gebhart/patrepeval huggingface dataset:
Quantitative small‐animal surrogate to evaluate drug efficacy in preventing wear debris‐induced osteolysis (2000)

Individuals who suffer from severe joint destruction caused by the various arthritidies often undergo total joint arthroplasty. A major limitation of this treatment is the development of aseptic loosening of the prosthesis in as many as 20% of patients. The current paradigm to explain aseptic loosening proposes that wear debris generated from the prosthesis initiates a macrophage-mediated inflammatory response by resident macrophages, leading to osteoclast activation and bone resorption at the implant interface. No therapeutic interventions have been proved to prevent or inhibit aseptic loosening. The development of therapeutic strategies is limited due to the absence of a quantitative surrogate in which drugs can be screened rapidly in large numbers of animals. We have previously described a model in which titanium particles implanted on mouse calvaria induce an inflammatory response with osteolysis similar to that observed in clinical aseptic loosening. Here, we present new methods by which the osteolysis in this model can be quantified. We determined that 6-8-week-old mice in normal health have a sagittal suture area of 50 (+/-6) microm2, which contains approximately five osteoclasts. As a result of the titanium-induced inflammation and osteolysis, the sagittal suture area increases to 197 (+/-27) microm2, with approximately 30 osteoclasts, after 10 days of treatment. The sagittal suture area and the number of osteoclasts in the calvaria of sham-treated mice remained unchanged during the 10 days. We also determined the effects of pentoxifylline, a drug that blocks the responses of tumor necrosis factor-alpha to wear debris, and the osteoclast inhibitor alendronate. We found that both drugs effectively block wear debris-induced osteolysis but not osteoclastogenesis. In conclusion, we found the measurements made with this model to be reproducible and to permit quantitative analysis of agents that are to be screened for their potential to prevent aseptic loosening.
New medical management techniques for acute exacerbations of chronic rhinosinusitis (2003)

In the past 2 years, intranasal nebulized medications have emerged as a widely prescribed treatment for medical management of chronic rhinosinusitis. This represents an innovative and advanced approach to treating acute exacerbations of chronic rhinosinusitis topically. The use of specially formulated medication compounds delivered by unique nebulization equipment is reviewed in the treatment of patients with chronic sinus disease. Scientific data including related upper and lower respiratory literature is included, as well as the important aspects of factors affecting nebulized medication delivery to the sinuses. The benefits, effectiveness, risks, and adverse effects of intranasal nebulized medications are also addressed. A treatment algorithm identifying appropriate use of nebulized medications in the treatment plan for chronic sinusitis patients is then presented in diagrammatic format.
Cytokine Profiling in Acute Anterior Cruciate Ligament Injury (2010)

Level IV, prognostic case series.
Cell Adhesion and Fertilization: Steps in Oocyte Transport, Sperm-Zona Pellucida Interactions, and Sperm-Egg Fusion1 (2003)

Fertilization in mammals requires the successful completion of many steps, starting with the transport of gametes in the reproductive tract and ending with sperm-egg membrane fusion. In this minireview, we focus on three adhesion steps in this multistep process. The first is oocyte "pick-up," in which the degree of adhesion between the extracellular matrix of the cumulus cells and oviductal epithelial cells controls the successful pick-up of the oocyte-cumulus complex and its subsequent transfer into the oviduct. The second part of this review is concerned with the interaction between the sperm and the zona pellucida of the egg. Evidence is discussed that a plasma membrane form of galactosyltransferase on the surface of mouse sperm binds to ZP3 in the zona pellucida and initiates an acrosome reaction. Additional evidence raises the possibility that initial sperm binding to the zona pellucida is independent of ZP3. Last, we address the relationship between sperm adhesion to the egg plasma membrane and membrane fusion, especially the role of ADAM family proteins on the sperm surface and egg integrins.
Subunit structure of a laminin-binding integrin and localization of its binding site on laminin (1989)

