gebhart/patrepeval huggingface dataset:
Quantitative proteomics of fractionated membrane and lumen exosome proteins from isogenic metastatic and nonmetastatic bladder cancer cells reveal differential expression of EMT factors (2013)

Cancer cells secrete soluble factors and various extracellular vesicles, including exosomes, into their tissue microenvironment. The secretion of exosomes is speculated to facilitate local invasion and metastatic spread. Here, we used an in vivo metastasis model of human bladder carcinoma cell line T24 without metastatic capacity and its two isogenic derivate cell lines SLT4 and FL3, which form metastases in the lungs and liver of mice, respectively. Cultivation in CLAD1000 bioreactors rather than conventional culture flasks resulted in a 13- to 16-fold increased exosome yield and facilitated quantitative proteomics of fractionated exosomes. Exosomes from T24, SLT4, and FL3 cells were partitioned into membrane and luminal fractions and changes in protein abundance related to the gain of metastatic capacity were identified by quantitative iTRAQ proteomics. We identified several proteins linked to epithelial-mesenchymal transition, including increased abundance of vimentin and hepatoma-derived growth factor in the membrane, and casein kinase II α and annexin A2 in the lumen of exosomes, respectively, from metastatic cells. The change in exosome protein abundance correlated little, although significant for FL3 versus T24, with changes in cellular mRNA expression. Our proteomic approach may help identification of proteins in the membrane and lumen of exosomes potentially involved in the metastatic process.
Chapter 4. Atomic Layer Deposition (2008)

Atomic layer deposition (ALD) is a special variant of chemical vapour deposition (CVD) technology used to grow high-quality thin films through alternate self-limiting surface reactions (Figure 4.1). ALD has gained considerable interest in recent years as a thin film deposition method to overcome man...
Telomerase in alveolar epithelial development and repair (2000)

Telomerase expression and activity were examined in the developing lung and in the adult lung during repair after injury. Both whole lung tissue and primary cultures of type 2 alveolar epithelial cells (AEC2) isolated from fetal and adult rodents were analyzed for 1) telomerase expression by immunohistochemistry and 2) telomerase activity with a telomerase repeat amplification protocol. We found that telomerase was expressed in a temporally regulated manner in fetal lung through the late stages of gestation, with peak expression just before birth. Expression persisted for a brief period in neonates, then decreased to nearly undetectable levels by postnatal day 9. Telomerase expression and activity were reinduced in normally quiescent adult lung by in vivo treatment with hyperoxia. In populations of AEC2 isolated from both developing and repairing lungs, telomerase expression and activity showed a strong correlation with the proliferation marker proliferating cell nuclear antigen. It has been suggested that telomerase expression and activity are hallmarks of stem or progenitor cells. Our observations suggest that a telomerase-positive subpopulation is present within the general AEC2 population. Telomerase may act as a marker for the proliferative status of this subpopulation.
Anisotropic voronoi diagrams and guaranteed-quality anisotropic mesh generation (2003)

We introduce anisotropic Voronoi diagrams, a generalization of multiplicatively weighted Voronoi diagrams suitable for generating guaranteed-quality meshes of domains in which long, skinny triangles are required, and where the desired anisotropy varies over the domain. We discuss properties of anisotropic Voronoi diagrams of arbitrary dimensionality---most notably circumstances in which a site can see its entire Voronoi cell. In two dimensions, the anisotropic Voronoi diagram dualizes to a triangulation under these same circumstances. We use these properties to develop an algorithm for anisotropic triangular mesh generation in which no triangle has an angle smaller than 20A, as measured from the skewed perspective of any point in the triangle.
Association of γ-Secretase with Lipid Rafts in Post-Golgi and Endosome Membranes (2004)

