gebhart/patrepeval huggingface dataset:
High expression of functional adenovirus DNA polymerase and precursor terminal protein using recombinant vaccinia virus (1988)

Initiation of Adenovirus (Ad) DNA replication occurs by a protein-priming mechanism in which the viral precursor terminal protein (pTP) and DNA polymerase (pol) as well as two nuclear DNA-binding proteins from uninfected HeLa cells are required. Biochemical studies on the pTP and DNA polymerase proteins separately have been hampered due to their low abundance and their presence as a pTP-pol complex in Ad infected cells. We have constructed a genomic sequence containing the large open reading frame from the Ad5 pol gene to which 9 basepairs from a putative exon were ligated. When inserted behind a modified late promoter of vaccinia virus the resulting recombinant virus produced enzymatically active 140 kDa Ad DNA polymerase. The same strategy was applied to express the 80 kDa pTP gene in a functional form. Both proteins were overexpressed at least 30-fold compared to extracts from Adenovirus infected cells and, when combined, were fully active for initiation in an in vitro Adenovirus DNA replication system.
Improvement of Diesel Combustion and Emissions with Addition of Various Oxygenated Agents to Diesel Fuels (1996)

&lt;div class="htmlview paragraph"&gt;The effect of eight kinds of oxygenated agents added to diesel fuels on the combustion and emissions was investigated in a DI diesel engine. The results showed significant smoke and particulate suppression without increases in NOx with every oxygenated agent. The emissions decreased linearly with increasing oxygen content in the fuels, almost regardless of the kind of oxygenated agent. The improvement in smoke and particulate emissions with the oxygenated agent addition was more significant for lower volatility fuels. Combustion analysis with the two-dimensional two color method showed that soot concentration in the flame during the combustion process decreased with the addition of the oxygenated agent while the flame temperature distribution was almost unchanged.&lt;/div&gt;
Knowledge based modelling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures (1987)

An approach is described for modelling the three-dimensional structure of a protein from the tertiary structures of several homologous proteins that have been determined by X-ray analysis. A method is developed for the simultaneous superposition of several protein molecules and for the calculation of an 'average structure' or 'framework'. Investigation of the convergence properties of this method, in the case of both weighted and unweighted least squares, demonstrates that both give a unique answer and the latter is robust for an homologous family of proteins. Multi-dimensional scaling is used to subgroup of the proteins with respect to structural homology. The framework calculated on the basis of the family of homologous proteins, or of an appropriate subgroup, is used to align fragments of the known protein structures of high sequence homology with the unknown. This alignment provides a basis for model building the tertiary structure. Different techniques for using the framework to model the mainchain of various globins and an immunoglobulin domain in the structurally conserved regions are investigated.
Characterization of Transcription Factors That Regulate the Type IV Secretion System and Riboflavin Biosynthesis in Wolbachia of Brugia malayi (2012)

The human filarial parasite Brugia malayi harbors an endosymbiotic bacterium Wolbachia (wBm) that is required for parasite survival. Consequently, targeting wBm is a promising approach for anti-filarial drug development. The Type IV secretion system (T4SS) plays an important role in bacteria-host interactions and is under stringent regulation by transcription factors. In wBm, most T4SS genes are contained in two operons. We show the wBm is active since the essential assembly factor virB8-1, is transcribed in adult worms and larval stages, and VirB8-1 is present in parasite lysates. We also identify two transcription factors (wBmxR1 and wBmxR2) that bind to the promoter region of several genes of the T4SS. Gel shift assays show binding of wBmxR1 to regions upstream of the virB9-2 and wBmxR2 genes, whereas wBmxR2 binds to virB4-2 and wBmxR1 promoter regions. Interestingly, both transcription factors bind to the promoter of the ribA gene that precedes virB8-1, the first gene in operon 1 of the wBm T4SS. RT-PCR reveals ribA and virB8-1 genes are co-transcribed as one operon, indicating the ribA gene and T4SS operon 1 are co-regulated by both wBmxR1 and wBmxR2. RibA encodes a bi-functional enzyme that catalyzes two essential steps in riboflavin (Vitamin B2) biosynthesis. Importantly, the riboflavin pathway is absent in B. malayi. We demonstrate the pathway is functional in wBm, and observe vitamin B2 supplementation partially rescues filarial parasites treated with doxycycline, indicating Wolbachia may supply the essential vitamin to its worm host. This is the first characterization of a transcription factor(s) from wBm and first report of co-regulation of genes of the T4SS and riboflavin biosynthesis pathway. In addition, our results demonstrate a requirement of vitamin B2 for worm health and fertility, and imply a nutritional role of the symbiont for the filarial parasite host.
Hammerhead ribozyme-mediated cleavage of the long terminal repeat RNA of human immunodeficiency virus type 1. (1992)

