gebhart/patrepeval huggingface dataset:
Fundamentals of Supported Catalysts for Atom Transfer Radical Polymerization (ATRP) and Application of an Immobilized/Soluble Hybrid Catalyst System to ATRP (2002)

A series of hybrid catalysts, comprising a tethered ligand immobilized catalyst operating in conjunction with a small amount of soluble catalyst, were evaluated for atom transfer radical polymerization (ATRP). The level of control over the ATRP of vinyl monomers was significantly improved by the addition of part per million levels of a soluble catalyst, or soluble catalyst precursor, to the immobilized catalyst. Use of a hybrid catalyst system for polymerization of vinyl monomers such as MMA, MA, and styrene provided polymers with a predetermined molecular weight and a narrow molecular weight distribution. The immobilized catalyst can be removed from the polymerization by simple filtration, or sedimentation, affording a colorless transparent polymer solution with a salient reduction in the concentration of any residual transition metal in the final polymeric products.
Subspace clustering of images using Ant colony Optimisation (2009)

Content-based image retrieval can be dramatically improved by providing a good initial clustering of visual data. The problem of image clustering is that most current algorithms are not able to identify individual clusters that exist in different feature subspaces. In this paper, we propose a novel approach for subspace clustering based on Ant Colony Optimisation and its learning mechanism. The proposed algorithm breaks the assumption that all of the clusters in a dataset are found in the same set of dimensions by assigning weights to features according to the local correlations of data along each dimension. Experiment results on real image datasets show the need for feature selection in clustering and the benefits of selecting features locally.
Neuraminidase from Trypanosoma cruzi: analysis of enhanced expression of the enzyme in infectious forms. (1987)

We purified the neuraminidase (sialidase, acylneuraminyl hydrolase, EC 3.2.1.18) from the protozoan parasite Trypanosoma cruzi, strain Y, and examined the developmental regulation of the enzyme. The detectable amount of enzyme activity increased 10- to 20-fold upon conversion of the parasite from the noninfectious epimastigote form to the infectious trypomastigote form. The enzyme was purified from membranes of trypomastigotes greater than 5000-fold to apparent homogeneity and migrated as an entity of Mr 60,000 under denaturing conditions. Antibodies produced in rabbits against the denatured protein recognized the neuraminidase in membrane extracts from the infectious stage but not from the noninfectious stage. Sera from a patient with acute chagasic disease also reacted strongly with the neuraminidase. Other T. cruzi strains exhibited similar neuraminidase activities and induction rates. The coincidence of infectivity and enhanced expression of neuraminidase in trypomastigotes suggests that this enzyme constitutes a virulence factor in T. cruzi.
ChemInform Abstract: Design of Chiral Bifunctional Secondary Amine Catalysts for Asymmetric Enamine Catalysis (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Protein Kinase C Inhibitor Generates Stable Human Tolerogenic Dendritic Cells (2013)

Tolerogenic dendritic cells (DCs) are a promising tool for a specific form of cellular therapy whereby immunological tolerance can be induced in the context of transplantation and autoimmunity. From libraries of bioactive lipids, nuclear receptor ligands, and kinase inhibitors, we screened conventional protein kinase C inhibitors (PKCIs) bisindolylmaleimide I, Gö6983, and Ro32-0432 with strong tolerogenic potential. PKCI-treated human DCs were generated by subjecting them to a maturation process after differentiation of immature DCs. The PKCI-treated DCs had a semimature phenotype, showing high production of IL-10, and efficiently induced IL-10-producing T cells and functional Foxp3(+) regulatory T cells from naive CD4(+) T cells, thus eliciting a strong immunosuppressive function. They also showed CCR7 expression and sufficient capacity for migration toward CCR7 ligands. Additionally, PKCI-treated DCs were highly stable when exposed to inflammatory stimuli such as proinflammatory cytokines or LPS. Conventional PKCIs inhibited NF-κB activation of both the canonical and noncanonical pathways of DC maturation, thus suppressing the expression of costimulatory molecules and IL-12 production. High production of IL-10 in PKCI-treated DCs was due to not only an increase of intracellular cAMP, but also a synergistic effect of increased cAMP and NF-κB inhibition. Moreover, PKCI-treated mouse DCs that had properties similar to PKCI-treated human DCs prevented graft-versus-host disease in a murine model of acute graft-versus-host disease. Conventional PKCI-treated DCs may be useful for tolerance-inducing therapy, as they satisfy the required functional characteristics for clinical-grade tolerogenic DCs.
The Origins of Femtomolar Protein−Ligand Binding:  Hydrogen-Bond Cooperativity and Desolvation Energetics in the Biotin−(Strept)Avidin Binding Site (2007)

