gebhart/patrepeval huggingface dataset:
Identification of 14-3-3σ as a Contributor to Drug Resistance in Human Breast Cancer Cells Using Functional Proteomic Analysis (2006)

Multidrug resistance (MDR) is a major obstacle to successful cancer treatment. To understand the mechanism of MDR, many cancer cell lines have been established, and various mechanisms of resistance, such as ATP-binding cassette (ABC) transporter-mediated drug efflux, have been discovered. Previously, a MDR cell line MCF7/AdVp3000 was selected from breast cancer cell line MCF7 against Adriamycin, and overexpression of ABCG2 was thought to cause MDR in this derivative cell line. However, ectopic overexpression of ABCG2 in MCF7 cells could not explain the extremely high drug resistance level of the selected MCF7/AdVp3000 cells. We hypothesized that MCF7/AdVp3000 cells must have other resistance mechanisms selected by Adriamycin. To test this hypothesis, we compared the global protein profiles between MCF7 and MCF7/AdVp3000 cells. Following two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis, 17 protein spots with differential levels between the two cell lines were identified. Although 14-3-3sigma, keratin 18, keratin 19, ATP synthase beta, protein disulfide isomerase, heat shock protein 27, cathepsin D, triose-phosphate isomerase, peroxiredoxin 6, and electron transfer flavoprotein were increased, nm23/H1, peroxiredoxin 2, nucleophosmin 1/B23, and inorganic pyrophosphatase were decreased in MCF7/AdVp3000 cells. The differential levels of these proteins were validated using Western blot. Furthermore, functional validation showed that the elevated 14-3-3sigma expression contributes considerably to the observed drug resistance in MCF7/AdVp3000 cells. We, thus, conclude that these proteins likely contribute to the resistance selected in the MCF7/AdVp3000 cells, and their altered expression in tumors may cause clinical resistance to chemotherapy.
Growth and Characterization of Epitaxial ZnO Thin Films on GaN(0001) Epilayers and ZnO{0001} Substrates Using Metalorganic Chemical Vapor Depositon (2005)

ZnO thin films were produced on GaN(0001) epilayers and ZnO(0001) substrates utilizing an iterative process requiring a structured low temperature (480&amp;deg;C) layer followed by a high temperature (800&amp;deg;C) densification step to create approximately 200 nm of contiguous film. This process is subsequently repeated to achieve thicker films with each iteration producing approximately 200 nm of dense film. Diethylzinc was used as the zinc source, UHP oxygen (O2) as the oxygen source, and UHP argon as both the carrier and diluent gas. Nitrous (N2O) and nitric oxide (NO2) were also used both as potential oxygen sources in the pure state as well as mixed with oxygen in the chamber and for nitrogen doping of the growing film. Major impurities of C, H, and N were incorporated into the films with the majority of the incorporation occurring during the low temperature step. Films grown using N2O + O2 contained an average of 5 x 1017 cm-3 atomic nitrogen while films using NO2 + O2 had an average nitrogen concentrations of 9 x 1019 cm-3. Needle microstructures were observed for low temperature layers using O2 and N2O + O2, while networked structures formed when using NO2 + O2. The surface of the densified films contained hexagonal pits that increased in number and depth with an increase in film thickness. Triple-axis XRD measurements indicated that the crystal structure of the films mimic the underlying substrates. A comparative analysis of undoped and N-doped films using capacitance voltage and photoluminescence measurements showed that the N-doped films were more insulating than the undoped films and the incorporation of nitrogen decreases the amount of excitonic peaks observed in the PL spectra. The 3.367 eV ionized donor bound exciton becomes dominant in N-doped films relative to the 3.361 eV donor bound exciton that dominates the undoped films. A preliminary inductively coupled plasma etching study determined that the smoothest sidewalls and surfaces were obtained using an ICP power of 600 W, a DC bias of 50 V, 5 mtorr total pressure, and 20 sccm of pure flowing BCl3 The etch rate under these conditions was 40 nm/min.
Zwitterion Functionalized Silica Nanoparticle Coatings: The Effect of Particle Size on Protein, Bacteria, and Fungal Spore Adhesion (2018)

