gebhart/patrepeval huggingface dataset:
Transduction of Passaged Human Articular Chondrocytes with Adenoviral, Retroviral, and Lentiviral Vectors and the Effects of Enhanced Expression of SOX9 (2004)

Chondrocytes form and maintain the extracellular matrix of cartilage. The cells can be isolated from cartilage for applications such as tissue engineering, but their expansion in monolayer culture causes a progressive loss of chondrogenic phenotype. In this work, we have investigated the isolation of human articular chondrocytes from osteoarthritic (OA) cartilage at joint replacement, their expansion in monolayer culture, and their transduction with adenoviral, retroviral, and lentiviral vectors, using the gene encoding green fluorescent protein as a marker gene. The addition of growth factors (transforming growth factor beta(1), fibroblast growth factor 2, and platelet-derived growth factor BB) during cell culture was found to greatly increase cell proliferation and thereby to selectively enhance the efficiency of transduction with retrovirus. With adenoviral and lentiviral vectors the transduction efficiency achieved was 95 and 85%, respectively. Using growth factor-supplemented medium with a retroviral vector, efficiency in excess of 80% was achieved. The expression was stable for several months with both retrovirus and lentivirus when analyzed by fluorescence-activated cell-sorting flow analysis and immunoblotting. Transduction with SOX9 was investigated as a method to reinitiate cartilage matrix gene expression in passaged human OA chondrocytes. Endogenous collagen II expression (both mRNA and protein) was increased in monolayer culture using both adenoviral and retroviral vectors. Furthermore, collagen II gene expression in chondrocytes retrovirally transduced with SOX9 was stimulated by alginate bead culture, whereas in control chondrocytes it was not. These results demonstrated methods for rapid expansion and highly efficient transduction of human OA chondrocytes and the potential for the recovery of key features of chondrocyte phenotype by transduction with SOX9.
Efficient Synthesis of Key Intermediate Toward Liphagal Synthesis (2010)

Liphagal (A) is a very potent and selective inhibitor of PI3Kα (p110α) and is under development for an oncolytic drug. We herein report the new and concise synthesis of key intermediates (7, 8), which have been used for liphagal synthesis and will be useful for generating liphagal-based chemical entities for drug discovery purposes.
Mice lacking all conventional MHC class II genes (1999)

MHC class II (MHC-II) molecules play a central role in the selection of the T cell repertoire, in the establishment and regulation of the adaptive immune response, and in autoimmune deviation. We have generated knockout mice lacking all four of the classical murine MHC-II genes (MHCII(Delta/Delta) mice), via a large (80-kilobase) deletion of the entire class II region that was engineered by homologous recombination and Cre recombinase-mediated excision. These mice feature immune system perturbations like those of Aalpha and Abeta knockout animals, notably a dearth of CD4(+) lymphocytes in the thymus and spleen. No new anatomical or physiological abnormalities were observed in MHCII(Delta/Delta) mice. Because these animals are devoid of all classical MHC-II chains, even unpaired chains, they make excellent recipients for MHC-II transgenes from other species, avoiding the problem of interspecies cross-pairing of MHC-II chains. Therefore, they should be invaluable for engineering "humanized" mouse models of human MHC-II-associated autoimmune disorders.
Pre‐operative removal of dentures (1991)

profoundly bradycardic and no ECG complexes or pulse waveform were seen for approximately 10 seconds.Sinus rhythm then resumed spontaneously at 45 beats/minute.After a further 0.4 mg of glycopyrronium subsequent elevation of the zygoma had no effect on the heart rate, which remained constant at 80 beats/minute.Glycopyrronium 0.2 mg falls within the manufacturer's initial dose range for adults of 0.2 mg-0.4 mg.However, in this patient, it was clear that 0.2mg was not adequate to block reflex vagal response during anaesthesia.In future I would recommend use of the upper limit of the manufacturer's dose range in an attempt to prevent reflex bradycardia occurring during surgical procedures that may involve vagal stimulation.
PEDOT:PSS films with significantly enhanced conductivities induced by preferential solvation with cosolvents and their application in polymer photovoltaic cells (2011)

