gebhart/patrepeval huggingface dataset:
Regulation of mTOR by Phosphatidic Acid? (2007)

Interest in the regulation of the mammalian target of rapamycin (mTOR) has increased substantially in recent years largely because of an apparent link between mTOR and survival signals in human cancer cells. Much has been learned about the regulation of mTOR in response to survival signals generated by phosphatidylinositol 3-kinase (PI3K). However, another mechanism for regulating mTOR has been proposed involving the generation of phosphatidic acid (PA). PA is the metabolic product of phospholipase D (PLD), whose activity is elevated in a large number of human cancers, and, like PI3K, has been implicated in the survival of human cancer cells. Although the regulation of mTOR by the PI3K signaling pathway is well established, a role for PLD and PA in regulating mTOR has been controversial. In this review, the evidence implicating PLD and PA in the regulation of mTOR is summarized, and the implications of this novel and potentially important mechanism for regulating mTOR are discussed.
An in vivo and in vitro Study of the Loss of Plasticizer from Soft Polymer-gel Materials (1991)

Polymer-gel materials used as short-term denture soft linings are blended with plasticizers to lower the glass transition temperature (Tg). A lower Tg allows for greater polymer chain mobility, thus producing a more flexible material. The present work evaluated the loss of plasticizers due to leaching both in vivo and in vitro. Two commercial denture soft-lining materials (A and B) were tested. These were both poly(ethyl methacrylate) polymers, blended with alcohol and phthalate esters. A clinical study was conducted in which patients wore, sequentially, dentures bearing (on separate occasions) each of the two soft-polymer lining materials. The two materials A and B were randomly assigned for each of ten patients and were worn for 14 and 30 days, respectively. With one exception, patients wore dentures with both lining materials, for a total of 19 clinical evaluations. The plasticizer loss occurring during the clinical trial was determined by GC analysis from the initial and terminal day sampling of plasticizer content of the soft polymer-gel materials. The results of this analysis were compared with results obtained from an in vitro leachability study by use of sink conditions in water at 37 degrees C for the same two commercial soft polymers conducted over the same time periods of 14 and 30 days. The results indicated that a higher loss of plasticizer occurred in vivo, compared with the in vitro tests for 17 of the 19 clinical evaluations. The average plasticizer lost in vivo from material A at 14 days was 122 +/- 58 mg/g, and for material B at 30 days it was 33 +/- 27 mg/g.(ABSTRACT TRUNCATED AT 250 WORDS)
Development of a quadrupole-based Secondary-Ion Mass Spectrometry (SIMS) system at Lewis Research Center (1990)

The design, construction, and initial use of an ion microprobe to carry out secondary ion mass spectrometry (SIMS) of solid samples is reported. The system is composed of a differentially pumped custom-made UHV (Ultra High Vacuum) chamber, a quadrupole mass spectrometer and a telefocus A-DIDA ion gun with the capability of producing beams of Cesium, as well as inert and reactive gases. The computer control and acquisition of the data were designed and implemented using a personal computer with plug-in boards, and external circuitry built as required to suit the system needs. The software is being developed by using a FORTH-like language. Initial tests aimed at characterizing the system, as well as preliminary surface and depth-profiling studies are presently underway.
Characterization of scFv-Ig Constructs Generated from the Anti-CD20 mAb 1F5 Using Linker Peptides of Varying Lengths (1999)

