gebhart/patrepeval huggingface dataset:
Rabbit skeletal muscle glycogenin. Molecular cloning and production of fully functional protein in Escherichia coli. (1992)

Glycogenin is a self-glucosylating protein involved in the initiation reactions of glycogen synthesis. Initiation occurs in two stages, requiring first the covalent attachment of a glucose residue to Tyr-194 of glycogenin and then elongation to form an oligosaccharide chain. The latter reaction is known to be catalyzed by glycogenin itself. The glycogenin sequence determined from the protein by Campbell and Cohen (Campbell, D. G., and Cohen, P. (1989) Eur. J. Biochem. 185, 119-125) was used to design oligonucleotide probes to screen a rabbit muscle lambda gt11 library. A cDNA was isolated that predicted an amino acid sequence identical to that of Campbell and Cohen, except that Cys residues replaced Ser-88 and Leu-97. Northern analysis indicated a strongly hybridizing message of 1.8 kilobases, present in most tissues including skeletal muscle, but much weaker in kidney and scarcely detectable in liver. A much weaker 3-kilobase message was also detected in muscle. Polymerase chain reaction was used to isolate DNA fragments encoding a portion of glycogenin from rat and cow. The sequence of this segment was > 90% identical at the amino acid level across the three species, indicating that glycogenin is a highly conserved protein. Using the pET-8c vector, the glycogenin protein was expressed in Escherichia coli. Incubation of the recombinant glycogenin with UDP-[14C]glucose and Mn2+ resulted in labeling of the glycogenin protein, indicating that the recombinant glycogenin was enzymatically active and capable of self-glucosylation. Furthermore, after incubation with UDP-glucose, the recombinant glycogenin could serve as a substrate for glycogen synthase, leading to the production of high M(r) polysaccharide. Therefore, production of functional glycogenin did not require the intervention of any other mammalian protein.
<b>DNA sequence of recombinase‐binding sites can determine Xer site‐specific recombination outcome</b> (1997)

Xer site-specific recombination functions in the stable inheritance of circular plasmids and bacterial chromosomes. Two related recombinases, XerC and XerD, mediate this recombination, which 'undoes' the potential damage of homologous recombination. Xer recombination on natural plasmid sites is preferentially intramolecular, converting plasmid multimers to monomers. In contrast, recombination at the Escherichia coli recombination site, dif, occurs both intermolecularly and intramolecularly, at least when dif is inserted into a multicopy plasmid. Here the DNA sequence features of a family of core recombination sites in which the XerC- and XerD-binding sites, which are separated by 6 bp, were analysed in order to ascertain what determines whether recombination will be preferentially intramolecular, or will occur both within and between molecules. Sequence changes in either the XerC- or XerD-binding site can alter the recombination outcome. Preferential intramolecular recombination between a pair of recombination sites requires additional accessory DNA sequences and accessory recombination proteins and is correlated with reduced affinities of recombinase binding to recombination core sites, reduced XerC-mediated cleavage in vitro, and an apparent increased overall bending in recombinase-core-site complexes.
An Analytical Expression for the Time-Varying Contact Length in Perfect Cylindrical Gears: Some Possible Applications in Gear Dynamics (1996)

This paper presents an analytical expression of the time-varying contact length between perfect involute spur and helical gears. It is shown that contact lengths can be expressed as Fourier series whose numerical expansions correlate very well with the results of numerical time-step simulations based on contact length discretization. Finally, some possible examples of application in gear dynamics are suggested.
APPLICATIONS OF SILICON NITRIDE (1961)

The paper summarizes the known physical, mechanical, and chemical properties of silicon nitride. These are compared with the properties of several ceramics and other materials in common use, and it is shown how the combination of certain properties in silicon nitride make it an ideal material for six general types of application. For example, it is shown how the combination of thermal shock-resistance and electrical resistivity can be used to develop high-temperature electrical insulators.
Serum anion gap, bicarbonate and biomarkers of inflammation in healthy individuals in a national survey (2009)

A higher serum anion gap and lower bicarbonate level were associated with higher levels of inflammatory biomarkers in a healthy sample of the general population. Further studies are needed to elucidate the relation between acid-base status and inflammation.
An amphipathic helical motif common to tumourolytic polypeptide NK‐lysin and pulmonary surfactant polypeptide SP‐B (1995)

