gebhart/patrepeval huggingface dataset:
Multi‐Color FISH Techniques (2004)

Traditional FISH analysis has employed, at most, two colors of detection, a red-fluorescing fluorochrome and a green-fluorescing fluorochrome. The improvements in fluorescent imaging and development of heartier fluorochromes/dyes have enabled investigators to use several different DNA probes in one experiment. This may involve all or combinations of locus-specific probes and chromosome paints. The value of such experiments lies in the investigator obtaining far more information from one specific cell at one time, rather then carrying out separate experiments on multiple specimens prepared from the same sample, then extrapolating results. The generic term for multi-color FISH assays is M-FISH, however, the technologies behind the manner in which the fluorochrome information is generated has spawned two different M-FISH systems: spectral karyotyping (SKY) and M-FISH. For both assays, the experimental procedures are identical: commercially available probes for all 24 (human) chromosomes are differentially labeled according to a labeling scheme and hybridized to metaphase spreads for 24 to 48 hr, followed by post-hybridization washes and, if required, antibody detection. The difference lies in the imaging: spectral karyotyping identifies the differentiation of the chromosomes based on their spectral properties, whereas M-FISH identifies the differentiation of the chromosomes based on that fluorochrome's presence or absence when visualized with specific filters. The resulting analysis for both methods is the same, revealing hidden translocations and insertions as well as the chromosomal components of marker chromosomes.
Electrocatalytic hydrogen oxidation by an enzyme at high carbon monoxide or oxygen levels (2005)

Use of hydrogen in fuel cells requires catalysts that are tolerant to oxygen and are able to function in the presence of poisons such as carbon monoxide. Hydrogen-cycling catalysts are widespread in the bacterial world in the form of hydrogenases, enzymes with unusual active sites composed of iron, or nickel and iron, that are buried within the protein. We have established that the membrane-bound hydrogenase from the beta-proteobacterium Ralstonia eutropha H16, when adsorbed at a graphite electrode, exhibits rapid electrocatalytic oxidation of hydrogen that is completely unaffected by carbon monoxide [at 0.9 bar (1 bar = 100 kPa), a 9-fold excess] and is inhibited only partially by oxygen. The practical significance of this discovery is illustrated with a simple fuel cell device, thus demonstrating the feasibility of future hydrogen-cycle technologies based on biological or biologically inspired electrocatalysts having high selectivity for hydrogen.
Purification and characterization of mitogen-activated protein kinase activator(s) from epidermal growth factor-stimulated A431 cells. (1992)

Two peaks of mitogen-activated protein (MAP) kinase activator activity are resolved upon ion exchange chromatography of cytosolic extracts from epidermal growth factor-stimulated A431 cells. Two forms of the activator (1 and 2) have been purified from these peaks, using chromatography on Q-Sepharose, heparin-agarose, hydroxylapatite, ATP-agarose, Sephacryl S-300, Mono S, and Mono Q. The two preparations each contained one major protein band with an apparent molecular mass of 46 or 45 kDa, respectively, on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Evidence identifying the MAP kinase activators as the 46- and 45-kDa proteins is presented. Using inactive mutants of MAP kinase as potential substrates, it was found that each preparation of MAP kinase activator catalyzes phosphorylation of the regulatory residues, threonine 188 and tyrosine 190, of Xenopus MAP kinase. These results support the concept that the MAP kinase activators are protein kinases. These MAP kinase kinases demonstrate an apparent high degree of specificity toward the native conformation of MAP kinase, although slow autophosphorylation on serine, threonine, and tyrosine residues and phosphorylation of myelin basic protein on serine and threonine residues is detected as well.
Time-Dependent Airway Epithelial and Inflammatory Cell Responses Induced by Influenza Virus A/PR/8/34 in C57BL/6 Mice (2007)

