gebhart/patrepeval huggingface dataset:
Endocytosis of Adeno-Associated Virus Type 5 Leads to Accumulation of Virus Particles in the Golgi Compartment (2002)

Among the adeno-associated virus (AAV) serotypes which are discussed as vectors for gene therapy AAV type 5 (AAV5) represents a candidate with unique advantages. To further our knowledge on AAV5-specific characteristics, we studied the entry pathway of wild-type virus in HeLa cells in the absence of helper virus by immunofluorescence and electron microscopy and by Western blot analysis. We found virus binding at the apical cell surface, especially at microvilli and, with increasing incubation time, virus accumulation at cell-cell boundaries. The different binding kinetics suggest different binding properties at apical versus lateral plasma membranes. Endocytosis of viruses was predominantly by clathrin-coated vesicles from both membrane domains; however, particles were also detected in noncoated pits. AAV5 particles were mainly routed to the Golgi area, where they could be detected within cisternae of the trans-Golgi network and within vesicles associated with cisternae and with the dictyosomal stacks of the Golgi apparatus. These data suggest that AAV5 makes use of endocytic routes that have hitherto not been described as pathways for virus entry.
Oxidative photodegradation of ocular tissues: Beneficial effects of filtering and exogenous antioxidants (2014)

The fact that light is necessary for life is generally accepted as an axiom. The extent to which light interacts and influences human biology, however, is often not fully appreciated. Exposure to sunlight, for instance, can both promote and degrade human health. There is now general scientific consensus that, although the eye evolved to respond to light, it is also damaged by excessive exposure. Light-mediated ocular damage is involved in the pathophysiology of many common forms of blindness. The type of ocular tissue damage induced by light exposure depends on the extent of exposure and wavelength. The tissues of the lens, cornea, and retina contain specific chemical moieties that have been proven to exhibit light-mediated oxidative degradation. Proteins and lipids present in the cornea, lens, and retina, meet all of the physical requirements known to initiate the process of oxidative photodegradation upon exposure to solar radiation. As such, different mechanisms have evolved in the lens, cornea, and retina to ameliorate such light-mediated oxidative damage. It appears, however, that such mechanisms are ill-matched to handle modern conditions: namely, poor diet and longer life-spans (and the degenerative diseases that accompany them). Hence, steps must be taken to protect the eye from the damaging effects of light. Preventative measures include minimizing actinic light exposure, providing exogenous filtering (e.g., through the use of protective lenses), and enhancing antioxidant defenses (e.g., through increased dietary intake of antioxidants). These strategies may yield long-term benefits in terms of reducing oxidative photodegradation of the ocular tissues.
Sensorless Vector Control of PMSM Drives Equipped With Inverter Output Filter (2006)

The paper presents a sensorless vector control method for a permanent magnet synchronous motor when the output voltage of the PWM inverter is filtered by an LC filter. The dynamics of the LC filter are taken into account in the design of the controller and adaptive full-order observer. The use of the output filter does not require additional current or voltage measurements. The speed adaptation is based on the estimation error of the inverter output current. Linearization analysis is used to design an observer that enables a wide operation region. Simulation and experimental results show the functionality of the proposed control method
45S5 Bioactive glass surface charge variations and the formation of a surface calcium phosphate layer in a solution containing fibronectin (2001)

This study investigated the effect of fibronectin adsorption on surface charge variations and calcium phosphate (Ca-P) layer formation kinetics on the surface of 45S5 bioactive glass (BG). We hypothesize that the adsorption of fibronectin on BG changes the surface charge and alters the kinetics of Ca-P layer formation on the glass surface. The charge at a material's surface modulates surface chemistry, protein adsorption, and interactions with bone cells. The zeta potential of BG in a solution containing human plasma fibronectin (TE-FN) was measured as a function of time by particle electrophoresis, and Ca-P layer formation was characterized using SEM, EDXA, and FTIR. Si, Ca, and P solution concentrations also were determined. It was found that the adsorption of fibronectin reduced the initial electronegativity of the BG surface and delayed the formation of both the amorphous and the crystalline Ca-P layers. The delayed formation of these surface layers may be attributed to the competitive binding of Ca2+ ions by the fibronectin molecule. In addition, the formation of an amorphous Ca-P layer correlated with the reversal from a negatively to a positively charged surface, independent of the presence of fibronectin. The addition of a single protein (in this case fibronectin) can significantly alter material surface parameters, such as charge, and subsequently affect the formation of a surface Ca-P layer. Furthermore, the formation of an amorphous Ca-P layer is an important event in the reactions leading to bioactive behavior, and proteins such as FN are actively involved in the transformation of the surface into a Ca-P layer. © 2000 Wiley & Sons, Inc. J Biomed Mater Res 54: 454–461, 2001
Homologous Up-regulation of KDR/Flk-1 Receptor Expression by Vascular Endothelial Growth Factor in Vitro (1998)

