gebhart/patrepeval huggingface dataset:
Differential expression of constitutive and inducible proteasome subunits in human monocyte‐derived DC differentiated in the presence of IFN‐α or IL‐4 (2008)

Several studies strongly suggest that DC differentiated in vitro in the presence of type I IFN acquire more potent immune stimulatory properties, compared with DC differentiated in vitro with IL-4. However, little is known about the molecular mechanisms underlying this phenomenon. To address this question, we compared the Ag-processing machinery (APM) profile in human DC grown in the presence of IFN-alpha ((IFN)DC) or IL-4 ((IL-4)DC). Using a panel of APM component-specific mAb in Western blot experiments, we found that (IFN)DC preferentially express inducible proteasome subunits (LMP2, LMP7, and MECL1) both at immature and mature stages. In contrast, immature (IL-4)DC co-express both constitutive (beta1, beta2, and beta5) and inducible subunits, as shown by Western blotting analysis. In addition, immature (IFN)DC express higher levels of TAP1, TAP2, calnexin, calreticulin, tapasin, and HLA class I molecules than (IL-4)DC. The different proteasome profiles of (IFN)DC and (IL-4)DC were associated with a greater ability of (IFN)DC to present an immunodominant epitope that requires LMP7 expression for its processing. In general, these data show the impact of cytokines on APM component expression and hence the Ag-processing ability of DC.
The large external domain is sufficient for the correct sorting of secreted or chimeric influenza virus hemagglutinins in polarized monkey kidney cells. (1987)

MA104.11 rhesus kidney cells express several characteristics of polarized epithelial cells, including the formation of "domes" on impermeable substrates, the establishment of a transmonolayer electrical resistance when grown on collagen gels, the polarized maturation of influenza and vesicular stomatitis viruses, and the expression of the glycoproteins of those viruses at a single surface domain. The polarized expression of the influenza virus hemagglutinin (HA) is maintained in MA104.11 cells infected with SV40-derived vectors carrying a cDNA gene for either the wild-type influenza virus HA, a truncated HA gene encoding a secreted form of HA (HAsec), or a chimeric gene encoding a hybrid protein with the external domain of the HA and the transmembrane and cytoplasmic domains of the vesicular stomatitis virus G protein (HAG). Thus, the recognition event separating glycoproteins, such as HA, destined for the apical surface from proteins, such as G, destined for the basolateral membranes involves features of the external domains of the proteins. The transmembrane and cytoplasmic domains of HA have no role in this process.
Economics modeling of multichip modules testing strategies (1998)

To produce high-quality and cost-effective multichip systems, they must be designed with test and fault diagnosis as critical design requirements. However, deciding on where and when to test, and whether to apply design for test (DFT) and built-in self test (BIST) at the IC, multichip module (MCM) or board level requires considerable study and evaluation to determine the economics of the various solutions and the payback. In this paper we explore the tradeoffs between various test and rework strategies for multichip module designs. Some of these strategies incorporate various DFT options at both the MCM and IC levels. We will analyze the impact of various cost, yield, and test effectiveness parameters on the final cost and quality of multichip modules. Experimental tradeoff analysis data generated for some leading-edge multichip designs will also be presented. The results clearly indicate that incorporating DFT and BIST with varying degrees at the chip or MCM levels is economically justifiable and results in cost reduction as well as quality improvement. The results also indicates that the MCM cost could vary by about 10–20% depending on the test strategy used. However, proper determination of where and how to test, and whether to employ DFT and BIST at the IC or MCM levels, requires an evaluation of the economics of the various solutions and the payback. That process is highly dependent on the design under consideration and the parameters associated with the available manufacturing environment(s). Hence, one has to be careful about generalizing the lessons learned from specific cases, since it could lead to non optimal solutions. A careful economic modeling of the various design, test and manufacturing parameters is clearly necessary for producing cost-effective high-quality products.
A ligand for the aryl hydrocarbon receptor isolated from lung (2002)