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each--NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.
A role for FOXO1 in BCR–ABL1-independent tyrosine kinase inhibitor resistance in chronic myeloid leukemia (2016)

Chronic myeloid leukemia (CML) patients who relapse on imatinib due to acquired ABL1 kinase domain mutations are successfully treated with second-generation ABL1-tyrosine kinase inhibitors (ABL-TKIs) such as dasatinib, nilotinib or ponatinib. However, ~40% of relapsed patients have uncharacterized BCR-ABL1 kinase-independent mechanisms of resistance. To identify these mechanisms of resistance and potential treatment options, we generated ABL-TKI-resistant K562 cells through prolonged sequential exposure to imatinib and dasatinib. Dual-resistant K562 cells lacked BCR-ABL1 kinase domain mutations, but acquired other genomic aberrations that were characterized by next-generation sequencing and copy number analyses. Proteomics showed that dual-resistant cells had elevated levels of FOXO1, phospho-ERK and BCL-2, and that dasatinib no longer inhibited substrates of the PI3K/AKT pathway. In contrast to parental cells, resistant cells were sensitive to growth inhibition and apoptosis induced by the class I PI3K inhibitor, GDC-0941 (pictilisib), which also induced FOXO1 nuclear translocation. FOXO1 was elevated in a subset of primary specimens from relapsed CML patients lacking BCR-ABL1 kinase domain mutations, and these samples were responsive to GDC-0941 treatment ex vivo. We conclude that elevated FOXO1 contributes to BCR-ABL1 kinase-independent resistance experienced by these CML patients and that PI3K inhibition coupled with BCR-ABL1 inhibition may represent a novel therapeutic approach.
Fully automated VMAT treatment planning for advanced-stage NSCLC patients (2017)

Clinically deliverable, high-quality autoVMAT plans can be generated fully automatically for the vast majority of advanced-stage NSCLC patients. For a subset of patients, autoVMAT allowed for tumor dose escalation.
Cross-Linking CD98 Promotes Integrin-like Signaling and Anchorage-independent Growth (2002)

CD98, an early marker of T-cell activation, is an important regulator of integrin-mediated adhesion events. Previous studies suggest that CD98 is coupled to both cellular activation and transformation and is involved in the pathogenesis of viral infection, inflammatory disease, and cancer. Understanding of the molecular mechanisms underlying CD98 activity may have far-reaching practical applications in the development of novel therapeutic strategies in these disease states. Using small cell lung cancer cell lines, which are nonadherent, nonpolarized, and highly express CD98, we show that, in vitro, under physiological conditions, CD98 is constitutively associated with beta1 integrins regardless of activation status. Cross-linking CD98 with the monoclonal antibody 4F2 stimulated phosphatidylinositol (PI) 3-kinase, PI(3,4,5)P(3), and protein kinase B in the absence of integrin ligation or extracellular matrix engagement. Furthermore, cross-linking CD98 promoted anchorage-independent growth. Using fibroblasts derived from beta1 integrin null stem cells (GD25), wild-type GD25beta1, or GD25 cells expressing a mutation preventing beta1 integrin-dependent FAK phosphorylation, we demonstrate that a functional beta1 integrin is required for CD98 signaling. We propose that by cross-linking CD98, it acts as a "molecular facilitator" in the plasma membrane, clustering beta1 integrins to form high-density complexes. This results in integrin activation, integrin-like signaling, and anchorage-independent growth. Activation of PI 3-kinase may, in part, explain cellular transformation seen on overexpressing CD98. These results may provide a paradigm for events involved in such diverse processes as inflammation and viral-induced cell fusion.
Elektromágneses hullámok mesterséges periodikus szerkezetekben = Electromagnetic waves in artificial periodical structures (2007)

