gebhart/patrepeval huggingface dataset:
Partial least squares: a versatile tool for the analysis of high-dimensional genomic data (2006)

Partial least squares (PLS) is an efficient statistical regression technique that is highly suited for the analysis of genomic and proteomic data. In this article, we review both the theory underlying PLS as well as a host of bioinformatics applications of PLS. In particular, we provide a systematic comparison of the PLS approaches currently employed, and discuss analysis problems as diverse as, e.g. tumor classification from transcriptome data, identification of relevant genes, survival analysis and modeling of gene networks and transcription factor activities.
Novel Synthetic Routes to Carbon-Nitrogen Thin Films (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel Synthetic Routes to Carbon-Nitrogen Thin FilmsJ. Kouvetakis, Michael Todd, Barry Wilkens, Anil Bandari, and Nigel CaveCite this: Chem. Mater. 1994, 6, 6, 811–814Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/cm00042a018https://doi.org/10.1021/cm00042a018research-articleACS PublicationsRequest reuse permissionsArticle Views1557Altmetric-Citations216LEARN 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 Get e-Alerts
Tyrosine Modification Is Not Required for Myeloperoxidase-induced Loss of Apolipoprotein A-I Functional Activities (2005)

Apolipoprotein A-I (apoAI), the major protein of high density lipoprotein, plays an important role in reverse cholesterol transport via its activity as an ABCA1-dependent acceptor of cellular cholesterol. We reported recently that myeloperoxidase (MPO) modification of apoAI inhibits its ABCA1-dependent cholesterol acceptor activity (Zheng, L., Nukuna, B., Brennan, M. L., Sun, M., Goormastic, M., Settle, M., Schmitt, D., Fu, X., Thomson, L., Fox, P. L., Ischiropoulos, H., Smith, J. D., Kinter, M., and Hazen, S. L. (2004) J. Clin. Invest. 114, 529-541). We also reported that MPO-mediated chlorination preferentially modifies two of the seven tyrosines in apoAI, and loss of parent peptides containing these residues dose-dependently correlates with loss in ABCA1-mediated cholesterol acceptor activity (Zheng, L., Settle, M., Brubaker, G., Schmitt, D., Hazen, S. L., Smith, J. D., and Kinter, M. (2005) J. Biol. Chem. 280, 38-47). To determine whether oxidative modification of apoA-I tyrosine residues was responsible for the MPO-mediated inactivation of cholesterol acceptor activity, we made recombinant apoAI with site-specific substitutions of all seven tyrosine residues to phenylalanine. ApoAI and the tyrosine-free apoAI were equally susceptible to dose-dependent MPO-mediated loss of ABCA1-dependent cholesterol acceptor activity, as well as lipid binding activity. MPO modification altered the migration of apoAI on SDS gels and decreased its alpha-helix content. MPO-induced modification also targeted apoAI tryptophan and lysine residues. Specifically, we detected apoAI tryptophan oxidation to mono- and dihydroxytryptophan and apoAI lysine modification to chlorolysine and 2-aminoadipic acid. Thus, tyrosine modification of apoAI is not required for its MPO-mediated inhibition of cholesterol acceptor activity.
Polyphenols from green tea and pomegranate for prevention of prostate cancer (2006)

Prostate cancer (PCa) is the most common non-cutaneous cancer diagnosed in North America with similar trends in many Western countries. Geographic, epidemiological and laboratory studies suggest a role for dietary constituents in the etiology as well as prevention of PCa. The rising incidence of PCa in several countries appears to be coincidental with adoption of western lifestyle. Increase in the incidence of PCa has also been found in Asian populations migrating to the west. These facts give numerous leads to explore testable PCa prevention strategies. There is growing evidence in support of use of dietary ingredients in prevention and treatment of PCa. While substantial data exists in favor of use of polyphenols from tea as PCa chemopreventive agent, interest in anti-cancer properties of polyphenols from pomegranate has recently emerged. This review summarizes current literature on the effects of polyphenols from green tea and pomegranate against PCa.
Trends in geometric and electronic properties of thiophene‐ and cyclopentadiene‐based polymers (1998)

