gebhart/patrepeval huggingface dataset:
Recombinant junctions formed by site-specific integration of adeno-associated virus into an episome (1995)

A model system using an episomal Epstein-Barr virus shuttle vector was recently developed to study the adeno-associated virus (AAV) site-specific integration event in chromosome 19q13.3-qter (C. Giraud, E. Winocour, and K.I. Berns, Proc. Natl. Acad. Sci. USA 91:10039-10043, 1994). In this study, we analyze the recombinant junctions generated after integration of the AAV genome into an Epstein-Barr virus shuttle vector carrying 8.2, 1.6, or 0.51 kb of the chromosome 19 preintegration sequence (AAVS1 locus). In most of the recombinants, one end of the viral genome was joined to a portion of the AAVS1 DNA previously shown to be a minimum target for AAV integration. Within this AAVS1 segment, the AAV insertion points were strikingly clustered around a binding site for the AAV regulatory protein. In all cases, the second junction with AAV occurred with vector DNA outside of the AAVS1 segment. With respect to the viral genome, one junction with the shuttle vector DNA occurred either within the AAV inverted terminal repeat (itr), or near the P5 promoter, approximately 100 nucleotides distal to a modified itr. The modified itr in 5 of 11 recombinants involved a head-to-tail organization. In one such instance, the AAV insert contained slightly more than one genome equivalent arranged in a head-to-tail manner with a junction close to the P5 promoter; the AAV insert in this recombinant episome could be rescued by adenovirus infection and replicated to virus particles. The significance of the head-to-tail organization is discussed in terms of the possible circularization of AAV DNA before or during integration.
Design of Protective and Therapeutic DNA Vaccines for the Treatment of Allergic Diseases (2005)

The DNA vaccine revolution has opened a vast scope of novel approaches for protective and therapeutic treatments of type I allergy. This review gives an overview on the current status of allergy DNA vaccines and presents advances in the design of vaccine constructs. An immense number of concurring studies have proven the stimulation of Th1 cells and the induction of a balanced Th1/Th2 cytokine milieu as the fundamental mechanisms underlying the anti-allergic effects of DNA vaccines. Basic vaccine formulations thus can be optimized by improving the cellular immunogenicity via co-administration of cytokines, co-expression or co-application of immunostimulatory DNA sequences or adapting the codon usage. The latter is a frequent and major reason for impaired vaccine expression (e.g. translation of plant allergen genes in mammal cells). Because of unwanted side effects during conventional specific immunotherapy with allergen extracts, safety is increasingly demanded for both, protein and DNA vaccines for allergy treatment. We discuss the creation of hypoallergenic DNA vaccines based on deliberate allergen gene fragmentation, the use of mutations and the routine production of hypoallergenic DNA vaccines by forced ubiquitination. Furthermore, allergen-expressing DNA replicon vaccines are introduced, which enable a drastic reduction of the vaccine dose without loss of anti-allergic efficacy. Finally, the development of DNA multi vaccines and fusion vaccines for protective and therapeutic applications against certain groups of allergens is addressed.
A Study of Translation Edit Rate with Targeted Human Annotation (2006)

We examine a new, intuitive measure for evaluating machine-translation output that avoids the knowledge intensiveness of more meaning-based approaches, and the labor-intensiveness of human judgments. Translation Edit Rate (TER) measures the amount of editing that a human would have to perform to change a system output so it exactly matches a reference translation. We show that the single-reference variant of TER correlates as well with human judgments of MT quality as the four-reference variant of BLEU. We also define a human-targeted TER (or HTER) and show that it yields higher correlations with human judgments than BLEU—even when BLEU is given human-targeted references. Our results indicate that HTER correlates with human judgments better than HMETEOR and that the four-reference variants of TER and HTER correlate with human judgments as well as—or better than—a second human judgment does. 1
The Impact of EGFR T790M Mutations and BIM mRNA Expression on Outcome in Patients with EGFR -Mutant NSCLC Treated with Erlotinib or Chemotherapy in the Randomized Phase III EURTAC Trial (2014)

