gebhart/patrepeval huggingface dataset:
Dependence of intrachromosomal recombination in mammalian cells on uninterrupted homology. (1988)

Recombination between a 360-base-pair (bp) segment of a wild-type thymidine kinase gene (tk) from each of three different strains (F, MP, and 101) of herpes simplex virus type one and a complete herpes simplex virus type 1 (strain F) tk gene containing an 8-bp insertion mutation was studied. The pairs of tk sequences resided as closely linked repeats within the genome of mouse LTK- cells. The frequency of recombination between sequences exhibiting 232 bp of uninterrupted homology and containing no mismatches other than the insertion mutation was comparable to the frequency of recombination between two sequences exhibiting four additional nucleotide mismatches distributed in such a way to preserve the 232-bp stretch of contiguous homology. In contrast, the placement of only two single-nucleotide mismatches (in addition to the insertion mutation) in such a manner to reduce the longest uninterrupted homology to 134 bp resulted in a 20-fold reduction in recombination. We conclude that the rate of intrachromosomal recombination in mammalian cells is determined by the amount of uninterrupted homology available and not by the total number of mismatches within a given interval of DNA. Furthermore, efficient recombination appears to require between 134 and 232 bp of uninterrupted homology; single-nucleotide heterologies are most likely sufficient to disrupt the minimal efficient recombination target. We also observed that if recombination was allowed to initiate within sequences exhibiting perfect homology, the event could propagate through and terminate within adjacent sequences exhibiting 19% base pair mismatch. We interpret this to mean that heterology exerts most of its impact on early rather than late steps of intrachromosomal recombination in mammalian cells.
Permissivity of the NCI-60 cancer cell lines to oncolytic Vaccinia Virus GLV-1h68 (2011)

Our findings have implications for the design of oncolytic therapies for cancer and offer insights into the nature of permissivity of tumor cells to viral infection.
Mechanisms of Estrogen Action (2001)

Our appreciation of the physiological functions of estrogens and the mechanisms through which estrogens bring about these functions has changed during the past decade. Just as transgenic mice were produced in which estrogen receptors had been inactivated and we thought that we were about to understand the role of estrogen receptors in physiology and pathology, it was found that there was not one but two distinct and functional estrogen receptors, now called ER alpha and ER beta. Transgenic mice in which each of the receptors or both the receptors are inactive have revealed a much broader role for estrogens in the body than was previously thought. This decade also saw the description of a male patient who had no functional ER alpha and whose continued bone growth clearly revealed an important function of estrogen in men. The importance of estrogen in both males and females was also demonstrated in the laboratory in transgenic mice in which the aromatase gene was inactivated. Finally, crystal structures of the estrogen receptors with agonists and antagonists have revealed much about how ligand binding influences receptor conformation and how this conformation influences interaction of the receptor with coactivators or corepressors and hence determines cellular response to ligands.
Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato (1999)

The Bs2 resistance gene of pepper specifically recognizes and confers resistance to strains of Xanthomonas campestris pv. vesicatoria that contain the corresponding bacterial avirulence gene, avrBs2. The involvement of avrBs2 in pathogen fitness and its prevalence in many X. campestris pathovars suggests that the Bs2 gene may be durable in the field and provide resistance when introduced into other plant species. Employing a positional cloning strategy, the Bs2 locus was isolated and the gene was identified by coexpression with avrBs2 in an Agrobacterium-mediated transient assay. A single candidate gene, predicted to encode motifs characteristic of the nucleotide binding site-leucine-rich repeat class of resistance genes, was identified. This gene specifically controlled the hypersensitive response when transiently expressed in susceptible pepper and tomato lines and in a nonhost species, Nicotiana benthamiana, and was designated as Bs2. Functional expression of Bs2 in stable transgenic tomatoes supports its use as a source of resistance in other Solanaceous plant species.
Receptors and lytic mediators regulating anti-tumor activity by the leukemic killer T cell line TALL-104 (2005)