Pórusos szilícium mintákban egydimenziós fotonikus kristályok állítottunk elő. Az elvégzett mérésekről és a hullámterjedés FDTD modellezéséről megjelent publikációink a közleményjegyzék 4., 7., 8., 11. és 21. tételei. FDTD modellezéssel vizsgáltuk a hullámterjedést kétdimenziós fotonikus kristályokban és beépített hullámvezető hibavonalak mentén. A kétdimenziós számításokról a jegyzék 16., valamint 12., 14., 19 és 20. tételeit közöltük. Előkészületeket tettünk az MTA MFA nanomegmunkáló laborjában, az egybeépített elektronmikroszkóp és fókuszált ionnyaláb alkalmazásával kétdimenziós fotonikus kristályok előállítására. A BME Fizikai Kémia Tanszékének kutatóival együttműködést kezdeményeztünk a Langmuir-Blodgett kísérleti módszer alkalmazására kétdimenziós fotonikus kristályok előállítása céljából. Ez az "önszerveződő maszkolási" eljárás teljesen újszerűnek bizonyult és erre vonatkozó publikációinkat komoly szakirodalmi sikernek tekintjük (a jegyzék 22-28. tételei). A témakör népszerűsítésére vonatkozó publikációink a jegyzék 1., 2., 3., 5. és 13. tételei. Két munkatársunk Japánban kapott 2 éves munkalehetőséget: Szabó Zsolt a 3 dimenziós FDTD módszer programkódjának elkészítésén, Volk János a kétdimenziós fotonikus kristály szerű ZnO szerkezetek előállításán és kísérleti vizsgálatán dolgozik. A beruházási keretből ''Nanocube'' típusú nanométer felbontású pozicionáló berendezést vásároltunk. | One dimensional photonic crystals have been prepared in Porous silicon samples. The experimental observations and the FDTD modeling of wave propagation in such structures have been published as the 4., 7., 8., 11. and 21. items of the publication list. Wave propagation has been studied in two dimensional photonic crystals and along wave-guides built therein using FDTD modeling. Publications on two dimensional structures are the 16., as well as the 12., 14., 19. and 20. items. We have attempted the preparation of two dimensional photonic crystals by applying focused ion beam in the nanofabrication lab of our MTA MFA institute. In cooperation with the Physical Chemistry Depertment of BME (BTU) we have intended to apply the Langmuir-Blodgett technique for the preparation of two dimensional photonic crystals. Asa result the ''self-assembled masking'' procedure proved to be a genuine novelty and our publications of the method are considered as works attracting serious impact (22.-28.items). In several publications we intended to disseminate popularizing information for wider community (1., 2., 3., 5. and 13. items of the list) Two colleagues work in Japan, Zsolt Szabó on coding of three dimensional FDTD modeling, János Volk on preparation and experimental study of periodic ZnO two dimensional structures. We have purchased a "Nanocube" type positioning device of nanometer acccuracy.
Application of Stabilization/Solidification Technology on Oil Refinery Sludge Contaminated by Heavy Metals (2004)