Three ribozymes targeted against different sites of the long terminal repeat RNA (LTR RNA) of human immunodeficiency virus type 1 cleaved a LTR RNA transcript 1,000 x less efficiently than corresponding short synthetic oligoribonucleotide substrates. Varying the stem lengths of the ribozyme resulted in changes of the catalytic efficiency. Almost no cleavage was observed for a ribozyme forming only 10 base pairs instead of 14 with the LTR RNA. Increasing the base pairs to 16 or elongation of the stem formed within the ribozyme revealed only small changes in kcat/Km. The influence of chemical modifications within the ribozyme on the cleavage of the LTR RNA was also examined. 2'-Fluorocytidine substitutions as well as four terminal phosphorothioate internucleotidic linkages influenced the catalytic efficiency of ribozymes only negligibly. However, substitution of uridine by 2'-fluorouridine resulted in a 5-fold decrease of kcat/Km. A ribozyme containing all these modifications revealed only a 7-fold lower catalytic efficiency but a markedly increased stability in cell culture supernatant. These results demonstrate that it is possible to increase the stability of ribozymes toward nucleases without a serious loss in catalytic efficiency.
Lactoferrin increases the output of neutrophil precursors and attenuates the spontaneous production of TNF-alpha and IL-6 by peripheral blood cells. (1999)

The aim of this report was to investigate the effects of bovine lactoferrin (BLF) taken orally (per os) by healthy individuals, on selected immune parameters. Three groups of volunteers (7 persons per group) were taken daily for 7 days, one capsule containing 2, 10 or 50 mg of BLF. A control group has taken placebo only. Venous blood was taken for tests a few hours before the first dose of BLF, one day and 14 days after the last dose of the preparation. For the evaluation of BLF action on the immune response system we have chosen 3 parameters: content of neutrophil precursors in the peripheral blood (in percentage), spontaneous production of interleukin 6 (IL-6) and tumor necrosis factor alpha (TNF-alpha) by unstimulated blood cell cultures. We found that oral treatment of volunteers with BLF caused a transient (one day after last dose) increase of immature forms of neutrophils in the circulating blood. That increase was more than 2-fold in the case of 10 mg dose. However, statistically significant increases in the percentage of neutrophil precursors were also registered at doses of 2 and 50 mg of BLF. No change in the immature cell content was observed in the placebo group. The treatment with BLF also resulted in a profound decrease of the spontaneous production of IL-6 and TNF-alpha by cultures of peripheral blood cells. This decrease was significant (10 mg/dose) one day following the last dose of BLF and persisted for additional 14 days. These results confirmed our earlier data on the effects of per os treatment with a nutritional preparation containing BLF. Furthermore, we were able to closer establish the optimal dose of BLF affecting selected immune indices.
Rat lymphoid cell lines with human T cell leukemia virus production. I. Biological and serological characterization. (1984)