The conductivity of poly(3,4-ethylene dioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) films was significantly enhanced by preferential solvations of the hydrophobic PEDOT and hydrophilic PSS chains with cosolvents. When a PEDOT:PSS film prepared from the PEDOT:PSS aqueous solution was treated with water or a common organic solvent like ethanol, iso-propyl alcohol (IPA), acetonitrile (ACN), acetone, or tetrahydrofuran (THF), its conductivity did not change remarkably. But the conductivity was significantly enhanced when the PEDOT:PSS film was treated with a cosolvent of water and one of these common organic solvents. The conductivity enhancement was affected by several factors, including the ratio of the organic solvent to water, the dielectric constant of the organic solvent, and the temperature during the treatment. The conductivity enhancement from 0.2 S cm−1 to 103 S cm−1 was observed. The significant conductivity enhancement is attributed to the preferential solvation of PEDOT:PSS with a cosolvent. Water and the organic solvent of the cosolvent preferentially solvate the hydrophilic PSS and hydrophobic PEDOT chains, respectively. The preferential solvation of a PEDOT:PSS film with a cosolvent induces the phase separation of the insulator PSSH chains from the PEDOT:PSS film, aggregation of PSSH segments in the PEDOT:PSS film, and the conformational change of the PEDOT chains from coiled to linear. The cosolvent-treated PEDOT:PSS films were quite smooth and could be used to replace indium tin oxide (ITO) as the transparent electrode of electronic devices. Polymer photovoltaic cells (PVs) with the cosolvent-treated PEDOT:PSS films as the transparent electrode exhibited high photovoltaic performance.
Thermal properties and stereoregularity of poly(3-hydroxybutyrate) prepared from optically active .beta.-butyrolactone with a zinc-based catalyst (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal properties and stereoregularity of poly(3-hydroxybutyrate) prepared from optically active .beta.-butyrolactone with a zinc-based catalystNaoki Tanahashi and Yoshiharu DoiCite this: Macromolecules 1991, 24, 20, 5732–5733Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://pubs.acs.org/doi/10.1021/ma00020a039https://doi.org/10.1021/ma00020a039research-articleACS PublicationsRequest reuse permissionsArticle Views396Altmetric-Citations56LEARN 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
Risk Factors for Candidemia in a Children's Hospital (1998)

Candida species are increasingly important nosocomial pathogens in critically ill children. A 2.3-fold increase in the rate of nosocomial candidemia at our 200-bed tertiary care children's hospital prompted a study to identify risk factors for this infection. Twenty-six cases were identified between 1992 and 1993, representing 21% of all nosocomial bloodstream infections. Candida albicans was the most frequent isolate (58%), followed by Candida parapsilosis (27%). A case-control study revealed that there was a statistically significant association between the occurrence of candidemia and placement of a central venous catheter in the femoral vein (P = .03), the use of a tunneled central venous catheter (P = .05), and prolonged hyperalimentation (P = .04). Patients with candidemia also were noted to have candiduria more often than controls (P = .003) and were more likely to have had topical antifungal agents prescribed (P = .04). Multivariate analysis showed that hyperalimentation was an independent risk factor for the development of candidemia. We conclude that measures must be taken to reduce these risk factors whenever possible.
Functionalizing Carbon Nanotubes by Plasma Modification for the Preparation of Covalent-Integrated Epoxy Composites (2006)

