gebhart/patrepeval huggingface dataset:
Truncation of the C-terminal acidic transcriptional activation domain of herpes simplex virus VP16 produces a phenotype similar to that of the in1814 linker insertion mutation (1997)

We examined the phenotype of a herpes simplex virus (HSV) type 1 mutant (V422) in which the C-terminal acidic activation domain of the virion transactivator VP16 is truncated at residue 422. The efficiency of plaque formation by V422 on Vero cells was boosted by approximately 100-fold by including hexamethylene bis-acetimide (HMBA) in the growth medium, as previously observed with the in1814 VP16 linker insertion mutant isolated by Preston and colleagues. V422 displayed severely reduced levels of the immediate-early transcripts encoding ICP0 and ICP4 during infection in the presence of cycloheximide, and this defect was partially overcome by the addition of HMBA. The defect in plaque formation exhibited by V422 and in 1814 was efficiently complemented in U2OS osteosarcoma cells, which had previously been shown to complement ICP0 null mutations. Taken in combination, these data confirm the key role of VP16 in triggering the onset of the HSV lytic cycle.
19F nuclear magnetic resonance imaging of drug distribution in vivo: The disposition of an antifolate anticancer drug in mice (1991)

The application of 19F nuclear magnetic resonance imaging to the study of drug distribution in vivo is discussed. CB3988 (C2-desamino-C2-methyl-N10-propargyl-2'-trifluoromethyl-5,8-dideazafolic acid) is a fluorinated representative of a class of quinazoline antifolates which act as inhibitors of thymidylate synthase and which are being evaluated for the treatment of human cancer. 19F images were obtained in vivo from the abdomen of mice following intravenous injection of CB3988 (500 mg/kg). Time resolutions of 4 and 20 min were achieved for two- and three-dimensional imaging, respectively. These images were consistent with the presence of high concentrations of drug (up to 26 mg/ml) in the gall bladder, urinary bladder, and small intestine, as confirmed ex vivo by extraction and HPLC analysis. The results indicate the potential value of 19F NMR imaging in pharmacokinetic studies.
Deletion of microsomal prostaglandin E synthase-1 augments prostacyclin and retards atherogenesis (2006)

Prostaglandin (PG) E(2) is formed from PGH(2) by a series of PGE synthase (PGES) enzymes. Microsomal PGES-1(-/-) (mPGES-1(-/-)) mice were crossed into low-density lipoprotein receptor knockout (LDLR(-/-)) mice to generate mPGES-1(-/-) LDLR(-/-)s. Urinary 11alpha-hydroxy-9, 15-dioxo-2,3,4,5-tetranor-prostane-1,20-dioic acid (PGE-M) was depressed by mPGES-1 deletion. Vascular mPGES-1 was augmented during atherogenesis in LDLR(-/-)s. Deletion of mPGES-1 reduced plaque burden in fat-fed LDLR(-/-)s but did not alter blood pressure. mPGES-1(-/-) LDLR(-/-) plaques were enriched with fibrillar collagens relative to LDLR(-/-), which also contained small and intermediate-sized collagens. Macrophage foam cells were depleted in mPGES-1(-/-) LDLR(-/-) lesions, whereas the total areas rich in vascular smooth muscle cell (VSMC) and matrix were unaltered. mPGES-1 deletion augmented expression of both prostacyclin (PGI(2)) and thromboxane (Tx) synthases in endothelial cells, and VSMCs expressing PGI synthase were enriched in mPGES-1(-/-) LDLR(-/-) lesions. Stimulation of mPGES-1(-/-) VSMC and macrophages with bacterial LPS increased PGI(2) and thromboxane A(2) to varied extents. Urinary PGE-M was depressed, whereas urinary 2,3-dinor 6-keto PGF(1alpha), but not 2,3-dinor-TxB(2), was increased in mPGES-1(-/-) LDLR(-/-)s. mPGES-1-derived PGE(2) accelerates atherogenesis in LDLR(-/-) mice. Disruption of this enzyme retards atherogenesis, without an attendant impact on blood pressure. This may reflect, in part, rediversion of accumulated PGH(2) to augment formation of PGI(2). Inhibitors of mPGES-1 may be less likely than those selective for cyclooxygenase 2 to result in cardiovascular complications because of a divergent impact on the biosynthesis of PGI(2).
Nonenzymatic Sugar Production from Biomass Using Biomass-Derived γ-Valerolactone (2014)

