gebhart/patrepeval huggingface dataset:
IMMUNOLOGIC BARRIERS TO HEPATIC ADENOVIRAL GENE THERAPY FOR TRANSPLANTATION (1997)

Adenoviral gene transfer has potential use to attenuate the immunogenicity of hepatic allografts. However, the clinical application of adenoviral gene therapy is currently impeded by the potent host immune response to the virus that limits the duration of its effects. In these studies, we identify the cellular and humoral immune responses to recombinant adenovirus in the liver of mice and define the immunologic barriers to the successful application of this technology to transplantation. The immunobiology of recombinant adenovirus was studied in mouse liver using vectors containing the lacZ and alkaline phosphatase marker genes. The duration of transgene expression was studied in various immunodeficient mice to determine the mechanism of viral clearance. Adoptive transfer of serum to B lymphocyte deficient mice and neutralizing antibody assays were used to define the antiviral humoral response. Hepatic adenoviral transgene expression was prolonged in animals deficient in CD4+ or CD8+ T cells indicating their importance in viral clearance. Unexpectedly, mice lacking B lymphocytes also had delayed elimination of virus suggesting that B cells play a role in the primary immune response. Effective repeat gene transfer was blocked by adenoviral-specific neutralizing antibody. Therefore, a T lymphocyte response results in viral elimination after a primary intravenous inoculation of recombinant adenovirus and a potent humoral response inhibits effective repeat adenoviral gene transfer. The immunogenicity of the vector must be overcome for adenoviral gene therapy to have therapeutic application for hepatic transplantation.
The Glycolytic Flux in Escherichia coli Is Controlled by the Demand for ATP (2002)

The nature of the control of glycolytic flux is one of the central, as-yet-uncharacterized issues in cellular metabolism. We developed a molecular genetic tool that specifically induces ATP hydrolysis in living cells without interfering with other aspects of metabolism. Genes encoding the F(1) part of the membrane-bound (F(1)F(0)) H(+)-ATP synthase were expressed in steadily growing Escherichia coli cells, which lowered the intracellular [ATP]/[ADP] ratio. This resulted in a strong stimulation of the specific glycolytic flux concomitant with a smaller decrease in the growth rate of the cells. By optimizing additional ATP hydrolysis, we increased the flux through glycolysis to 1.7 times that of the wild-type flux. The results demonstrate why attempts in the past to increase the glycolytic flux through overexpression of glycolytic enzymes have been unsuccessful: the majority of flux control (>75%) resides not inside but outside the pathway, i.e., with the enzymes that hydrolyze ATP. These data further allowed us to answer the question of whether catabolic or anabolic reactions control the growth of E. coli. We show that the majority of the control of growth rate resides in the anabolic reactions, i.e., the cells are mostly "carbon" limited. Ways to increase the efficiency and productivity of industrial fermentation processes are discussed.
Lewis acid-catalyzed reactions in protic media. Lanthanide-catalyzed reactions of indoles with aldehydes or ketones (1996)

Lanthanide triflates were found to be effective catalysts for reactions of indoles with aldehydes or ketones in aqueous solution.
Intelligence Compensation Theory: A Critical Examination of the Negative Relationship Between Conscientiousness and Fluid and Crystallised Intelligence (2009)

Abstract This study investigates the negative relationship between fluid and crystallised intelligence and Conscientiousness subfactors within the New Zealand workplace. Fluid and crystallised intelligence were assessed via the General Reasoning Test Battery 2 (GRT2; N = 1629). Two personality inventories were employed: The Fifteen-Factor Questionnaire (15FQ; N = 546), and the Occupational Personality Profile (OPP; N = 1083). 15FQ subfactors of Conscientious and Disciplined negatively correlated with fluid and crystallised intelligence. OPP subfactors of Detail-Conscious and Conformity also negatively correlated with fluid and crystallised intelligence. Subfactors for both personality measures correlated more strongly with crystallised than fluid intelligence. This finding is contrary to an earlier finding that Conscientiousness negatively correlates with fluid, but not crystallised intelligence (Moutafi, Furnham, &amp; Paltiel, 2004). An explanation for this difference is discussed and the Intelligence Compensation Theory is introduced as an explanation for the observed relationships.
Data management of musical information (1987)