The oily sludge produced by petroleum refineries is classified as a solid hazardous waste, according to European regulations. The objective of this work was to investigate whether stabilization/solidification can be used as a management method for the oily sludge. The sludge samples used originated from a petroleum-storing tank and a centrifuge unit of two Greek refineries. The experiments were designed to study the leachability of the heavy metals Pb, Cr, Cd, Ni, and Cu, which are contained in the sludge, using the Toxicity Characteristic Leaching Procedure (TCLP). Despite the fact that the metals were immobilized in a cement-based environment in the presence of organic load, leaching tests have shown a low metal leachability, less than 5%. Acid Neutralizing Capacity (ANC) tests were employed in order to estimate the acid resistance of the stabilized/solidified waste. In addition to ANC, a sequential TCLP test was employed in order to understand how the pH affects the leachability of Ni from the stabilized/solidified specimen.
Photoprotection due to pigmentation and epidermal thickness after repeated exposure to ultraviolet light and psoralen plus ultraviolet A therapy (1995)

Tanning and thickening of the epidermis are cardinal defensive responses of human skin to ultraviolet (UV) radiation that lead to increased photoprotection. Earlier studies have shown that skin pigmentation can be used to predict minimal erythema dose and minimal phototoxic dose. In this study it was calculated how much of the increase in photoprotection after 4 weeks of repeated exposure to suberythemogenic doses of either UVA or UVB radiation sources or psoralen plus UVA (PUVA) therapy that was attributable to melanogenesis. The backs of 12 volunteers were exposed to 6 different UVA and UVB radiation sources 9 times during 4 weeks. Skin pigmentation was assessed by skin reflectance measuring. Photoprotection was determined from the minimal erythema dose. Melanogenesis accounted for 63-95% of the increase in photoprotection after 4 weeks of exposure to UVA radiation. Exposure to two UVB sources induced a significant increase in photoprotection but not in pigmentation. Melanogenesis accounted only for 6-11% of the increase in photoprotection after 4 weeks of UVB exposure. The pigmentary and photoprotective responses to PUVA therapy were followed in 14 patients. After 2 weeks of exposure, the increase in photoprotection was significantly higher than predicted from the increase in skin pigmentation. After 4 weeks, melanogenesis accounted for only 36% of the increase in photoprotection. This study shows that melanogenesis accounts for the increased photoprotection after 2 weeks of exposure to UVA radiation, but after 4 weeks other protective mechanisms occur. During suberythemal UVB exposure and during PUVA therapy the importance of skin pigmentation in the overall photoprotection gradually decreases during a 4-week irradiation period.
Series hybrid electric vehicle supervisory control based on off-line efficiency optimization (2012)

A supervisory control system (SCS) is developed for a dynamic model of a series hybrid electric vehicle. The powertrain steady-state behavior is analyzed to produce a control map offline which maximizes the vehicle energy efficiency for any driving condition. This map can be accessed on a real-time basis during driving at low computational cost to locally optimize efficiency. The vehicle transient response is considered to ensure efficient, stable and healthy operation. Simulations using standard drive cycles verify that the designed Efficiency Maximizing Map (EMM) control allows smoother operation of the powertrain and it brings reductions in fuel consumption as compared to a Thermostat control scheme.
Treatment and Prognosis of Anaplastic Thyroid Carcinoma: Experience from a Single Institution in China (2013)

We found that the elevated peripheral PLT count may be an adverse prognostic factor of ATC patients. The prognosis for ATC is especially poor for patients with distant metastasis, a WBC count ≥ 10.0×10(9)/L, a PLT count ≥ 300.0 × 10(9)/L, or age ≥ 55 years. WBC count at presentation and surgery with or without postoperative radiotherapy independently influenced the prognosis. Intensive treatment combining surgery with postoperative radiotherapy is recommended for ATC patients with stage IVA/B disease.
Transient Behavior of Annular Pressure Build-up in HP/HT Wells (2004)