Widespread production of biomass-derived fuels and chemicals will require cost-effective processes for breaking down cellulose and hemicellulose into their constituent sugars. Here, we report laboratory-scale production of soluble carbohydrates from corn stover, hardwood, and softwood at high yields (70 to 90%) in a solvent mixture of biomass-derived γ-valerolactone (GVL), water, and dilute acid (0.05 weight percent H2SO4). GVL promotes thermocatalytic saccharification through complete solubilization of the biomass, including the lignin fraction. The carbohydrates can be recovered and concentrated (up to 127 grams per liter) by extraction from GVL into an aqueous phase by addition of NaCl or liquid CO2. This strategy is well suited for catalytic upgrading to furans or fermentative upgrading to ethanol at high titers and near theoretical yield. We estimate through preliminary techno-economic modeling that the overall process could be cost-competitive for ethanol production, with biomass pretreatment followed by enzymatic hydrolysis.
Direct Cutaneous Gene Delivery in a Human Genetic Skin Disease (1997)

The skin is an accessible somatic tissue for therapeutic gene transfer and, depending on therapeutic goals, a variety of cutaneous gene delivery approaches are currently available. Recent advances in direct injection of naked DNA into intact skin have shown promise and are less labor-intensive than approaches involving grafting of genetically modified cells. We have regenerated skin from transglutaminase 1 (TGase1)-deficient patients with the genetic skin disease lamellar ichthyosis (LI) on nude mice to examine the corrective impact of direct naked plasmid injection. Regenerated LI patient skin receiving repeated in vivo injections with a TGase1 expression plasmid displayed restoration of TGase1 expression in the correct tissue location in the suprabasal epidermis. Unlike LI skin regenerated from keratinocytes, first transduced in vitro with a retroviral expression vector for TGase1 prior to grafting, however, directly injected LI skin displayed a nonuniform TGase1 gene expression pattern. In further contrast, direct injection failed to correct the central histologic and functional abnormalities of the disease. These data demonstrate that partial restoration of gene expression can be achieved via direct injection of naked DNA in human genetic skin disease tissue but underscore the need for new advances to achieve efficient and sustained plasmid-based gene delivery to the skin.
Optimized expression and specific activity of IL-12 by directed molecular evolution (2003)

DNA delivery of IL-12 has shown promise in reducing the toxic side effects associated with administration of recombinant human (h)IL-12 protein while maintaining the ability to inhibit tumor growth and abolish tumor metastases in animal models. We have developed a more potent version of IL-12 by using DNA shuffling and screening to improve its expression in human cells and specific activity on human T cells. The most improved evolved IL-12 (EvIL-12) derived from seven mammalian genes encoding both the p35 and p40 subunits of IL-12 showed a 128-fold improvement in human T cell proliferation compared with native hIL-12 during the initial screening of supernatants from transected cells. When purified hIL-12 and EvIL-12 proteins were compared in vitro in human T cell proliferation and Th1 differentiation assays, it was demonstrated that EvIL-12 exhibited a concomitant 10-fold increase in the specific activity of the protein compared with hIL-12. Furthermore, DNA shuffling improved the level of expression and homogeneity of the heterodimer synthesized by 293 human embryonic kidney cells transfected with EvIL-12 by at least 10-fold. Molecular analysis of the variant revealed strategic placement of amino acid substitutions that potentially may facilitate heterodimer formation and product expression. The enhanced expression and biological activity of EvIL-12 may improve the effectiveness of IL-12 gene-based vaccines and therapeutics without the toxic side effects sometimes associated with hIL-12 protein administration.
Characterizing structural relationships in scenes using graph kernels (2011)