This dissertation explores various issues related to the application of computer data management techniques to musical information. The contribution of this work is twofold: (1) It extends an existing data model (the entity-relationship model) to support a database schema for musical information. (2) It develops particular data management access methods to effectively manipulate information in the musical database.
Various types of musical information are analyzed, focusing particularly on the conceptual representations necessary to formally encode musical scores expressed in Common Musical Notation (CMN). The entity-relationship model is taken as a starting point for a CMN database schema.
A new feature is added to the entity-relationship model to represent the notion of ordered sets of entities. This property is called hierarchical ordering. Such a relationship occurs, for example, when an ordered set of notes constitutes a chord, or an ordered set of measures forms a movement of a composition.
A method is proposed for representing attribute inheritance among entities, and various approaches to the problem of managing this inheritance among entities within the music database are considered. Several examples demonstrate that inheritance under hierarchical ordering is more complex than that supported by standard generalization hierarchies.
Using these two data modeling tools, hierarchical ordering and attribute inheritance, a schema is developed for CMN. Entities from the CMN schema are divided into groups according to various aspects of the information: temporal, timbral, and graphical.
To implement hierarchical ordering using existing relational database technology, extensions to relational access methods are developed. Entity ordering is supported by the introduction of ordered relations.
A data structure is developed for ordered relations which provides a general solution for the support of user-defined aggregate functions computed over ordered sets, and user-defined orderings, including hierarchical orderings.
The dissertation closes with a summary of questions left open by the present research, particularly those remaining issues that need be addressed in order to develop a functional database system appropriate to the management of musical information.
Managing scientific metadata (2001)

Metacat is a network-enabled database framework that lets users store, query, and retrieve XML documents with arbitrary schemas in SQL-compliant relational database systems. The system (available from the Knowledge Network for Biocomplexity, http://knb.ecoinformatics.org/) incorporates RDF-like methods for packaging data sets to allow researchers to customize and revise their metadata. It is extensible and flexible enough to preserve utility and interpretability working with future content standards. Metacat solves several key challenges that impede data confederation efforts in ecological research, or any field in which independent agencies collect heterogeneous data that they wish to control locally while enabling networked access. This distributed solution integrates with existing site infrastructures because it works with any SQL-compliant database system. The framework's open-source based components are widely available, and individual sites can extend and customize the system to support their data and metadata needs.
Developing an adaptive model of thermal comfort and preference (1998)

The adaptive hypothesis predicts that contextual factors and past thermal history modify building occupants' thermal expectations and preferences. One of the predictions of the adaptive hypothesis is that people in warm climate zones prefer warmer indoor temperatures than people living in cold climate zones. This is contrary to the static assumptions underlying the current ASHRAE comfort standard 55-92. To examine the adaptive hypothesis and its implications for Standard 55-92, the ASHRAE RP-884 project assembled a quality-controlled database from thermal comfort field experiments worldwide (circa 21,000 observations from 160 buildings). Our statistical analysis examined the semantics of thermal comfort in terms of thermal sensation, acceptability, and preference, as a function of both indoor and outdoor temperature. Optimum indoor temperatures tracked both prevailing indoor and outdoor temperatures, as predicted by the adaptive hypothesis. The static predicted means vote (PMV) model was shown to be partially adaptive by accounting for behavioral adjustments, and fully explained adaptation occurring in HVAC buildings. Occupants in naturally ventilated buildings were tolerant of a significantly wider range of temperatures, explained by a combination of both behavioral adjustment and psychological adaptation. These results formed the basis of a proposal for a variable indoor temperature standard.
Single-Molecule Study of Protein-Protein and Protein-DNA Interaction Dynamics (2005)

Protein-protein and protein-DNA interactions play critical roles in biological systems, and these interactions often involve complex mechanisms and inhomogeneous dynamics. Single-molecule spectroscopy is a powerful and complimentary approach to decipher such spatially and temporally inhomogeneous protein interaction systems, providing new information that are not obtainable from static structure analyses, thermodynamics characterization, and ensemble-averaged measurements. To illustrate the single-molecule spectroscopy and imaging technology and their applications on studying protein-ligand interactions, this chapter focuses on discussing two recent single-molecule spectroscopy studies on protein-protein interaction in cell signaling process and on protein-DNA interactions in DNA damage recognition process.
Soluble HLA class I molecules induce natural killer cell apoptosis through the engagement of CD8: evidence for a negative regulation exerted by members of the inhibitory receptor superfamily (2002)