Alzheimer's disease-associated beta-amyloid peptides (Abeta) are generated by the sequential proteolytic processing of amyloid precursor protein (APP) by beta- and gamma-secretases. There is growing evidence that cholesterol- and sphingolipid-rich membrane microdomains are involved in regulating trafficking and processing of APP. BACE1, the major beta-secretase in neurons is a palmitoylated transmembrane protein that resides in lipid rafts. A subset of APP is subject to amyloidogenic processing by BACE1 in lipid rafts, and this process depends on the integrity of lipid rafts. Here we describe the association of all four components of the gamma-secretase complex, namely presenilin 1 (PS1)-derived fragments, mature nicastrin, APH-1, and PEN-2, with cholesterol-rich detergent insoluble membrane (DIM) domains of non-neuronal cells and neurons that fulfill the criteria of lipid rafts. In PS1(-/-)/PS2(-/-) and NCT(-/-) fibroblasts, gamma-secretase components that still remain fail to become detergent-resistant, suggesting that raft association requires gamma-secretase complex assembly. Biochemical evidence shows that subunits of the gamma-secretase complex and three TGN/endosome-resident SNAREs cofractionate in sucrose density gradients, and show similar solubility or insolubility characteristics in distinct non-ionic and zwitterionic detergents, indicative of their co-residence in membrane microdomains with similar protein-lipid composition. This notion is confirmed using magnetic immunoisolation of PS1- or syntaxin 6-positive membrane patches from a mixture of membranes with similar buoyant densities following Lubrol WX extraction or sonication, and gradient centrifugation. These findings are consistent with the localization of gamma-secretase in lipid raft microdomains of post-Golgi and endosomes, organelles previously implicated in amyloidogenic processing of APP.
Comparison of Vietnamese and US isolates of Edwardsiella ictaluri (2013)

We compared Edwardsiella ictaluri from striped catfish in Vietnam with US channel catfish isolates. Biochemical analyses and sequencing of the 16S rRNA gene confirmed that the Vietnamese isolates were E. ictaluri. Comparison using rep-PCR fingerprinting demonstrated no significant differences between the isolates, but plasmid analysis indicated that the Vietnamese isolates grouped into 4 plasmid profiles, each different from the typical pEI1 and pEI2 plasmid profile found in the US isolates. Sequencing plasmids representative of the 4 profiles indicated that all contained derivatives of the E. ictaluri plasmid pEI1, whereas only 1 contained a plasmid derivative of the E. ictaluri plasmid pEI2. The pEI2 encoded type III secretion effector, EseI, and its chaperone, EscD, were found to be present on the chromosome in isolates lacking a pEI2 derivative. In addition, 1 isolate carried a 5023 bp plasmid that does not have homology to either pEI1 or pEI2. Furthermore, Vietnamese isolates were PCR positive for the type III and type VI secretion system genes esrC and evpC, respectively, and the urease enzyme, but were PCR-negative for the putative type IV secretion system gene virD4. A monoclonal antibody against the lipopolysaccharide of E. ictaluri ATCC 33202 did not react with the Asian isolates or with the more recent US isolates. Antibiotic resistance patterns were variable and did not correlate to the presence of any particular plasmid profile. Finally, the Vietnamese isolates were avirulent and had a significantly reduced capacity for intracellular replication within head-kidney-derived channel catfish macrophages.
Decentralized Master-Slave Communication and Control Architecture of a Battery Swapping Station (2018)

The aim of this paper is to provide an overview of communication protocols that could be used to establish communication between different battery packs within energy management system of battery swapping station. In order to compare similarities and differences, the overview of communication within battery pack is also provided. For the choice of the most appropriate communications solution, it is of vital importance to consider energy management system operating conditions within the battery swapping station. For the time being, CAN protocol is widely accepted for the communication between battery packs and electric vehicle energy management system and it would be convenient to employ it also to the battery management system (BMS) because of its robustness to noise problem and compatibility with other hardware involved in BMS.
Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies (2021)