Low-level pretreatment T790M mutations can frequently be detected and can be used for customizing treatment with T790M-specific inhibitors. BCL2L11 mRNA expression is a biomarker of survival in EGFR-mutant NSCLC and can potentially be used for synthetic lethality therapies.
Acquired homozygosity (isodisomy) of chromosome 3 during clonal evolution of a uveal melanoma: Association with morphologic heterogeneity (1996)

Cytogenetic investigation of untreated uveal melanoma has shown that the most frequent abnormality is monosomy 3, which occurs in approximately 60% of cases. One of our cases showed distinct pigmented and nonpigmented areas at gross dissection; representative tissue was collected separately from each area, cultured, and harvested using standard cytogenetic techniques. On histologic examination, the pigmented area was found to be composed of small epithelioid cells, whereas the nonpigmented area contained large, pleomorphic epithelioid cells. The karyotype of the pigmented tumor revealed monosomy 3, whereas the nonpigmented tumor showed two apparently normal chromosomes 3. Our purpose in the present study was to investigate the two tumor areas by molecular techniques to determine whether the karyotype of the nonpigmented tumor evolved directly from the pigmented tumor with duplication of the remaining chromosome 3 or whether the two sublines evolved in a divergent fashion from a common precursor stemline. DNA was extracted from normal lymphocytes and separately from both areas of the tumor. The DNA was analyzed using the polymerase chain reaction for polymorphic dinucleotide and tetranucleotide repeat sequences on chromosome 3. Both pigmented and nonpigmented areas of the tumor showed loss of heterozygosity at all informative loci on chromosome 3 that were tested. These results support our hypothesis that an abnormality on chromosome 3 plays a central role in the molecular pathogenesis of uveal melanoma and that some melanomas develop acquired homozygosity (isodisomy) by loss and duplication of the remaining, presumably abnormal, chromosome 3.
Influence of Cannabinoids on Somatic Cells <i>in vivo</i> (1980)

Chromosomal and nuclear aberrations in bone marrow cells were studied in hybrid mice of genotype (C57BL x C3H)F1 following treatment with specific cannabinoids. In the subacute series, mice were treated for 5 consecutive days with delta 9-tetrahydrocannabinol (THC), cannabinol or cannabidiol at a dose of 10 mg/kg, the percentage of micronuclei in cannabinoid-treated mice was 3- to 5-fold greater than in the dimethyl sulfoxide controls. In the acute series, polychromatic erythrocytes were scored after a single exposure. In one acute series there was an approximately twofold increase in the incidence of micronuclei in the cannabinoid-treated mice; in the other acute series of cannabinoid-treated animals the micronuclei values were as high as 6 times the control values. Interaction between dose and frequency of exposure was assessed for THC; the number of micronuclei was affected by THC dosage, but not by frequency of exposure. Further confirmation of nuclear aberrations was obtained from assessment of bone marrow mitosis. In this limited study of mitotic cells the incidence of metaphase aberrations in cannabinoid-treated animals was 5-7 times greater than in controls.
The Phosphinoboration Reaction (2014)

The synthesis of phosphinoboronate esters containing a single P-B bond is reported, together with preliminary reactivity studies towards a range of organic substrates. These compounds add readily to aldehydes, ketones, aldimines, and α,β-unsaturated enones to give primarily the corresponding 1,2-addition products containing a new P-C bond. The first examples of transition-metal-catalyzed phosphinoborations of C-C multiple bonds in which P-C and B-C bonds are formed in a single step are also disclosed; allenes react by a highly regioselective 1,2-addition whereas terminal alkynes undergo a formal 1,1-addition.
Evidence for interactions of acyl carrier protein with glycerol‐3‐phosphate acyltransferase, an inner membrane protein of Escherichia coli (1989)