Cocultivation of spleen cells, lymph node cells, and thymocytes of female Wistar-King-Aptekman rats with short-term cultured male adult T cell leukemia (ATL) cells in the presence of 5-bromo-2'-deoxyuridine (BrdUrd) resulted in the establishment of rat lymphoid cell lines, TARS-1, TARL-2, and TART-1. Cytogenetic analysis of the three cell lines showed a female rat karyotype with 42 chromosomes. The surface phenotypes of TARS-1 and TART-1 were those of rat T cells. TARL-2 was only positive for rat Ia and leukocyte common antigens. The cell lines continuously produced a type C retrovirus, human T cell leukemia virus (HTLV) and expressed ATL-associated antigens. TARS-1 and TART-1, but not TARL-2 were transplantable into newborn syngeneic rats and nude mice. These results strongly indicate that HTLV not only immortalizes, but also transforms rat T cells in vitro. Adult rats immunized with either TARS-1 or TARL-2 produced antibodies specific for HTLV. The biochemical analysis of the antigens that reacted with rat sera revealed that they are the two HTLV-specific polypeptides, p24 and p28.
Atrial-selective pharmacological therapy for atrial fibrillation: hype or hope? (2008)

Efforts to develop atrial-selective antiarrhythmics are bearing fruit, but such compounds will need to exhibit equal or superior safety and efficacy compared with multichannel blockers such as dronedarone for atrial fibrillation suppression in order to prove their worth. It is still too early to tell whether atrial selectiveness is just hype or truly a hope for antiarrhythmic drug treatment of atrial fibrillation.
Analysis of a restored maxillary second premolar tooth by using three‐dimensional finite element method (1999)

In the first part of this study some physical properties of restorative materials, amalgam, glass-ionomer and composite resin were measured experimentally. In the second part a numerical study was carried out, for which the maxillary second premolar tooth was used. The tooth model was restored with composite resin and amalgam on glass-ionomer, which was used as the base material. The stress distribution investigated was the resultant of the stresses which come from the mastication force and those resulting from the contraction and expansion of restorative materials. All calculations were carried out using the finite element method and programs were written using FORTRAN 77. A load of 450 N, at an angle of 45 degrees to the longitudinal axis was applied on the occlusal margin of the tooth. The tooth was assumed isotropic, homogenous, elastic and unsymmetrical. The distribution of compressive, tensile and shear stresses were plotted for the whole tooth structure.
THE PATH OF CARBON IN PHOTOSYNTHESIS. XXXI. THE ROLE OF LECTINS (2014)

Abstract Radish (Raphanus sativus) and Swiss Chard (Beta vulgaris) seedlings, grown hydroponically, exhibited significantly greater increases in height and weight in medium containing α-mannoside supplemented with calcium and manganese salts, than in control treatments lacking one or more of those components. Furthermore, seeds sown on medium containing α-mannoside plus Ca2+and Mn2+showed accelerated germination. Calcium and manganese are necessary to maintain the protein conformation of mannose-binding lectins. In the presence of those cations, glycosides displace specific sugars bound to lectins, making them available to support plant growth. Keywords: plant growthseed germinationlectinglycosidecalciummanganese ACKNOWLEDGMENT We greatly appreciate the clarity of expression contributed by our colleague and past co-author in the series, Professor Emerita Valrie A. Gerard. Elucidation of concepts is brought to the forefront by her profound understanding of the field.
Characteristics of 3,5,3′-Triiodothyronine Sulfate Metabolism in Euthyroid Man* (1991)