Owing to the limitations of the present efforts on drug discovery against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the lack of the understanding of the biological regulation mechanisms underlying COVID-19, alternative or novel therapeutic targets for COVID-19 treatment are still urgently required. SARS-CoV-2 infection and immunity dysfunction are the two main courses driving the pathogenesis of COVID-19. Both the virus and host factors are potential targets for antiviral therapy. Hence, in this study, the current therapeutic strategies of COVID-19 have been classified into "target virus" and "target host" categories. Repurposing drugs, emerging approaches, and promising potential targets are the implementations of the above two strategies. First, a comprehensive review of the highly acclaimed old drugs was performed according to evidence-based medicine to provide recommendations for clinicians. Additionally, their unavailability in the fight against COVID-19 was analyzed. Next, a profound analysis of the emerging approaches was conducted, particularly all licensed vaccines and monoclonal antibodies (mAbs) enrolled in clinical trials against primary SARS-CoV-2 and mutant strains. Furthermore, the pros and cons of the present licensed vaccines were compared from different perspectives. Finally, the most promising potential targets were reviewed, and the update of the progress of treatments has been summarized based on these reviews.
Role of materials surface topography on mammalian cell response (2011)

Many approaches are used to modify the surface topography of implant materials. Some produce unordered surfaces using, for example, classical implant surface treatments, whereas others produce ordered surfaces by micro- and nanopatterning techniques. Surface topographies can be characterised by several methods that can acquire two-dimensional profiles or three-dimensional measurements and calculate different roughness parameters. The importance of using systematically several roughness parameters for correlation with biological response, and of consider these parameters at different scales will be demonstrated. Furthermore, it will be described, from a general point of view, how cells are able to identify and respond to surface topography. The role of membrane receptors, cytoskeleton, filopods and intracellular signal transduction in the response to topography will be considered and discussed. A critical review of more than 300 papers provides the basis for illustrating how mammalian cells respond to surface topography and how their rugophilia, the increased cell response to rougher surfaces, is a function of cell phenotype. For the first time, the rugophilia of cells from different tissue origins is compared in a synthetic table.
Oxidative DNA and RNA damage in the livers of Sprague-Dawley rats treated with the hepatocarcinogen 2-nitropropane. (1989)

2-Nitropropane (2-NP), a widely used industrial chemical, is a mutagen in bacteria and a powerful hepatocarcinogen in Sprague-Dawley rats. In contrast, 1-nitropropane (1-NP) is not mutagenic and does not appear to be carcinogenic. Thus far, the mechanism of carcinogenicity of 2-NP has not been examined. We report in the present work that i.p. treatment of male Sprague-Dawley rats with 100 mg/kg 2-NP results in a 3.6-fold increase (P less than 0.01) in the levels of 8-hydroxydeoxyguanosine as well as in the appearance of an additional electrochemically active species, presumably a modified deoxynucleoside, in liver DNA hydrolysates 6 h after dosing. Treatment with 2-NP also induces an 11-fold increase (P less than 0.0001) in the levels of 8-hydroxyguanosine in rat liver RNA, and results in the appearance of two new electrochemically active species (RX1 and RX2), presumably modified nucleosides. Small, statistically not significant increases of 8-hydroxyguanosine in RNA and of 8-hydroxydeoxyguanosine in DNA, as well as the induction of much smaller amounts of RX2 (but apparently not RX1) in rat liver RNA, are also observed following analogous treatment with 1-NP. Since the presence of 8-hydroxyguanine, a product of the attack of hydroxyl radicals (or other reactive oxygen species) on guanine, can cause DNA misreplication [Kuchino et al., Nature (Lond.), 327: 77-79, 1987], our findings are consistent with a mechanism of hepatocarcinogenicity of 2-NP based on damage to nucleic acids from the intracellular generation of reactive forms of oxygen and/or the 2-NP free radical.
Multiplexed <i>in Vivo</i> His-Tagging of Enzyme Pathways for <i>in Vitro</i> Single-Pot Multienzyme Catalysis (2012)

Protein pathways are dynamic and highly coordinated spatially and temporally, capable of performing a diverse range of complex chemistries and enzymatic reactions with precision and at high efficiency. Biotechnology aims to harvest these natural systems to construct more advanced in vitro reactions, capable of new chemistries and operating at high yield. Here, we present an efficient Multiplex Automated Genome Engineering (MAGE) strategy to simultaneously modify and co-purify large protein complexes and pathways from the model organism Escherichia coli to reconstitute functional synthetic proteomes in vitro. By application of over 110 MAGE cycles, we successfully inserted hexa-histidine sequences into 38 essential genes in vivo that encode for the entire translation machinery. Streamlined co-purification and reconstitution of the translation protein complex enabled protein synthesis in vitro. Our approach can be applied to a growing area of applications in in vitro one-pot multienzyme catalysis (MEC) to manipulate or enhance in vitro pathways such as natural product or carbohydrate biosynthesis.
Repeatability of the “flash-replenishment” method in contrast-enhanced ultrasound for the quantitative assessment of hepatic microvascular perfusion (2018)