We [(1989) FEBS Lett., in press] have previously shown that membrane vesicles from Escherichia coli contain protein-binding sites for the acyl carrier protein (ACP). We report now that membrane vesicles prepared from a strain amplified for glycerol-3-phosphate acyltransferase (GPAT) contain a higher number of ACP-binding sites than the membrane vesicles prepared from a wild type strain. In addition, we show that GPAT is retained specifically on an ACP-Sepharose affinity column and that [3H]ACP binds to the enzyme solubilized by detergent. We conclude that GPAT, an inner membrane protein which catalyses the transesterification of a fatty acyl group from acyl coenzyme A or acyl ACP to glycerol-3-phosphate, possesses a binding site for ACP.
New photodefinable glass etch masks for entirely dry photolithography: Plasma deposited organosilicon hydride polymers (1993)

The low energy plasma induced dehydrogenative polymerization of various monosubstituted silanes (RSiH3) is shown to provide photosensitive films characterized as organosilicon hydride network materials with extensive Si—Si bonding. Plasma deposited films may be photo-oxidatively patterned with mid-deep ultraviolet light producing glasslike Si–O–Si crosslinked materials in exposed areas. Patterns can be developed by chlorine reactive ion etching with up to 5:1 selectivity, and transferred into underlying organic layers with ≳50:1 selectivity and sub-half-micron resolution. This provides a versatile, completely dry photolithographic process useful with current exposure and etching tools and is well-suited for integration into cluster tool technologies.
MR‐based hippocampal volumetry in the diagnosis of Alzheimer's disease (1992)

We evaluated a new magnetic resonance (MR)-based technique for performing volumetric measurements of temporal lobe structures. The technique was designed to assist in making the clinical diagnosis of dementia of the Alzheimer type (DAT). We chose specific anatomic regions of interest because of their known involvement in memory function and in the neuropathology of DAT and used a regression model to assess the effects of age on the volumes of the anterior temporal lobe (ATL) and the hippocampal formation (HF). These measurements were normalized by total intracranial volume (TIV). The volumetric measurements of both the normalized ATL and HF were significantly smaller (p less than 0.001) in DAT patients (N = 20) than in controls (N = 22), but the HF volumes provided much better separation between the two groups. Eighty-five percent of the DAT patients fell below the range of the HF/TIV measurement for the control subjects. This separation held up over the entire age range studied. Normalized volumes of both the HF and ATL decreased with age significantly for both the DAT patients and the controls. These results support the contention that MR-based HF volumetric measurements are accurate in differentiating DAT patients from cognitively normal elderly individuals. This technique may be a useful adjunct in making the clinical diagnosis of DAT.
NASA's revitalized role in satellite communications (1980)

The early efforts of NASA in space communications development strengthened the general level of confi. dence in the use of satellite technology for telecommunications. Soon afterward, the formation of organizations such as INTELSAT and the Comsat Corporation and their subsequent progress brought reliable communications via satellite at affordable rates. These capabilities have grown worldwide through new industries that are fostering the principles of the 1958 Space Act to exploit the peaceful benefits of space for the betterment of mankind. As a result of this recognized success arid the pressures of budget cutting, NASA's role in this pioneering effort was slowed in 1973. The flight projects then under development, the Applications Technology Satellite Six (ATS-6) and the Communications Technology Satellite (CTS) were allowed to continue but the research projects were reduced to a small ground-based effort directed toward long-term high-risk components and techniques. Now, as we enter the 1980's, the situation is reversed. The principal NASA spacecrafts are retired, but the program for research and development and flight experiments is revived.
Glutamine repeats as polar zippers: their possible role in inherited neurodegenerative diseases. (1994)

Four inherited neurodegenerative diseases are linked to abnormally expanded repeats of glutamine residues in the affected proteins. Molecular modeling followed by optical, electron, and x-ray diffraction studies of a synthetic poly(L-glutamine) shows that it forms beta-sheets strongly held together by hydrogen bonds. Glutamine repeats may function as polar zippers, for example, by joining specific transcription factors bound to separate DNA segments. Their extension may cause disease either by increased, nonspecific affinity between such factors or by gradual precipitation of the affected proteins in neurons.
Cellular and subcellular immunolocalization of vasopressin-regulated water channel in rat kidney. (1993)