In this work, we present theoretical evidence illustrating that cyano derivatives of conducting polymers such as polythiophene, polycyclopentadiene, and polyfulvene have smaller intrinsic band gaps than those of their parent polymers. The geometric and electronic properties of the parent and the derivative polymers were studied with the use of two methodologies: (1) the pseudo-one-dimensional band-structure calculations performed using the semi-empirical molecular orbital theory (MNDO, AM1) and (2) oligomer calculations performed using the ab initio molecular orbital theory both at the Hartree–Fock and configuration interaction levels. In particular, we found that an organic polymer, poly(dicyanomethylene cyclopentadifulvene) (PCNFv), has a comparable (possibly lower) band gap to the one observed in poly(dicyanomethylene cyclopentadithiophene) (PCNTH) (which has a band gap of 0.8 eV). The precursor of PCNFv is poly(dicyanomethylene cyclopentadicyclopentadiene) (PCNCY) in which two cyclopentadiene rings are connected by a dicyanomethylene group. The additional bond conjugation (in contrast to PCNCY) perpendicular to the chain axis makes PCNFv very rigid and fully planar. Trends in structural properties indicate that the lower band gaps in the cyano-substituted polymers, in comparison to their parent polymers, are accompanied by a decrease in bond alternations in the aromatic or trans–cisoid forms and by an increase in bond alternations in the quinoid or cis–transoid forms. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 229–240, 1998
Interleukin‐21 Induces Proliferation and Proinflammatory Cytokine Profile of Fibroblast‐like Synoviocytes of Patients with Rheumatoid Arthritis (2015)

Fibroblast-like synoviocytes (FLS) play a pivotal role in the pathogenesis of rheumatoid arthritis (RA) through aggressive proliferation and invasion, and certain proinflammatory cytokines may affect synoviocyte proliferation. To evaluate whether interleukin-21 (IL-21) could promote proliferation and proinflammatory cytokine production by RA-FLS, immunohistochemistry and immunoblotting were performed to observe the expression of IL-21 receptor (IL-21R) in synovial tissues and FLS from RA and osteoarthritis (OA) patients. The MTS assay was used to analyse RA-FLS proliferation. The concentrations of IL-6 and tumour necrosis factor-α (TNF-α) in culture supernatants were determined by enzyme-linked immunosorbent assay (ELISA). The signalling pathways triggered by IL-21 were characterized by immunoblotting. IL-21R was upregulated in the synovial tissues and FLS of RA patients as compared with OA patients. IL-21 stimulated RA-FLS proliferation and promoted the production of TNF-α and IL-6 and blockade of IL-21/IL-21R pathway with IL-21R.Fc attenuated IL-21-induced proliferation and secretion of TNF-α and IL-6. Moreover, IL-21 induced activation of the ERK1/2, PI3K/AKT and STAT3 pathways, and blockade of these pathways attenuated IL-21-induced proliferation and secretion of TNF-α and IL-6. These results suggest that IL-21 could promote RA-FLS proliferation and production of proinflammatory cytokines. Therefore, therapeutic strategies targeting IL-21 might be effective for the treatment of RA.
Assignment of the proton and carbon NMR spectra of the indoloquinoline alkaloid cryptolepine (1991)

Abstract The relatively rare alkaloid cryptolepine, 5‐methyl‐5 H ‐indolo[3,2‐ b ]quinoline, was isolated from Cryptolepis sanguinolenta (Lindl.) Schlecter ( Asclepiadaceae ). Unequivocal proton and carbon nmr assignments in dimethyl sulfoxide are reported based on two‐dimensional nmr methods, including COSY, inverse‐detected direct (HMQC), and long‐range (HMBC) correlations. Several of the assignments were confirmed using one‐dimensional SIMBA spectra ‐ a new, selective, one‐dimensional analogue of the proton‐detected long‐range heteronuclear shift correlation experiment (HMBC). The SIMBA experiment was also used in an attempt to observe a two‐bond coupling from the H11 proton to C10a at several optimizations.
Hybrid eye tracking for computer-aided retinal surgery. (1996)

We describe initial results of a new hybrid digital and analog design for tracking the retina and controlling the laser beam. The results demonstrate tracking rates which exceed the equivalent of 50 degrees per second in the eye, with automatic lesion pattern creation and robust loss of lock detection. Robotically-assisted laser surgery to treat conditions such as diabetic retinopathy, macular degeneration, and retinal tears can now be realized under clinical conditions with requisite safety using standard video hardware and inexpensive optical components.
FGFR3-targeted mAb therapy for bladder cancer and multiple myeloma (2009)