We investigated the possibility that vascular endothelial growth factor (VEGF) treatment could regulate KDR/Flk-1 receptor expression in endothelial cells. Bovine adrenal cortex endothelial cells were incubated with 200 pM rhVEGF165 for 0-7 days. Western blot analysis showed a 3-5-fold increase in total KDR protein following 4-day VEGF treatment. Scatchard analysis revealed that VEGF induced a 2-3-fold increase in high affinity receptor number (5.0 x 10(4)/cell versus 2. 4 x 10(4)/cell) without significantly affecting receptor binding affinity (Kd 76 pM versus 72 pM). Quantitative polymerase chain reaction analysis demonstrated a 3-fold increase in KDR mRNA levels following VEGF exposure. VEGF-induced KDR expression primarily occurred at the transcriptional level as demonstrated by a luciferase reporter assay system. Receptor selective mutants with wild-type KDR binding and decreased Flt-1 binding also induced KDR up-regulation; in contrast, mutants with decreased KDR binding and wild-type Flt-1 binding did not, suggesting that KDR receptor signaling mediated the increase in KDR expression. Inhibition of tyrosine kinase, Src tyrosine kinase, protein kinase C, and mitogen-activated protein kinase activities all blocked VEGF-induced KDR up-regulation. Finally, co-incubation of nitric-oxide synthase inhibitors with VEGF had no significant effect on KDR expression, but 100 microM sodium nitroprusside, a NO donor, significantly inhibited VEGF-induced KDR up-regulation, indicating that NO negatively regulates KDR expression. In conclusion, our data demonstrate that VEGF binding to the KDR receptor tyrosine kinase results in an increase in KDR receptor gene transcription and protein expression. Thus, KDR up-regulation induced by VEGF may represent an important positive feedback mechanism for VEGF action in tumor and ischemia-induced angiogenesis.
A Defined and Xeno-Free Culture Method Enabling the Establishment of Clinical-Grade Human Embryonic, Induced Pluripotent and Adipose Stem Cells (2010)

Our results demonstrate that human ESCs, iPSCs and ASCs can be maintained in the same defined xeno-free medium formulation for a prolonged period of time while maintaining their characteristics, demonstrating the applicability of the simplified xeno-free medium formulation for the production of clinical-grade stem cells. The basic xeno-free formulation described herein has the potential to be further optimized for specific applications relating to establishment, expansion and differentiation of various stem cell types.
HLAand HIV-1: Heterozygote Advantage andB*35-Cw*04Disadvantage (1999)

A selective advantage against infectious disease associated with increased heterozygosity at the human major histocompatibility complex [human leukocyte antigen (HLA) class I and class II] is believed to play a major role in maintaining the extraordinary allelic diversity of these genes. Maximum HLA heterozygosity of class I loci (A, B, and C) delayed acquired immunodeficiency syndrome (AIDS) onset among patients infected with human immunodeficiency virus-type 1 (HIV-1), whereas individuals who were homozygous for one or more loci progressed rapidly to AIDS and death. The HLA class I alleles B*35 and Cw*04 were consistently associated with rapid development of AIDS-defining conditions in Caucasians. The extended survival of 28 to 40 percent of HIV-1-infected Caucasian patients who avoided AIDS for ten or more years can be attributed to their being fully heterozygous at HLA class I loci, to their lacking the AIDS-associated alleles B*35 and Cw*04, or to both.
ChemInform Abstract: Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality. (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.
Virtualizing FPGAs for Cloud Computing Applications (2014)