The sulfated conjugate of T3 (T3S) has long been recognized as a normal product of peripheral thyroid hormone metabolism. In order to better understand the role that T3S may play in this process, the metabolic handling of T3S was studied in euthyroid man. After the iv administration of [125I]T3S in man, T3S was found to be rapidly metabolized with estimated mean MCR of 135 +/- 15 liters/day (L/D) after a bolus injection and 127 +/- 8 L/D employing a constant infusion. The primary route of T3S disposal was by deiodination with an efficiency of 92%. The administration of propylthiouracil (PTU, 300 mg every 6 h x 5 days) and iopanoic acid (IA, 500 mg every day x 5 days), both inhibitors of deiodination, decreased clearance compared to control (87 +/- 9 L/D, P less than 0.01 and 46 +/- 10 L/D, P less than 0.002, respectively). A 3-day fast also reduced the clearance of T3S (56 +/- 10 L/D, P less than 0.002). All three maneuvers decreased the total urinary deiodination fraction of tracer T3S (control 91 +/- 2%, PTU 70 +/- 9%, P less than 0.04, IA 26 +/- 3%, P less than 0.0001, and fasting 58 +/- 6%, P less than 0.01). A strong correlation between T3S clearance and deiodination was noted for fasting and IA only (r = 0.78, P less than 0.003). However, no relationship between clearance and deiodination was noted with PTU administration presumably as a result of a compensatory increase in biliary losses of T3S. The urinary thyronine excretion pattern demonstrated the presence of small amounts of labeled T3,3,3'-T2, and 3,3'-T2S with the major metabolite being T3S itself. TSH levels were not influenced by the infusion of stable T3S designed to achieve a serum value greater than 50 ng/dL. No absorption of intact T3S was detected after its oral ingestion. In conclusion, T3S is rapidly cleared from the serum, primarily by deiodination, may undergo nondeiodinative disposal when hepatic deiodination is inhibited by PTU but not with IA or fasting, and has no intrinsic biological activity. Thus, T3S may serve as a metabolite of T3 for its rapid deiodinative disposal. Although the precise role T3S plays in human thyroid hormone metabolism has not been defined, the metabolic characteristics of T3S appear similar to that of an unidentified alternate T4 metabolite formed in low T3 states of fasting and nonthyroidal illness.
Solid Phase Peptide Synthesis. II. The Synthesis of Bradykinin (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolid Phase Peptide Synthesis. II. The Synthesis of BradykininR. B. MerrifieldCite this: J. Am. Chem. Soc. 1964, 86, 2, 304–305Publication Date (Print):January 1, 1964Publication History Published online1 May 2002Published inissue 1 January 1964https://pubs.acs.org/doi/10.1021/ja01056a056https://doi.org/10.1021/ja01056a056research-articleACS PublicationsRequest reuse permissionsArticle Views1178Altmetric-Citations216LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cloning and functional characterization of a subunit of the transporter associated with antigen processing (1997)

The transporter associated with antigen processing (TAP) is essential for the transport of antigenic peptides across the membrane of the endoplasmic reticulum. In addition, TAP interacts with major histocompatibility complex class I heavy chain (HC)/beta2-microglobulin (beta2-m) dimers. We have cloned a cDNA encoding a TAP1/2-associated protein (TAP-A) corresponding in size and biochemical properties to tapasin, which was recently suggested to be involved in class I-TAP interaction (Sadasivan, B., Lehner, P. J., Ortmann, B., Spies, T. & Cresswell, P. (1996) Immunity 5, 103-114). The cDNA encodes a 448-residue-long ORF, including a signal peptide. The protein is predicted to be a type I membrane glycoprotein with a cytoplasmic tail containing a double-lysine motif (-KKKAE-COOH) known to maintain membrane proteins in the endoplasmic reticulum. Immunoprecipitation with anti-TAP1 or anti-TAP-A antisera demonstrated a consistent and stoichiometric association of TAP-A with TAP1/2. Class I HC and beta2-m also were coprecipitated with these antisera, indicating the presence of a pentameric complex. In pulse-chase experiments, class I HC/beta2-m rapidly dissociated from TAP1/2-TAP-A. We propose that TAP is a trimeric complex consisting of TAP1, TAP2, and TAP-A that interacts transiently with class I HC/beta2-m. In peptide-binding assays using cross-linkable peptides and intact microsomes, TAP-A bound peptides only in the presence of ATP whereas binding of peptides to TAP1/2 was ATP-independent. This suggests a direct role of TAP-A in peptide loading onto class I HC/beta2-m dimer.
Zymophagy, a Novel Selective Autophagy Pathway Mediated by VMP1-USP9x-p62, Prevents Pancreatic Cell Death* (2010)