The tumour-lysing and antimicrobial polypeptide NK-lysin and the pulmonary surfactant-associated polypeptide SP-B exhibit 24% residue identities (49% similarities), including six half-cystine residues in the same disulphide bonding pattern, and similar far-UV circular dichroism spectra corresponding to 45-55% alpha-helix and 20-25% beta-sheet structures. From this, we conclude that the conformations of NK-lysin and SP-B are similar. In contrast, the functional properties of the two proteins are dissimilar: SP-B does not exhibit antibacterial activity and NK-lysin does not significantly effect phospholipid spreading at an air/water interface. Saposins, which solubilize lipids and activate lysosomal hydrolases, the pore-forming amoebapores, and parts of acid sphingomyelinase and acyloxyacylhydrolase, also share 18-27% sequence identities with NK-lysin (and SP-B), including the six conserved half-cystine residues. The inclusion of NK-lysin extends the family of saposin-like polypeptides, all members of which appear to interact with lipids. Strictly conserved structural features with implications for helix topology and lipid interactions are observed.
Sensitivity of GBM cells to cAMP agonist-mediated apoptosis correlates with CD44 expression and agonist resistance with MAPK signaling (2016)

In some cell types, activation of the second messenger cAMP leads to increased expression of proapoptotic Bim and subsequent cell death. We demonstrate that suppression of the cAMP pathway is a common event across many cancers and that pharmacological activation of cAMP in glioblastoma (GBM) cells leads to enhanced BIM expression and apoptosis in specific GBM cell types. We identified the MAPK signaling axis as the determinant of cAMP agonist sensitivity in GBM cells, with high MAPK activity corresponding to cAMP resistance and low activity corresponding to sensitization to cAMP-induced apoptosis. Sensitive cells were efficiently killed by cAMP agonists alone, while targeting both the cAMP and MAPK pathways in resistant GBM cells resulted in efficient apoptosis. We also show that CD44 is differentially expressed in cAMP agonist-sensitive and -resistant cells. We thus propose that CD44 may be a useful biomarker for distinguishing tumors that may be sensitive to cAMP agonists alone or cAMP agonists in combination with other pathway inhibitors. This suggests that using existing chemotherapeutic compounds in combination with existing FDA-approved cAMP agonists may fast track trials toward improved therapies for difficult-to-treat cancers, such as GBM.
Renal transplantation between identical twins: A review (1986)

Abstract The experience of transplantation between identical twins, occurring primarily at the Peter Bent Brigham Hospital, is reviewed. The remarkable success of this human experiment beginning in 1954 and ending, at least for the present in our hospital, in 1976, has confirmed early hopes that clinical renal transplantation may be an extremely effective treatment for end‐stage renal failure. Based largely on this seminal experience, investigations into experimental aspects of transplantation immunology, autoimmunity, and the general host responses, as well as developments in the field of nephrology and overall care of patients with endstage renal disease, have burgeoned. Indeed, during recent years, transplantation of several organs including heart, heart‐lung, liver, and kidney have proven remarkably successful. As knowledge and application in this field continues to expand, increasing numbers of patients with organ failure can expect to return to relatively normal lives .
Buried and graded/buried LDD structures for improved hot-electron reliability (1986)

New buried and graded/buried lightly doped drain (LDD) structures have been demonstrated, for the first time, to improve significantly the hot-electron reliability of NMOS devices. Both LDD structures have peak doping of the n- spacer implant approximately 1000 A below the Si-SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> interface forming a "buried" n- spacer near the drain region. In the graded/buried LDD structure the junction of the "buried" n- spacer is further graded by an additional low-dose phosphorus spacer implant.
Optimization of heterologous protein production in Chinese hamster ovary cells under overexpression of spliced form of human X-box binding protein (2014)

Our data suggest the T-REx system overexpressing human XBP-1(s) can be successfully used in CHO-K1 cells for human immunoglobulin production.
Lipid binding by fragments of apolipoprotein C-III-1 obtained by thrombin cleavage (1977)