Gain-of-function mutations in FGF receptor 3 (FGFR3) have been implicated in severe skeletal dysplasias and in a variety of cancers. In their study in this issue of the JCI, Qing et al. used specific shRNA probes to demonstrate that FGFR3 functions as an important driver of bladder carcinoma cell proliferation (see the related article beginning on page 1216). A unique anti-FGFR3 mAb was shown to exhibit antitumor activity in human bladder carcinoma cells in vitro and in mouse bladder cancer or multiple myeloma xenograft tumor models bearing either wild-type or mutant FGFR3. These results suggest that clinical development of anti-FGFR3 mAbs should be considered for targeted therapy of cancer and other diseases.
Object modeling by geometric matching for a prospective portable 3D scanner (1999)

With the evolution of 3D-scanner technology, the combined measurement of color and geometry of objects and scenes becomes feasible within a portable device. It opens new perspectives for the generation of virtual 3D models and applies to domains like multimedia, museography, reverse engineering... Several scanner technologies and object modeling schemes are possible. This paper discusses some of these possibilities and shows why the modeling by geometric matching of object views efficiently assists a universal portable device in the modeling task. It introduces the concept of a global architecture involving a remote portable 3D scanner linked to a powerful modeling facility and presents examples for the expected results.
In vitro activity of fosfomycin against 'problem' gram-positive cocci. (1992)

Fosfomycin was active in vitro against 54 of 60 'problem' Gram-positive cocci (20 methicillin-resistant Staphylococcus aureus, 20 coagulase-negative staphylococci and 20 enterococci). Its activity was significantly greater under anaerobic conditions, especially against coagulase-negative staphylococci. Mutants resistant to fosfomycin were readily demonstrated, but their growth was prevented by rifampicin or ciprofloxacin. The combinations rifampicin+fosfomycin and ciprofloxacin+fosfomycin showed MIC synergy. It is concluded that fosfomycin in an appropriate combination would be a valuable addition to the small and dwindling range of antibiotics active against problem Gram-positive cocci.
Influence of hydrogen treatment and annealing processes upon the Schottky barrier height of Au/n-GaAs and Ti/n-GaAs diodes (2004)

After annealing in a H2 atmosphere at different temperatures, ⟨100⟩-oriented n-GaAs substrates were metallized with Au and Ti layers of different thicknesses to form Au/n-GaAs and Ti/n-GaAs Schottky diodes. The Schottky barrier height (SBH) variation and its dependence on subsequent N2 annealing for these Schottky diodes have been studied by different measurement techniques (I–V, C–V and BEEM) to obtain reliable values. These methods show that pre-metallization annealing leads to a less homogeneous metal semiconductor (MS) interface. In case of thick Au layers the effective barrier height is reduced as soon as the H2 annealing temperature reaches 300 °C. However, GaAs samples covered with thin Au layers or Ti layers do not exhibit such a barrier height reduction. The lower value in the case of thick Au layers is attributed to H+ groups, present at the interface due to the annealing in H2 atmosphere, forming interfacial dipoles with Au, leading to an inhomogeneous barrier and a decrease of the effective barrier height. It seems that these dipoles disappear again in the case of thin Au layers or are not formed with Ti. Post-metallization N2 annealing at higher temperatures lowers the barrier height for all samples. The resulting barrier inhomogeneities are explained and analysed using the bond polarization theory of Tung (2001 Phys. Rev. B 64 205310, 2001 Mater. Sci. Eng. R 35), a recent Schottky barrier formation model and the pinch-off model (Tung 1992 Phys. Rev. B 45 13509).
Amino Acid-Functionalized Dendrimers with Heterobifunctional Chemoselective Peripheral Groups for Drug Delivery Applications (2010)