Autophagy has recently elicited significant attention as a mechanism that either protects or promotes cell death, although different autophagy pathways, and the cellular context in which they occur, remain to be elucidated. We report a thorough cellular and biochemical characterization of a novel selective autophagy that works as a protective cell response. This new selective autophagy is activated in pancreatic acinar cells during pancreatitis-induced vesicular transport alteration to sequester and degrade potentially deleterious activated zymogen granules. We have coined the term "zymophagy" to refer to this process. The autophagy-related protein VMP1, the ubiquitin-protease USP9x, and the ubiquitin-binding protein p62 mediate zymophagy. Moreover, VMP1 interacts with USP9x, indicating that there is a close cooperation between the autophagy pathway and the ubiquitin recognition machinery required for selective autophagosome formation. Zymophagy is activated by experimental pancreatitis in genetically engineered mice and cultured pancreatic acinar cells and by acute pancreatitis in humans. Furthermore, zymophagy has pathophysiological relevance by controlling pancreatitis-induced intracellular zymogen activation and helping to prevent cell death. Together, these data reveal a novel selective form of autophagy mediated by the VMP1-USP9x-p62 pathway, as a cellular protective response.
Spectroscopic properties of nitrogen doped hydrogenated amorphous carbon films grown by radio frequency plasma-enhanced chemical vapor deposition (2001)

Nitrogen doped hydrogenated amorphous carbon thin films have been deposited by rf plasma-enhanced chemical vapor deposition using CH4 as the source of carbon and with different nitrogen flow rates (N2/CH4 gas ratios between 0 and 3), at 300 K. The dependence modifications of the optical and the structural properties on nitrogen incorporation were investigated using different spectroscopic techniques, such as, Raman spectroscopy, Fourier transform infrared spectroscopy, x-ray photoelectron spectroscopy, ultraviolet-visible (UV-VIS) spectroscopy, electron spin resonance (ESR), photoluminescence (PL) and spectroscopic ellipsometry (SE). Raman spectroscopy and IR absorption reveal an increase in sp2-bonded carbon or a change in sp2 domain size with increasing nitrogen flow rate. It is found that the configuration of nitrogen atoms incorporated into an amorphous carbon network gradually changes from nitrogen atoms surrounded by three (σ bonded) to two (π bonded) neighboring carbons with increasing nitrogen flow rate. Tauc optical gap is reduced from 2.6 to 2.0 eV, and the ESR spin density and the peak-to-peak linewidth increase sharply with increasing nitrogen flow rate. Excellent agreement has been found between the measured SE data and modeled spectra, in which an empirical dielectric function of amorphous materials and a linear void distribution along the thickness have been assumed. The influence of nitrogen on the electronic density of states is explained based on the optical properties measured by UV-VIS and PL including nitrogen lone pair band.
Role of the androgen receptor in triple-negative breast cancer. (2016)

Triple-negative breast cancer (TNBC) is an aggressive disease with outcomes inferior to those of other breast cancer subtypes. No targeted therapies are currently approved for TNBC, and newer treatment approaches are critically needed. It is increasingly recognized that TNBC is a heterogeneous disease, and the role of androgen signaling in a subset of TNBC is emerging. Although the degree of androgen receptor (AR) expression in TNBC varies widely depending on the assay methodology, cutoff for positivity, and patient population, existing evidence suggests an association between a higher level of AR expression and improved outcomes. Despite lower pathologic complete response (pCR) rates with neoadjuvant therapy, patients with AR-dependent TNBCs have a better prognosis than those with TNBCs that are not AR-dependent. Furthermore, gene expression profiling has been used to identify a luminal androgen receptor subtype of TNBC that is dependent on AR signaling. Early clinical studies investigating agents targeting AR in advanced TNBC have produced promising results. We review herein the literature on the biology of AR in breast cancer and its prognostic and predictive role in TNBC, and we describe the results of early clinical trials with antiandrogens in this population. We also present our vision of the future development of newer therapeutic strategies in AR-dependent TNBC.
Determination of the Neutralization Number for Biodiesel Fuel Production (1997)

Abstract The titration methods used for the determination of the Neutralization Number for biodiesel fuel production are discussed. Two new methods determining strong acids and free fatty acids in one measurement separately are described, one method (of main interest) with potentiometric indication and the other with a couple of suitable acid‐base indicators.