Herein, we show that CD8(dull), CD8(intermediate), and CD8(bright) natural killer (NK) cell clones can be identified. Triggering of CD8 with its natural ligand(s), represented by soluble HLA class I (sHLA-I), isolated either from serum of healthy donors or from HLA-I(-) 721.221 lymphoblastoid cell line transfected with HLA-A2, -Cw4, and -Bw46 alleles, or HLA-G1 leads to NK cell apoptosis. The magnitude of this effect directly correlated with the level of CD8 expression. sHLA-I-induced apoptosis depends on the interaction with CD8, as it was inhibited by masking this molecule with specific monoclonal antibodies (mAbs). Moreover, sHLA-I or CD8 cross-linking with specific mAbs elicited intracellular calcium increases, Fas ligand (FasL) messenger RNA transcription, and FasL secretion, which were needed for delivering the death signal. Indeed, this apoptosis was inhibited by preincubation of NK cell clones with Fas or FasL antagonist mAbs, indicating that the Fas/FasL pathway is involved. Furthermore, members of the inhibitory receptor superfamily, such as CD94/NKG2 complex or killer inhibitory receptors, were shown to exert an inhibitory effect on sHLA-I-mediated apoptosis and secretion of FasL. These findings suggest that interaction between sHLA-I and CD8 evokes an apoptotic signal that is down-regulated by inhibitory receptor superfamily that function as survival receptors in NK cells.
Blocking of collagenase secretion by estramustine during in vitro tumor cell invasion. (1988)

The effects of the antitumorigenic drug estramustine on tumor cell membrane penetration (invasion) were investigated in vitro by utilizing a synthetic basement membrane system (a modified Boyden chamber). Tumor cells were plated on a "partition barrier," consisting of a porous filter (8-micron pores) which was coated with a reconstituted basement membrane matrix (Matrigel), and induced to migrate across the barrier with conditioned medium obtained from 9DU 145 human prostatic tumor cells (passage 9). Quantitative radiolabeling studies demonstrated that specially isolated lines (isolated by several passages through the Matrigel) of DU 145 cells, A2058 melanoma, and B16-F10 melanoma cells were highly invasive such that 15 to 20% migrated across a 1-mm-thick Matrigel layer within 5 h at 37 degrees C. NIH-3T3 cells, mouse fibroblasts, and 20DU 145 cells (passage 20) exhibited little or no membrane invasive behavior. Micromolar concentrations of estramustine (30 to 120 microM) inhibited invasion by the invasive cell lines in a dosage-dependent fashion. Quantitative enzymatic assays and radioimmune assays demonstrated that estramustine inhibited membrane invasion by blocking type IV collagenase secretion. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blots confirmed that 30 to 60 microM estramustine blocked secretion of a Mr 105,000 collagenase protein. Indirect studies showed that a collagenase antibody raised against the Mr 105,000 protein and inhibitors of proteinase activity, including a metalloproteinase inhibitor, and 1,10-phenanthroline, blocked invasion. Because the antibodies inhibited type IV collagenase digestion of 3H-mouse type IV collagen, and invasion simultaneously, it is proposed that collagenolytic activity is involved in invasion. These data demonstrate that estramustine blocks proteinase secretion, and suggest that estramustine may be a useful therapeutic drug for the prevention of metastasis.
A randomized investigator‐blind trial of different passes of microdermabrasion therapy and their effects on skin biophysical characteristics (2008)

MDA may have remarkable effects on skin barrier function changes resulting in skin clinical improvements (Cochrane Skin Group identifier: CSG No. 37).
Relationship between Complement Membrane Attack Complex, Chemokine (C-C Motif) Ligand 2 (CCL2) and Vascular Endothelial Growth Factor in Mouse Model of Laser-induced Choroidal Neovascularization (2011)