The aryl hydrocarbon receptor (AHR) is a ligand-inducible transcription factor that is best known because it mediates the actions of polycyclic and halogenated aromatic hydrocarbon environmental toxicants such as 3-methylcholanthrene and 2,3,7,8-tetrachlorodibenzo-p-dioxin. We report here the successful identification of an endogenous ligand for this receptor; approximately 20 microg was isolated in pure form from 35 kg of porcine lung. Its structure was deduced as 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester from extensive physical measurements and quantum mechanical calculations. In a reporter gene assay, this ligand activates the AHR with a potency five times greater than that of beta-naphthoflavone, a prototypical synthetic AHR ligand. 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester competes with 2,3,7,8-[(3)H]tetrachlorodibenzo-p-dioxin for binding to human, murine, and fish AHRs, thus showing that AHR activation is caused by direct receptor binding, and that recognition of this endogenous ligand is conserved from early vertebrates (fish) to humans.
Mastermind mediates chromatin-specific transcription and turnover of the Notch enhancer complex (2002)

Signaling through the Notch pathway activates the proteolytic release of the Notch intracellular domain (ICD), a dedicated transcriptional coactivator of CSL enhancer-binding proteins. Here we show that chromatin-dependent transactivation by the recombinant Notch ICD-CBF1 enhancer complex in vitro requires an additional coactivator, Mastermind (MAM). MAM provides two activation domains necessary for Notch signaling in mammalian cells and in Xenopus embryos. We show that the central MAM activation domain (TAD1) recruits CBP/p300 to promote nucleosome acetylation at Notch enhancers and activate transcription in vitro. We also find that MAM expression induces phosphorylation and relocalization of endogenous CBP/p300 proteins to nuclear foci in vivo. Moreover, we show that coexpression with MAM and CBF1 strongly enhances phosphorylation and proteolytic turnover of the Notch ICD in vivo. Enhanced phosphorylation of the ICD and p300 requires a glutamine-rich region of MAM (TAD2) that is essential for Notch transcription in vivo. Thus MAM may function as a timer to couple transcription activation with disassembly of the Notch enhancer complex on chromatin.
Evaluation of Specific Absorption Rate as a Dosimetric Quantity for Electromagnetic Fields Bioeffects (2013)

SAR actually refers to thermal effects, while the vast majority of the recorded biological effects from man-made non-ionizing environmental radiation are non-thermal. Even if SAR could be accurately estimated for a whole tissue, organ, or body, the biological/health effect is determined by tiny amounts of energy/power absorbed by specific biomolecules, which cannot be calculated. Moreover, it depends upon field parameters not taken into account in SAR calculation. Thus, SAR should not be used as the primary dosimetric quantity, but used only as a complementary measure, always reporting the estimating method and the corresponding error. Radiation/field intensity along with additional physical parameters (such as frequency, modulation etc) which can be directly and in any case more accurately measured on the surface of biological tissues, should constitute the primary measure for EMF exposures, in spite of similar uncertainty to predict the biological effect due to non-linearity.
THE ROLE OF EXTRACELLULAR DNA IN THE TRANSFER OF INFORMATION FROM T TO B HUMAN LYMPHOCYTES IN THE COURSE OF AN IMMUNE RESPONSE (1980)

Human lymphocytes obtained from donors exhibiting different allotypes were separated into B- and T-enriched subpopulations and cultured in the presence or absence of Herpes simplex virus inactivated by U.V. Isolated B or T cell suspensions did not produce any antiherpetic activity. The B lymphocytes cultured in the presence of the supernatant collected from virus-exposed T cells or in the presence of DNA extracted from this supernatant, synthesized an antiherpetic antibody carrying allotypic markers of the T cell donor.
Adherent cell function in murine T-lymphocyte antigen recognition. IV. Enhancement of murine T-cell antigen recognition by human leukocytic pyrogen. (1979)

A macrophage-dependent, antigen-specific murine T-cell proliferation assay was utilized to examine the role of soluble products of murine and human adherent cells in the activation of T lymphocytes. Highly purified human leukocytic pyrogen, and supernates from both murine and human mononuclear phagocytes-macrophages stimulated the immune T-cell proliferative response to the multideterminant antigens dinitrophenyl-ovalbumin and keyhole limpet hemocyanin. The implications of these studies and the relationship of leukocytic pyrogen to human lymphocyte-activating factor are discussed.
Uroplakin IIIb, a urothelial differentiation marker, dimerizes with uroplakin Ib as an early step of urothelial plaque assembly (2002)