The major histocompatibility complex nonrestricted cytotoxic leukemic T cell line T acute lymphoblastic leukemia (TALL)-104 is being pursued as a therapeutic agent for cancer. However, the receptors and effector mechanisms responsible for its broad tumoricidal function remain undefined. Here, we examined the roles played by natural cytotoxicity receptors (NCR), killer cell immunoglobulin-like receptors, cytolytic granule components, and tumor necrosis factor (TNF) family members in tumor recognition and lysis by TALL-104 cells. The perforin-granzyme pathway, TNF-related apoptosis-inducing ligand (TRAIL), and Fas were each involved in the lysis of particular tumor targets by TALL-104. Furthermore, phorbol 12-myristate 13-acetate/ionomycin treatment induced surface expression of Fas-L and TRAIL. In addition, supernatants from CD3-stimulated TALL-104 cultures exhibited antiproliferative activity, which was blocked 50-90% by anti-TNF-alpha monoclonal antibody (mAb). Although negative for the NCR natural killer (NK)p44, this cell line was found to express NKp46. An anti-NKp46 antibody strongly blocked TALL-104-mediated lysis of certain targets and directly induced cytokine production, granule release, and redirected lysis responses. Anti-NKG2D and anti-2B4 also stimulated redirected cytotoxicity by TALL-104. By contrast, anti-NKG2A mAb did not stain the cells or inhibit killing responses. Alternatively, KIR3DL2 was detected on TALL-104, and expression of its reported ligand, human leukocyte antigen (HLA)-A, on target cells provided protection from cytotoxicity. Thus, NKp46, NKG2D, and 2B4 are activating receptors, and KIR3DL2 is an inhibitory receptor on TALL-104. The data demonstrate the ability of TALL-104 cells to recognize a wide variety of tumors with NK cell receptors and kill them with a broad arsenal of cytolytic effector mechanisms, including cytolytic granules and TNF family ligands.
Charge-Injection and Charge-Coupled Devices in Practical Chemical Analysis (1983)

The increasing demand on multispecie chemical analysis and use of highly sophisticated computer controlled instrumentation has made significant changes in the modern laboratory. Optical spectroscopy ranging from Raman through Atomic is under considerable pressure to replace the "tried and true" photomultiplier tube (PMT) with multichannel devices. Two classes of solid state devices, the Charge Coupled Device (CCD) and the Charge Injection Device (CID), hold great promise for meeting this need. Operating modes of these devices are reviewed. Characteristics pertinent to analytical spectroscopy are presented.
Stable Concentrations of Zidovudine, Stavudine, Lamivudine, Abacavir, and Nevirapine in Serum and Cerebrospinal Fluid during 2 Years of Therapy (2002)

For a number of antiretroviral drugs, prolonged suppression of viral replication is related to drug exposure. Therefore, it is important to maintain stable concentrations during prolonged therapy. While studies suggest that saquinavir concentrations decrease over time, we show that concentrations of zidovudine, stavudine, lamivudine, abacavir, and nevirapine in serum and cerebrospinal fluid are stable during 2 years of therapy.
Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes (2014)

Background. Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results. A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions. This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.
AAV-1–mediated gene transfer to skeletal muscle in humans results in dose-dependent activation of capsid-specific T cells (2009)

In a clinical trial for adeno-associated virus serotype 1 (AAV-1)-mediated gene transfer to muscle for lipoprotein lipase (LPL) deficiency, 1 subject from the high-dose cohort experienced a transient increase in the muscle enzyme creatine phosphokinase (CPK) 4 weeks after gene transfer. Simultaneously, after an initial downward trend consistent with expression of LPL, plasma triglyceride levels returned to baseline. We characterized B- and T-cell responses to the vector and the transgene product in the subjects enrolled in this study. IFN-gamma enzyme-linked immunosorbent spot (ELISpot) and intracellular cytokine staining assays performed on peripheral blood mononuclear cells (PBMCs) from the subject who experienced the CPK elevation showed the activation of capsid-specific CD4(+) and CD8(+) T cells. Four of 8 subjects had detectable T-cell responses to capsid with dose-dependent kinetics of appearance. Subjects with detectable T-cell responses to capsid also had higher anti-AAV-1 IgG3 antibody titer. No subject developed B- or T-cell responses to the LPL transgene product. These findings suggest that T-cell responses directed to the AAV-1 capsid are dose-dependent. Whether they also limit the duration of expression of the transgene at higher doses is unclear, and will require additional analyses at later time points.
Effects of deglycosylation on the architecture of ovine submaxillary mucin glycoprotein. (1984)