Modeling virtual environments is a time consuming and expensive task that is becoming increasingly popular for both professional and casual artists. The model density and complexity of the scenes representing these virtual environments is rising rapidly. This trend suggests that data-mining a 3D scene corpus could be a very powerful tool enabling more efficient scene design. In this paper, we show how to represent scenes as graphs that encode models and their semantic relationships. We then define a kernel between these relationship graphs that compares common virtual substructures in two graphs and captures the similarity between their corresponding scenes. We apply this framework to several scene modeling problems, such as finding similar scenes, relevance feedback, and context-based model search. We show that incorporating structural relationships allows our method to provide a more relevant set of results when compared against previous approaches to model context search.
Apolipoprotein E distribution among human plasma lipoproteins: role of the cysteine-arginine interchange at residue 112. (1990)

Human apolipoprotein (apo) E occurs as three common isoforms (apoE4, E3, and E2), all of which influence plasma cholesterol levels. Although both apoE4 and E3 bind with equal effectiveness to the low density lipoprotein receptor, they associate preferentially with different classes of plasma lipoproteins: apoE4 with very low density lipoproteins, apoE3 with high density lipoproteins. The primary structure of apoE3 differs from that of apoE4 at only a single site; apoE3 has its sole cysteine residue at position 112, while apoE4 contains arginine at position 112 and completely lacks cysteine. The present study investigated how this structural difference between apoE4 and E3 determines their distribution among plasma lipoproteins, and analyzed the role of the disulfide-linked heterodimer apoE-A-II (which apoE4 cannot form) in determining the distribution. Human plasma was incubated with 125I-labeled apoE, and lipoproteins were separated by agarose chromatography. Both apoE3 that had been reduced and alkylated with iodoacetamide and apoE3-A-II distributed with high density lipoproteins, indicating that a combination of an inherent property of the monomeric apoE3 structure and apoE-A-II formation account for distribution of apoE3 to the high density lipoproteins. Cysteamine modification of apoE3 resulted in an apoE4-like distribution, demonstrating that a positive charge at position 112 determined the apoE4 distribution and that the effect was not exclusively due to the presence of arginine at this position.(ABSTRACT TRUNCATED AT 250 WORDS)
Ring formation and the structural and electronic properties of tetrahedral amorphous carbon surfaces (1998)

In this paper, we report first-principles structural models of surfaces of tetrahedral amorphous carbon $(ta\ensuremath{-}\mathrm{C})$. The topology and defect structure of the amorphous surfaces are analyzed at the atomistic level. We examine the transition of the local bonding environment from the bulk to the surface. Comparing the surface with the bulk, many more surface atoms are threefold coordinated and planar rings or chains are formed with the ${\mathrm{sp}}^{2}$ bonds. This ``graphization'' character of the $ta\ensuremath{-}\mathrm{C}$ surface also significantly influences its electronic properties. Electrons are easily delocalized within these surface ${\mathrm{sp}}^{2}$ rings/chains and some of the surface electronic eigenstates become extended along the surface through such rings/chains. The implications of surface graphization for the growth and surface conduction are briefly discussed.
Using locally weighted regression for robot learning (2002)

The use of locally weighted regression in memory-based robot learning is explored. A local model is formed to answer each query, using a weighted regression in which close points (similar experiences) are weighted more than distant points (less relevant experiences). This approach implements a philosophy of modeling a complex function with many simple local models. The author explains how an appropriate distance metric or measure of similarity can be found, and how the distance metric is used. How irrelevant input variables and terms in the local model are detected is also explained. An example from the control of a robot arm is used to compare this approach with other robot control and learning techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Current status of endocrine therapy in localized prostate cancer: cure has become a strong possibility (2004)