A laminin receptor was isolated from human MG-63 osteosarcoma cells by affinity chromatography on human laminin. The isolated receptor was defined as the alpha 3 beta 1 integrin by immunoprecipitation with subunit-specific antibodies. A previously unclassified laminin-binding integrin from rat cells was shown also to contain the alpha 3 subunit. Both receptors bound to human and mouse laminin in a radioreceptor assay. They also both bound to some extent to fibronectin in this assay, but only the MG-63 cell receptor showed binding to type IV collagen. The binding of the radiolabeled receptor to insoluble laminin was inhibited by unlabeled receptor, by soluble laminin, and by chymotryptic fragments of laminin that have previously been shown to contain neurite-promoting and cell attachment-promoting activities. Moreover, the receptor binding was also inhibited by monoclonal antibodies capable of inhibiting the neurite-promoting activity of laminin and known to bind to laminin near the junction of the long arm and its terminal globule. One of these antibodies was reactive with fusion proteins expressed from laminin cDNA clones. The immunoreactive clones corresponded to the COOH-terminal end of the B1 subunit. These results identify the integrin-type laminin receptor isolated from the osteosarcoma cells as the alpha 3 beta 1 integrin and localize its binding site in close proximity of the B1 subunit COOH terminus.
Dedoop (2012)

We demonstrate a powerful and easy-to-use tool called Dedoop (&lt;u&gt;De&lt;/u&gt;duplication with Ha&lt;u&gt;doop&lt;/u&gt;) for MapReduce-based entity resolution (ER) of large datasets. Dedoop supports a browser-based specification of complex ER workflows including blocking and matching steps as well as the optional use of machine learning for the automatic generation of match classifiers. Specified workflows are automatically translated into MapReduce jobs for parallel execution on different Hadoop clusters. To achieve high performance Dedoop supports several advanced load balancing strategies.
DNA Damage Mediated by Metal Ions with Special Reference to Copper and Iron (2018)

This chapter relates to work with copper and iron. The author believes that these metals are good choices for metal-mediated DNA damage because copper and iron are two major transition metals in the biological environment that can catalyze extensive DNA damage in vitro and in vivo. The chapter discusses that DNA lesions created by these metals can be related to clinical conditions, since it is well established that overload of copper or iron in humans or rodents leads to specific diseases associated with oxidative DNA damage and an increased incidence of cancer. The DNA in many human disorders, including xeroderma pigmentosum, ataxia telangiectasia, Hutchinson-Gilford progeria, retinoblastoma, Fanconi's anemia, Bloom's, Cockayne's, and Werner's syndromes, and possibly Down syndrome, show increased sensitivity to the induction of damage. DNA damage also develops as a secondary effect in the course of other diseases such as rheumatoid arthritis and various inflammatory conditions.
Monolithic Two-dimensional Surface-emitting Arrays Of GaAs/AlGaAs Diode Lasers (2005)

Monolithic two-dimensional arrays with light emission normal to the surface were obtained by fabricating edge-emitting quantum well GaAs/AlGaAs lasers with deflecting mirrors adjacent to both laser facets. The facets and mirrors were formed by ion-beam-assisted etching. Proton bombardment between adjoining lasers was used to prevent lasing in the transverse direction. At the highest pulsed current used in these experiments, 10.5 A, the power output of a 22-element array was 1.6 W, which corresponds to a power density of 160 W/sq.cm. At this level, the power output was still linear with current.
Desktop teleoperation via the World Wide Web (2002)

We built a system that allows a robot manipulator to be teleoperated via the WWW. Although the field of teleoperation dates back over 50 years, the WWW provides a low-cost and widely-available interface that can make teleoperated resources accessible to anyone with a desktop or laptop computer and modem. The "Mercury Project" consists of an industrial robot arm fitted with a CCD camera and a pneumatic system. We placed a sandbox filled with buried artifacts in the robot workspace. Using the ISMAP feature of HTTP, users can remotely move the camera to view desired locations or direct a short burst of compressed air into the sand to view the newly cleared region. To our knowledge, the Mercury Project is the first system to permit WWW users to remotely view and alter the real world. This paper focuses on interface design, robot hardware, and system architecture.
Analysis of the Pathogenicity Locus inClostridium difficileStrains (2000)