Vasopressin (antidiuretic hormone) regulates body water balance by controlling water permeability of the renal collecting ducts. The control mechanisms may involve alterations in the number or unit conductance of water channels in the apical plasma membrane of collecting-duct cells. How this occurs is unknown, but indirect evidence exists for the "shuttle" hypothesis, which states that vasopressin causes exocytic insertion of water channel-laden vesicles from the apical cytosol. To test key aspects of the shuttle hypothesis, we have prepared polyclonal antisera against the recently cloned collecting-duct water channel protein and used the antisera in immunolocalization studies (light and electron microscopic levels) in thin and ultrathin cryosections from rat kidney. Labeling was seen exclusively in collecting-duct principal cells and inner medullary collecting-duct cells. Apical membrane labeling was intense. There was heavy labeling of abundant small subapical vesicles and of membrane structures within multivesicular bodies. In addition, labeling of basolateral plasma membranes in inner medullary collecting ducts was present. Depriving rats of water for 24 or 48 hr markedly increased collecting-duct water-channel protein expression determined by immunoblotting and immunolabeling. These results are compatible with at least two complementary modes of water-channel regulation in collecting-duct cells: (i) control of channel distribution between the apical membrane and a reservoir in subapical vesicles (shuttle hypothesis) and (ii) regulation of the absolute level of expression of water-channel protein.
Characterization of a Vaccinia Virus Mutant with a Deletion of the D10R Gene Encoding a Putative Negative Regulator of Gene Expression (2005)

The D9 and D10 proteins of vaccinia virus are 25% identical to each other, contain a mutT motif characteristic of nudix hydrolases, and are conserved in all sequenced poxviruses. Previous studies indicated that overexpression of D10 and, to a lesser extent, D9 decreased the levels of capped mRNAs and their translation products. Here, we further characterized the D10 protein and showed that only trace amounts are associated with purified virions and that it is expressed exclusively at late times after vaccinia virus infection. A viable deletion mutant (vdeltaD10) produced smaller plaques and lower virus yields than either wild-type virus or a D9R deletion mutant (vdeltaD9). Purified vdeltaD10 virions appeared normal by microscopic examination and biochemical analysis but produced 6- to 10-fold-fewer plaques at the same concentration as wild-type or vdeltaD9 virions. When 4 PFU per cell of wild-type or vdeltaD9 virions or equal numbers of vdeltaD10 virions were used for inoculation, nearly all cells were infected in each case, but viral early and late transcription was initiated more slowly in vdeltaD10-infected cells than in the others. However, viral early transcripts accumulated to higher levels in vdeltaD10-infected cells than in cells infected with the wild type or vdeltaD9. In addition, viral early and late mRNAs and cellular actin mRNA persisted longer in vdeltaD10-infected cells than in others. Furthermore, analysis of pulse-labeled proteins indicated prolonged synthesis of cellular and viral early proteins. These results are consistent with a role for D10 in regulating RNA levels in poxvirus-infected cells.
Survival after autologous hematopoietic stem cell transplantation for patients with inflammatory breast carcinoma (1999)

Combining HDC and ABM or PBSC for patients with IBC may yield an improved OS and DFS.
Mass Spectrometry: Recent Advances in Direct Open Air Surface Sampling/Ionization (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMass Spectrometry: Recent Advances in Direct Open Air Surface Sampling/IonizationMaría Eugenia Monge†, Glenn A. Harris‡, Prabha Dwivedi†, and Facundo M. Fernández*†View Author Information† School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States‡ Department of Biochemistry and the Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States*E-mail: [email protected]. Phone: 404 385 4432. Fax: 404 385 3399.Cite this: Chem. Rev. 2013, 113, 4, 2269–2308Publication Date (Web):January 9, 2013Publication History Received31 July 2012Published online9 January 2013Published inissue 10 April 2013https://pubs.acs.org/doi/10.1021/cr300309qhttps://doi.org/10.1021/cr300309qreview-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views11266Altmetric-Citations426LEARN 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 SUBJECTS:Desorption,Ionization,Ions,Lasers,Solvents Get e-Alerts
Progressive Multiple Sclerosis (2019)