The present study examines the kinetics of airway epithelial remodeling and inflammation in the airways of C57BL/6J mice infected with influenza virus A/PR/8/34 (PR8). Mice were intranasally instilled with 50 plaque forming units (pfu) of virus or its respective vehicle, saline, and then were sacrificed at 3, 7, 10, 15, or 21 days postinfection (dpi). PR8 treatment resulted in airway epithelial cell regeneration as suggested by proliferating cell nuclear antigen (PCNA) positive staining at 7 and 10 dpi and mucous cell metaplasia (MCM) evident at 10, 15, and 21 dpi. PR8 treatment resulted in a classic pattern of inflammation observed in bronchoalveolar lavage fluid (BALF), in which neutrophils peaked at 3 and 7 dpi and monocytes, lymphocytes, and eosinophils peaked at 10 dpi before returning to background levels of detection. Chemokine (MCP-1) and cytokine (IL-6, TNF-alpha, IFN-gamma, IL-5, IL-4, and IL-9) levels peaked at 7 dpi in BALF. IL-13 levels were unaffected by PR8 treatment. Concurrent with inflammation, MUC5AC gene expression was markedly increased by PR8 treatment at 7 dpi. Collectively, the results of this study indicate that the onset of MCM in airway epithelium occurs during the remodeling process and persists after the inflammatory response has diminished.
Functional Analysis of Elements Affecting Expression of the β-Actin Gene of Carpt (1990)

Regulatory regions of the beta-actin gene of the common carp (Cyprinus carpio) have been examined by linking upstream, 5'-flanking sequences and regions of the first intron to a bacterial chloramphenicol acetyltransferase (CAT) reporter gene. By analysis of the mRNA products and encoded CAT activity, we have identified four putative regions that influence expression: (i) a negative regulatory region 2,300 to 1,100 base pairs (bp) ahead of the gene; (ii) a proximal promoter element, containing the highly conserved CCAAT, CC(A/T)6GG, and TATA boxes, that is within the first 204 bp upstream of the initiation site; (iii) a negative element of 426 bp in the 5' region of the first intron; and (iv) a positive 304-bp element near the end of the first intron that contains highly conserved sequences found in all characterized beta-actin genes. The positive intron element is not a classical enhancer; it is position and orientation dependent, as has been observed in other housekeeping genes in vertebrates. Depending on the elements joined together, CAT gene expression can be modulated more than 500-fold in transfected mouse cells.
Preparation of Optically Active Polyhedral Borane Derivatives (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of Optically Active Polyhedral Borane DerivativesW. R. HertlerCite this: J. Am. Chem. Soc. 1964, 86, 14, 2949–2950Publication Date (Print):July 1, 1964Publication History Published online1 May 2002Published inissue 1 July 1964https://pubs.acs.org/doi/10.1021/ja01068a047https://doi.org/10.1021/ja01068a047research-articleACS PublicationsRequest reuse permissionsArticle Views54Altmetric-Citations8LEARN 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
A multigene family encodes the human cytomegalovirus glycoprotein complex gcII (gp47-52 complex) (1988)

The HXLF (HindIII-X left reading frame) gene family is a group of five genes that share one or two regions of homology and are arranged in tandem within the short unique component of the human cytomegalovirus genome (K. Weston and B.G. Barrell, J. Mol. Biol. 192:177-208, 1986). These genes were cloned into an SP6 expression vector in both the sense and antisense orientations. An abundant 1.62-kilobase (kb) bicistronic mRNA, predicted to originate from HXLF1 and HXLF2, was detected in the cytoplasm of infected human fibroblast cells by Northern (RNA) blot analysis. Less abundant RNAs of 1.0 and 0.8 kb, predicted to originate from the HXLF5 and HXLF2 genes, respectively, were also detected. Monocistronic, bicistronic, and polycistronic RNAs synthesized in vitro by using SP6 polymerase were translated in rabbit reticulocyte lysates with or without canine pancreatic microsomal membranes. The HXLF1 or the HXLF1 and HXLF2 translation products were detected when the above mRNAs were used. The HXLF3, HXLF4, and HXLF5 gene products were not detected by in vitro translation of the SP6-derived polycistronic mRNA. Nonglycosylated or glycosylated HXLF1 and HXLF2 gene products were immunoprecipitated by monoclonal antibody 9E10, which is specific for a virion envelope glycoprotein complex designated gcII (gp47-52 complex). In addition, the monoclonal antibody 9E10 immunoprecipitated a diffuse glycoprotein band, designated gp47-52, from HCMV-infected cell lysates. The amino acid composition of gp47-52 purified from viron envelopes has the highest similarity to the predicted amino acid composition of the HXLF1 plus HXLF2 open reading frames, but it is more similar to HXLF2 than to HXLF1. The Northern blot results imply that gp47-52 is synthesized predominantly from the abundant 1.62-kb bicistronic mRNA encoded by the HXLF1 and HXLF2 genes. However, the glycoprotein could also be synthesized by the monocistronic 0.8-kb mRNA encoded by the HXLF2 gene as well as by the mRNAs predicted from the other HXLF genes.
A Phase II pilot trial of 13-cis retinoic acid and interferon-? in patients with advanced pancreatic carcinoma (1998)