We have used thrombin to cleave apolipoprotein C-III-1 into two fragments constituting residues 1-40 (apoLP-C-III-A) and 41-79 (apoLP-C-III-B). The lipid binding properties of these fragments with dimyristoyl- and 1-palmitoyl-2-oleoylphosphatidylcholines have been determined using circular dichroic and intrinsic tryptophan fluorescence spectroscopy. The peptide-phospholipid mixtures were fractionated by density gradients of cesium chloride. ApoLP-C-III-A showed disordered structure in the absence and presence of DMPC and no significant amount of peptide-phospholipid complex was isolated. ApoLP-C-III-B showed conformational changes in the circular dichroic spectrum and a shift in the intrinsic tryptophan fluorescence spectrum. Ultracentrifugation in cesium chloride gradients yielded peptide-phospholipid complexes isolated between density 1.10 and 1.18. The molar ratio of lipid to protein was 12:1. The results of these studies and the examination of space filling models of apoLP-C-III provide evidence that an amphipathic alpha helix which contains a nonpolar face and a polar face is the basic structural unit for binding of phospholipid by the plasma apolipoproteins. These results also provide direct evidence that the hydrophobicity of the nonpolar face is important in lipid binding since the nonpolar face of residues 1-40 is considerably less hydrophobic than the nonpolar face of residues 41-79.
Prostate-specific antigen: any successor in sight? (2013)

Prostate cancer (PCa) is the most frequently diagnosed malignancy and the second leading cause of cancer death in men in the United States and other parts of the world. The lifetime risk of being diagnosed with PCa is approximately 16%. At present, the only widely accepted screening tools for PCa are prostate-specific antigen (PSA) and digital rectal examination. PSA is known to be prostate specific, but not PCa specific, and hence lacks the sensitivity to detect a large number of tumors, especially during the early stages. The PSA level is also known to be affected by many factors, such as medication, inflammation (benign prostatic hyperplasia and prostatitis), and urologic manipulation; hence, the controversy regarding the appropriate level of serum PSA that should trigger a biopsy or have clinical relevance to prostate metastases. Attempts to determine the level of prostate cells in peripheral blood by reverse transcriptase polymerase chain reaction did not significantly improve cancer diagnosis or predict postoperative failure. Therefore, the search continues for a novel biomarker or a panel of markers as well as other possible interventions to improve the use of PSA. This article reviews several possibilities.
Simulation and visualization support for user-defined formalisms using meta-modeling and hierarchical formalism transformation (2002)

A software environment which is dedicated to modeling and simulation of complex technological systems incorporating various domains has to cover a wide range of schematics and graphical formalisms. Usually, these formalisms are based on different computational models and include continuous as well as discrete-event dynamics. Furthermore, in order to improve the design process, an environment of that kind should provide means for adopting additional formalisms tailored to the needs of a specific domain. In the paper a hierarchical formalism refinement concept is presented. It allows us to introduce efficiently user-defined formalisms along with simulation and analysis facilities into a modeling environment by deriving them from already defined formalisms. This concept has been realized using the modeling language Modelica as the basic model representation and the meta-modeling tool DOME for specifying the graphical editors and the formalism transformations. For the purpose of illustration a basic statechart tool is refined twice. First, a new tool is created which support compound transitions. Then, this new formalism is extended again by introducing differential equations.
A comparative analysis of the properties of regulated promoter systems commonly used for recombinant gene expression in Escherichia coli (2013)

The choice of expression system needs to be evaluated for each specific case, but we believe that the standardized vectors developed for this study can be used to more easily identify the nature of case-specific bottlenecks. By then taking into account the relevant characteristics of each expression cassette it will be easier to make the best choice with respect to the goal of achieving high levels of protein expression in functional or non-functional form.
Characterization of nickel Germanide thin films for use as contacts to p-channel Germanium MOSFETs (2005)

We have measured the physical properties and resistivity of nickel germanide thin films formed by the rapid thermal annealing of nickel metal on p-type germanium substrates. Rutherford back scattering and high-resolution electron diffraction confirm that the stoichiometry of the resulting nickel germanide film corresponds to NiGe and has an orthorhombic unit cell with dimensions comparable to that of bulk samples. Transmission electron microscopy shows a poly-crystalline film structure with grain size > 0.1 μm. The resistivity values for films annealed in the range 350/spl deg/C-500/spl deg/C are comparable to those of metal silicides. Measurements of the specific contact resistance suggest that values approaching 2 × 10/sup -7/ /spl Omega/.cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> can be realized using NiGe formed on heavily doped p-type germanium.
Inhibition of visceral pain by electrical stimulation of the periaqueductal gray matter (1976)