The genes for Clostridium difficile toxins A and B (tcdA and tcdB) are part of a 19.6-kb pathogenicity locus (PaLoc) that includes the genes tcdD, tcdE, and tcdC. To determine whether the C. difficile PaLoc is a stable and conserved genetic unit in toxigenic strains, a multiplex polymerase chain reaction was used to analyze 50 toxigenic, 39 nontoxigenic, and 2 toxin-defective isolates. The respective amplicons were identified for tcdA-E in the toxigenic isolates; these were absent in the nontoxigenic isolates. C. difficile P-829 lacked at least a fragment of tcdD, tcdB, tcdE, and tcdC, but tcdA was present. C. difficile 8864 had deletions in the tcdA and tcdC genes. These data suggest that the PaLoc is highly stable in toxigenic C. difficile, nontoxigenic isolates lack the unit, and isolates with a defective PaLoc can still cause clinical disease. Further studies are needed to define the role of individual genes in the pathogenesis of C. difficile-associated diarrhea.
In Vitro Maturation of Viable Islets from Partially Digested Young Pig Pancreas (2013)

Isolation of islets from market-sized pigs is costly, with considerable islet losses from fragmentation occurring during isolation and tissue culture. Fetal and neonatal pigs yield insulin unresponsive islet-like cell clusters that become glucose-responsive after extended periods of time. Both issues impact clinical applicability and commercial scale-up. We have focused our efforts on a cost-effective scalable method of isolating viable insulin-responsive islets. Young Yorkshire pigs (mean age 20 days, range 4-30 days) underwent rapid pancreatectomy (<5 min) and partial digestion using low-dose collagenase, followed by in vitro culture at 37°C and 5% CO2 for up to 14 days. Islet viability was assessed using FDA/PI or Newport Green, and function was assessed using a glucose-stimulated insulin release (GSIR) assay. Islet yield was performed using enumeration of dithizone-stained aliquots. The young porcine (YP) islet yield at dissociation was 12.6 ± 2.1 × 10(3) IEQ (mean ± SEM) per organ and increased to 33.3 ± 6.4 × 10(3) IEQ after 7 days of in vitro culture. Viability was 97.3 ± 7% at dissociation and remained over 90% viable after 11 days in tissue culture (n = ns). Glucose responsiveness increased throughout maturation in culture. The stimulation index (SI) of the islets increased from 1.7 ± 2 on culture day 3 to 2.58 ± 0.5 on culture day 7. These results suggest that this method is both efficient and scalable for isolating and maturing insulin-responsive porcine islets in culture.
Fluorescence Lifetime Measurements and Biological Imaging (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTFluorescence Lifetime Measurements and Biological ImagingMikhail Y. Berezin* and Samuel Achilefu*View Author Information Department of Radiology, Washington University School of Medicine, 4525 Scott Ave, St. Louis, USA* To whom correspondence should be addressed. Tel. 314-747-0701 (M.Y.B.); 314-362-8599 (S.A.). Fax: 314-747-5191. E-mail: [email protected] (M.Y.B.); [email protected] (S.A.).Cite this: Chem. Rev. 2010, 110, 5, 2641–2684Publication Date (Web):March 31, 2010Publication History Received19 October 2009Published online31 March 2010Published inissue 12 May 2010https://pubs.acs.org/doi/10.1021/cr900343zhttps://doi.org/10.1021/cr900343zreview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views41161Altmetric-Citations1762LEARN 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:Biological imaging,Dyes and pigments,Fluorescence,Fluorescence imaging,Fluorophores Get e-Alerts
[Expression of vascular endothelial growth factor and endostatin in peritoneal fluid of patients with endometriosis]. (2004)

Both VEGF and endostatin may play a role in the regulation of angiogenesis of endometriosis, and the balance of angiogenic stimulators and inhibitors may be critical to the development of endometriosis.
Topical Tretinoin Improves Photoaged Skin (1988)