A novel method for preparing a fully integrated nanotube composite material through the use of functionalized multi-walled carbon nanotubes (MWNTs) is presented in this study. The functionalization of MWNTs was performed via plasma treatment; subsequently, maleic anhydride (MA) was grafted onto the MWNTs (CNTs-MA). Nanotube-reinforced epoxy polymer composites were prepared by first mixing the CNTs-MA and a diamine curing agent, followed by a further reaction with the epoxy matrix. In this hybrid nanocomposite system, the CNTs-MA were covalently integrated into the epoxy matrix and became part of the cross-linked structure rather than just a separate component. Fourier transform infrared (FT-IR) and high resolution X-ray photoelectron (XPS) spectroscopes were used to characterize the functional groups on the surface of the MWNTs after the plasma modification. In addition, observations of scanning electronic microscopy (SEM) and transmission electron microscopy (TEM) images showed that the functionalized nanotubes, CNTs-MA, had a better dispersion than the unfunctionalized nanotubes, u-CNTs, on either the composite fracture surfaces or inside the epoxy matrix. Moreover, CNTs-MA/epoxy nanocomposites presented obvious improvements in mechanical properties and conductivity (from 10-12 to 10-4 S/m) with only a small quantity (0.1−1.0 wt %) of the CNTs-MA addition.
Proliferative potential of human meningiomas of the brain: A cell kinetics study with bromodeoxyuridine (1986)

Twenty patients with intracranial meningiomas were given a 1-hour intravenous infusion of bromodeoxyuridine (BrdU), 200 mg/m2, at the time of surgery to label tumor cells in the DNA synthesis phase (S phase). The excised tumor specimens were fixed with 70% ethanol, embedded in paraffin, sectioned, and stained by an indirect immunoperoxidase method using anti-BrdU monoclonal antibody as the first antibody. The BrdU labeling index (LI), or S-phase fraction, was determined by counting the number of BrdU-labeled cells in the tissue sections. The average LIs for nonmalignant (11 cases) and histologically malignant meningiomas (seven cases) were 0.45% and 3.9% respectively (P less than 0.05). Two hemangiopericytic variants showed average LIs of 0.53% and 4.1%. Four of seven malignant meningiomas and both hemangiopericytomas were recurrent tumors. Nine of 20 meningiomas had an LI greater than 1%, and six of those nine (67%) were recurrent. Thus, meningiomas with an LI greater than 1% appear to grow faster and recur more frequently than those with LIs less than 1%; the higher LI may indicate biological malignancy. The measurement of BrdU LI in meningioma may prove valuable in establishing the diagnosis of "malignant meningioma."
Reduction of Amine N-Oxides by Diboron Reagents (2011)

Facile reduction of alkylamino-, anilino-, and pyridyl-N-oxides can be achieved via the use of diboron reagents, predominantly bis(pinacolato)- and in some cases bis(catecholato)diboron [(pinB)(2) and (catB)(2), respectively]. Reductions occur upon simply mixing the amine N-oxide and the diboron reagent in a suitable solvent, at a suitable temperature. Extremely fast reductions of alkylamino- and anilino-N-oxides occur, whereas pyridyl-N-oxides undergo slower reduction. The reaction is tolerant of a variety of functionalities such as hydroxyl, thiol, and cyano groups, as well as halogens. Notably, a sensitive nucleoside N-oxide has also been reduced efficiently. The different rates with which alkylamino- and pyridyl-N-oxides are reduced has been used to perform stepwise reduction of the N,N'-dioxide of (S)-(-)-nicotine. Because it was observed that (pinB)(2) was unaffected by the water of hydration in amine oxides, the feasibility of using water as solvent was evaluated. These reactions also proceeded exceptionally well, giving high product yields. In constrast to the reactions with (pinB)(2), triethylborane reduced alkylamino-N-oxides, but pyridine N-oxide did not undergo efficient reduction even at elevated temperature. Finally, the mechanism of the reductive process by (pinB)(2) has been probed by (1)H and (11)B NMR.
Reactions of L-&alpha;-Tosylamido-&beta;-propiolactone. I. : Synthesis, Reactions with Amines and Derivation to L-Serine (1969)

