gebhart/patrepeval huggingface dataset:
Human Immunoglobulin G Recognizing Fibrinogen-Binding Surface Proteins Is Protective against both Staphylococcus aureus and Staphylococcus epidermidis Infections In Vivo (2006)

A human donor-selected immunoglobulin G for intravenous injection (IGIV) product with elevated titers against the staphylococcal fibrinogen-binding MSCRAMM proteins ClfA and SdrG (INH-A21) was tested in vitro and in vivo. INH-A21 contained a significantly increased ability to inhibit the fibrinogen-binding activity of recombinant forms of both ClfA and SdrG. Evaluation of the opsonizing potential of INH-A21 was evaluated using fluorescently labeled bacteria; this assay indicated an increase in phagocytic activity compared to normal IGIV. The prophylactic efficacy of INH-A21 against an intraperitoneal challenge of methicillin-resistant Staphylococcus epidermidis (MRSE) was evaluated in a neonatal rat model. INH-A21 was also evaluated for prophylactic and therapeutic efficacy in a rabbit model of catheter-induced aortic valve infective endocarditis caused by either MRSE or methicillin-resistant Staphylococcus aureus (MRSA). Results from the in vivo models demonstrated potent prophylactic and therapeutic efficacy against both MRSE and MRSA. These data suggest that INH-A21 may be an important tool for the prevention and treatment of staphylococcal infections, especially in high-risk populations.
Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation (2013)

As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C > A/G > T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.
A Review of Mechanical Adjuncts in Wound Healing: Hydrotherapy, Ultrasound, Negative Pressure Therapy, Hyperbaric Oxygen, and Electrostimulation (2003)

Chronic or non-healing wounds may develop in the setting of many diseases and are the source of considerable morbidity as well as health costs. These wounds demand an aggressive, multifactorial approach including surgical debridement, revascularization, antibiotics and dressings. In addition several adjuvant treatment methods have been developed to further stimulate healing. Whirlpool, although used frequently, has not been proven to be of benefit. However, pulsed lavage does show a promising future. Ultrasound has demonstrated beneficial effects but further controlled studies are needed. Subatmospheric pressure therapy is associated with few complications and is fast becoming a mainstay of adjuvant therapy. Hyperbaric oxygen therapy has been shown to be effective for many types of wounds. Unfortunately, cost and access to chambers may prohibit its use on a routine basis. Finally, electrostimulation may be one of the up and coming therapies for the future. Though, more studies are needed to determine the mode of delivery for various types of wounds.
O-Allyl protection of guanine and thymine residues in oligodeoxyribonucleotides (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTO-Allyl protection of guanine and thymine residues in oligodeoxyribonucleotidesYoshihiro Hayakawa, Masaaki Hirose, and Ryoji NoyoriCite this: J. Org. Chem. 1993, 58, 20, 5551–5555Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://pubs.acs.org/doi/10.1021/jo00072a050https://doi.org/10.1021/jo00072a050research-articleACS PublicationsRequest reuse permissionsArticle Views655Altmetric-Citations60LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Chemistry and biological applications of photo-labile organic molecules (2009)

Photo-labile molecules have been widely used not only in organic synthesis but also in biological study. The chemistry of the typical photo-labile organic molecules, including their structure, mechanism underlying their photo-lability and strategies to integrate them with biomolecules, is reviewed to illustrate the structural basis for photo-activable caged compounds. Biological applications of representative photo-labile caged molecules were also illustrated for a general understanding on the important roles of caged compounds in dynamic biological studies. This tutorial review would provide an interdisciplinary overview on the important area of chemical biological study making use of photo-labile caged compounds.
Novel Tripeptide Model of Nickel Superoxide Dismutase (2009)

Nickel superoxide dismutase (Ni-SOD) catalyzes the disproportionation of superoxide to molecular oxygen and hydrogen peroxide, but the overall reaction mechanism has yet to be determined. Peptide-based models of the 2N:2S nickel coordination sphere of Ni-SOD have provided some insight into the mechanism of this enzyme. Here we show that the coordination sphere of Ni-SOD can be mimicked using the tripeptide asparagine-cysteine-cysteine (NCC). NCC binds nickel with extremely high affinity at physiological pH with 2N:2S geometry, as demonstrated by electronic absorption and circular dichroism (CD) data. Like Ni-SOD, Ni-NCC has mixed amine/amide ligation that favors metal-based oxidation over ligand-based oxidation. Electronic absorption, CD, and magnetic CD (MCD) data collected for Ni-NCC are consistent with a diamagnetic Ni(II) center bound in square-planar geometry. Ni-NCC is quasi-reversibly oxidized with a midpoint potential of 0.72(2) V (vs Ag/AgCl) and breaks down superoxide in an enzyme-based assay, supporting its potential use as a model for Ni-SOD chemistry.
Dietary treatment of homocystinuria. (1966)