The negative impacts that arise from biological fouling of surfaces have driven the development of coatings with unique physical and chemical properties that are able to prevent interactions with fouling species. Here, we report on low-fouling hydrophilic coatings presenting nanoscaled features prepared from different size silica nanoparticles (SiNPs) functionalized with zwitterionic chemistries. Zwitterionic sulfobetaine siloxane (SB) was reacted to SiNPs ranging in size from 7 to 75 nm. Particle stability and grafting density were confirmed using dynamic light scattering and thermogravimetric analysis. Thin coatings of nanoparticles were prepared by spin-coating aqueous particle suspensions. The resulting coatings were characterized using scanning electron microscopy, atomic force microscopy, and contact angle goniometry. SB functionalized particle coatings displayed increased hydrophilicity compared to unmodified particle coating controls while increasing particle size correlated with increased coating roughness and increased surface area. Coatings of zwitterated particles demonstrated a high degree of nonspecific protein resistance, as measured by quartz crystal microgravimetry. Adsorption of bovine serum albumin and hydrophobin proteins were reduced by up to 91 and 94%, respectively. Adhesion of bacteria ( Escherichia coli) to zwitterion modified particle coatings were also significantly reduced over both short and long-term assays. Maximum reductions of 97% and 94% were achieved over 2 and 24 h assay periods, respectively. For unmodified particle coatings, protein adsorption and bacterial adhesion were generally reduced with increasing particle size. Adhesion of fungal spores to SB modified SiNP coatings was also reduced, however no clear trends in relation to particle size were demonstrated.
Trisomy in the fetal backcross progeny of male and female metacentric heterozygotes of the mouse. I. (1974)

In the backcross progeny of single (Robertsonian) metacentric heterozygotes of the mouse, segregational impairment of fertility and reduced litter size are initiated by misdivision of trivalents in meiotic anaphase I. Males heterozygous for the metacentrics Rbl, Rb4, Rb5, and Rb7Bnr of the tobacco mouse series and for the Rb8–10Bnr metacentrics derived from other feral domestic mice produce variable rates of meiotic malsegregation, ranging from 4 % to 26 % unbalanced M II figures. Chromosomally unbalanced gametes become involved in fertilization and produce aneusomic zygotes. Fetal aneuploidy causes developmental breakdown and prenatal death. Mono-somic zygotes are eliminated at an early stage of development. Most aneuploid embryos observed beyond day 8 or 10 of gestation were trisomics. Aneuploidy (trisomy) of the zygotes was considerably more frequent in the progeny of heterozygous females than in that of heterozygous males. There was evidence that this disparity might be the result of a higher nondisjunction rate in the female gametogenesis. Mechanisms of selection against unbalanced male germ cells might operate on a small scale. The highest incidences of aneuploid implants were found (with decreasing frequencies) in the backcross progeny of the Rb(1.3)l, Rb(16.17)7, and Rb(11.13)4Bnr female heterozygotes. With the experimental design used in this study, several trisomic conditions could be observed and their phenotype and developmental profiles described, namely, trisomies (Ts) 1, 3, 4, 10, 11, 12, 13, 16, and 17. Among these, Ts 3, 11, and 17 were characterized by severe developmental impairment and relatively early death, whereas the others could survive until day 13 to 15 or, as in the case of Ts 12, even until day 17. Ts 1 displayed a syndrome of general hypoplasia (fetal runting), whereas exencephaly was found in Ts 12. It was the only trisomy observed in this study that was associated with gross malformation.
Biochemical and molecular characterization of the Alcaligenes eutrophus pyruvate dehydrogenase complex and identification of a new type of dihydrolipoamide dehydrogenase (1994)