Cloud computing has become a multi-billion dollar industry, and represents a computing paradigm where all resources are virtualized, flexible and scalable. Field Programmable Gate Arrays (FPGAs) have the potential to accelerate many cloud-based applications, but as of yet are not available as cloud resources because they are so different from the conventional microprocessors that virtual machines (VMs) are based on. This thesis presents a first attempt at virtualizing and integrating FPGAs into cloud computing systems, making them available as generic cloud resources to end users. A novel architecture enabling this integration is presented and explored, and several custom hardware applications are evaluated on a prototype system. These applications show that Virtualized FPGA Resources can significantly outperform VMs in certain classes of common cloud computing applications, showing the potential to increase user compute power while reducing datacenter power consumption and operating costs.
Electrospray ionization mass spectrometry for the study of non‐covalent complexes: an emerging technology (1998)

The detection of non-covalent complexes in the mass range 19000–34000 Da, using electrospray ionization mass spectrometry (ESI-MS), is reviewed. The examples discussed include (1) a protein–ligand interaction (ras–GDP), (2) an inhibitor–protein–ligand interaction (SCH 54292/SCH 54341-ras–GDP), (3) a protein–protein interaction (γ-IFN homodimer) and (4) a protein–metal complex [HCV (1–181)–Zn]. In each case, the ESI-MS method is capable of releasing the intact non-covalent complex from its native solution state into the gas phase in the form of multiply-charge ions. The molecular masses of these complexes were determined with a mass accuracy of better than 0.01%, which is far superior to the traditional methods of sodium dodecyl sulfate polyacrylamide gel electrophoresis and gel permeation chromatography. The method provides the researcher with a quick, reliable and reproducible method for probing difficult biological problems. The key to success in the study of non-covalent complexes depends on careful understanding and manipulation of ESI source parameters and sample solution conditions; special care must be taken with the source orifice potential and the solution pH and organic co-solvents must be avoided. This paper also illustrates the usefulness of ESI-MS for addressing biological problems leading to the discovery of new therapeutics; the approach involves the rapid screening of potential drug candidates, such as weakly bound inhibitors. © 1998 John Wiley & Sons, Ltd.
Electric Field Induced Texture Changes in Certain Nematic/Cholesteric Liquid Crystal Mixtures (1973)

Abstract In dielectrically positive mixtures of the nematic N4 with cholesteryl-chloride an unusual texture transition was observed which can be applied in a storage effect. The variation of several characteristic parameters of these mixtures with concentration and temperature was measured.
The Phylogenetic Position of Streptococcus and Enterococcus (1985)

Streptococcus pyogenes, S. equinus, S. bovis, S. salivarius, S. sanguis, S. mutans, S. rattus, S. cricetus, S. lactis, S. raffinolactis and Enterococcus faecalis have been characterized by oligonucleotide cataloguing of their 16S ribosomal RNA. All the organisms form a loose but coherent group that is phylogenetically equivalent to those of lactobacilli, bacilli, the Brochothrix and Listeria group, and related taxa that constitute one of several sublines within the 'Clostridium' branch of Gram-positive eubacteria. Within the Steptococcus-Enterococcus group, organisms fall into three moderately related clusters defined by Enterococcus, the lactic acid streptococci and streptococci of the pyogenic and oral groups, respectively.
Mode Coupling Effects in Ring-Core Fibers for Space-Division Multiplexing Systems (2016)

An optical fiber with weak mode coupling is desirable for future ultrahigh capacity space-division multiplexing (SDM) systems because mode coupling in an optical fiber results in extrinsic loss of the fiber and crosstalk between guided optical modes. To study the feasibility of a ring-core fiber (RCF) for SDM systems, in this paper, we investigate the mode coupling in the RCF supporting five or seven guided mode groups (MGs) at a wavelength of 1550 nm. For this purpose, the coupled mode/power theory with identified spatial power spectrum of random perturbations of fiber axis is used to estimate the bend loss/crosstalk of the RCF due to microbending. It is shown that based on the identified parameters for the spatial power spectrum in the 5/7-MG RCF, the estimated bend loss/crosstalk of the RCF agrees well with experimental results. In addition, the impact of the gradient parameter α and refractive index contrast Δ of the fiber refractive index profile on bend loss and crosstalk of the RCF is explored. Simulation results indicate that the Δ instead of the α significantly affects bend loss and crosstalk of the RCF. The magnitude improvement in bend loss by increasing the Δ is dependent on the spatial power spectrum.
Abstract 428: Creating Biocompatible 3-D Scaffolds for Engineering Cardiovascular Tissues: Heart, Lung, and Kidney (2007)

