D-JH recombination products can be rearranged to the H chains of both classical and HCAbs. This suggests that for these V domains the presence of a L chain to constitute the Ag-binding site is entirely optional. As such, the capacity of this promiscuous VH(4) family to participate in two distinct Ab formats significantly contributes to the breadth of the camelid Ag-binding repertoire. This was illustrated by the isolation of stable, dendritic cell-specific VH(4) single domains from a VH(4)-HCAb phage display library. The high degree of homology with human VH(4) sequences is promising in that it may circumvent the need for "humanization" of such single-domain Abs in therapeutic applications.
Potent effects of aerosol compared with intravenous treprostinil on the pulmonary circulation (2005)

Inhaled vasodilator therapy for pulmonary hypertension may decrease the systemic side effects commonly observed with systemic administration. Inhaled medications only reach ventilated areas of the lung, so local vasodilation may improve ventilation-perfusion matching and oxygenation. We compared the effects of intravenous vs. aerosolized treprostinil on pulmonary and systemic hemodynamics in an unanesthetized sheep model of sustained acute pulmonary hypertension. Acute, stable pulmonary hypertension was induced in instrumented unanesthetized sheep by infusing a PGH(2) analog, U-44069. The sheep were then administered identical doses of treprostinil either intravenously or by aerosol. Systemic and pulmonary hemodynamics were recorded during each administration. Both intravenous and aerosol delivery of treprostinil reduced pulmonary vascular resistance and pulmonary arterial pressure, but the effect was significantly greater with aerosol delivery (P < 0.05). Aerosol delivery of treprostinil had minimal effects on systemic hemodynamics, whereas intravenous delivery increased heart rate and cardiac output and decreased left atrial pressure and systemic blood pressure. Aerosol delivery of the prostacyclin analog treprostinil has a greater vasodilatory effect in the lung with minimal alterations in systemic hemodynamics compared with intravenous delivery of the drug. We speculate that this may result from treprostinil stimulated production of vasodilatory mediators from pulmonary epithelium.
Sialyllactotetraosylceramide, a Ganglioside Marker for Human Malignant Gliomas (1988)

The ganglioside composition of surgically removed human glioma tissue was shown to differ from that of normal adult brain tissue. First, it contained reduced amounts of the major normal brain gangliosides of the gangliotetraose series. Second, it contained increased proportions of gangliosides not detected in normal brain tissue. One of these was isolated and established as being sialyllactotetraosylceramide 3'-isoLM1. Radioimmunoassay for this ganglioside antigen in human glioma tissue revealed that 14/14 specimens of grades III and IV were positive but only 1/4 of grade II. Normal brain tissue was negative. These results suggest that sialyllactotetraosylceramide is a marker for human malignant gliomas.
Gova/b alloantigen system on human platelets (1990)

In this report we describe a platelet alloantigen system that is carried on a novel platelet protein of 175 Kd. Antisera against the two alleles (Gova/Govb) were found in two patients who had received large numbers of platelet transfusions. The anti-Gov alloantibodies could not be detected using a whole platelet solid phase enzyme immunoassay, or by a platelet glycoprotein capture enzyme immunoassay using monoclonal antibodies against glycoproteins Ib/IX, Ia/IIa, and IIb/IIIa. Using radioimmunoprecipitation techniques, a protein was precipitated that migrated at 175 Kd (reduced). Under nonreduced conditions, a 150-Kd protein was detected with a minor component at 175Kd. The detection of the alloantigens was not activation-dependent. Using immunodepletion studies, we demonstrated that each alloantiserum recognized an epitope on a discrete population of the 175-Kd platelet protein. Family studies demonstrated that the alloantigens designated as Gova and Govb were inherited in an autosomal codominant fashion. The phenotypic frequencies were Gova/Gova, 26%; Gova/Govb, 55%; Govb/Govb, 19%; giving gene frequencies of 0.532 and 0.468 for Gova and Govb, respectively (n = 33).
Integration and Germ-Line Transmission of a Pseudotyped Retroviral Vector in Zebrafish (1994)