The heavy (VH) and light (VL) chain variable regions of the murine anti-human CD20 mAb 1F5 were cloned, and four single-chain Ab (scFv) molecules were constructed using linker peptides of variable lengths to join the VH and VL domains. Three constructs were engineered using linker peptides of 15, 10, and 5 aa residues consisting of (GGGGS)3, (GGGGS)2, and (GGGGS)1 sequences, respectively, whereas the fourth was prepared by joining the VH and VL domains directly. Each construct was fused to a derivative of human IgG1 (hinge plus CH2 plus CH3) to facilitate purification using staphylococcal protein A. The aggregation and CD20 binding properties of these four 1F5 scFv-Ig derivatives produced were investigated. Both size-exclusion HPLC column analysis and Western blots of proteins subjected to nonreducing SDS-PAGE suggested that all four 1F5 scFv-Ig were monomeric with m.w. of approximately 55 kDa. The CD20 binding properties of the four 1F5 scFv-Ig were studied by ELISA and flow cytometry. The 1F5 scFv-Ig with the 5-aa linker (GS1) demonstrated significantly superior binding to CD20-expressing target cells, compared with the other scFv-Ig constructs. Scatchard analysis of the radiolabeled monovalent GS1 scFv-Ig revealed a binding avidity of 1.35 x 108 M-1 compared with an avidity of 7.56 x 108 M-1 for the native bivalent 1F5 Ab. These findings suggest that the GS1 scFv-Ig with a short linker peptide of approximately 5 aa is the best of the engineered constructs for future studies.
HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis (2012)

The HemaExplorer (http://servers.binf.ku.dk/hemaexplorer) is a curated database of processed mRNA Gene expression profiles (GEPs) that provides an easy display of gene expression in haematopoietic cells. HemaExplorer contains GEPs derived from mouse/human haematopoietic stem and progenitor cells as well as from more differentiated cell types. Moreover, data from distinct subtypes of human acute myeloid leukemia is included in the database allowing researchers to directly compare gene expression of leukemic cells with those of their closest normal counterpart. Normalization and batch correction lead to full integrity of the data in the database. The HemaExplorer has comprehensive visualization interface that can make it useful as a daily tool for biologists and cancer researchers to assess the expression patterns of genes encountered in research or literature. HemaExplorer is relevant for all research within the fields of leukemia, immunology, cell differentiation and the biology of the haematopoietic system.
Abstract: Global LNG — Existing and New Markets (2003)

Abstract The Asia Pacific LNG market has grown at a faster rate than energy demand in general since an exciting but modest start in 1969 with the Alaskan and Brunei projects. Gas demand continues to grow in the region driven by strong economic growth and an increased recognition of the flexibility and environmental benefits of gas consumption. Pipeline gas will play an important role in meeting this demand and will be one element that sets the scene for LNG demand and pricing. The LNG trade is also becoming more global in nature with LNG ships trading between the Atlantic Basin and Asia Pacific and Middle East projects able to play a swing role between the two regions. In this region, new markets and production areas are emerging for the next decade. India, China, Northern Taiwan and the American west coast will join the traditional buyers of Japan, Korea and Taiwan within this decade. These traditional markets are also changing as they face deregulation and lower barriers to entry. Increasingly, they have to develop new ways of doing business, which in turn provide challenges and opportunities for all the participants in the LNG value chain. There has been a lot of discussion in the industry around the direction of LNG prices. Recent deals have had to take into account a wide range of factors including new markets with different value drivers. On the production side, technical change, innovation and larger plant economics will help to meet the cost challenges of a more competitive market. Presented at: 2005 South East Asia Petroleum Exploration Society (SEAPEX) Conference, Singapore, 2003
Extracellular matrix elasticity directs stem cell differentiation. (2008)