Combination therapy with 13-cis RA and IFN-alpha is feasible and well tolerated in patients with advanced pancreatic carcinoma. Based on the median survival rates observed in this study this combination should be investigated further in Phase III trials.
Targeted Drug Delivery to Lymphocytes: A Route to Site-Specific Immunomodulation? (2010)

Lymphocytes are central to the progression of autoimmune disease, transplant rejection, leukemia, lymphoma and lymphocyte-resident viral diseases such as HIV/AIDs. Strategies to target drug treatments to lymphocytes, therefore, represent an opportunity to enhance therapeutic outcomes in disease states where many current treatment regimes are incompletely effective and promote significant toxicities. Here we demonstrate that highly lipophilic drug candidates that preferentially access the intestinal lymphatics after oral administration show significantly enhanced access to lymphocytes leading to improved immunomodulatory activity. When coadministered with such drugs, lipids enhance lymphocyte targeting via a three tiered action: promotion of drug absorption from the gastrointestinal tract, enhancement of lymphatic drug transport and stimulation of lymphocyte recruitment into the lymphatics. This strategy has been exemplified using a highly lipophilic immunosuppressant (JWH015) where coadministration with selected lipids led to significant increases in lymphatic transport, lymphocyte targeting and IL-4 and IL-10 expression in CD4+ and CD8+ lymphocytes after ex vivo mitogen stimulation. In contrast, administration of a 2.5-fold higher dose of JWH015 in a formulation that did not stimulate lymph transport had no effect on antiinflammatory cytokine levels, in spite of equivalent drug exposure in the blood. The current data suggest that complementary drug design and delivery strategies that combine highly lipophilic, lymphotropic drug candidates with lymph-directing formulations provide enhanced selectivity, potency and therapeutic potential for drug candidates with lymphocyte associated targets.
Taz1, an Outer Mitochondrial Membrane Protein, Affects Stability and Assembly of Inner Membrane Protein Complexes: Implications for Barth Syndrome (2005)

The Saccharomyces cerevisiae Taz1 protein is the orthologue of human Tafazzin, a protein that when inactive causes Barth Syndrome (BTHS), a severe inherited X-linked disease. Taz1 is a mitochondrial acyltransferase involved in the remodeling of cardiolipin. We show that Taz1 is an outer mitochondrial membrane protein exposed to the intermembrane space (IMS). Transport of Taz1 into mitochondria depends on the receptor Tom5 of the translocase of the outer membrane (TOM complex) and the small Tim proteins of the IMS, but is independent of the sorting and assembly complex (SAM). TAZ1 deletion in yeast leads to growth defects on nonfermentable carbon sources, indicative of a defect in respiration. Because cardiolipin has been proposed to stabilize supercomplexes of the respiratory chain complexes III and IV, we assess supercomplexes in taz1delta mitochondria and show that these are destabilized in taz1Delta mitochondria. This leads to a selective release of a complex IV monomer from the III2IV2 supercomplex. In addition, assembly analyses of newly imported subunits into complex IV show that incorporation of the complex IV monomer into supercomplexes is affected in taz1Delta mitochondria. We conclude that inactivation of Taz1 affects both assembly and stability of respiratory chain complexes in the inner membrane of mitochondria.
[Leflunomide inhibits PAF induced DNA synthesis in rabbit synovial cells and PAF production from rat peritoneal macrophages]. (1994)