Dendrimers have emerged as multifunctional carriers for targeted drug delivery, gene delivery and imaging. Improving the functional versatility at the surface for carrying multiple conjugation reactions is becoming vital. Typically, generation four polyamidoamine (G4-PAMAM) dendrimers bear approximately 64 symmetrical end groups, often requiring different spacers to conjugate various functional groups (drugs and targeting moities), increasing the synthetic steps. In the present study, a simple one-step synthesis to convert each symmetrical end group of G4-PAMAM dendrimers into two reactive, distinct orthogonal and chemoselective groups is described. A near-complete end-capping of the dendrimers (87-93%) with amino acids results in heterobifunctional G4-PAMAM dendrimers bearing a very high (> or = 110) diverse peripheral end groups (OH+NHBoc, OH+COOMe, SH+NHBoc, and COOH+NHBoc). Postfunctionalization ability of these dendrimers was evaluated. The heterobifunctional groups at the dendrimer periphery could be chemoselectively conjugated to multiple moities such as drugs (indomethacin and dexamethasone) and drugs and imaging agents (dexamethasone and FITC). These conjugations could be achieved in immediate succession without functional group conversions, eliminating the additional elaborate synthetic steps traditionally required to append specific linkers. Furthermore, one of the two functional handles at periphery was used to develop in situ forming hydrogels, whereas the other handle could be used for conjugating the drugs (e.g., dexamethasone). The heterobifunctional dendrimers with either "NH(2) or SH (thiopyridyl protected form)" terminations showed in situ hydrogel formation by cross-linking with N-hydroxysuccinimide or thiol-terminated multiarm polyethylene glycol (20 kDa). The choice of amino acids as versatile linkers would enable biocompatible dendrimer scaffolds for use in drug delivery. Zeta-potential measurements showed drastic lowering of the charge on G4-PAMAM-NH(2) dendrimers by end-capping with amino acids, whereas in the case of neutral G4-PAMAM-OH dendrimers, the charge did not increase or decrease substantially. The in vitro cytotoxicity and hemolysis assay showed that the heterobifunctional dendrimers were noncytotoxic in the 100 ng/mL to 1 mg/mL concentration range. With this study, we demonstrate the development of biocompatible dendrimers bearing multiple orthogonal surface groups, enabling the attachment of drugs, imaging agents, and gel formation using minimal synthetic steps.
Chlamydia trachomatis RNA polymerase alpha subunit: sequence and structural analysis (1995)

We describe the cloning and sequence analysis of the region surrounding the gene for the alpha subunit of RNA polymerase from Chlamydia trachomatis. This region contains genes for proteins in the order SecY, S13, S11, alpha, and L17, which are equivalent to Escherichia coli and Bacillus subtilis r proteins. The incorporation of chlamydial alpha subunit protein into the E. coli RNA polymerase holoenzyme rather than its truncated variant lacking the amino terminus suggests the existence of structural conservation among alpha subunits from distantly related genera.
Twelve immunotherapy drugs that could cure cancers (2008)

Immune T cells can kill cancer cells. Cancer vaccines function by increasing the number of immune T cells. There are exceedingly strict biologic limits imposed on the immune system to prevent excessive T-cell activation and expansion. The same biological restrictions limit cancer vaccines. Immunotherapeutic agents that circumvent the biological restrictions have been invented and formulated, including (i) dendritic cell activators and growth factors, (ii) vaccine adjuvants, (iii) T-cell stimulators and growth factors, (iv) immune checkpoint inhibitors, and (v) agents to neutralize or inhibit suppressive cells, cytokines, and enzymes. Few of these agents are broadly available for the development of effective multiple component regimens. The major problem facing immunotherapy today is a lack of broad availability of agents already in existence. The National Cancer Institute has developed a well-vetted ranked list of agents with high potential to serve as immunotherapeutic drugs. This review focuses on 12 of the agents, all with proven ability to augment T-cell responses. Alone, each has little chance of making substantial inroads into cancer therapy. In combinations dictated by biology, the agents are overwhelmingly likely to have an impact. Future availability of these agents for development of innovative combination cancer therapy regimens will provide a benchmark for the resolve of the national cancer therapy translational research enterprise.
Environmentally Benign Formation of Polymeric Microspheres by Rapid Expansion of Supercritical Carbon Dioxide Solution with a Nonsolvent (2001)