Background . Biocompatibility is an essential property of any extracellular matrix (ECM) used in tissue engineering. Perfusion decellularized whole cadaveric organs could provide novel scaffolds for organogenesis but their long term biocompatibility remains unknown. . Hypothesis: Perfusion decellularization of mammalian organs yields a biocompatible matrix that influences cell growth differentially in non-perfused 2-D tissue culture conditions. Methods . Adult F344 rats were euthanized after systemic heparinization. Heart, lung, liver, and kidney were removed, canulated, and perfused with SDS to remove cellular debris. Subsequent washing with 1% Triton-X-100 and PBS was performed to remove detergent. Biocompatibility was assessed by co-culture of ECM from each organ with either rat skeletal myoblasts (SKMBs) or mouse embryonic stem cells (mESCs). Decellularized tissue was cut into 0.5x1cm pieces and seeded with 40K cells each. Cells were fed daily and photographed on day 3, 9, 13, 17 (SKMB) or day 3, 5, 10, 12, 14, 20, 24 (mESC). Double-blinded high powered field (HPF) analysis was used to quantify cell growth over time. At day 17 or 24 tissues were harvested for histological analysis and TUNEL assays to assess cell number and viability. Results . Cell viability was &gt;90% in all cases but showed no organ preference. heart + SKMB 90.2 ± 2.4 and mESC 98.3 ± 1.1; lung + SKMB 96.3 ± 1.9 and mESC 96.4 ± 1.0; liver + SKMB 90.3 ± 3.2 and mESC 97.7 ± 1.6; kidney + SKMB 89.5 ± 4.5 and mESC 98.1 ± 1.4 Cell number on the other hand increased in all ECM coculture conditions (Table 1 ;) but with two distinct patterns depending on the organ. Maximal cell density was observed in Kidney followed by Liver, Lung and Heart (Table 1 ). Conclusion. SDS-based perfusion decellularization of cadaveric heart, lung, liver, and kidney provides biocompatible scaffolds that are conducive to cell growth and viability. Kidney and liver scaffolds allowed for greatest cell proliferation over time.
Expression of immediate early gene and growth factor mRNAs in a focal cerebral ischemia model in the rat. (1993)

Results are in agreement with the contention that increased c-fos and jun B expression leads to increased AP-1 binding activity, which in turn has been linked to the enhanced expression of neurotrophin genes.
Modulation of doxorubicin resistance by valinomycin (NSC 122023) and liposomal valinomycin in Chinese hamster ovary cells. (1989)

Recently, we have reported that the toxicity of the membrane-active agent valinomycin (VM) can be reduced with maintenance and/or enhancement of its antitumor activity by incorporation in liposomes (S. S. Daoud and Juliano, Cancer Res., 46:5518-5525, 1986). Since the underlying defect(s) in multidrug resistance reside mainly in the cell membrane, it seems reasonable to attempt to overcome multidrug resistance with membrane-active drugs. Here, we report on the in vitro restoration of Adriamycin (ADR) sensitivity in a resistant Chinese hamster ovary cell line (CHRC5) by treatment with nontoxic doses of valinomycin or of liposomal valinomycin. During a 1-h drug exposure, the sensitivity of CHRC5 to ADR was enhanced 21- to 28-fold when 20 or 40 nM VM was present, doses which are not toxic to CHRC5 cells. At the same time, modest synergistic toxicity could be seen in the parent drug-sensitive cell line (AUX B1). At 100 nM VM, the sensitivity of CHRC5 to ADR was restored to almost that of the sensitive AUX B1 cells. The effects of liposomal VM on ADR sensitivity were similar to the effects produced by free VM. At nontoxic doses and with continuous exposure of the drug, valinomycin was highly active in restoring ADR sensitivity in CHRC5 cells. In cells treated for 72 h, valinomycin enhanced the sensitivity to ADR 208- to 250-fold in CHRC5 and 3- to 5-fold in AUX B1 cells. Measurements of ADR uptake and efflux indicate that, unlike other multidrug resistance modifiers, valinomycin exerts its actions in modulating ADR resistance by mechanism(s) other than increasing intracellular accumulation of Adriamycin. The possible mechanisms of the restoration of ADR sensitivity by valinomycin are discussed.
Structural characterization of the epitopes of the monoclonal antibodies 473HD, CS-56, and MO-225 specific for chondroitin sulfate D-type using the oligosaccharide library (2004)