Urothelial plaques consist of four major uroplakins (Ia, Ib, II, and III) that form two-dimensional crystals covering the apical surface of urothelium, and provide unique opportunities for studying membrane protein assembly. Here, we describe a novel 35-kD urothelial plaque-associated glycoprotein that is closely related to uroplakin III: they have a similar overall type 1 transmembrane topology; their amino acid sequences are 34% identical; they share an extracellular juxtamembrane stretch of 19 amino acids; their exit from the ER requires their forming a heterodimer with uroplakin Ib, but not with any other uroplakins; and UPIII-knockout leads to p35 up-regulation, possibly as a compensatory mechanism. Interestingly, p35 contains a stretch of 80 amino acid residues homologous to a hypothetical human DNA mismatch repair enzyme-related protein. Human p35 gene is mapped to chromosome 7q11.23 near the telomeric duplicated region of Williams-Beuren syndrome, a developmental disorder affecting multiple organs including the urinary tract. These results indicate that p35 (uroplakin IIIb) is a urothelial differentiation product structurally and functionally related to uroplakin III, and that p35-UPIb interaction in the ER is an important early step in urothelial plaque assembly.
Covalent Capture of Self-Assembled Rosette Nanotubes (2012)

Rosette nanotubes (RNTs) are self-assembled tubular architectures which have extensive chemical and physical tuning capabilities, owing to their ease of surface functionalization and flexible inner channel design. To marry these tunable features of the RNTs with the enhanced stability of a covalent polymer, here we demonstrate the covalent capture of the RNT supramolecular structure by polymerizing alkyldiamine functional groups expressed on their outer periphery in the presence of adipoyl chloride (nylon-6,6 process). The resulting polymeric materials were characterized using proton nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, dynamic light scattering, and differential scanning calorimetry. Transmission and scanning electron microscopy revealed the formation of fibers and films composed of RNTs.
Molecular cloning and characterization of avian sarcoma virus circular DNA molecules (1980)

Supercoiled DNA molecules were used for the molecular cloning of full-length avian sarcoma virus (ASV) DNA. Viral DNA produced by the Schmidt-Ruppin A (SR-A) strain of ASV was isolated from acutely infected transformed quail cells. Supercoiled DNA was separated from linear and open circular DNA by acid phenol extraction, opened into a full-length linear form by cleavage with the restriction endonuclease SacI, and cloned into lambda gtWES x lambda B. Four different cloned viral DNA molecules were isolated: SRA-1 contains two copies of the 330-base pair terminal redundancy normally found at each end of the linear DNA molecules, but harbors a 63-base pair deletion that spans the site at which the two copies of the terminal redundancy are joined in circular DNA molecules; SRA-2 contains two complete copies of the terminal redundancy; SRA-3 probably contains only one copy of the terminal redundancy but in all other respects appears to be similar to SRA-2; SRA-4 contains a 2,500-base pair deletion that removes all of the src gene (the gene responsible for transformation by ASVs) plus additional nucleotides adjacent to the src gene whose precise locations have not been determined. Transfection of chicken embryo fibroblasts by either SRA-1 or SRA-2 resulted both in the appearance of transformed cells and in the production of infectious virus. These results demonstrate that the cloned DNA molecules are functionally identical to viral DNA produced in vivo; therefore, molecular cloning did not cause any major alterations of the DNA. The infectivity of SRA-1 DNA indicates that the 63 base pairs missing from that molecule are not required for the initiation of viral RNA synthesis, even though the deletion is located in a copy of the terminal redundancy thought to carry a promoter for RNA synthesis. This suggests that the deletion does not remove any sequences required for the initiation of transcription.
Genetic vaccination with Flt3-L and GM-CSF as adjuvants: Enhancement of cellular and humoral immune responses that results in protective immunity in a murine model of hepatitis C virus infection (2006)