Pressure build-up due to fluid thermal expansion in sealed annuli of HP/HT wells can have serious consequences such as casing failure or tubing collapse. To determine whether mitigation was required for a HP/HT development, annular pressures in an appraisal well were studied with a dedicated field test, which consisted of running a pressure/temperature memory gauge in a casing/casing annulus of a well and testing the well several times during a 3-month period, after which the gauge was retrieved and the data were read out.First of all, comparison of the magnitude of the observed annular pressures with the burst and collapse ratings of the casings, shows that annular pressure build-up is a serious consideration in casing design. Such design is to be based on theoretical models for annular pressure build-up. The data acquired with the test serve to validate these models.The data demonstrated that in the lower temperature range (20 to 40 °C), on average, pressure development in the annulus agreed reasonably well with theoretical model predictions, based on thermal expansion of the annular fluids and casings, and ballooning and compression of the casing strings. The influence of these factors could be established by analyzing the transient pressure response of the annulus. At higher temperatures the theoretical models overestimate pressure build-up. This is probably to be attributed to the properties of the completion fluids differing from the properties of the base fluid, water. Estimates on the basis of pure water properties can be considered a worst-case estimate for pressure build-up.Leak-off of the annular fluids, which was seen to dominate pressure development during a previous test in a well with a cement shortfall between casings, did not play a significant role in this fully cemented and sealed annulus.
Abstract 13287: Anti-Apoptotic BAG3 Gene in Tako-Tsubo Cardiomyopathy (2012)

Background and aim: Tako-tsubo cardiomyopathy (TTC) is a stress related acute cardiac condition characterized by transient myocardial stunning inducing left ventricular systolic dysfunction in abse...
Lost in Transgenesis (2012)

The advent of modern mouse genetics has benefited many fields of diseased-based research over the past 20 years, none perhaps more profoundly than cardiac biology. Indeed, the heart is now arguably one of the easiest tissues to genetically manipulate, given the availability of an ever-growing tool chest of molecular reagents/promoters and "facilitator" mouse lines. It is now possible to modify the expression of essentially any gene or partial gene product in the mouse heart at any time, either gain or loss of function. This review is designed as a handbook for the nonmouse geneticist and/or junior investigator to permit the successful manipulation of any gene or RNA product in the heart, while avoiding artifacts. In the present review, guidelines, pitfalls, and limitations are presented so that rigorous and appropriate examination of cardiac genotype-phenotype relationships can be performed. This review uses examples from the field to illustrate the vast spectrum of experimental and design details that must be considered when using genetically modified mouse models to study cardiac biology.
Abstract 2127: The role of FOXD3 in resistance to PLX4032/4720-induced cell death in mutant B-RAF melanoma cells (2011)

Abstract Melanoma cells driven by mutant B-RAF are highly resistant to chemotherapeutic treatment. Recent phase I results with PLX4032/RG7204, which selectively inhibits BRAF/MEK/ERK1/2 signaling in mutant B-RAF cells, has given encouragement to this struggling field. Despite initial tumor shrinkage, most responders in the trial experienced tumor relapse over time. Furthermore, 19% of patients failed to show any significant tumor regression. These findings indicate that both intrinsic and acquired resistance will hamper the clinical efficacy of PLX4032. We have previously shown that the stemness factor, FOXD3, is up-regulated following inhibition of mutant B-RAF-MEK signaling in mutant B-RAF melanoma cells. Here, we show that up-regulation of FOXD3 after PLX4032 and PLX4720 (the non-clinical tool compound for PLX4032) treatment confers resistance to cell death. siRNA-mediated knockdown of FOXD3 significantly enhanced the cell death response after PLX4032/4720 treatment in mutant B-RAF melanoma cell lines. Additionally, up-regulation of FOXD3 after PLX4720 treatment was attenuated in non-adherent conditions and correlated with enhanced cell death. Ectopic expression of FOXD3 in non-adherent cells significantly reduced cell death in response to PLX4720 treatment. Together, these data indicate that up-regulation of FOXD3 is an adaptive response to B-RAF inhibitors that promotes a state of drug resistance. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2127. doi:10.1158/1538-7445.AM2011-2127