The variation in the sulfation profile of chondroitin sulfate (CS)/dermatan sulfate (DS) chains regulates central nervous system development in vertebrates. Notably, the disulfated disaccharide D-unit, GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate), correlates with the promotion of neurite outgrowth through the DSD-1 epitope that is embedded in the CS moiety of the proteoglycan DSD-1-PG/phosphacan. Monoclonal antibody (mAb) 473HD inhibits the DSD-1-dependent neuritogenesis and also recognizes shark cartilage CS-D, which is characterized by the prominent D-unit and is also recognized by two other mAbs, CS-56 and MO-225. We investigate the oligosaccharide epitope structures of these CS-D-reactive mAbs by ELISA and oligosaccharide microarrays using lipid-derivatized CS oligosaccharides. CS-56 and MO-225 recognized the octa- and larger oligosaccharides, though the latter also bound one unique hexasaccharide D-A-D, where A denotes the disaccharide A-unit GlcUA-GalNAc(4-O-sulfate). The octasaccharides reactive with CS-56 and MO-225 shared a core A-D tetrasaccharide, whereas the neighboring structural elements located on the reducing and/or nonreducing sides of the A-D gave a differential preference additionally to the recognition sequence for each antibody. In contrast, 473HD reacted with multiple hexa- and larger oligosaccharides, which also contained A-D or D-A tetrasaccharide sequences. Consistent with the distinct specificity of 473HD as compared with CS-56 and MO-225, the 473HD epitope displayed a different expression pattern in peripheral mouse organs as revealed by immunohistology, extending the previously reported CNS-restricted expression. The epitope of 473HD, but not of CS-56 or MO-225, was eliminated from DSD-1-PG by digestion with chondroitinase B, suggesting the close association of L-iduronic acid with the 473HD epitope. Despite such supplemental information, the integral epitope remains to be isolated for identification and comprehensive analytical characterisation. Thus novel information on the sugar sequences containing the A-D tetrasaccharide core was obtained for the epitopes of these three useful mAbs.
Semi-synthetic aequorins with improved sensitivity to Ca2+ ions (1989)

Thirty-seven coelenterazine analogues were synthesized and incorporated into apo-aequorin, yielding 30 semi-synthetic aequorins that have the capacity to emit a significant amount of light in the presence of Ca2+. The properties of resultant photoproteins were investigated. The most prominent feature of those photoproteins was the wide range in their sensitivities to Ca2+ concentration. The relative intensity of Ca2+-triggered luminescence of the photoproteins ranged from 0.01 to 190 when compared with natural aequorin (relative intensity 1.0) at pCa 6 for the cases where the relative intensity is less than 1 and at pCa 7 for the cases where the relative intensity is higher than 1. Eight of the semi-synthetic aequorins belonged to the class of e-aequorin. With two of those photoproteins, the degree of dependence of the luminescence intensity ratio I400/I465 on pCa was greater than that with e-aequorin, suggesting that these two photoproteins are possibly superior to e-aequorin in measuring Ca2+ concentration by the ratio method.
Talisman (1996)

A new 3D graphics and multimedia hardware architecture, codenamed Talisman, is described which exploits both spatial and temporal coherence to reduce the cost of high quality animation. Individually animated objects are rendered into independent image layers which are composited together at video refresh rates to create the final display. During the compositing process, a full affine transformation is applied to the layers to allow translation, rotation, scaling and skew to be used to simulate 3D motion of objects, thus providing a multiplier on 3D rendering performance and exploiting temporal image coherence. Image compression is broadly exploited for textures and image layers to reduce image capacity and bandwidth requirements. Performance rivaling highend 3D graphics workstations can be achieved at a cost point of two to three hundred dollars.
Thin-Film Inductor Designs and Materials for High-Current Low-Voltage Power (2003)

Thin-film inductors for dc-to-dc converters for microprocessor power delivery are discussed. Thin-film inductors offer small size and fast transient response as required by the application. The choice of magnetic material and design of the inductor are discussed. Composite granular metal-nonmetal films applied in a Vgroove stucture show strong promise for this application. The possibility of using magnetic films with stripe domains is also discussed.