The zebrafish is rapidly becoming a popular model system for the study of vertebrate development because it is ideal for both embryological studies and genetic analysis. To determine if a retroviral vector pseudotyped with the envelope glycoprotein of the vesicular stomatitis virus could infect zebrafish embryos, and in particular, the cells destined to become the germ line, a pseudotyped virus was injected into blastula-stage zebrafish embryos. Fifty-one embryos were allowed to develop and eight transmitted proviral DNA to their progeny. Founders were mosaic, but as expected, transgenic F1's transmitted proviral DNA in a Mendelian fashion to the F2 progeny. Transgenic F1 fish inherited a single integrated provirus, and a single founder could transmit more than one viral integration to its progeny. These results demonstrate that this pantropic pseudotyped vector, originally developed for human gene therapy, will make the use of retroviral vectors in zebrafish possible.
Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression (2021)

PE2 directs high-fidelity editing of a single base in a TFBS leading to cell-specific loss in expression of an mRNA/long noncoding RNA gene pair. The PE2 platform expands the genome editing toolbox for modeling and correcting relevant noncoding SNVs in the mouse.
Lower Bounds for Constant Multiplication Problems (2007)

Lower bounds for problems related to realizing multiplication by constants with shifts, adders, and subtracters are presented. These lower bounds are straightforwardly calculated and have applications in proving the optimality of solutions obtained by heuristics.
The dynamic factory pattern (2008)

The Dynamic Factory pattern describes a factory that can create product instances based on concrete type definitions stored as external metadata. This facilitates adding new products to a system without having to modify code in the factory class.
Synthesis of monosubstituted derivatives of closo-decahydrodecaborate(2-). X-ray crystal structures of [closo-2-B10H9CO]- and [closo-2-B10H9NCO]2- (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of monosubstituted derivatives of closo-decahydrodecaborate(2-). X-ray crystal structures of [closo-2-B10H9CO]- and [closo-2-B10H9NCO]2-Kenneth Shelly, Carolyn B. Knobler, and M. Frederick HawthorneCite this: Inorg. Chem. 1992, 31, 13, 2889–2892Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://pubs.acs.org/doi/10.1021/ic00039a041https://doi.org/10.1021/ic00039a041research-articleACS PublicationsRequest reuse permissionsArticle Views340Altmetric-Citations49LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The Microclimate Chamber: Morphological Aspects of Experimental Deep Burns Treated Topically with Continuous Humidified Oxygen (1983)

Scanning electron and transmission electron micrographs of tissue biopsies from experimental third-degree burns treated topically with 96% oxygen for twenty-five days, without modifying the environment of the whole animal, revealed a marked promotion of collagen maturation. The O2-treated wounds showed a high ratio of collagen-ground substance; assembling of distinct fibers to form bundles with individual fibers of 1,360 +/- 95 A in diameter and an organized orientation; a highly aggregated rough endoplasmic reticulum of the fibroblasts, consisting of large cisternae and abundant ribosomes. The control burn wounds exposed to ambient air exhibited a low ratio of collagen-ground substance; a loose, rough endoplasmic reticulum; fiber diameter of 700 +/- 70 A, with haphazard orientation of the fibers; and a poor tendency to form bundles. These findings suggest that topical treatment of experimental deep burns with 96% O2 promoted collagen maturation and organization as well as collagen synthesis.
Antitumor Activity of IFN-λ in Murine Tumor Models (2006)