Homocystinuria was described in 1962 by Field, Carson, Cusworth, Dent, and Neil and later in the same year by
Successful Readministration of Adeno-Associated Virus Vectors to the Mouse Lung Requires Transient Immunosuppression during the Initial Exposure (1998)

The airway is an important target for gene transfer to treat cystic fibrosis and other diseases that affect the lung. We previously found that marker gene expression did not persist in the bronchial epithelium following adeno-associated virus (AAV) vector administration to the rabbit lung. In an attempt to promote continued expression, we tested repeat vector administration, but no additional transduction was observed, and the block to transduction correlated with the appearance of neutralizing antibodies to the viral capsid. Here we show that mice exhibit a similar response but that treatment with anti-CD40 ligand antibody (MR1) and a soluble CTLA4-immunoglobulin fusion protein (CTLA4Ig) at the time of primary AAV vector exposure allowed successful repeat transduction and prevented production of neutralizing antibodies. We also tested the possibility that an immune response caused the loss of marker-positive cells in the epithelial population in rabbits by evaluating AAV vector expression in immunocompetent and immunodeficient mice. In contrast to results in rabbits, marker protein expression persisted in the lung in both groups of mice. AAV vector transduction occurred in alveolar cells, airway epithelial cells, and smooth muscle cells, and vector expression persisted for at least 8 months. Although data on persistence of AAV vector expression in the human lung are not available, it is likely that repeat transduction will be necessary either due to loss of expression or to the need for repeat administration to deliver effective amounts of AAV vectors. Results presented here indicate that transient immunosuppression will allow such repeat vector treatment of the lung.
Vitamin D3 binding protein (group-specific component) is a precursor for the macrophage-activating signal factor from lysophosphatidylcholine-treated lymphocytes. (1991)

A brief (30 min) treatment of mouse peritoneal cells (mixture of nonadherent lymphocytes and adherent macrophages) with 1-20 micrograms of lysophosphatidylcholine (lyso-PC) per ml in serum-supplemented RPMI medium 1640, followed by a 3-hr cultivation of the adherent cells alone, results in a greatly enhanced Fc receptor-mediated phagocytic activity of macrophages. This rapid process of macrophage activation was found to require a serum factor, the vitamin D3 binding protein (the human protein is known as group-specific component; Gc). Efficient activation of macrophages was achieved by using medium containing purified human Gc protein. Analysis of intercellular signal transmission among nonadherent (B and T) cells revealed that lyso-PC-treated B cells modify Gc protein to yield a proactivating factor, which can be converted by T cells to the macrophage-activating factor. This rapid generation process of the macrophage-activating factor was also demonstrated by stepwise incubation of Gc protein with lyso-PC-treated B-cell ghosts and untreated T-cell ghosts, suggesting that Gc protein is modified by preexisting membranous enzymes to yield the macrophage-activating factor. Incubation of Gc protein with a mixture of beta-galactosidase and sialidase efficiently generated the macrophage-activating factor. Stepwise incubation of Gc protein with B- or T-cell ghosts and sialidase or beta-galactosidase revealed that Gc protein is modified by beta-galactosidase of B cells and sialidase of T cells to yield the macrophage-activating factor. Administration to mice of a minute amount (4-10 pg per mouse) of in vitro, enzymatically generated macrophage-activating factor resulted in a greatly enhanced (3- to 7-fold) ingestion activity of macrophages.
Identification of differentially expressed genes in classical and atypical multidrug-resistant gastric carcinoma cells. (2003)

The phenomenon of multidrug resistance (MDR) in human cancers is the major cause of failure of chemotherapy. To better understand the molecular events associated with the development of different types of MDR, a classical MDR P-glycoprotein expressing gastric carcinoma cell line and an atypical MDR P-glycoprotein-negative variant were analyzed by cDNA array hybridization. Of 588 cDNAs spotted on the array, a total of 9 genes showed differences in mRNA expressions. An enhanced expression level of 3 genes could be detected in both different MDR models (HLH, IR21, CCT5, Tx P-1), 4 genes were overexpressed solely in classical MDR cells (Hsp27, Rcl, aldehyde dehydrogenase 1, vimentin), whereas the expression of one gene was increased in atypical MDR cells (ProTa). Furthermore, the mRNA expressions of 3 genes were down-regulated in atypical MDR cells (Hsp27, vimentin, JNK2), whereas a decrease in mRNA expression in classical MDR cells could be determined for none of them. These differences were confirmed by a semiquantitative RT-PCR approach. Further characterization of these factors may provide more insight into the biology and development of different types of MDR in human gastric carcinomas. Moreover, these genes may be potential candidate factors for the diagnostics and/or prognosis of clinical drug resistance.
Roles of mast cells in the pathogenesis of inflammatory myopathy (2014)