Numerous recent studies demonstrated that electrical stimulation of the periaqueductal gray matter (PGM) can result in powerful analgesia to pain of somatic origin. In the present study, we have developed a visceral pain test employing intraperitoneal injection of hypertonic saline which yields a writhing response in the adult rat more reliably than other pain-producing substances. With this test we show that writhing as well as the response to radiant heat (tail flick test) are completely inhibited in all animals with PGM electrode placements.
Clinical Outcome in Stage I to III Breast Carcinoma and eIF4E Overexpression (1998)

Patients with stage I to III breast cancer and high eIF4E overexpression had a higher rate of cancer recurrence and a higher rate of cancer-related death when compared to similar-stage breast cancer patients with low eIF4E overexpression. Therefore, eIF4E protein overexpression may be of prognostic value in stage I to III breast carcinoma.
Split-level I/O scheduling (2015)

We introduce split-level I/O scheduling, a new framework that splits I/O scheduling logic across handlers at three layers of the storage stack: block, system call, and page cache. We demonstrate that traditional block-level I/O schedulers are unable to meet throughput, latency, and isolation goals. By utilizing the split-level framework, we build a variety of novel schedulers to readily achieve these goals: our Actually Fair Queuing scheduler reduces priority-misallocation by 28x; our Split-Deadline scheduler reduces tail latencies by 4x; our Split-Token scheduler reduces sensitivity to interference by 6x. We show that the framework is general and operates correctly with disparate file systems (ext4 and XFS). Finally, we demonstrate that split-level scheduling serves as a useful foundation for databases (SQLite and PostgreSQL), hypervisors (QEMU), and distributed file systems (HDFS), delivering improved isolation and performance in these important application scenarios.
Enhancement of electron emission efficiency and stability of molybdenum-tip field emitter array by diamond like carbon coating (1997)

The effect of diamond like carbon (DLC) films, coated by a layer-by-layer technique using PECVD (plasma enhanced chemical vapor deposition) on the electron emission characteristics of molybdenum (Mo)-tip field emitter array (FEA) is examined. The turn-on voltage was lowered from 80 V for the Mo-tip to 65 V for the DLC-coated Mo-tip FEA while the maximum emission current was increased from 140 μA for the Mo-tip to 320 μA for the DLC-coated Mo-tip FEA composed of 900 emitters. For an anode current of 0.1 (μA/emitter) the gate voltage for the DLC-coated Mo-tip FEA and Mo-tip FEA was about 87 and 107 V, respectively. It was also confirmed that the emission current of a DLC-coated Mo-tip FEA was more stable than that of a Mo-tip FEA.
Liposomes from ionic, single-chain amphiphiles (1978)

In studies of the minimum physiochemical requirements for lipid membrane formation, we have made liposomes from dilute, aqueous dispersions of C(8)-C(18) single-chain amphiphiles. In general, membrane formation from ionic soaps and detergents requires the presence of uncharged amphiphiles. Vesicles were characterized by phase-contrast microscopy, by trapping of ionic dyes, as well as by negativestain and freez-frature electron microscopy. They were typically heterogeneous in size, but the average diameter could be experimentally varied in some cases over the range of 1 to 100 micrometer. Uni-, oligo-, and multilamellar vesicles were observed. Membrane permeability to various solutes was determined in part by a new technique which utilized phase-contract microscopy; when impermeable vesciles exclude added solutes such as sucrose, refractive index differences are created between vesicle contents and surrounding medium, so that the vesicles appear bright in the phase microscope. Permeant solutes do not produce this effect. Spectrophotometric permeability determinations confirmed the results of this technique and provided quantitative measures of permeability. Monoalkyl liposomes have potential uses as models of biomembranes and in drug delivery. They are also relevant to the prebiotic origin of biomembranes.
<i>Glycyrrhiza uralensis</i> Flavonoids Present in Anti‐Asthma Formula, ASHMI<sup>TM</sup>, Inhibit Memory Th2 Responses <i>in Vitro</i> and <i>in Vivo</i> (2012)