The present study investigated the interactions among the complement membrane attack complex (MAC), CCL2, and VEGF that occur in vivo during the development of choroidal neovascularization (CNV). We first investigated the sequential expression of MAC, CCL2, and VEGF during laser-induced CNV in C57BL/6 mice. Increased MAC deposition was detected at 1 h, CCL2 increased at 3 h, and VEGF was up-regulated at day 3 post-laser treatment. These results suggested that during laser-induced CNV, MAC, CCL2 and VEGF are formed and/or expressed in the following order: MAC → CCL2 → VEGF. To determine the cross-talk between MAC, CCL2, and VEGF during laser-induced CNV, neutralizing antibodies were injected both systemically and locally to block the bioactivity of each molecule. Blocking MAC formation inhibited CCL2 and VEGF expression and also limited CNV formation, whereas neutralization of CCL2 bioactivity did not affect MAC deposition; however, it reduced VEGF expression and CNV formation. When bioactivity of VEGF was blocked, CNV formation was significantly inhibited, but MAC deposition was not affected. Together, our results demonstrate that MAC is an upstream mediator and effect of MAC on the development of laser-induced CNV can be attributed to its direct effect on VEGF as well as its effect on VEGF that is mediated by CCL2. Understanding the interplay between immune mediators is critical to gain insight into the pathogenesis of CNV.
Passive optical methods in measurement of the structure parameter of the air refractive index (2015)

A passive optical method for estimating the level of atmospheric turbulence (structure parameter of the air refractive index C n 2) from the image jitter is considered. It is proposed to use a high-speed digital video camera and effective two-dimensional parallel algorithms of image processing for measuring C n 2 in real time. Results obtained by the active and passive optical methods, as well as by an acoustic method, are compared.
Differential expression of myostatin and its receptor in the porcine anterior pituitary gland (2008)

ABSTRACT Myostatin (MSTN), known as growth and differentiation factor 8 (GDF‐8), is a member of the transforming growth factor β (TGF‐β) superfamily that negatively regulates skeletal muscle mass. Myostatin binds with high affinity to the receptor serine threonine kinase activin receptor type IIB (ActRIIB). Activins that also belong to the TGF‐β superfamily, stimulate follicle‐stimulating hormone production in gonadotrophs and suppress growth hormone and adrenocorticotropic hormone production in somatotrophs and corticotrophs, respectively. The aim of the present paper was therefore to clarify the endocrine action of MSTN in adenohypophysis. The present study details the expression and cellular localization of MSTN and ActRIIB in porcine anterior pituitary gland. The mRNA of MSTN and ActRIIB was consistently expressed in RT‐PCR. Immunohistochemistry of MSTN and specific hormones showed that MSTN localized in thyrotrophs and gonadotrophs, in which most of the MSTN immunoreactive cells were identified as thyrotrophs. The immunostaining of ActRIIB was restricted to corticotrophs. These results indicate that MSTN was mainly produced in thyrotrophs and its receptor, ActRIIB, was restrictively contained in corticotrophs. Interestingly, thyrotrophs immunoreactive for MSTN were frequently close to corticotrophs immunoreactive for ActRIIB. The present study suggests that MSTN from thyrotrophs may regulate corticotroph function as a paracrine mediator among the porcine anterior pituitary cells.
Identification of an Insulin-responsive, Slow Endocytic Recycling Mechanism in Chinese Hamster Ovary Cells (1998)

In adipocytes, the insulin-regulated aminopeptidase (IRAP) is trafficked through the same insulin-regulated recycling pathway as the GLUT4 glucose transporter. We find that a chimera, containing the cytoplasmic domain of IRAP fused to transmembrane and extracellular domains of the transferrin receptor, is slowly recycled and rapidly internalized in Chinese hamster ovary cells. Morphological studies indicate that the chimera is slowly trafficked through the general endosomal recycling compartment rather than being sorted to a specialized recycling pathway. A chimera in which a di-leucine sequence within the cytoplasmic domain of IRAP has been mutated to alanines is rapidly internalized and rapidly recycled, indicating that this di-leucine is required for the slow recycling but not for the rapid internalization. Insulin stimulates a 2-3-fold increase in the recycling of the chimera and only a 1.2-fold increase in the recycling of the transferrin receptor. The effect of insulin on the recycling of the chimera is blocked by wortmannin, a phosphatidylinositol 3'-kinase inhibitor. GTPgammaS (guanosine 5'-3-O-(thio)triphosphate) increases the recycling of the chimera by 50% but has no effect on the recycling of the transferrin receptor. In these studies, we have identified in Chinese hamster ovary cells a novel, slow endocytic recycling mechanism that is regulated by insulin.
Agrobacterium tumefaciens‐mediated sorghum transformation using a mannose selection system (2005)