Sequence analysis of a 6.3-kbp genomic EcoRI-fragment of Alcaligenes eutrophus, which was recently identified by using a dihydrolipoamide dehydrogenase-specific DNA probe (A. Pries, S. Hein, and A. Steinbüchel, FEMS Microbiol. Lett. 97:227-234, 1992), and of an adjacent 1.0-kbp EcoRI fragment revealed the structural genes of the A. eutrophus pyruvate dehydrogenase complex, pdhA (2,685 bp), pdhB (1,659 bp), and pdhL (1,782 bp), encoding the pyruvate dehydrogenase (E1), the dihydrolipoamide acetyltransferase (E2), and the dihydrolipoamide dehydrogenase (E3) components, respectively. Together with a 675-bp open reading frame (ORF3), the function of which remained unknown, these genes occur colinearly in one gene cluster in the order pdhA, pdhB, ORF3, and pdhL. The A. eutrophus pdhA, pdhB, and pdhL gene products exhibited significant homologies to the E1, E2, and E3 components, respectively, of the pyruvate dehydrogenase complexes of Escherichia coli and other organisms. Heterologous expression of pdhA, pdhB, and pdhL in E. coli K38(pGP1-2) and in the aceEF deletion mutant E. coli YYC202 was demonstrated by the occurrence of radiolabeled proteins in electropherograms, by spectrometric detection of enzyme activities, and by phenotypic complementation, respectively. A three-step procedure using chromatography on DEAE-Sephacel, chromatography on the triazine dye affinity medium Procion Blue H-ERD, and heat precipitation purified the E3 component of the A. eutrophus pyruvate dehydrogenase complex from the recombinant E. coli K38(pGP1-2, pT7-4SH7.3) 60-fold, recovering 41.5% of dihydrolipoamide dehydrogenase activity. Microsequencing of the purified E3 component revealed an amino acid sequence which corresponded to the N-terminal amino acid sequence deduced from the nucleotide sequence of pdhL. The N-terminal region of PdhL comprising amino acids 1 to 112 was distinguished from all other known dihydrolipoamide dehydrogenases. It resembled the N terminus of dihydrolipoamide acyltransferases, and it contained one single lipoyl domain which was separated by an adjacent hinge region from the C-terminal region of the protein that exhibited high homology to classical dihydrolipoamide dehydrogenases.
Low noise chirped pulse mode-locked laser using an intra-cavity Fabry-Pérot etalon (2011)

This work presents an extensive investigation of the performance characteristics of a semiconductor-based Theta cavity design laser with an intra-cavity Fabry-Pérot etalon operating at 100 MHz repetition rate. The Theta laser being an external cavity harmonically mode-locked semiconductor laser exhibits supermode noise that impairs its performance. A fiberized Fabry-Pérot periodic filter inserted within the Theta laser cavity mitigates the contribution of the supermode noise to the pulse-to-pulse energy variance by 20 times. The laser has both a compressed output with picosecond pulse duration and a uniform intensity quasi-CW linearly chirped pulse output with 10 nm bandwidth. Long-term stability is attained by referencing the cavity length to the etalon using an intra-cavity Hänsch-Couillaud locking scheme.
Anticancer drugs that target metabolism: Is dichloroacetate the new paradigm? (2010)

Recent findings in the fields of oncogenic regulation of metabolism, mitochondrial function and macromolecular synthesis have brought tumor metabolism and the Warburg effect back into the scientific limelight. A number of metabolic pathways that seem to be important for tumor growth are being touted as novel targets for anticancer drug development. One of the candidates in this class of drugs being investigated is dichloroacetate (DCA), a molecule used for over 25 years in the treatment of children with inborn errors in mitochondrial function. This pyruvate mimetic compound stimulates mitochondrial function by inhibiting the family of regulatory pyruvate dehydrogenase kinases (PDK1-4). The stimulation of mitochondrial function, at the expense of glycolysis, reverses the Warburg effect and is thought to block the growth advantage of highly glycolytic tumors. Interestingly, some of the recent in vitro findings have shown very modest "antitumor cell activity" of DCA when cells are treated in a dish. However, several studies have reported "antitumor activity" in model tumors. This apparent paradox raises the question, how do we evaluate cancer drugs designed to target tumor metabolism? Traditional approaches in cancer drug development have used in vitro assays as a first pass to evaluate potential lead compounds. The fact that DCA has better in vivo activity than in vitro activity suggests that there are unique aspects of solid tumor growth and metabolism that are difficult to recapitulate in vitro and may be important in determining the effectiveness of this class of drugs.
Van der Waals Picture of Liquids, Solids, and Phase Transformations (1983)

The van der Waals picture focuses on the differing roles of the strong short-ranged repulsive intermolecular forces and the longer ranged attractions in determining the structure and dynamics of dense fluids and solids. According to this physical picture, the attractive interactions help fix the volume of the system, but the arrangements and motions of molecules within that volume are determined primarily by the local packing and steric effects produced by the repulsive forces. This very useful approach, its limitations, and its successful application to a wide variety of static and dynamic phenomena in condensed matter systems are reviewed.
R-Ras Signals through Specific Integrin α Cytoplasmic Domains to Promote Migration and Invasion of Breast Epithelial Cells (1999)