Leflunomide (LFM, HWA 486) is an isoxazol derivative with antiphogistic and novel immunomodulating properties. It has been shown to be very effective in preventing and curing arthritis. In this report we found that platelet-activating factor (PAF) at 0.1-10 micrograms.ml-1 significantly stimulated DNA synthesis in cultured rabbit synovial cells. While LFM and its metabolite A771726 elicited inhibitory effects on this action of PAF. These two agents were also shown to markedly inhibit A23187 induced PAF production from rat peritoneal macrophages. The inhibition was dose and time-dependent. The inhibitory effects of LFM and A771726 on DNA synthesis in synovial cells and PAF production from macrophages may play an important role in the antiinflammatory effects of LFM.
Two step Deposited Rugged Surface (TDRS) Storagenode and Self Aligned Bitline-Contact-Penetrating Cellplate (SABPEC) for 64MbDRAM STC Cell (1991)

In this paper, the 1.5mum2 STC is reported with Two step Deposited Rugged Surface Poly-Si (TDRS) enabling fin shape storagenode and also with a Self-Aligned Bitline-contact by PEnetrating Cellplate (SABPEC) to increase projective storagenode area, reducing pattern tolerance.
A structural view of CD4 and CD8 (1995)

CD4 and CD8 are cell-surface glycoproteins that participate in molecular complexes involved in both T cell development and antigen recognition by T cells. CD4 and CD8 interact with nonpolymorphic regions of class II and class I major histocompatibility complex (MHC) molecules, respectively, and these interactions result in increased intercellular adhesion and enhanced stimulation of T cells. A src-like tyrosine kinase, p56lck, is associated with the cytoplasmic domain of both CD4 and CD8 and may be involved in transmembrane signaling. Crystal structures of extracellular regions of CD4 and CD8 have been determined and have provided a basis for understanding and probing CD4 and CD8 function. The structures of CD4 and CD8 are reviewed here, along with the implications of these structures for CD4 and CD8 function.
Interleaved T1 and T2 relaxation time mapping for cardiac applications (2009)

The interleaved sequence acquires data for the calculation of T(1) and T(2) maps in only one scan without the need for registration. This technique has the potential to differentiate between acute and chronic MI by estimating the concentration of gadolinium diethylenetriamine pentaacetic acid (Gd-DTPA) in the necrotic tissue and to assess the extent of edema from T(2) maps.
When oral agents fail: optimizing insulin therapy in the older adult. (2009)

Basal insulin therapy, basal-bolus insulin therapy, and premixed insulin therapy are useful options for older patients inadequately controlled on one or more oral agents. Older patients who require additional postprandial control may benefit from GLP-1 analogs or DPP-4 inhibitors. Additional research is needed to determine optimal therapy in older adults treated with oral agents who require more intensive therapy.
Strongyloides stercoralis: a model for translational research on parasitic nematode biology (2007)

Because of their free-living life cycle alternatives, Strongyloides and related nematode parasites may represent the best models for translating C. elegans science to the study of nematode parasitism. S. stercoralis, a significant pathogen of humans, can be maintained in laboratory dogs and gerbils. Biosafety precautions necessary for work with S. stercoralis, though unfamiliar to many C. elegans researchers, are straightforward and easily accomplished. Although specialized methods are necessary for large-scale culture of the free-living stages of S. stercoralis, small-scale cultures for experimental purposes may be undertaken using minor modifications of standard C. elegans methods. Similarly, the morphological similarities between C. elegans and the free-living stages of S. stercoralis allow investigational methods such as laser cell ablation and DNA transformation by gonadal microinjection to be easily adapted from C. elegans to S. stercoralis. Comparative studies employing these methods have yielded new insights into the neuronal control of the infective process in parasites and its similarity to regulation of dauer development in C. elegans. Furthermore, we have developed a practical method for transient transformation of S. stercoralis with vector constructs having various tissue- and cell-specific expression patterns and have assembled these into a modular vector kit for distribution to the community.
Coffee Consumption Is Associated With Higher Plasma Adiponectin Concentrations in Women With or Without Type 2 Diabetes (2008)