A novel method is reported for forming polymer microparticles, which reduce atmospheric emissions of environmentally harmful volatile organic compounds such as toluene and xylene used as paint solvent in paint industry. The polymer microparticles have formed through rapid expansion from supercritical solution with a nonsolvent (RESS-N). Solubilization of poly(styrene)-b-(poly(methyl methacrylate)-co-poly (glycidyl methacrylate)) copolymer(PS-b-(PMMA-co-PGMA), MW = 5000, PS/PMMA/PGMA = 2/5/3), poly(ethylene glycol) (PEG, M. W = 4000), bisphenol A type epoxy resin (EP, MW = 3000), poly(methyl methacrylate) (PMMA; MW = 15000, 75000, 120000), and poly(oxyalkylene) alkylphenyl ether (MW = 4000) in carbon dioxide (CO2) was achieved with the use of small alcohols as cosolvents. The solubility of the PS-b-(PMMA-co-PGMA) is extremely low in either CO2 or ethanol but becomes 20 wt % in a mixture of the two. Because ethanol is a nonsolvent for the polymer, it can be used as a cosolvent in rapid expansion from supercritical solution to produce 1-3 microm particles that do not agglomerate. Obtained polymer particles by RESS-N were applied as powder coatings. The resulting coatings have a smooth and coherent film. The particle size distribution of microspheres was controlled by changing the polymer concentration, preexpansion pressure, temperature, and injection distance. The feed compositions were more effective than the other factors in controlling the particle size. The polymeric microparticles formed by RESS-N method can be utilized to make the thin coating film without anytoxic organic solvents and/or surfactants.
IFN- beta production by macrophages obtained from mice undergoing graft vs host disease. (1988)

We have previously shown that when splenocytes are obtained from mice undergoing graft vs host disease (GVHD), and then placed in culture, IFN-beta is produced spontaneously in supernatants without any stimulus. Thus, when B10.D2 spleen cells are injected into sublethally irradiated BALB/c recipient mice, in vitro splenic IFN-beta production is readily apparent between days 10 to 20 post-transplantation. In the present study, experiments were carried out to characterize the cell population(s) responsible for spontaneous IFN-beta production from GVHD spleen cells. Specific antibody and C lysis of selected cell types, including T cells, B cells, and NK cells, failed to abrogate in vitro IFN production. However, IFN-producing cells from GVHD splenocytes were nylon wool adherent and could be isolated using discontinuous Percoll gradient centrifugation from the upper most large cell fractions. IFN production was also partially resistant to irradiation. Using indirect immunofluorescence and flow cytometry, IFN production was shown to be associated with MAC-1 positive cells. MAC-1 negative splenocytes demonstrated no spontaneous IFN production. Treatment of GVHD spleen cells with silica, a selective toxin for phagocytic cells, resulted in a complete inhibition of IFN production. Thus, in vitro IFN production from GVHD splenocytes appeared to come from cells having a phenotype associated with macrophages. This in vitro IFN production by macrophages represents a unique aspect of GVHD which is not typically found in tissues of normal mice.
Detection of terahertz radiation in gated two-dimensional structures governed by dc current (2006)

We present theoretical and experimental studies of the direct current effect on the detection of subterahertz and terahertz radiation in gated two-dimensional structures. We developed a theory of the current-driven detection both for resonant case, when the fundamental frequency of plasma oscillation is large compared to inverse scattering time, ${\ensuremath{\omega}}_{0}\ensuremath{\tau}⪢1$, and for the nonresonant case, ${\ensuremath{\omega}}_{0}\ensuremath{\tau}⪡1$, when the plasma oscillations are damped. We predict that, in the nonresonant case, even a very small dc current would increase the detection amplitude up to two orders of magnitude. Physically, this increase is related to an abrupt transition from the linear to saturation region near the knee of the current-voltage characteristic. When the current increases up to the saturation value, the electron concentration near the drain becomes very low and can be strongly affected by a small external field. As a consequence, the two-dimensional channel becomes extremely sensitive to external perturbations. In the resonant case, the detection amplitude has maxima when the radiation frequency is equal to fundamental plasma frequency and its harmonics. We predict that the effective linewidths of the respective resonances would decrease with the increasing current. Physically, this happens because dc current shifts the system towards the plasma wave instability. At some critical current value, the width corresponding to the fundamental frequency would turn to zero, indicating the onset of plasma waves generation. Our experimental measurements performed on $\mathrm{GaAs}$ HEMT confirm the theoretical predictions.