Stem cell differentiation is regulated by a variety of cues including growth factors and extracellular matrix (ECM), although the role that the ECM has in this process is less understood. Here we provide examples of how the composition, concentration, and elastic modulus of matrix as well as its temporal and spatial location plays a key role in regulating cell fate. Natural variation of matrix elasticity (Figure 1A), ranging from soft brain tissue to calcified bone, plays an important developmental role for tissues: muscle cells want compliant matrix such that they can deform it during contractions whereas bone cells want a less compliant matrix which they can mineralize. Differentiation of naive mesenchymal stem cells (MSCs) in a microenvironment with a controlled elastic modulus (Figure 1B) mirrors tissue-level elasticity: soft matrices that mimic brain are neurogenic, stiffer matrices that mimic muscle are myogenic, and comparatively rigid matrices that mimic collagenous bone prove osteogenic (Figure 1C). Responses are observed at all levels from RNA to protein production to morphology and cell stiffness. Inhibition of elasticity-directed lineage specification in MSCs and ES cells occurs when non-muscle myosin-II is blocked without strongly perturbing many other aspects of cell function and shape. However, such responses act synergistically with chemical factors where only the combination of both results in differentiation marker expression similar to that of differentiated cell lines. Although growth factors likely have increased influence earlier in development compared to matrix as they signal to cells to produce matrix, ECM maintains the ability to stimulate similar cell responses in embryonic stem (ES). Over the initial week of ES cell differentiation, expression of Nanog, a self-renewal gene, drops 10-fold and is followed by a 3-fold up-regulation in ECM, suggesting an inverse relationship between matrix expression and self-renewal. This is supported by co-localization of matrix and germ layer markers (e.g., GATA4, SOX1, etc.) along with decreased levels of matrix and Nanog. When the elasticity of this matrix was increased by the introduction of cross-linking agents, loss of self-renewal and germ layer commitment is accelerated. Taken together, it appears that stem cells can be significantly influenced by both the chemical and physical aspects of their microenvironment, which should be considered for therapeutic uses of stem cells. Extracellular matrix elasticity directs stem cell differentiation
A VR-based CAD System (2001)

The performance of current Computer-Aided Design (CAD) systems is still far from the satisfaction of conceptual designers. This paper presents a VR-based CAD system for conceptual design by applying VR interfaces and geometric modelling techniques to improve the human computer interaction. The system uses an electronic data glove as an input device so that conceptual designers are allowed to use hand gestures to conduct various geometric shape operations instead of depending solely on keyboard and 2D mouse. We employ the 3D GUIs for enhancing the gesture interface. The implemented shape modelling techniques offered by the system include: destruction, construction, and techniques for freeform feature creation and modification. The destructive techniques allow the user to arbitrarily sculpt an existing part by means of sculpting tools. The constructive techniques allow the user to assemble an object by using a collection of feature objects, by either adding or subtracting feature objects from the model. The system also offers several novel methods for facilitating intuitive modification of freeform curves and surfaces.
Challenges of human-robot communication in telerobotics (2002)

Some general considerations are presented on bilateral human-telerobot control and information communication issues. Advances are reviewed related to the more conventional human-telerobot communication techniques, and some unconventional but promising communication methods are briefly discussed. Future needs and emerging application domains are briefly indicated.
A Survey of Network Isolation Solutions for Multi-Tenant Data Centers (2016)

The infrastructure-as-a-service model is one of the fastest growing opportunities for cloud-based service providers. It provides an environment that reduces operating and capital expenses while increasing agility and reliability of critical information systems. In this multitenancy environment, cloud-based service providers are challenged with providing a secure isolation service combining different vertical segments, such as financial or public services, while nevertheless meeting industry standards and legal compliance requirements within their data centers. In order to achieve this, new solutions are being designed and proposed to provide traffic isolation for a large numbers of tenants and their resulting traffic volumes. This survey highlights key challenges that cloud-based service providers might encounter while providing multitenant environments. It also succinctly describes some key solutions for providing simultaneous tenant and network isolation, as well as highlights their respective advantages and disadvantages. We begin with generic routing encapsulation introduced in 1994 in “RFC 1701,” and will conclude with today's latest solutions. We detail 15 of the newest architectures and then compare their complexities, the overhead they induce, their VM migration abilities, their resilience, their scalability, and their multidata center capacities. This paper is intended for, but not limited to, cloud-based service providers who want to deploy the most appropriate isolation solution for their needs, taking into consideration their existing network infrastructure. This survey provides details and comparisons of various proposals while also highlighting possible guidelines for future research on issues pertaining to the design of new network isolation architectures.
Double LDD concave (DLC) structure for sub-half micron MOSFET (2003)

A novel concave-structure MOSFET named a double lightly doped drain concave (DLC) structure was developed for sub-half-micron MOSFETs which can operate at a 5 V supply voltage. This structure has an impurity profile of n/sup +/-n/sup -/-p/sup -/-p along the side wall of the groove. It has been shown that the DLC MOSFET has excellent characteristics, such as (1) high drain sustaining voltage, (2) a reduced short-channel effect, (3) high current drivability, and (4) high reliability. The high current drivability provides high-speed switching.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phosphorylation of eukaryotic initiation factor 2 during physiological stresses which affect protein synthesis. (1987)

Phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF-2) is a major mechanism regulating protein synthesis in rabbit reticulocytes. To determine whether phosphorylation of eIF-2 alpha is a likely regulatory mechanism in the Ehrlich cell, we have measured the percent of cellular eIF-2 alpha which is phosphorylated in cells exposed to heat shock, 2-deoxyglucose, or amino acid deprivation, conditions which rapidly decrease the concentration of 40 S initiation complexes and inhibit protein synthesis. eIF-2 alpha and eIf-2 alpha (P) were separated by isoelectric focusing and were detected by immunoblotting with a monoclonal antibody we developed for this purpose. Under the above three inhibitory conditions, phosphorylation of eIF-2 alpha increased rapidly, and this increase correlated in time with the rapid inhibition of protein synthesis. In heat-shocked cells which were returned to 37 degrees C, both phosphorylation and protein synthesis remained unchanged for 10 min and then returned toward control values slowly and in parallel. The close temporal correspondence between changes in protein synthesis and phosphorylation supports an important regulatory role for phosphorylation in protein synthesis. An increase of 25-35 percentage points, to 50-60% phosphorylation from control levels of 20-30% phosphorylation, correlated with an 80-100% inhibition of protein synthesis. This steep curve of inhibition is consistent with a mechanism in which eIF-2 alpha (P) saturates and inhibits the guanine-nucleotide exchange factor.
Refolding of Escherichia coli produced membrane protein inclusion bodies immobilised by nickel chelating chromatography (1998)

Two distinctly different membrane proteins, which produced inclusion bodies in Escherichia coli, have been refolded to reconstitute properties appropriate to their native counterparts. The method employed utilises nickel chelating chromatography, where the solubilised inclusion bodies bind, refold and elute. Our aims were to release a large pool of membrane protein for functional, mutational and crystallisation screening studies. It is hoped that the methods described here will have a general application for other membrane proteins which have formed inclusion bodies.
Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis (1993)

Acetyl coenzyme A (CoA) carboxylase catalyzes the synthesis of malonyl-CoA, the first intermediate of fatty acid synthesis. The Escherichia coli enzyme is encoded by four subunits located at three different positions on the E. coli chromosome. The accBC genes lie in a small operon at min 72, whereas accA and accD are located at min 4.3 and 50, respectively. We examined the expression of the genes that encode the E. coli acetyl-CoA carboxylase subunits (accA, accBC, and accD) under a variety of growth conditions by quantitative Northern (RNA) blot analysis. We found a direct correlation between the levels of transcription of the acc genes and the rate of cellular growth. Consistent results were also obtained upon nutritional upshift and downshift experiments and upon dilution of stationary-phase cultures into fresh media. We also determined the 5' end of the accA and accD mRNAs by primer extension and did transcriptional fusion analysis of the previously reported accBC promoter. Several interesting features were found in the promoter regions of these genes, including a bent DNA sequence and an open reading frame within the unusually long leader mRNA of the accBC operon, potential stem-loop structures in the accA and accD mRNA leader regions, and a stretch of GC-rich sequences followed by AT-rich sequences common to all three promoters. In addition, both accA and accD are located in complex gene clusters. For example, the accA promoter was localized within the upstream polC gene (which encodes the DNA polymerase III catalytic subunit), suggesting that additional regulatory mechanisms exist.
De - link R 을 이용한 폐고무 재활용 (1) (2001)

It goes to be serious with environmental pollution cause waste rubber. That is why there are lot of studies for efficient recycle. The purpose of this study is to improve the physical properties of EPDM powder by using De-link system. We changed on the size of waste rubber powder and De-link contents. we examined the physical, rheological, mechanical properties. And also examined cross-link state at various De-link. Also we carried out morphological studies after making the weather strip`s feature by optical microscope.
Altered glycosylation of proteins produced by malignant cells, and application for the diagnosis and immunotherapy of tumours (2005)