It is clear that all available means should be taken to diagnose prostate cancer early and to use efficient therapy immediately in order to prevent prostate cancer from migrating to the bones where treatment becomes extremely difficult and cure or even long-term control of the disease is an exception. The only means of preventing prostate cancer from migrating to the bones and becoming incurable is efficient treatment at the localized stage of the disease. In fact, since radical prostatectomy, radiotherapy and brachytherapy can achieve cure in about 50% of cases, these approaches are all equally valid choices as first treatment of localized prostate cancer. However, in view of the current knowledge and available data, nowadays, androgen blockade should also be considered as first line treatment. While showing the high efficacy of hormonal therapy in localized prostate cancer, present knowledge clearly indicate that long-term treatment with the best available hormonal drugs, somewhat similar to the 5 years of Tamoxifen in breast cancer, is required for optimal control of prostate cancer. It is also clear from the data analyzed that combined androgen blockage alone could well be an efficient therapy of localized prostate cancer while it has already been recognized as the best therapy for metastatic disease. This paper presents and discusses the current knowledge available on the use and results of endocrine therapy in localized prostate cancer.
Activation, regulation, and inhibition of DYRK1A (2010)

Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase with diverse functions in neuronal development and adult brain physiology. Higher than normal levels of DYRK1A are associated with the pathology of neurodegenerative diseases and have been implicated in some neurobiological alterations of Down syndrome, such as mental retardation. It is therefore important to understand the molecular mechanisms that control the activity of DYRK1A. Here we review the current knowledge about the initial self-activation of DYRK1A by tyrosine autophosphorylation and propose that this mechanism presents an ancestral feature of the CMGC group of kinases. However, tyrosine phosphorylation does not appear to regulate the enzymatic activity of DYRK1A. Control of DYRK1A may take place on the level of gene expression, interaction with regulatory proteins and regulated nuclear translocation. Finally, we compare the properties of small molecule inhibitors that target DYRK1A and evaluate their potential application and limitations. The β-carboline alkaloid harmine is currently the most selective and potent inhibitor of DYRK1A and has proven very useful in cellular assays.
Confocal differential interference contrast (DIC) microscopy: including a theoretical analysis of conventional and confocal DIC imaging (1992)

SUMMARY A technique for obtaining differential interference contrast (DIC) imaging using a confocal microscope system is examined and its features compared to those of existing confocal differential phase contrast (DPC) techniques as well as to conventional Nomarski DIC. A theoretical treatment of DIC imaging is presented, which takes into account the vignetting effect caused by the finite size of the lens pupils. This facilitates the making of quantitative measurements in DIC and allows the user to identify and select the most appropriate system parameters, such as the bias retardation and lateral shear of the Wollaston prism.
Differential gene expression between normal and tumor-derived ovarian epithelial cells. (2000)

The majority of ovarian tumors arise from the transformation of the ovarian surface epithelial cells, a single layer of cells surrounding the ovary. To identify genes that may contribute to the malignant phenotype of ovarian cancers, cDNA representational difference analysis was used to compare expressed genes in primary cultures of normal human ovarian surface epithelium (HOSE) and ovarian tumor-derived epithelial cells from the Cedars-Sinai Ovarian Cancer (CSOC) repository. A total of 255 differentially expressed genes were identified, of which 160 and 95 were specifically expressed in HOSE and CSOC cells, respectively. Using cDNA array hybridization, the expression profiles of the genes identified by cDNA-representational difference analysis were examined in an additional 5 HOSE and 10 CSOC lines. The comparison of average signal of each gene revealed 44 HOSE-specific and 16 CSOC-specific genes that exhibited at least a 2.5-fold difference in expression. A large number of genes identified in this study encode membrane-associated or secreted proteins and, hence, may be useful as targets in the development of serum-based diagnostic markers for ovarian cancer. Very few genes associated with protein synthesis or metabolism were identified in this study, reflecting the lack of observable differences in phenotypic or growth characteristics between HOSE and CSOC cells. Northern blot analysis on a subset of these genes demonstrated comparable levels of gene expression as observed in the cDNA array hybridization.
Predicting technical communication in product development organizations (1995)

This work explores prediction of technical communication patterns within product development organizations. Our methodology involves first predicting the patterns of communication and then measuring the actual communications to see if the anticipated linkages are realized. We applied this methodology to a commercial product development project in the electronics industry. In this case study we found that: 81% of all coordination type communication linkages were predicted in advance; occurrences of frequent communications were more accurately predicted than infrequent communications; and two-way communication exchange was most often observed, even where oneway information transfer was predicted. For the management of product development projects, these results imply that certain aspects of organizational design can be planned by anticipating the technical communication linkages required for project execution. Finally, a critical analysis of our methodology suggests improvements for future work.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Chirality in ocular agents (2007)