A dual-marker plasmid containing the selectable marker gene, manA, and the reporter gene, sgfp, was used to transform immature sorghum embryos by employing an Agrobacterium-mediated system. Both genes were under the control of the ubi1 promoter in a binary vector pPZP201. The Escherichia coli phosphomannose isomerase (PMI) gene, pmi, was used as the selectable marker gene and mannose was used as the selective agent. The sgfp gene encoding green fluorescence protein (GFP) was the reporter gene and served as a visual screening marker. A total of 167 transgenic plants were obtained from nine different embryogenic callus lines grown on a selection medium containing 1%-2% mannose. Embryoids and shoots regenerated via embryogenesis, that showed strong GFP fluorescence, were selected from two sorghum genotypes: C401, an inbred line, and Pioneer 8505, a commercial hybrid. The GFP accumulation in transgenic plants was observed with a dissecting stereomicroscope. The integration and expression of the manA gene was confirmed by Southern blot and Western blot analyses, and the feasibility of manA selection was demonstrated by the chlorophenol red (CPR) assay. Our results indicated that transgenes segregated in the Mendelian fashion in the T1 generation. The conversion of mannose to a metabolizable fructose carbon source is beneficial to plants. In addition, except in soybean and a few legumes, no endogenous PMI activity has been detected in plant species, indicating that PMI is useful in the transformation of sorghum. In addition, PMI has no sequence homology to known allergens. Optimization of this selection system for sorghum transformation provides an efficient way to produce transgenic plants without using antibiotic or herbicidal agents as selectable markers, and our results showed that the transformation efficiency reached 2.88% for Pioneer 8505 and 3.30% for C401, both values higher than in previously published reports.
The tomato lectin consists of two homologous chitin-binding modules separated by an extensin-like linker (2003)

A cDNA encoding a putative lectin expressed in tomato leaves was identified and analysed. The lectin consists of two homologous chitin-binding modules interconnected by a short proline-rich domain containing a single Ser[Pro]( n ) repetitive motif. Each module comprises two in-tandem-arrayed hevein domains separated by a tetrapeptide linker. Besides the chitin-binding modules and proline-rich domain, the lectin contains two short unrelated domains located at the N- and C-termini of the protein respectively. Eventual elucidation of the molecular structure of the tomato lectin confirms the presumed chimaeric nature of the Solanaceae lectins but also indicates that all previously proposed models need to be revised.
VEGF Trap complex formation measures production rates of VEGF, providing a biomarker for predicting efficacious angiogenic blockade (2007)

VEGF is the best characterized mediator of tumor angiogenesis. Anti-VEGF agents have recently demonstrated impressive efficacy in human cancer trials, but the optimal dosing of such agents must still be determined empirically, because biomarkers to guide dosing have yet to be established. The widely accepted (but unverified) assumption that VEGF production is quite low in normal adults led to the notion that increased systemic VEGF levels might quantitatively reflect tumor mass and angiogenic activity. We describe an approach to determine host and tumor production of VEGF, using a high-affinity and long-lived VEGF antagonist now in clinical trials, the VEGF Trap. Unlike antibody complexes that are usually rapidly cleared, the VEGF Trap forms inert complexes with tissue- and tumor-derived VEGF that remain stably in the systemic circulation, where they are readily assayable, providing unprecedented capability to accurately measure VEGF production. We report that VEGF production is surprisingly high in non-tumor-bearing rodents and humans, challenging the notion that systemic VEGF levels can serve as a sensitive surrogate for tumor load; tumor VEGF contribution becomes significant only with very large tumor loads. These findings have the important corollary that anti-VEGF therapies must be sufficiently dosed to avoid diversion by host-derived VEGF. We further show that our assay can indicate when VEGF is optimally blocked; such biomarkers to guide dosing do not exist for other anti-VEGF agents. Based on this assay, VEGF Trap doses currently being assessed in clinical trials are in the efficacious range.