Most secretory and membrane-bound proteins produced by mammalian cells contain covalently linked sugar chains. Alterations of the sugar chain structures of glycoproteins have been found to occur in various tumours. Because the sugar chains of glycoproteins are essential for the maintenance of the ordered social behaviour of differentiated cells in multicellular organisms, alterations to the sugar chains are the molecular basis of abnormal social behaviours in tumour cells, such as invasion into the surrounding tissues and metastasis. In this review, the structure and enzymatic basis of typical alterations of the N-linked sugar chains, which are found in various tumours, are introduced. These data are useful for devising diagnostic methods and immunotherapies for the clinical treatment of tumours. Three beta-N-acetylglucosaminyltransferases, GnT-III, -IV and -V, play roles in the structural alteration of the complex-type sugar chains in various tumours. In addition, transcriptional changes in various glycosyltransferases, together with the transporters of sugar nucleotides and sulfate, which are responsible for the formation of the outer chain moieties of complex-type sugar chains, are the keys to inducing the alterations.
DNA Polymerase β:  Multiple Conformational Changes in the Mechanism of Catalysis (1997)

Stopped-flow fluorescence assay was applied to identify conformational changes in the catalytic cycle of DNA polymerase beta (Pol beta), using a synthetic DNA primer/template containing 2-aminopurine (2-AP) at the template position opposite the incoming dNTP. Two phases of fluorescence change were observed in the stopped-flow fluorescence assay of the incorporation of the correct nucleotide dTTP. The rate of the slow phase corresponds to that of product formation. This slow phase was identified as the result of a rate-limiting conformational change step before chemistry because this slow phase was also observed with a dideoxynucleotide at the 3' end of the primer which prevents chemical bond formation. The fast phase was also attributed to a conformational change step since its dependence on [dTTP] is hyperbolic. The rates of the two phases and their dependence on [dTTP] and [Mg2+] suggest that the fast conformational change is induced by the binding of MgdNTP and the slow conformational change is induced by the binding of the catalytic Mg2+ ion. The same biphasic kinetics with different rates were also observed with the thio analog dTTPalphaS and incorrect nucleotides dATP, dGTP, and dCTP. The structural nature for the two conformational changes has been discussed in relation to the available structural information of this enzyme. The results could help to explain how a polymerase controls and achieves its fidelity with a multiple conformational change mechanism.
Biochemical characterization and biosynthesis of the Ki-1 antigen in Hodgkin-derived and virus-transformed human B and T lymphoid cell lines. (1987)

The Hodgkin-associated Ki-1 antigen was analyzed in different cell lines. In Hodgkin analogous L428 cells, biosynthetically labeled with radioactive amino acids, the Ki-1 antibody precipitated three glycoproteins with 90, 105, and 120 kDa, respectively. Surface-labeling revealed that the two larger components were membrane-associated forms of the Ki-1 antigen, although the 90-kDa molecule was shown in pulse-chase experiments to be the precursor of the 105- and 120-kDa forms. All three forms of the Ki-1 antigen possess a tunicamycin-sensitive 6-kDa N-linked carbohydrate moiety. O-Linked oligosaccharides could not be detected. Thus, the differences in m.w. are probably not due to glycosylation. The ionophore monensin prevented the appearance of the membrane-associated molecules, which demonstrated that they are assembled between the transcompartment of the Golgi complex and their insertion into the cell membrane. The 90-kDa precursor molecule cannot be generated by disulfide reduction from the two larger forms. After internal labeling with P-32, only the 105- and 120-kDa bands became visible, indicating that the Ki-1 molecule is phosphorylated after its processing into the two larger membrane-associated forms. Analysis of the Ki-1 antigens from other cell lines demonstrated that after external labeling of two other Hodgkin-derived cell lines, six Epstein-Barr virus lymphoblastoid cell lines and one human T leukemia virus I-positive T cell line, both the 105- and the 120-kDa membrane molecules could be detected, regardless of the presence or type of virus integrated.