IFN-lambda 1, -lambda 2 and -lambda 3 have been discovered as the latest members of the class II cytokine family and shown to possess antiviral activity. Murine B16 melanoma and Colon26 cancer cells were transduced with mouse IFN-lambda to determine whether IFN-lambda possesses antitumor activity. Overexpression of IFN-lambda induced cell surface MHC class I expression and Fas/CD95 Ag, induced significant caspase-3/7 activity, and increased p21(Waf1/Cip1) and dephosphorylated Rb (Ser(780)) in B16 cells in vitro. IFN-lambda expression in tumor cell lines markedly inhibited s.c. and metastatic tumor formation in vivo compared with mock transfections (p < 0.05). Moreover, IFN-lambda expression induced lymphocytic infiltrates, and an Ab-mediated immune cell depletion assay showed that NK cells were critical to IFN-lambda-mediated tumor growth inhibition. Hydrodynamic injection of IFN-lambda cDNA successfully targeted liver metastatic foci of Colon26 cells, and moderately decreased the mortality of mice with tumors. IFN-lambda overexpression in the liver increased NK/NKT cells and enhanced their tumor-killing activity, and suggested the activation of innate immune responses. Thus, IFN-lambda induced both tumor apoptosis and NK cell-mediated immunological tumor destruction through innate immune responses. These findings suggested that local delivery of IFN-lambda might prove a useful adjunctive strategy in the clinical treatment of human malignancies.
Differential expression of chemokine receptors on peripheral blood, synovial fluid, and synovial tissue monocytes/macrophages in rheumatoid arthritis (2001)

Objective Since it is likely that monocytes utilize chemokines to migrate to the rheumatoid arthritis (RA) joint, we investigated the expression of C-C chemokine receptors (CCR) 1–6 and C-X-C receptor 3 (CXCR3) in the peripheral blood (PB), synovial fluid (SF), and synovial tissue of patients with RA as well as in the PB of normal subjects. Methods We compared chemokine receptor expression on CD14+ monocytes from normal PB, RA PB, and RA SF using 2-color flow cytometry. Correlations with patient clinical data were determined. Chemokine and receptor expression were investigated in RA synovial tissue by immunohistochemistry and 2-color immunofluorescence to identify CD68+ macrophages. Results Most normal PB monocytes expressed CCR1 (87%) and CCR2 (84%), but not CCRs 3, 4, 5, or 6 or CXCR3. RA PB monocytes expressed CCR1 (56%) and CCR2 (76%), with significantly more expressing CCR3 (18%), CCR4 (38%), and CCR5 (17%) compared with normal PB monocytes. Significantly fewer SF monocytes from RA patients expressed CCR1 (17%), CCR2 (24%), and CCR4 (6%) while significantly more expressed CCR3 (35%) and CCR5 (47%) compared with RA and normal PB monocytes; CCR6 and CXCR3 were rarely detected. Clinically, the erythrocyte sedimentation rate was inversely correlated with the expression of CCR1 and CCR4 by RA PB, and CCR5 expression by RA SF was correlated with the SF white blood cell count. CCR1-, CCR2-, and CCR5-immunoreactive cells were found in RA synovial tissue and colocalized with CD68+ macrophages. RA synovial tissue RANTES (regulated upon activation, normally T cell expressed and secreted chemokine)– and monocyte chemoattractant protein 1–immunoreactive cells colocalized with CCR1 and CCR2, respectively, on serial sections. Macrophage inflammatory protein 1α (MIP-1α) was principally restricted to vascular endothelium, and MIP-1β+ macrophages were found throughout the sections. Conclusion Monocytes mainly express CCR1 and CCR2 in normal and RA PB, CCR3 and CCR5 in RA PB and RA SF, and CCR4 in RA PB. The differential expression of chemokine receptors suggests that certain receptors aid in monocyte recruitment from the circulation while others are important in monocyte retention in the joint.
Synthesis of novel silanes with functional head groups, surface modifications, and characterization (2008)