Our data support the view that plasmid DNA vaccination is a promising approach for HCV immunization, and may provide a general adjuvant vaccination strategy against malignancies and other pathogens.
Thin electroless barrier for copper films (1998)

Electroless barrier deposition for copper metallization potentially provides many advantages, among which are the selectivity to dielectrics, possibility of an amorphous alloy deposition, binary alloy properties enhancement by an addition of a third component, high conformity and low cost. Electroless cobalt-rich CoWP ternary alloys with high phosphorus content (approximately 11 weight percent) and a low weight percent of the third component, tungsten (approximately 2 percent), were deposited in basic solution onto copper and cobalt in integrated circuit structures. A capability of the electroless CoWP deposition to form thin selective and conformal barrier/protection films was demonstrated. Extendibility of these thin films to extremely small, nano- scale dimensions was observed. Conformal 10 nm thick CoWP layer was formed on the sidewalls of 30 - 40 nm wide seam of aspect ratio about 5:1 on the top of 0.4 micrometer wide in- laid Cu line. Thermal stability of electroless CoWP/Cu films investigated by Rutherford Backscattering Spectroscopy (RBS), Auger Electron Spectroscopy (AES) and Secondary Ion Mass Spectroscopy (SIMS) was extended to 500 degrees Celsius for 15 nm thick barrier. Atomic Force Microscopy (AFM) images of the electroless CoWP film surface and sectional analysis showed small grain sizes of CoWP on either electroless or Physical Vapor Deposited (PVD) Cu films. Several passivation schemes to protect the exposed Cu surface and adhesion promotion/barrier layers to stabilize the Cu/dielectric interface in a damascene process were demonstrated.
Syntheses of (Diacetoxyiodo)arenes or Iodylarenes from Iodoarenes, with Sodium Periodate as the Oxidant (2001)

- Easy, safe, and effective novel methods for preparing either (diacetoxyiodo)-arenes, ArI(OAc)2, or iodylarenes, ArIO2, from the corresponding iodoarenes, ArI, using sodium periodate as the oxidant are presented in this paper. In order to obtain 2- and 4-iodylbenzoic acids, the respective sodium salts of 2- and 4-iodobenzoic acids should be used as the starting substrates, because mixtures containing the corresponding iodosyl derivatives as the main products along with the intended iodyl compounds are produced from the free parent acids.
Molecular Cloning and Characterization of NKT, a Gene Product Related to the Organic Cation Transporter Family That Is Almost Exclusively Expressed in the Kidney (1997)

We have identified a gene product (NKT) encoding an apparently novel transcript that appears to be related to the organic ion transporter family and is expressed almost exclusively in the kidney. Analysis of the deduced 546-amino acid protein sequence indicates that NKT is a unique gene product which shares a similar transmembrane domain hydropathy profile as well as transporter-specific amino acid motifs with a variety of bacterial and mammalian nutrient transporters. Nevertheless, the overall homology of NKT to two recently cloned organic ion transport proteins (NLT and OCT-1) is significantly greater; together these three gene products may represent a new subgroup of transporters. The NKT was characterized further with respect to its tissue distribution and its expression during kidney development. A 2.5-kilobase transcript was found in kidney and at much lower levels in brain, but not in a number of other tissues. Studies on the embryonic kidney indicate that the NKT transcript is developmentally regulated with significant expression beginning at mouse gestational day 18 and rising just before birth, consistent with a role in differentiated kidney function. Moreover, in situ hybridization detected specific signals in mouse renal proximal tubules. NKT was mapped by linkage disequilibrium to mouse chromosome 19, the same site to which several mouse mutations localize, including that for osteochondrodystrophy (ocd). Although initial experiments in a Xenopus oocyte expression system failed to demonstrate transport of known substrates for OCT-1, the homology to OCT-1 and other transporters, along with the proximal tubule localization, raise the possibility that this gene may play a role in organic solute transport or drug elimination by the kidney.
Purification and characterization of the α‐agarase from Alteromonas agarlyticus (Cataldi) comb. nov., strain GJ1B (1993)