In a 16-week randomized, double-blind, vehicle-controlled study of topical tretinoin in the treatment of photoaging, all patients applied topical tretinoin to one forearm and vehicle cream to the other. Half of the patients received tretinoin to the face, and half received vehicle cream. All 30 patients who completed the study showed statistically significant improvement in photoaging on the tretinoin-treated forearms, but not on the vehicle-treated forearms. Fourteen of the 15 patients who received tretinoin to the face had improvement in photoaging, whereas none of the vehicle-treated patients' faces improved, a statistically significant difference in response between the two groups. Statistically significant histologic changes were seen in forearm skin treated with tretinoin, but not with vehicle cream. Side effects were limited to irritation of tretinoin-exposed skin.
Plasticity and Permeability in Carbonates: Dependence on Stress Path and Porosity (1998)

Abstract Pore collapse and the plastic behavior of high porosity chalks is well known but the extent to which harder, more moderate porosity carbonates are plastic is not as clear. We have experimentally determined the elastic and plastic deformation and effect of that deformation on permeability for a suite of carbonate rocks spanning the porosity range of 14% to 42%. The depositional environment of the carbonates was a shallow marine reef with some secondary porosity development. Biaxial compression tests were carried out along various stress paths where the ratio of axial to radial effective stress change was kept constant. Yield and failure surfaces and strain hardening response were mapped as a function of porosity. Variation in permeability and compressibility as a function of porosity, lithology, and stress path were determined. The results were modeled with a critical state-cap plasticity model. The deformation of the carbonates generally followed a critical state cap model. The yield cap and hardening function were strongly dependent on porosity. Even moderate porosity samples (15-22%) showed significant plastic strain under stress conditions attainable in many petroleum reservoirs. The compressibility of the samples in the plastic regime was a strong function of both porosity and stress path. One aspect of the observed deformation that did not fit critical state theory was the long transition from elastic to fully plastic behavior. We found we could represent this behavior with two cap surfaces: an initial yield surface and final hardening surface. Permeability reduction was a strong function of stress path. Permeability reduced less for a given increase in mean stress along stress paths with higher differential stress increments. Permeability reduction due to compaction was offset by permeability enhancement due to microcracking depending on stress path and differential stress. P. 485
A gas chromatographic air analyzer fabricated on a silicon wafer (1979)

A miniature gas analysis system has been built based on the principles of gas chromatography (GC). The major components are fabricated in silicon using photolithography and chemical etching techniques, which allows size reductions of nearly three orders of magnitude compared to conventional laboratory instruments. The chromatography system consists of a sample injection valve and a 1.5-m-long separating capillary column, which are fabricated on a substrate silicon wafer. The output thermal conductivity detector is separately batch fabricated and integrably mounted on the substrate wafer. The theory of gas chromatography has been used to optimize the performance of the sensor so that separations of gaseous hydrocarbon mixtures are performed in less than 10 s. The system is expected to find application in the areas of portable ambient air quality monitors, implanted biological experiments, and planetary probes.
Conformational Changes and Fusion Activity of Vesicular Stomatitis Virus Glycoprotein:  [125I]Iodonaphthyl Azide Photolabeling Studies in Biological Membranes (1997)

The interaction of VSV glycoprotein (VSV G) with biological membranes was studied by photosensitized labeling. The method is based on photosensitized activation by the fluorescent lipid analog 3,3'-dioctadecyloxacarbocyanine (DiO) of a hydrophobic probe, [125I]iodonaphthyl azide (125INA), that rapidly partitions into the membrane bilayer of virus and cells. 125INA labeling of proteins and lipids can be confined to the site of chromophore localization by photosensitized labeling. Photoactivation using visible light of target membrane labeled with DiO and 125INA, to which unlabeled virions are bound, results in exclusive labeling of envelope glycoproteins inserted into the target membrane [Pak et al. (1994) J. Biol. Chem. 269, 14614]. In this study, we labeled lipid symmetric erythrocyte ghosts with 125INA and DiO. Photosensitized activation of VSV prebound to labeled ghosts with visible light resulted in VSV G labeling under fusogenic conditions. Photoactivation of 125INA by UV light, which is nonspecific, produced labeled VSV G at both acidic and neutral pH. Photosensitized labeling of VSV G by DiO-125INA-ghosts was also observed at pH 5.5, 4 degrees C, in the absence of mixing between viral and cellular lipids, suggesting insertion of the ectodomain of VSV G. Soluble VSV G lacking the transmembrane domain inserted into DiO-125INA-ghosts under the same conditions as intact VSV G. DiO inserted into intact VSV appeared to be a suitable fluorophore for continuous kinetic measurements of membrane fusion by fluorescence dequenching. Our photosensitized labeling results establish biochemical correlates for the three states of VSV G, which we had proposed based on kinetic data [Clague et al., Biochemistry 29, 1303]. In addition, we found that VSV G insertion into the target membrane is reversible, suggesting a "velcro"-like attachment of the fusogenic domain with the target membrane.
Isolation, physicochemical properties, and macromolecular composition of zona pellucida from porcine oocytes (1980)