The structural features of native and deglycosylated ovine submaxillary mucin (OSM) were determined by electron microscopy of platinum unidirectionally shadowed preparations and by ultracentrifugation. Thin filamentous molecules, of which 90% were 100-230 nm in length with estimated diameters of 1.0-1.4 nm, were observed with dilute samples of OSM in high ionic strength solvents (5-30 micrograms/ml in 0.8 M NaCl or NH4Ac). Ultracentrifugation studies indicated that these filamentous structures were monomers and/or dimers. At higher mucin concentrations or in lower ionic strength solvents, OSM molecules were oligomers that appeared as long rope-like strands. Removal of sialic acid residues by incubation with Clostridium perfringens neuraminidase yielded filamentous structures similar to those observed with OSM and some smaller less extended structures. Subsequent removal of the GalNAc residues of asialo-OSM with C. perfringens alpha-N-acetylgalactosaminidase resulted in a dramatic change in appearance, from an extended filament to a globular form. The frictional ratios of OSM and deglycosylated OSM were consistent with the marked structural differences of these molecules. Native OSM had a frictional ratio of 3.09, comparable to that of highly asymmetric tropomyosin (3.22); deglycosylated OSM had a frictional ratio of 1.11, comparable to that of globular ovalbumin (1.08).
High Oxidation State Multiple Metal−Carbon Bonds (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh Oxidation State Multiple Metal−Carbon BondsRichard R. SchrockView Author Information Department of Chemistry 6-331, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 Cite this: Chem. Rev. 2002, 102, 1, 145–180Publication Date (Web):December 19, 2001Publication History Received18 June 2001Published online19 December 2001Published inissue 1 January 2002https://pubs.acs.org/doi/10.1021/cr0103726https://doi.org/10.1021/cr0103726research-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views6697Altmetric-Citations821LEARN 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:Chemical structure,Hydrocarbons,Ligands,Metals,X-rays Get e-Alerts
Rolling-circle amplification in DNA diagnostics: the power of simplicity (2002)

Due to its robustness and simplicity, the rolling replication of circular DNA probes holds a distinct position in DNA diagnostics among other isothermal methods of target, probe or signal amplification. Major rolling-circle amplification approaches to DNA detection via posthybridization probe/signal turn-by-turn enhancement are briefly overviewed here with an emphasis on the new concepts and latest progress in the field, including the single-molecule and single-mutation detection assays as exemplary applications. Underlying mechanisms, current controversies and principal advantages of rolling-circle amplification are also considered. Possible future directions for the further advancement of this diagnostic methodology are outlined.
A dictionary of genetics 7000 entries (2006)

'a welcome update of the most useful and reliable reference work in the area' - Joseph G. Gall, Department of Embryology, Carnegie Institution of Washington
Checkpoint kinase inhibitor synergizes with DNA‐damaging agents in G1 checkpoint‐defective neuroblastoma (2010)

Checkpoint kinase inhibitors can enhance the cancer killing action of DNA-damaging chemotherapeutic agents by disrupting the S/G(2) cell cycle checkpoints. The in vitro and in vivo effects of the Chk1/2 inhibitor AZD7762 when combined with these agents were examined using neuroblastoma cell lines with known p53/MDM2/p14(ARF) genomic status. Four of four p53 mutant lines and three of five MDM2/p14(ARF) abnormal lines were defective in G(1) checkpoint, correlating with failure to induce endogenous p21 after treatment with DNA-damaging agents. In cytotoxicity assays, these G(1) checkpoint-defective lines were more resistant to DNA-damaging agents when compared to G(1) checkpoint intact lines, yet becoming more sensitive when AZD7762 was added. Moreover, AZD7762 abrogated DNA damage-induced S/G(2) checkpoint arrest both in vitro and in vivo. In xenograft models, a significant delay in tumor growth accompanied by histological evidence of increased apoptosis was observed, when AZD7762 was added to the DNA-damaging drug gemcitabine. These results suggest a therapeutic potential of combination therapy using checkpoint kinase inhibitor and chemotherapy to reverse or prevent drug resistance in treating neuroblastomas with defective G(1) checkpoints.
Peripheral blood-derived stem cell collections for use in autologous transplantation after high dose chemotherapy: an alternative approach. (1990)

Peripheral blood-derived hematopoietic stem cells (PBHSC) can be utilized to reconstitute hematopoiesis in patients after high dose myeloablative chemotherapy. We have performed PBHSC reinfusion in 18 patients who have or had a history of tumor involving the bone marrow or a hypocellular bone marrow. The PBHSC were collected by continuous flow leukapheresis and subsequently cryopreserved. A median of 31.9 X 10(9) (range 18 X 10(9)-67.2 X 10(9)) mononuclear cells or a median of 4.85 X 10(8) mononuclear cells/kg (range 2.7 X 10(8)-11.0 X 10(8)) were collected. Fifteen patients had in vitro assays of granulocyte-monocyte colony-forming cells (CFU-GM) performed with a median of 2.7 X 10(4) (range 0-11.5 X 10(4)) CFU-GM/kg. To date, of the 18 patients collected, all have undergone high dose chemotherapy and PBHSC reinfusion. For the evaluable patients, granulocyte recovery (greater than 500 X 10(6)/ml) has occurred in a median of 15 days and platelet recovery (greater than 50 X 10(9)/ml without transfusion support) has occurred in a median of 43 days. Four patients have had prolonged thrombocytopenia and still require platelet transfusion at 80+, 97+, 124+, and 270+ days. PBHSC collection is safe and effective for hematopoietic reconstitution after high dose chemotherapy in the majority of patients; however incomplete hematopoietic reconstitution has been observed in 4/18 evaluable patients. This procedure requires further investigation.
LITREF-a microcomputer based information retrieval system supporting stroke diagnosis, design, and development (2003)