L-α-Tosylamido-β-propiolactone (V) was obtained by diazotization of L-2-tosylamido-3-aminopropionic acid (III), which was derived from L-asparagine (I), in aqueous organic acid solution at low temperature. N-Tosyl-L-serine (IV) and L-2-tosylamido-3-chloropropionic acid (VI) were selectively prepared from III in the other proper diazotization conditions. V was quantitatively hydrolyzed with water to yield IV, which afforded L-serine (VII) by the usual detosylation. Treatment of V with amines afforded the corresponding three type products, which were amino acid types (A), amide types (B) and betaine types (C).
PI3K/Akt/mTOR pathway as a target for cancer therapy (2005)

The PI3K/Akt/mTOR pathway regulates several normal cellular functions that are also critical for tumorigenesis, including cellular proliferation, growth, survival and mobility. Components of this pathway are frequently abnormal in a variety of tumors, making them an attractive target for anti-cancer therapy. Inhibition of mTOR in patients with cancer became more feasible after the development of rapamycin analogs with improved pharmacologic properties. The promising activity of these agents in early clinical trials has led to the development of ongoing phase III trials in renal cell carcinoma and breast cancer. Future studies are needed to identify the patients most likely to benefit from this form of therapy, and to define its role in combination with chemotherapy, hormones and growth factor inhibitors.
IRB/FDA requirements relevant to HIV/AIDS clinical trials in correctional settings. (2001)

Federally funded research involving inmates in US correctional facilities requires the approval of the Office for Protection from Research Risks (now called the Office for Human Research Protections [OHRP] and located in the Office of the Secretary of the Department of Health and Human Services). Trials that are carried out by pharmaceutical companies (not federally funded) fall under the jurisdiction of the FDA. This article reviews OHRP and FDA guidelines relevant to the conduct of HIV/AIDS clinical trials in correctional settings.
Synthesis and damage specificity of a novel probe for the detection of abasic sites in DNA (1993)

The abasic site (apurinic/apyrimidinic site) is the most common lesion in DNA and is suggested to be an important intermediate in mutagenesis and carcinogenesis. We have recently reported a novel assay for the detection and quantitation of abasic sites in DNA [Kubo, K., Ide, H., Wallace, S. S., & Kow, Y. W. (1992) Biochemistry 31, 3703-3708]. In this assay, the aldehyde group in an abasic site is first modified by a probe bearing a biotin residue, called the Aldehyde Reactive Probe (ARP) and then the tagged biotin is quantified by an ELISA-like assay. However, in the previous study, ARP was prepared only in a crude form, and no solid chemical data concerning the structure and specificity of ARP were reported. In this study, an improved method for the preparative synthesis of ARP has been established, and its structure has been unambiguously characterized using spectroscopic means. In order to elucidate the specificity of ARP to DNA damages, ARP was incubated with a variety of damaged bases or nucleosides and the reaction mixtures were analyzed by HPLC. Of the 14 compounds tested for their reactivity to ARP, 2-deoxyribose (a model compound for an abasic site) and 5-formyluracil reacted with ARP. Interestingly, compounds bearing a formamide group such as formamidopyrimidine and deoxyribosylformamide did not react with ARP, indicating that ARP is specific to damages having an alkyl or allyl aldehyde group. Furthermore, the ability of ARP synthesized by the defined chemical route to detect abasic sites has been substantiated using natural DNA containing abasic sites. Potential applications and limitations of the ARP assay are discussed.
Senescent Cells: A Novel Therapeutic Target for Aging and Age-Related Diseases (2012)