Specificity and modulation of integrin function have important consequences for cellular responses to the extracellular matrix, including differentiation and transformation. The Ras-related GTPase, R-Ras, modulates integrin affinity, but little is known of the signaling pathways and biological functions downstream of R-Ras. Here we show that stable expression of activated R-Ras or the closely related TC21 (R-Ras 2) induced integrin-mediated migration and invasion of breast epithelial cells through collagen and disrupted differentiation into tubule structures, whereas dominant negative R-Ras had opposite effects. These results imply novel roles for R-Ras and TC21 in promoting a transformed phenotype and in the basal migration and polarization of these cells. Importantly, R-Ras induced an increase in cellular adhesion and migration on collagen but not fibronectin, suggesting that R-Ras signals to specific integrins. This was further supported by experiments in which R-Ras enhanced the migration of cells expressing integrin chimeras containing the alpha2, but not the alpha5, cytoplasmic domain. In addition, a transdominant inhibition previously noted only between integrin beta cytoplasmic domains was observed for the alpha2 cytoplasmic domain; alpha2beta1-mediated migration was inhibited by the expression of excess alpha2 but not alpha5 cytoplasmic domain-containing chimeras, suggesting the existence of limiting factors that bind the integrin alpha subunit. Using pharmacological inhibitors, we found that R-Ras induced migration on collagen through a combination of phosphatidylinositol 3-kinase and protein kinase C, but not MAPK, which is distinct from the other Ras family members, Rac, Cdc42, and N- and K-Ras. Thus, R-Ras communicates with specific integrin alpha cytoplasmic domains through a unique combination of signaling pathways to promote cell migration and invasion.
Virulence of Escherichia coli in relation to host factors in women with symptomatic urinary tract infection (1988)

The relationship between bacterial characteristics and the severity of urinary tract infection in adults has not been clarified. In this study, Escherichia coli strains (n = 178) were prospectively collected from women with community-acquired urinary tract infection. The isolates were identified by O:K:H serotype and characterized for adherence, hemolysin production, and serum bactericidal resistance. The patients had acute pyelonephritis with or without complicating factors and acute cystitis. Nine serotypes (O1:K1:H7, O1:K1:H-, O2:K1:H-, O4:K12:H1, O7:K1:H-, O9:K34:H-, O16:K1:H6, O16:K1:H-, and O75:K5:H-) comprised 65% of the strains in uncomplicated pyelonephritis, but were significantly less often encountered in complicated pyelonephritis or cystitis. Adherence was the single property most characteristic of the pyelonephritogenic clones. Adhesins specifically recognizing Gal alpha 1----4Gal beta-containing receptors occurred in 80% of strains in uncomplicated pyelonephritis, in 50% of strains in complicated infections, and in 37% of cystitis strains. Hemolysin production and serum resistance did not correlate with any disease pattern. Advanced age did not seem to reduce the selection of virulent E. coli to cause pyelonephritis. These results demonstrate in women a relationship between E. coli virulence and the severity of urinary tract infection analogous to that previously observed in pediatric populations and also illustrate the balance between host resistance and bacterial virulence in the urinary tract.
La experiencia coreana en promover la adopcion del negocio electronico en pequenas y micro empresas (2004)

In Korea, around 3.1 million small enterprises (99.2 percent of the total) operate with less than 50 employees. Micro & small businesses (MSBs), however, have lagged well behind in the adoption of IT, largely due to insufficient financial, human and technological resources. To address this, Korea has taken bold measures to help MSBs exploit the potential of ICT as a driver of productivity and growth.
An efficient and accurate integration of mini-Mu transposons in vitro: a general methodology for functional genetic analysis and molecular biology applications (1999)

Transposons are mobile genetic elements and have been utilized as essential tools in genetics over the years. Though highly useful, many of the current transposon-based applications suffer from various limitations, the most notable of which are: (i) transposition is performed in vivo, typically species specifically, and as a multistep process; (ii) accuracy and/or efficiency of the in vivo or in vitro transposition reaction is not optimal; (iii) a limited set of target sites is used. We describe here a genetic analysis methodology that is based on bacteriophage Mu DNA transposition and circumvents such limitations. The Mu transposon tool is composed of only a few components and utilizes a highly efficient and accurate in vitro DNA transposition reaction with a low stringency of target preference. The utility of the Mu system in functional genetic analysis is demonstrated using restriction analysis and genetic footprinting strategies. The Mu methodology is readily applicable in a variety of current and emerging transposon-based techniques and is expected to generate novel approaches to functional analysis of genes, genomes and proteins.
Corroles-Porphyrins: A Teamwork for Gas Sensor Arrays (2015)