Many important agents exist as a mixture of two different stereoisomers. Both isomers may produce a pharmacological effect; however, these effects may be different from one another and one isomer may even give a result opposite from the desired pharmacological effect. Here we examine published findings on ocular medications relating to their chiral nature and summarize the possible ways chirality affects the activity of a few ocular agents. Many more ocular medications have not been investigated to ascertain their chiral properties. This review adds to the recent emphasis on investigating stereo-isomers for individual selectivity of beneficial and adverse profiles.
Object-oriented programming using SOM and DSOM (1994)

It provides a language-neutral environment for building object-oriented class libraries. It promotes optimum software reuse and features multiple language bindings that enhance bridge-building between object-oriented and procedural languages. Totally CORBA compliant, it represents a viable strategic solution to multiplatform, multivendor computing-providing transparent access to objects distributed across different address spaces on different machines. It is IBM's System Object Model (SOM), a remarkable new paradigm for developing and packaging object-oriented software on AIX/6000, OS/2, and Windows. In this new hands-on guide, programmers, system architects, and managers will discover exactly what SOM is and learn how it can best be used to design and implement object-oriented applications. Written in a clear, lucid style, Objected-Oriented Programming Using SOM and DSOM first delivers a global overview of SOM, clarifying the basic steps involved in creating SOM objects, and profiling the complete SOM system - exploding classes, metaclasses, inheritance, and method-resolution. From here, the guide shows how SOM complements C++ and breaks new ground in such important areas as Distributed Objects, Persistence Objects, and Replication.
Generation of an anti-tumour immune response in a non-immunogenic tumour: HSVtk killing in vivo stimulates a mononuclear cell infiltrate and a Th1-like profile of intratumoural cytokine expression (1997)

Direct delivery of the herpes simplex virus thymidine kinase (HSVtk) gene, in combination with the prodrug ganciclovir (GC), has been used for the treatment of localised, inoperable tumours. Several groups have shown that when rodent tumours are ablated in vivo with suicide genes, anti-tumour immunity can also be generated. Hence, this approach may also be useful in treating disseminated disease. Here we have studied the mechanisms associated with this anti-tumour immunity. In B16 HSVtk+ tumours being killed in vivo with GC treatment, we observed the induction of a pronounced intratumoural infiltrate of macrophages, CD4+ and CD8+ T cells. In addition, using reverse transcriptase polymerase chain reaction, expression of interleukin (IL)-2, IL-12, interferon-gamma (IFN-gamma), tumor necrosis factor-alpha (TNF-alpha) and granulocyte/macrophage colony-stimulating factor (GM-CSF) but not IL-4, IL-6 or IL-10, was observed, a profile of cytokine expression which resembles that of a Th1 immune response. To complement these findings, we also investigated the mechanisms by which expression of HSVtk leads to cell death. Our data show that B16/HSVtk+ cells die predominantly by necrosis, rather than apoptosis, on exposure to GC, a process which may be associated with the generation of anti-tumour inflammatory responses. From these data we propose a model for the induction of anti-tumour immunity using suicide genes and discuss the development of improved vectors for gene therapy to augment these effects in vivo.
Towards automated code parallelization through program comprehension (2002)

Currently available parallelizing tools are biased in favor of a particular parallel execution model for generating the output parallel program. This obviously limits the generality of these tools, since programs may be parallelized according to different programming paradigms. In this paper we propose a novel approach to automated code parallelization that tries to overcome these limitations. This approach consists in recognizing first the paradigm that as best suited to a given program to be parallelized, and then applying paradigm-specific transformation to generate the final parallel code. We argue that the recognition phase can be fully automated using techniques developed in the framework of automated program understanding. With the help of a case study, we discuss how this new approach could be implemented and propose the basic structure of a paradigm-oriented parallelizer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>