Progressive MS remains a diagnostic challenge, and the pathogenesis underlying progression is complex. Significant overlap in the biology and clinical and imaging features of progressive MS exists with relapsing forms of the disease. The use of disease-modifying and symptomatic treatments may improve the quality of life for patients with progressive MS.
Expression of the neural cell adhesion molecule NCAM in endocrine cells. (1989)

We examined the expression of the neural cell adhesion molecule NCAM in a number of endocrine tissues of adult rat and in an endocrine tumor cell line. NCAM was found by immunoelectron microscopy to be present on the surface of all endocrine cells in the three lobes of the hypophysis, although staining was relatively less intense in the intermediate lobe, and in pancreatic islets. Pituicytes, hypophyseal glial cells, were also labeled for NCAM. A rat insulinoma cell line (RIN A2) also expressed NCAM as judged by immunocytochemistry. Analysis of NCAM antigenic determinants (Mr 180, 140, and 120 KD) revealed large variations in the relative proportions of NCAM polypeptides present in the different tissues. Although all tissues and cell lines expressed NCAM-140, NCAM-180 was not detected in the adenohypophysis, pancreas, or adrenal medulla, and NCAM-120 was found in none of the endocrine tissues or cell lines except at low levels in the neurohypophysis. The tumor cell line expressed significant levels of NCAM-180, which was most abundant in the neurohypophysis. These results show that NCAM expression appears to be a general property of endocrine cells, although the antigenic composition differs markedly from that in brain tissue. These data are discussed with regard to the embryological origins of the different endocrine tissues, and possible functional implications are suggested.
Primary Human Immunodeficiency Virus Type 2 (HIV-2) Isolates, Like HIV-1 Isolates, Frequently Use CCR5 but Show Promiscuity in Coreceptor Usage (1999)

Coreceptor usage of primary human immunodeficiency virus type 1 (HIV-1) isolates varies according to biological phenotype. The chemokine receptors CCR5 and CXCR4 are the major coreceptors that, together with CD4, govern HIV-1 entry into cells. Since CXCR4 usage determines the biological phenotype for HIV-1 isolates and is more frequent in patients with immunodeficiency, it may serve as a marker for viral virulence. This possibility prompted us to study coreceptor usage by HIV-2, known to be less pathogenic than HIV-1. We tested 11 primary HIV-2 isolates for coreceptor usage in human cell lines: U87 glioma cells, stably expressing CD4 and the chemokine receptor CCR1, CCR2b, CCR3, CCR5, or CXCR4, and GHOST(3) osteosarcoma cells, coexpressing CD4 and CCR5, CXCR4, or the orphan receptor Bonzo or BOB. The indicator cells were infected by cocultivation with virus-producing peripheral blood mononuclear cells and by cell-free virus. Our results show that 10 of 11 HIV-2 isolates were able to efficiently use CCR5. In contrast, only two isolates, both from patients with advanced disease, used CXCR4 efficiently. These two isolates also promptly induced syncytia in MT-2 cells, a pattern described for HIV-1 isolates that use CXCR4. Unlike HIV-1, many of the HIV-2 isolates were promiscuous in their coreceptor usage in that they were able to use, apart from CCR5, one or more of the CCR1, CCR2b, CCR3, and BOB coreceptors. Another difference between HIV-1 and HIV-2 was that the ability to replicate in MT-2 cells appeared to be a general property of HIV-2 isolates. Based on BOB mRNA expression in MT-2 cells and the ability of our panel of HIV-2 isolates to use BOB, we suggest that HIV-2 can use BOB when entering MT-2 cells. The results indicate no obvious link between viral virulence and the ability to use a multitude of coreceptors.