To test whether the beneficial effects of coffee consumption in metabolism might be explained by changes in circulating levels of adiponectin, we evaluated self-reported habitual coffee and tea consumption and caffeine intake as predictors of plasma adiponectin concentrations among 982 diabetic and 1,058 nondiabetic women without cardiovascular disease from the Nurses' Health Study. Women with and without diabetes who drank >or=4 cups of coffee per day had significantly higher adiponectin concentrations than those who didn't drink coffee regularly (7.7 vs. 6.1 microg/ml, respectively, in diabetic women, P = 0.004; 15.0 vs. 13.2 microg/ml in nondiabetic women, P = 0.04). Similar associations were observed for caffeine intake. We confirm previously reported inverse associations of coffee consumption with inflammatory markers, C-reactive protein, and tumor necrosis factor-alpha receptor II. Adjustment for adiponectin did not weaken these associations, and adjustment for inflammatory markers did not attenuate the association between coffee consumption and adiponectin concentrations. High consumption of caffeine-containing coffee is associated with higher adiponectin and lower inflammatory marker concentrations.
Transgenic rainbow trout expressed sGnRH-antisense RNA under the control of sGnRH promoter of Atlantic salmon (2000)

A recombinant vector containing antisense DNA complementary to Atlantic salmon (Salmo salar) sGnRH cDNA driven by specific promoter Pab derived from a corresponding sGnRH gene was introduced into rainbow trout (Oncorhynchus mykiss) eggs. This resulted in transgenic animals that had integrated one copy of the transgene into their genome and transmitted it through the germline. Antisense-sGnRH mRNA (AS) was expressed mainly in the brain of transgenic AS(+) fish. Levels of sGnRH endogenous mRNA in the brain were lower in 11-month-old AS(+) fish compared with nontransgenic AS(-) individuals from the same F2 progeny. sGnRH levels significantly decreased in the pituitary of transgenic males and females around the maturation period and in the brain of AS(+) immature females compared with controls. No reliable statistical difference was found in the levels of FSH and LH between AS(+) and AS(-) groups either in immature or mature fish. The majority of transgenic fish reached maturity at the same time as did nontransgenic individuals, although the maturation of AS(+) animals seemed to be more asynchronous. For the first time, the influence of antisense messengers on endogenous mRNA in transgenic fish and the corresponding protein is described.
Functional Analysis of the TAN-1 Gene, a Human Homolog of Drosophila Notch (1994)

The TAN-1 gene was originally discovered at the breakpoint of a recurrent (7;9)(q34;q34.3) chromosomal translocation found in a subset of human T-lymphoblastic leukemias (Reynolds et al. 1987; Smith et al. 1988; Ellisen et al. 1991). This translocation joins roughly the 3′ half of TAN-1 head-to-head with the 3′ portion of the β T-cell-receptor gene (TCRB) beginning at the 5′ boundary of one or the other J segment. Intact TAN-1 is normally transcribed into an 8.2-kb transcript that is present in many tissues, most abundantly in developing thymus and spleen (Ellisen et al. 1991). This tissue distribution and the apparent involvement of an altered version of the gene in T-cell cancers have suggested that TAN-1 normally has some special function in lymphocytes or their precursors.
The Size of the Human Proteome: The Width and Depth (2016)

This work discusses bioinformatics and experimental approaches to explore the human proteome, a constellation of proteins expressed in different tissues and organs. As the human proteome is not a static entity, it seems necessary to estimate the number of different protein species (proteoforms) and measure the number of copies of the same protein in a specific tissue. Here, meta-analysis of neXtProt knowledge base is proposed for theoretical prediction of the number of different proteoforms that arise from alternative splicing (AS), single amino acid polymorphisms (SAPs), and posttranslational modifications (PTMs). Three possible cases are considered:<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mo stretchy="false">(</mml:mo><mml:mn fontstyle="italic">1</mml:mn><mml:mo stretchy="false">)</mml:mo></mml:math>PTMs and SAPs appear exclusively in the canonical sequences of proteins, but not in splice variants;<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mo stretchy="false">(</mml:mo><mml:mn fontstyle="italic">2</mml:mn><mml:mo stretchy="false">)</mml:mo></mml:math>PTMs and SAPs can occur in both proteins encoded by canonical sequences and in splice variants;<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M3"><mml:mo stretchy="false">(</mml:mo><mml:mn fontstyle="italic">3</mml:mn><mml:mo stretchy="false">)</mml:mo></mml:math>all modification types (AS, SAP, and PTM) occur as independent events. Experimental validation of proteoforms is limited by the analytical sensitivity of proteomic technology. A bell-shaped distribution histogram was generated for proteins encoded by a single chromosome, with the estimation of copy numbers in plasma, liver, and HepG2 cell line. The proposed metabioinformatics approaches can be used for estimation of the number of different proteoforms for any group of protein-coding genes.