The phenotypic features of strain GJ1B, an unidentified marine bacterium that degrades agar [Young, K. S. Bhattacharjee, S. S. & Yaphe, W. (1978) Carbohydr. Res. 66, 207-212], were investigated and its agarolytic system was characterized using 13C-NMR spectroscopy to analyse the agarose degradation products. The bacterium was assigned to the genus Alteromonas and the new combination A. agarlyticus (Cataldi) is proposed. An alpha-agarase, i.e. specific for the alpha(1-->3) linkages present in agarose, was purified to homogeneity from the culture supernatant by affinity chromatography on cross-linked agarose (Sepharose CL-6B) and by anion-exchange chromatography (Mono Q column). The major end product of agarose hydrolysis using the purified enzyme was agarotetraose. Using SDS/PAGE, the purified alpha-agarase was detected as a single band with a molecular mass of 180 kDa. After the affinity-chromatography step, however, the native molecular mass was approximately 360 kDa, suggesting that the native enzyme is a dimer which is dissociated to active subunits by anion-exchange chromatography. The isolectric point was estimated to be 5.3. Enzyme activity was observed using agar as the substrate over the pH range 6.0-9.0 with a maximum value at pH 7.2 in Mops or Tris buffer. The enzyme was inactivated by prolonged treatment at a pH below 6.5, or by temperatures over 45 degrees C or by removing calcium. In addition, a beta-galactosidase specific for the end products of the alpha-agarase was present in the alpha-agarase affinity-chromatography fraction, probably as part of a complex with this enzyme. The degradation of agarose by this agarase complex yielded a mixture of oligosaccharides in the agarotetraose series and the agarotriose series, the latter consisting of oligosaccharides with an odd number of galactose residues.
Metabolic Engineering of Escherichia coli for Short Chain Length-Medium Chain Length Polyhydroxyalkanoate Biosynthesis (2006)

Polyhydroxyalkanoates (PHA)s are microbially produced polyesters that are biodegradable and have a wide variety of uses. PHAs can be divided into three groups dependent on the size of the monomers incorporated into the polymer. Shortchain-length (SCL) PHAs are composed of C3-C5 monomers and are thermoplastic in nature, while medium-chain-length (MCL) PHAs are composed of C6-C14 monomers and are elastomeric in nature. SCL-MCL PHAs are composed of monomers C3-C14 in length and where the properties of the polymer vary based on the mol% composition of SCL and MCL monomers. This study compares various monomersupplying pathways in recombinant Escherichia coli used for PHA production from non-related carbon sources to supply SCL and MCL PHA monomers. In addition, data describing the composition and thermal properties of polymers produced in recombinant E. coli using engineered PHA synthases and fatty acid biosynthesis enzymes are presented.
Cardiovascular Medicine at the Turn of the Millennium: Triumphs, Concerns, and Opportunities (1997)

Tthe end of every century it is customary to reflect on the events of the past hundred years and to look toward the future, and in this lecture I should like to do this for cardiovascular disease. This is also an especially opportune time to comment on progress in cardiovascular disease, because both the National Heart, Lung, and Blood Institute and the American Heart Association are celebrating their golden anniversaries within the next 18 months. These two organizations have had the most profound influence on the development of research on cardiovascular disease during the 20th century. A bewildering amount of . . .
Cloning and Characterization of an Uncoupling Protein Homolog: A Potential Molecular Mediator of Human Thermogenesis (1997)

We have identified a novel cDNA encoding a protein highly homologous to the mammalian brown fat uncoupling protein (UCP). Unlike the known UCP, which is expressed specifically in brown adipose tissue, the UCP homolog (UCPH) mRNA is expressed in a variety of tissues, with predominant expression in human white adipose tissue and skeletal muscle. In the white adipose tissue of ob/ob and db/db mice, the UCPH transcript is induced approximately fivefold relative to lean littermate controls. Expression of murine UCPH in yeast results in growth inhibition under conditions that require aerobic respiration, but does not affect growth under anaerobic conditions. Furthermore, UCPH expression in yeast causes a decrease in the mitochondrial membrane potential, as judged by staining with the potential-sensitive dye DiOC6. These observations suggest that UCPH, like UCP, uncouples oxidative phosphorylation. The possibility that the UCPH protein is an important mediator of human thermogenesis is discussed.