Allergic asthma is associated with Th2-mediated inflammation. Several flavonoids were isolated from Glycyrrhiza uralensis, one of the herbs in the anti-asthma herbal medicine intervention. The aim of this investigation was to determine whether Glycyrrhiza uralensis flavonoids have inhibitory effects on memory Th2 responses in vitro and antigen-induced Th2 inflammation in vivo. The effects of three Glycyrrhiza uralensis flavonoids on effector memory Th2 cells, D10.G4.1 (D10 cells), were determined by measuring Th2 cytokine production. Isoliquiritigenin, 7, 4'-dihydroxyflavone (7, 4'-DHF) and liquiritigenin significantly suppressed IL-4 and IL-5 production in a dose-dependent manner, 7, 4'-DHF being most potent. It was also evaluated for effects on D10 cell proliferation, GATA-3 expression and IL-4 mRNA expression, which were suppressed, with no loss of cell viability. Chronic treatment with 7, 4'-DHF in a murine model of allergic asthma not only significantly reduced eosinophilic pulmonary inflammation, serum IgE levels, IL-4 and IL-13 levels, but also increased IFN-γ production in lung cell cultures in response to antigen stimulation.
Round-Optimal Password-Based Authenticated Key Exchange (2010)

We show a general framework for constructing password-based authenticated key-exchange protocols with optimal round complexity — one message per party, sent simultaneously — in the standard model, assuming the existence of a common reference string. When our framework is instantiated using bilinear-map-based cryptosystems, the resulting protocol is also (reasonably) efficient. Somewhat surprisingly, our framework can be adapted to give protocols in the standard model that are universally composable while still using only one (simultaneous) round. 1 Password-Based Authenticated Key Exchange Protocols for authenticated key exchange enable two parties to generate a shared, cryptographically strong key while communicating over an insecure network under the complete control of an adversary. Such protocols are among the most widely used and fundamental cryptographic primitives; indeed, agreement on a shared key is necessary before “higher-level ” tasks such as encryption and message authentication become possible. Parties must share some information in order for authenticated key exchange to be possible. It is well known that shared cryptographic keys — either in the form of public keys or a long,
Expansion of Polyfunctional HIV-Specific T Cells upon Stimulation with mRNA Electroporated Dendritic Cells in the Presence of Immunomodulatory Drugs (2012)

Recently, it has been demonstrated that disease progression during HIV infection is not determined merely by the number of HIV-specific T cells but also by their quality (J. R. Almeida, et al., J. Exp. Med. 204:2473-2485, 2007; C. T. Berger, et al., J. Virol. 85:9334-9345, 2011; M. R. Betts, et al., Blood 107:4781-4789, 2006; V. V. Ganusov, et al., J. Virol. 85:10518-10528, 2011; P. Kiepiela, et al., Nat. Med. 13:46-53, 2007; and F. Pereyra, et al., J. Infect. Dis. 197:563-571, 2008). Therefore, strategies to specifically enhance or induce high-quality, HIV-specific T-cell responses are necessary to develop effective immune therapies. Thalidomide, lenalidomide, and pomalidomide have a strong capacity to boost immune responses and are therefore referred to as immunomodulatory drugs (IMiDs). We evaluated the effects of lenalidomide and pomalidomide on HIV-specific T cells. We found that the presence of IMiDs during in vitro T-cell stimulation with dendritic cells electroporated with Gag- or Nef-encoding mRNA resulted in higher numbers of cytokine-secreting HIV-specific CD8(+) T cells, particularly inducing polyfunctional HIV-specific CD8(+) T cells with an enhanced lytic capacity. Furthermore, CD8(+) T-cell responses were detected upon stimulation with lower antigenic peptide concentrations, and a higher number of Gag epitopes was recognized upon addition of IMiDs. Finally, IMiDs reduced the proliferation of the HIV-specific CD4(+) T cells while increasing the number of polyfunctional CD4(+) T cells. These results provide new information about the effects of IMiDs on antigen-specific T cells and suggest that these drugs increase the efficacy of immune therapies for infectious diseases and cancer.
사이버 교육의 효과:위성강좌에 대한 상명대학교 학생들의 반응 (1998)

This study investigates the effect of satellite lectures via students' responses. Six criteria were asked for the evaluation : the reason for taking the course, the content of the lecture, facilities, the degree of access to the relevant internet site, re