The aim of this thesis was to investigate novel techniques to create complex hierarchical chemical patterns on silica or quartz surfaces with micro to nanometer sized features.These modified surfaces were used for functional group-selective surface reactions and site-selective assembly of colloidal particles.For this purpose, novel functionalized triethoxysilanes were synthesized by a modular convergent approach, coupling 3-aminopropyltriethoxysilane and an amino-reactive fragment.After deposition of these silanes as molecular layers onto planar silica and quartz surfaces, the functional groups of these silanes form new functional surfaces (by liquid-or vapor phase silanization) or even lateral functional patterns (by micro-contact printing or photolithography) that allow further chemical reactions at these surfaces.By the above mentioned modular approach triethoxysilanes with terminal t-butyl-, maleimide-, succinimidyl-, and alkyne moieties were synthesized and surface layers were prepared with them.Kinetic experiments with varying hydrolysis-and incubation times were performed while monitoring changes in hydrophilicity of the functional surfaces and the layer thickness to study the efficiency of silanization process.From these results the hydrolysis conditions could be optimized in order to form uniform and well defined self-assembled surface layers.In model reactions it was shown that their head groups can further bind appropriate molecules due to their characteristic chemical reactivities.Furthermore, a series of novel photosensitive silanes with 1-(4,5-dimethoxy-2nitrophenyl)ethanol (CH 3 -NVoc) protected -OH, -COOH and -NH 2 functionalities, and 3,5-dimethoxybenzoin (Bzn)-protected -NH 2 group were synthesized and characterized.UV-Vis spectra of both CH 3 -NVoc and Bzn silanes were recorded in solution phase and as SAMs on quartz surfaces for different irradiation times at the respective deprotection wavelengths to optimize the photodeprotection step.By irradiation through a gold mask in a UV mask aligner (365 nm) or a crosslinker (254 nm), both CH 3 -NVoc and Bzn SAMs could be patterned with functional (photodeprotected / irradiated) and protected (unirradiated) regions, respectively.The obtained functional pattern could be visualized by site-selective staining with fluorescent probes.Furthermore, site-selective colloid absorption could be observed on the photosensitive silane layer patterns after local deprotection with light.
The lens as a model for fibrotic disease (2011)

Fibrosis affects multiple organs and is associated with hyperproliferation, cell transdifferentiation, matrix modification and contraction. It is therefore essential to discover the key drivers of fibrotic events, which in turn will facilitate the development of appropriate therapeutic strategies. The lens is an elegant experimental model to study the processes that give rise to fibrosis. The molecular and cellular organization of the lens is well defined and consequently modifications associated with fibrosis can be clearly assessed. Moreover, the avascular and non-innervated properties of the lens allow effective in vitro studies to be employed that complement in vivo systems and relate to clinical data. Using the lens as a model for fibrosis has direct relevance to millions affected by lens disorders, but also serves as a valuable experimental tool to understand fibrosis per se.
Hemojuvelin and bone morphogenetic protein (BMP) signaling in iron homeostasis (2014)

Mutations in hemojuvelin (HJV) are the most common cause of the juvenile-onset form of the iron overload disorder hereditary hemochromatosis. The discovery that HJV functions as a co-receptor for the bone morphogenetic protein (BMP) family of signaling molecules helped to identify this signaling pathway as a central regulator of the key iron hormone hepcidin in the control of systemic iron homeostasis. This review highlights recent work uncovering the mechanism of action of HJV and the BMP-SMAD signaling pathway in regulating hepcidin expression in the liver, as well as additional studies investigating possible extra-hepatic functions of HJV. This review also explores the interaction between HJV, the BMP-SMAD signaling pathway and other regulators of hepcidin expression in systemic iron balance.
Clustera (2008)

This paper introduces Clustera, an integrated computation and data management system. In contrast to traditional cluster-management systems that target specific types of workloads, Clustera is designed for extensibility, enabling the system to be easily extended to handle a wide variety of job types ranging from computationally-intensive, long-running jobs with minimal I/O requirements to complex SQL queries over massive relational tables. Another unique feature of Clustera is the way in which the system architecture exploits modern software building blocks including application servers and relational database systems in order to realize important performance, scalability, portability and usability benefits. Finally, experimental evaluation suggests that Clustera has good scale-up properties for SQL processing, that Clustera delivers performance comparable to Hadoop for MapReduce processing and that Clustera can support higher job throughput rates than previously published results for the Condor and CondorJ2 batch computing systems.