Oocytes released en masse from pig ovaries were isolated in large quantities by using sieving techniques. The isolated oocytes were gently homogenized, and the largely intact zona pellucida "ghosts" were purified by using sieving techniques. Sufficient amounts of zonae were recovered to permit, for the first time, adequate characterization of the zona pellucida in chemical, physical, and macromolecular terms. The isolated zonae were greater than 93% pure as determined by chemical, enzymatic, and microscopic criteria. The zonae were completely solubilized by a variety of conditions that do not break covalent bonds. The extent of solubilization was a function of pH, ionic strength, temperature, and the presence of various solubilizing agents such as detergents and urea. Chemically, the zonae were composed predominantly of protein (71%) and carbohydrate (19%). After acid hydrolysis of the zonae, no unusual amounts or types of amino acids were detected. The monosaccharides present after hydrolysis were those typically found in animal glycoproteins (Fuc, Man, Gal, GalNAc, and GlcNAc). Sialic acid in glycosidic linkage and sulfate and phosphate esters were present and were considered to be true constituents of the zona pellucida. Other substances detected, but considered contaminants rather than true constituents, included fatty acids (esterified and free) and uronic acids. The binding by several fluorescein-conjugated plant lectins to the in situ zona pellucida was determined by using light microscopy. The binding of the lectins to the zona pellucida was not uniform, indicating that the carbohydrate moieties of the zona pellucida were asymmetrically distributed. The zona pellucida was composed of at least three macromolecules as indicated by immunodiffusion and sodium dodecyl sulfate gel electrophoresis experiments. Determination of the number of macromolecules composing the zona pellucida was compromised by the aggregation and/or microheterogeneity of its constituent macromolecules. We conclude that the zona pellucida is composed of several glycoprotein macromolecules; interaction of these macromolecules to form supramolecular complexes and the integral zona pellucida is dependent on noncovalent forces.
Therapeutic efficacy of trehalose eye drops for treatment of murine dry eye induced by an intelligently controlled environmental system. (2012)

Trehalose application restored ocular surface integrity, suppressed inflammatory and proteolytic MMP-9 and HSP70 expression, and keratinization in mice with dry eye damaged by a desiccative model.
Synthesis and Biological Studies of 5-Aminolevulinic Acid-Containing Dendrimers for Photodynamic Therapy (2001)

Using a convergent growth approach, a series of novel 5-aminolevulinic acid (ALA)-containing dendrimers have been synthesized. In these molecules, ALA residues are attached to the periphery by ester linkages, with amide bonds connecting the dendrons. Three first-generation dendrimers, bearing either 6 or 9 ALA residues, were synthesized by attachment of a tris(Boc-protected ALA)-containing wedge (1) to a di- or tripodent aromatic, or tripodent aliphatic core. Two second generation 18-ALA-containing dendrimers were also synthesized using a 3,3'-iminodipropionic acid spacer unit between wedge 1 and the aromatic core. These compounds differed only in the distance between the core and the linker unit. The Boc-protected dendrimers were deprotected using trifluoroacetic acid and isolated as their TFA salts. The potential of these ALA ester dendrimers as macromolecular prodrugs for photodynamic therapy has been demonstrated in the tumorigenic keratinocyte PAM 212 cell line.