This study aimed to evaluate the feasibility and repeatability of the flash-replenishment method in contrast-enhanced ultrasound (CEUS) perfusion imaging and assess quantitatively microvascular perfusion in the liver. Twenty healthy New Zealand rabbits were submitted to CEUS perfusion imaging with continuous intravenous infusion. Using flash-replenishment kinetics, the dynamic process of depletion and refilling of microbubble contrast agent was recorded. The hepatic microvascular perfusion parameters were calculated, including region of interest, peak intensity (PI), area under the curve (AUC), and hepatic artery to vein transit time (HA-HVTT). A consistency test was performed for multiple measurements by the same operator and blind measurements by two different operators. The hepatic perfusion imaging of 3×108 bubbles/min had minimal error and the best imaging effect and repeatability. The variability of the perfusion parameter measured at 3 cm depth under the liver capsule was at a minimum with coefficient of variation of 3.9%. The interclass correlation coefficient (ICC) of measurements taken by the same operator was 0.985, (95% confidence interval, CI=0.927-0.998). Measurements taken by two operators had good consistency and reliability, with the ICC of 0.948 (95%CI=0.853-0.982). The PI and AUC of liver parenchyma after reperfusion were lower than before blocking; and HA-HVTT was significantly longer than before blocking (P<0.05). The flash-replenishment method in CEUS perfusion imaging showed good stability and repeatability, which provide a valuable experimental basis for the quantitative assessment of hepatic microvascular perfusion in clinical practice.
The rel-associated pp40 protein prevents DNA binding of Rel and NF-kappa B: relationship with I kappa B beta and regulation by phosphorylation. (1991)

The product of proto-oncogene Rel associates with a number of cellular proteins. We have studied the effect of one of them, a phosphoprotein of 40 kD (pp40), on the DNA-binding activity of the Rel protein. We demonstrate that purified pp40 not only inhibits the binding of Rel, but also NF-kappa B (p50-p65) heterocomplex to DNA. Additionally, I kappa B beta, but not I kappa B alpha, also prevented the binding of Rel to the kappa B site. I kappa B beta and pp40 are related proteins because (1) they share a number of common tryptic peptides, (2) their inhibitory effect on DNA binding can be abolished by preincubation with pp40-specific antiserum, and (3) labeled I kappa B beta can be immunoprecipitated with pp40 antibodies. pp40 is part of the Rel complex present in the cytoplasm and nuclear extracts of WEHI-231 cells. The activity of pp40 to inhibit the DNA binding of Rel and NF-kappa B is modulated by phosphorylation.
RFLP Mapping of Resistance to Southern Root‐Knot Nematode in Soybean (1997)

In the USA, the southern root‐knot nematode [ Meloidogyne incognita (Kofoid and White) Chitwood] (Mi) is a serious pathogen soybean [ Glycine max (L.) Merrill]. The objectives of this study were the following: (i) to use restriction fragment length polymorphism (RFLP) to identify markers associated with quantitative trait loci (QTL) conferring Mi resistance, (ii) to estimate the relative contribution to resistance of each QTL, and (iii) to locate each QTL on the molecular map of the soybean genome. PI96354, a plant introduction with a high level of resistance to Mi, was crossed with ‘Bossier’, a highly susceptible cultivar, and 110 F 2 plants were produced and mapped with 121 RFLP markers. A greenhouse screening procedure was used to determine the level of galling for the F 2:3 lines. Data were analyzed using single‐factor and two‐factor analysis of variance and interval mapping. Two QTL were identified which mapped to LG‐O and LG‐G of the USDA/ARS‐Iowa State Univ. (USDA/ARS‐ISU) soybean RFLP Map. Results showed a major resistance QTL ( R 2 = 31%) linked to marker G248A‐1 on LG‐O. The second QTL (R 2 = 14%) was localted on LG‐G in the interval from K493H‐1 to Cs008D‐1 and was dominant with respect to resistance. The two QTL explained 39% of the variation in Mi galling in a multiple QTL model. Marker G248A‐1 may be closely linked to the Rmi 1 gene. When galling data was classified into three distinct classes, it mapped distally to G248A‐1 on LG‐O. Mi resistance also was linked to G248A‐1 through simulated marker analysis. The root‐knot nematode resistance QTL identified were found in duplicated DNA segments.
MICROPARTICULATE DRUG DELIVERY SYSTEM: A REVIEW (2011)