Mast cells are involved in the pathogenesis of inflammatory myopathy.
Integrating compression and execution in column-oriented database systems (2006)

Column-oriented database system architectures invite a re-evaluation of how and when data in databases is compressed. Storing data in a column-oriented fashion greatly increases the similarity of adjacent records on disk and thus opportunities for compression. The ability to compress many adjacent tuples at once lowers the per-tuple cost of compression, both in terms of CPU and space overheads.In this paper, we discuss how we extended C-Store (a column-oriented DBMS) with a compression sub-system. We show how compression schemes not traditionally used in row-oriented DBMSs can be applied to column-oriented systems. We then evaluate a set of compression schemes and show that the best scheme depends not only on the properties of the data but also on the nature of the query workload.
Bovine Sperm Adenylate Cyclase: Inhibition by Adenosine and Adenosine Analogs (1984)

Since both adenosine and cAMP affect sperm motility and metabolism, the authors have studied the mode of interaction of adenosine with the adenylate cyclase activity in either the presence or the absence of 15 mM caffeine. In general, structural analogs of adenosine containing alterations of the purine structure produce little or no inhibition, whereas analogs containing alterations of the ribose structure are effective inhibitors. Cyclic AMP and caffeine also inhibit the enzyme activity. The kinetics of the adenosine inhibition most closely resemble the linear noncompetitive type. Adenosine is a more effective inhibitor of adenylate cyclase activity in the presence of Mn2+ rather than Mg2+, and is more effective at higher metal ion concentrations. These observations are consistent with a P-site interaction of adenosine with adenylate cyclase.
RNA interference directed against ribosomal protein S3a suggests a link between this gene and arrested ovarian development during adult diapause in Culex pipiens (2009)

Arrested ovarian development is a key characteristic of adult diapause in the mosquito Culex pipiens. In this study we propose that ribosomal protein S3a (rpS3a), a small ribosomal subunit, contributes to this shutdown. RpS3a is consistently expressed in females of C. pipiens that do not enter diapause, but in females programmed for diapause, expression of the rpS3a transcript is dramatically reduced for a brief period in early diapause (7-10 days after adult eclosion). RNA interference directed against rpS3a in nondiapausing females arrested follicle development, mimicking the diapause state. The effect of the dsRNA injection faded within 10 days, allowing the follicles to grow again, thus the suppression of rpS3a caused by RNAi did not permanently block ovarian development, implying that a brief suppression of rpS3a is not the only factor contributing to the diapause response. The arrest in development that we observed in dsRNA-injected females could be reversed with a topical application of juvenile hormone III, an endocrine trigger known to terminate diapause in this species. Though we speculate that many genes contribute to the diapause syndrome in C. pipiens, our results suggest that a shut down in the expression of rpS3a is one of the important components of this developmental response.
Core substructure of the hemiellipsoidal phycobilisome from the red alga Porphyridium cruentum. (1993)

The allophycocyanin core of hemiellipsoidal phycobilisomes from the red alga, Porphyridium cruentum, was isolated by chromatography on hydroxylapatite and subsequent density gradient centrifugation. Electron microscopy of negatively stained core complexes revealed a tricylindrical structure with a width of 21 to 23 nm in face view and a depth of 12 to 14 nm in side view. Fluorescence emission spectra of these complexes were similar to those of whole phycobilisomes confirming the presence of the two "terminal energy acceptors" allophycocyanin B (APB) and the high molecular linker polypeptide LCM. The polypeptide composition analyzed by SDS-PAGE showed the "anchor" polypeptide LCM, alpha AP, alpha APB, beta AP subunits, a low molecular weight linker with M(r) 13,500 and a blue-colored polypeptide of M(r) 19,800. A complex containing APB could be isolated from a "trimeric" allophycocyanin fraction of the density gradient by agarose gel electrophoresis in the presence of ampholytes. This complex shows a polypeptide composition of (alpha APB alpha AP2 beta AP3).L13.5C and contributes to the core with 30 to 35% of total "trimers". In comparison to the allophycocyanin cores from hemidiscoidal phycobilisomes of cyanobacteria and red algae, all data concerning the core of the hemiellipsoidal phycobilisomes from Porphyridium cruentum strongly suggest that there is no increase in size but an increase in its APB content. A model comprising the allophycocyanin core and the membrane integral photosystem II particles presents the structural and possible functional consequences of the results.
Experience-Associated Structural Events, Subependymal Cellular Proliferative Activity, and Functional Recovery After Injury to the Central Nervous System (2000)