Porphyrins provide an excellent material for chemical sensors, and they have been used for sensing species both in air and solution. In the gas phase, the broad selectivity of porphyrins is largely dependant on molecular features, such as the metal ion complexed at the core of the aromatic ring and the peripheral substituents. Although these features have been largely exploited to design gas sensor arrays, so far, little attention has been devoted to modify the sensing properties of these macrocycles by variation of the molecular aromatic ring. In this paper, the gas sensing properties of a porphyrin analog, the corrole, are studied in comparison with those of the parent porphyrin. Results show that changes in the aromatic ring have important consequences on the sensitivity and selectivity of the sensors and that porphyrins and corroles can positively cooperate to enhance the performance of sensor arrays.
Immunological studies of the disulfide bridge region of Pseudomonas aeruginosa PAK and PAO pilins, using anti-PAK pilus and antipeptide antibodies (1989)

Pseudomonas aeruginosa is an opportunistic pathogen that attaches to host cells via their pili. The pilus of P. aeruginosa PAK consists of a polymer of a single subunit, pilin, which is a 144-residue polypeptide. The C-terminal end of this protein is semiconserved in a number of strains and contains a disulfide bridge. We have synthesized the C-terminal peptide PAK (128-144)-OH in both its reduced and oxidized forms and the analog PAK(A-129) (128-144)-OH, in which cysteine-129 was substituted by alanine. These three peptides were used to immunize rabbits and prepare antipeptide antisera. It was found that antipeptide antisera to reduced peptide (17-R) and to oxidized peptide (17-O) bound to native PAK pili and cross-reacted with strain PAO pili in direct enzyme-linked immunosorbent assay (ELISA) and immunoblot experiments. However, the antiserum to the peptide immunogen PAK(A-129)(128-144)-OH, which does not have the ability to form the disulfide bridge, did not bind to either PAK or PAO pili. Competitive ELISA experiments with reduced and oxidized peptides of Ac-PAK(128-144)-OH showed that there was no difference in binding between the two peptides for 17-R or 17-O immunoglobulin G. When immunoglobulin G from native PAK antipilus antiserum was used in competitive or direct ELISA experiments, there was also no preference in binding to reduced or oxidized Ac-PAK(128-144)-OH or to PAK(A-129)(128-144)-OH. This result showed that the disulfide bridge in Pseudomonas pili is not critical to the immunogenicity of this region. However, the disulfide bridge is important in the immunogenicity of the C-terminal peptide when preparing antipeptide antisera that are cross-reactive with pili from different strains, since only the disulfide bridge peptide antisera cross-reacted well with the PAO pili as shown by competitive ELISA, suggesting that this region could be an important candidate for development of a synthetic vaccine.
Real-World Cost of Care for Commercially Insured versus Medicare Patients with Metastatic Pancreatic Cancer Who Received Guideline-Recommended Therapies. (2021)

The treatment patterns varied across the regimens but were largely consistent between the commercially insured and the Medicare patients who received the same regimen for metastatic pancreatic cancer; the ratio of total cost of care was 3:1 (commercially insured to Medicare). The total costs of care were similar across the regimens in each cohort, but the components of the total cost varied. These results can inform clinical guidelines and pathways for pancreatic cancer therapy as new evidence and treatment options emerge, and in the context of increasing value-based care models.
Narrow-linewidth bandpass filters with diffractive thin-film layers (2001)

Bandpass filters based on guided-mode resonance effects in waveguide-grating structures are obtained by use of a genetic algorithm search-and-optimization routine. Calculated examples show that narrow linewidths, high peaks, and low sideband transmittances can be achieved in thin-film diffractive devices with few layers. A filter with a linewidth of 0.2 nm at a central wavelength of 0.55 microm is demonstrated in a two-layer-two-grating structure. At 10.6-microm wavelength, a filter consisting of a single binary grating is obtained that has a linewidth of 12.7 nm and extended, low sideband transmittance. A three-layer device with a surface relief Si grating and two underlying homogeneous layers of SiO(2) and Si yields a high-efficiency filter centered at 1.55 microm with a linewidth of 0.1 nm.