Aging is the main risk factor for most chronic diseases, disabilities, and declining health. It has been proposed that senescent cells--damaged cells that have lost the ability to divide--drive the deterioration that underlies aging and age-related diseases. However, definitive evidence for this relationship has been lacking. The use of a progeroid mouse model (which expresses low amounts of the mitotic checkpoint protein BubR1) has been instrumental in demonstrating that p16(Ink4a)-positive senescent cells drive age-related pathologies and that selective elimination of these cells can prevent or delay age-related deterioration. These studies identify senescent cells as potential therapeutic targets in the treatment of aging and age-related diseases. Here, we describe how senescent cells develop, the experimental evidence that causally implicates senescent cells in age-related dysfunction, the chronic diseases and disorders that are characterized by the accumulation of senescent cells at sites of pathology, and the therapeutic approaches that could specifically target senescent cells.
Phase transition of aqueous solutions of poly(N-isopropylacrylamide) and poly(N-isopropylmethacrylamide) (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhase transition of aqueous solutions of poly(N-isopropylacrylamide) and poly(N-isopropylmethacrylamide)Shouei Fujishige, K. Kubota, and I. AndoCite this: J. Phys. Chem. 1989, 93, 8, 3311–3313Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://pubs.acs.org/doi/10.1021/j100345a085https://doi.org/10.1021/j100345a085research-articleACS PublicationsRequest reuse permissionsArticle Views5278Altmetric-Citations1035LEARN 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 options Get e-Alerts
The Place of the Ice Water Test (IWT) in the Evaluation of the Patients with Traumatic Spinal Cord Injury. (2012)

In the last decades, functional Urology developed itself as a subspecialty, and, although is strongly linked to Urology, it has its own language, devices and dedicated people. The ice water test (IWT) was first described in 1957 and gained its place in the armamentarium of functional urologists for the coming years. Now, when urodynamic devices are more and more complex and sensitive, when neuromodulation and neurostimulation are gaining popularity and with the terminology changes of the last decade, one can wonder if a 50 years old test may still be of some use. We performed a prospective study using the ice water test in 150 consecutive patients referred to us for urodynamics in order to identify if there is any improvement in the diagnostic process. The patients were referred for varied indications, but a large number of them were neurogenic, given the special profile of our unit. We classified the patients in four different groups and analyzed the data for each group. The results showed that, while there is no use of the IWT as a routine procedure, the test might prove extremely useful in selected cases.
Vagal nerve stimulation for epilepsy (2000)

Editor,—It is timely that “Archivist” has taken an interest in vagal nerve stimulation for epilepsy. The comments do not suggest however that Archivist was fully informed.

It is true to say that the mechanism by which the effect is achieved is not known, but there is considerable animal evidence that both serotoninergic and noradrenergic pathways from afferent vagus terminations to the thalamus are involved.1 …
Packing bag-of-features (2009)

One of the main limitations of image search based on bag-of-features is the memory usage per image. Only a few million images can be handled on a single machine in reasonable response time. In this paper, we first evaluate how the memory usage is reduced by using lossless index compression. We then propose an approximate representation of bag-of-features obtained by projecting the corresponding histogram onto a set of pre-defined sparse projection functions, producing several image descriptors. Coupled with a proper indexing structure, an image is represented by a few hundred bytes. A distance expectation criterion is then used to rank the images. Our method is at least one order of magnitude faster than standard bag-of-features while providing excellent search quality.
Precise alias analysis for static detection of web application vulnerabilities (2006)

The number and the importance of web applications have increased rapidly over the last years. At the same time, the quantity and impact of security vulnerabilities in such applications have grown as well. Since manual code reviews are time-consuming, error-prone and costly, the need for automated solutions has become evident. In this paper, we address the problem of vulnerable web applications by means of static source code analysis. To this end, we present a novel, precise alias analysis targeted at the unique reference semantics commonly found in scripting languages. Moreover, we enhance the quality and quantity of the generated vulnerability reports by employing a novel, iterative two-phase algorithm for fast and precise resolution of file inclusions.We integrated the presented concepts into Pixy~\cite{jovanovic06:pixy_short}, a high-precision static analysis tool aimed at detecting cross-site scripting vulnerabilities in PHP scripts. To demonstrate the effectiveness of our techniques, we analyzed three web applications and discovered 106 vulnerabilities. Both the high analysis speed as well as the low number of generated false positives show that our techniques can be used for conducting effective security audits.