Considerable structural plasticity is possible in the damaged neocortex and connected brain areas, and the potential for significant functional recovery remains even during the chronic phases of the recovery process. In this article, the authors review the literature on use-dependent morphologic events, focusing on the direct interaction of behavioral experience and structural changes associated with plasticity and degeneration. Experience-associated neural changes have the potential to either hinder or enhance functional recovery; therefore, issues concerning the nature, timing, and intensity of behavior-based intervention strategies are addressed.
Tris(2,4,6-trimethoxyphenyl)phosphine (TTMPP): A Novel Catalyst for Selective Deacetylation (2001)

Abstract Chemo- and stereoselective deacetylation was achieved by the use of a catalytic amount of tris(2,4,6-trimethoxyphenyl)phosphine (TTMPP).
Gas6/Axl mediates tumor cell apoptosis, migration and invasion and predicts the clinical outcome of osteosarcoma patients (2013)

Dysregulation of the receptor tyrosine kinase Axl and its ligand Gas6 has been shown to promote multiple tumorigenic processes, as well as to correlate with worse prognosis in many different tumor types. However, studies of Axl expression and function in osteosarcoma have rarely been reported. In this study, we report that activated Axl is highly expressed in osteosarcoma cells, and this expression is significantly correlated with the recurrence and lung metastasis of osteosarcoma patients. High expression of activated Axl was an independent predictor for worse prognosis in osteosarcoma. Additionally, we confirmed a strong positive correlation between P-Axl and MMP-9 expression in those osteosarcoma patients. In osteosarcoma cell lines MG63 and U2OS, 200 ng/ml rhGas6 could cause obvious increase of P-Axl expression within 30 min, consistent with the expression of P-AKT. In both of the cell lines, Axl activated by rhGas6 could protect the tumor cells from apoptosis caused by serum starvation, and promote tumor cells' migration and invasion in vitro. Together with previous data, these studies suggest that activated Axl participate in the progression of osteosarcoma by resisting tumor cells apoptosis and promoting their migration and invasion, which may be linked to the expression of MMP-9. In the mechanism, AKT signaling pathway may contribute to the function of P-Axl in osteosarcoma rather than ERK pathway.
Optical sensor arrays for chemical sensing: the optoelectronic nose (2013)

A comprehensive review is presented on the development and state of the art of colorimetric and fluorometric sensor arrays. Optical arrays based on chemoresponsive colorants (dyes and nanoporous pigments) probe the chemical reactivity of analytes, rather than their physical properties. This provides a high dimensionality to chemical sensing that permits high sensitivity (often down to ppb levels), impressive discrimination among very similar analytes and exquisite fingerprinting of extremely similar mixtures over a wide range of analyte types, both in the gas and liquid phases.
Macrophage activation for antileishmanial defense by an apparently novel mechanism. (1987)

Activation of macrophages by lymphokines (including interferon-gamma; IFN-gamma) is presently considered to be a major host defense mechanism against a number of intracellular microorganisms. In a series of earlier studies that made use of mice undergoing spontaneous resolution of footpad infections with Leishmania major, we obtained evidence suggesting that a subpopulation of Leishmania-sensitized lymph node T lymphocytes could activate antimicrobial effects in Leishmania-infected macrophages by an apparently lymphokine-independent mechanism. These effector lymphocytes are not cytotoxic to host cells, and their effects are antigen specific and genetically restricted. To more rigorously investigate this apparently novel mechanism of macrophage activation, we examined the effect of blocking lymphokine production with cyclosporin A (CSA) on the capacity of these effector lymphocytes to exert macrophage activating function. Although CSA blocked lymphokines that activate antileishmanial effects, it did not inhibit the antimicrobial capacity of the effector lymphocytes. We also confirmed that IFN-gamma is the major macrophage-activating lymphokine that induces antileishmanial effects; treatment of lymphokine-containing supernatants with anti-IFN-gamma antibody markedly reduced their antimicrobial effects. In contrast, treatment of effector lymphocytes with this antibody failed to reduce their macrophage-activating capacity. We conclude that there exists an apparently novel macrophage-activating mechanism for antimicrobial defense that is independent of soluble lymphokine mediators.
Serial changes in 14C-deoxyglucose and 201Tl uptake in autoimmune myocarditis in rats. (2001)

In the acute phase of autoimmune myocarditis in rats, cardiac uptake of DG was accelerated by severe inflammation. Cardiac uptake of 201Tl, on the other hand, was suppressed. Our results suggest that GLUT1 expression accelerates DG uptake by cells in areas of severe inflammation.