Drug delivery systems (DDS) that can precisely control the release rates or target drugs to a specific body site have an enormous impact on the health care system. Carrier technology offers an intelligent approach for drug delivery by coupling the drug to a carrier particle such as microsphere, nanoparticles etc, which modulates the release and absorption characteristics of the drug. Microspheres/microparticles constitute an important part of this particulate drug delivery system by virtue of their small size and efficient carrier characteristics. These delivery systems offer numerous advantages compared to conventional dosage forms, which include improved efficacy, reduced toxicity, improved patient compliance and convenience. Such systems often use macromolecules as carriers for the drugs. The present review highlights several carriers used in the preparation of microparticles, preparation methods of microparticles, their release mechanisms, evaluation parameters, their advantages and applications. Therefore microparticles open up new vistas of research in the development of novel drug delivery systems. Drug delivery systems (DDS) that can precisely control the release rates or target drugs to a specific body site have an enormous impact on the health care system. Carrier technology offers an intelligent approach for drug delivery by coupling the drug to a carrier particle such as microsphere, nanoparticles etc, which modulates the release and absorption characteristics of the drug. Microspheres/microparticles constitute an important part of this particulate drug delivery system by virtue of their small size and efficient carrier characteristics. These delivery systems offer numerous advantages compared to conventional dosage forms, which include improved efficacy, reduced toxicity, improved patient compliance and convenience. Such systems often use macromolecules as carriers for the drugs. The present review highlights several carriers used in the preparation of microparticles, preparation methods of microparticles, their release mechanisms, evaluation parameters, their advantages and applications. Therefore microparticles open up new vistas of research in the development of novel drug delivery systems.
Polymeric optical waveguide films with 45°mirrors formed with a 90° V-shaped diamond blade (1997)

A novel method for forming high quality 45° mirrors in polymeric waveguides is described. Singlemode and multimode polymeric waveguide films with 45° mirrors were fabricated by cutting the waveguide with a 90° V-shaped diamond blade. The mirror losses were as low as 0.1 dB for the singlemode and 0.3 dB for the multimode waveguides.
Prevention of Maternal and Congenital Cytomegalovirus Infection (2012)

Congenital cytomegalovirus (CMV) infection is an important cause of hearing impairment, mental retardation, and cerebral palsy. Principal sources of infection during pregnancy are young children and intimate contacts. Prevention of maternal and congenital CMV infection depends on counseling women regarding the sources of infection and hygienic measures that might prevent infection. There is currently insufficient evidence to support use of antiviral treatment or passive immunization for postexposure prophylaxis of pregnant women or as a maternal treatment aimed at preventing fetal infection. Vaccines for CMV are under development but it will be a number of years before one is licensed.
Performance of low-rate orthogonal convolutional codes in DS-CDMA applications (1997)

Low-rate orthogonal convolutional codes (LROCC), originally proposed by A.J. Viterbi (1971), can be used in a direct-sequence code-division multiple access (DS-CDMA) system to achieve both spreading of the data and providing coding gain. The implementation of this type of multiplexing in a practical DS-CDMA system is presented, and the theoretical performance of the proposed system under "other-user" noise, additive white Gaussian noise (AWGN), intercell interference, and thermal noise is established using a computer simulation. The improvement in system performance, gained through the use of a nonspreading randomizing sequence on the encoded output symbols, is also studied. Performance curves for a rate 1/64 orthogonal convolutional code are shown, and the impact of code rate, quantization methods, and constraint length on the overall system performance are discussed.