An online bibliographic retrieval system, called the literature reference (Litref) system, is presented. It is designed to run on a high-end microcomputer to support the stroke consultant system (Maiestro). Litref interprets a Boolean command language derived from knowledge-index to provide fast, efficient browsing of abstracts from the stroke literature. User feedback on keywords derived from a relational thesaurus is used to enhance the original query. The system is designed to work in a microcomputer environment. Features and goals, design principles, and system architecture are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Chemical Modification of Influenza CD8+ T-Cell Epitopes Enhances Their Immunogenicity Regardless of Immunodominance (2016)

T cells are essential players in the defense against infection. By targeting the MHC class I antigen-presenting pathway with peptide-based vaccines, antigen-specific T cells can be induced. However, low immunogenicity of peptides poses a challenge. Here, we set out to increase immunogenicity of influenza-specific CD8 + T cell epitopes. By substituting amino acids in wild type sequences with non-proteogenic amino acids, affinity for MHC can be increased, which may ultimately enhance cytotoxic CD8 + T cell responses. Since preventive vaccines against viruses should induce a broad immune response, we used this method to optimize influenza-specific epitopes of varying dominance. For this purpose, HLA-A*0201 epitopes GILGFVFTL, FMYSDFHFI and NMLSTVLGV were selected in order of decreasing MHC-affinity and dominance. For all epitopes, we designed chemically enhanced altered peptide ligands (CPLs) that exhibited greater binding affinity than their WT counterparts; even binding scores of the high affinity GILGFVFTL epitope could be improved. When HLA-A*0201 transgenic mice were vaccinated with selected CPLs, at least 2 out of 4 CPLs of each epitope showed an increase in IFN- responses of splenocytes. Moreover, modification of the low affinity epitope NMLSTVLGV led to an increase in the number of mice that responded. By optimizing three additional influenza epitopes specific for HLA-A*0301, we show that this strategy can be extended to other alleles. Thus, enhancing binding affinity of peptides provides a valuable tool to improve the immunogenicity and range of preventive T cell-targeted peptide vaccines.
Picoliter DNA sequencing chemistry on an electrowetting‐based digital microfluidic platform (2010)

The results of investigations into performing DNA sequencing chemistry on a picoliter-scale electrowetting digital microfluidic platform are reported. Pyrosequencing utilizes pyrophosphate produced during nucleotide base addition to initiate a process ending with detection through a chemiluminescence reaction using firefly luciferase. The intensity of light produced during the reaction can be quantified to determine the number of bases added to the DNA strand. The logic-based control and discrete fluid droplets of a digital microfluidic device lend themselves well to the pyrosequencing process. Bead-bound DNA is magnetically held in a single location, and wash or reagent droplets added or split from it to circumvent product dilution. Here we discuss the dispensing, control, and magnetic manipulation of the paramagnetic beads used to hold target DNA. We also demonstrate and characterize the picoliter-scale reaction of luciferase with adenosine triphosphate to represent the detection steps of pyrosequencing and all necessary alterations for working on this scale.
Migraine Prophylactic Medication Usage Patterns in the Netherlands (2003)

This study aims to investigate usage patterns of specific migraine prophylactic medications in ergotamine and triptan patients commencing this treatment for the first time during 1 January 1992 until 31 December 1998. Usage patterns of specific migraine prophylactic drugs were evaluated for each patient by accessing data from a large prescription database and were characterized as continued, switch or stop use during the patient observation period. Several patient and medication-related factors were explored in order to identify a possible relationship with the specific usage pattern defined. Approximately 75% of the study population (n = 729) had terminated (stop or switch) prophylactic treatment after 1 year. Age < 40 years (relative risk (RR) 1.9; 95% confidence interval (CI) 1.2-3.2) and the concomitant use of non-steroidal anti-inflammatory drugs (RR 3.2; 95% CI 1.2-5.5) or specific abortive migraine drugs resulted in a faster onset of treatment modification (switch). Overall, migraine prophylactic treatment is used for a relatively short period, probably attributable to the common limitations associated with migraine prophylaxis, such as poor compliance and/or limited therapeutic efficacy. Patterns of use can be influenced by a variety of factors, including age, type of prescriber and certain co-medication. Patient interview studies are required to clarify these issues further.
Autonomic trigger patterns and anti-arrhythmic treatment of paroxysmal atrial fibrillation: data from the Euro Heart Survey (2008)

This study is the first to address the issue of autonomic trigger patterns and AF in a large population. Autonomic trigger patterns were seen frequently in paroxysmal AF patients. Autonomic influences should be taken into consideration since non-recommended treatment may result in aggravation of vagal AF.