gebhart/patrepeval huggingface dataset:
Rapid selection for an N-linked oligosaccharide by monoclonal antibodies directed against the V3 loop of human immunodeficiency virus type 1 (1996)

The V3 loop of the human immunodeficiency virus (HIV) surface protein, gp 120, constitutes a principal neutralizing determinant. HIV strains lacking a naturally conserved N-linked oligosaccharide (at position 306) within the V3 loop are highly sensitive to neutralization. We subjected molecular clones of HIV(LAI) lacking this 306N-glycan to in vitro immune selection with MAbs directed against the V3 loop. In all, ten clones were characterized, and all proved resistant to V3-directed neutralization. Sequencing of the V3 loop revealed that six of the clones had become resistant at least partly by reacquisition of the 306N-glycan. Only two of the clones possessed mutations within the binding site of the antibody itself, while the two remaining clones did not display changes within the V3 loop itself. Thus, HIV strains lacking the 306N-glycan primarily develop resistance to V3-directed neutralization through acquisition of the specific oligosaccharide. This demonstrates that protein glycosylation can be a primary modifier of virus antigenicity of possible importance for the interaction of HIV with the host immune response.
The effect of defects on the electronic and magnetic properties of Fe2MnSi Heusler alloy (2011)

Abstract Density functional theory (DFT) calculations were performed by using FP‐LAPW method to investigate the effect of defects on the electronic and magnetic structure of Fe 2 MnSi Heusler alloy. The formation energies were calculated for antisite, swap, and vacancy defects. We found that three defects, namely Mn Fe and Mn Si antisite as well as Fe–Mn swap defects may spontaneously occur as they have negative formation energies. Whereas, Mn and Si vacancies, Fe–Si swap, and Fe Mn antisite defects are unlikely to occur. However, the rest of the defects (Fe Si , Mn Si , and Si Fe ) antisites, Mn–Si swap, and Fe vacancy defects have relatively low formation energies that suggest higher probabilities to occur. The band gaps of the defected structures are found to be smaller than the ideal structure with almost zero values in the cases of Fe Si antisite and Fe–Si swap defects. The structure with Fe vacancy defect, however, exhibits almost the same energy gap as that of the ideal structure. The magnetic structure was also affected by the presence of defects except for Fe–Mn and Mn–Si swap defects that show the same total magnetic moment of 3 µ B /f.u. as the ideal structure.
A multicenter study to evaluate a novel assay for quantitation of soluble interleukin 2 receptor in renal transplant recipients. (1992)

The clinical utility of monitoring soluble interleukin 2 receptor (sIL-2R) as an indicator of immune stimulation in renal transplant patients was evaluated in a retrospective study at 3 centers. Serum samples (n = 2360) were obtained from 86 (17 living related donor, 69 cadaver) transplant recipients. The patients had received either triple therapy (n = 35) or antilymphocyte antibody induction therapy followed by triple therapy (n = 51). The mean period of postoperative observation was 118 days (range, 6-349 days). Serum sIL-2R concentrations were quantitated by an automated microparticle enzyme immunoassay (MEIA) (Abbott Diagnostics) in which sIL-2R was captured by 7G7/B6 monoclonal antibody-coated microparticles and detected by an immunospecific rabbit antihuman sIL-2R-alkaline phosphatase conjugate. A distinct advantage of the technique was rapid turn-around time: 1-24 results were obtained in less than 50 min. Cyclosporine trough concentrations were determined by radioimmunoassay or high-performance liquid chromatography. Diagnosis of rejection was established by clinical and histological criteria. The mean sIL-2R concentration in patients receiving antilymphocyte antibody induction therapy increased from 3486 +/- 1729 U/ml (+/- SD) at the time of transplant to a maximum of 7395 +/- 7101 U/ml on the third day posttransplant; this increase was not observed in patients receiving triple therapy (P less than 0.0001). By the sixth day of posttransplant, there were no differences in sIL-2R levels in the two groups. Fifty rejection episodes were observed in 29 patients on triple therapy. The mean sIL-2R concentration rose from 3022 U/ml at the data point prior to rejection to 3524 U/ml at the time of rejection. Thirty-four rejection episodes were observed in 26 patients receiving induction therapy. The mean sIL-2R concentration was 3015 U/ml at the data point prior to rejection and 4815 U/ml at the time of rejection. The sIL-2R concentrations began increasing earlier and rose higher in rejecting patients who received induction therapy than in those receiving triple therapy. Early posttransplant sIL-2R levels increased significantly more in cadaver recipients than in LRD recipients, reaching a maximum on day 2 posttransplant (P less than 0.001). Prerejection sIL-2R concentrations were significantly lower in LRD recipients than in cadaver recipients (2248 U/ml vs. 4290 U/ml, P less than 0.02), as were sIL-2R levels at the time of diagnosis of rejection (2800 U/ml vs. 4832 U/ml, P = 0.01). The mean sIL-2R level in stable long-term graft recipients was 2110 U/ml, with approximately 90% of values less than 3000 U/ml.(ABSTRACT TRUNCATED AT 400 WORDS)
Electrospinning: A Fascinating Method for the Preparation of Ultrathin Fibers (2007)

Electrospinning is a highly versatile method to process solutions or melts, mainly of polymers, into continuous fibers with diameters ranging from a few micrometers to a few nanometers. This technique is applicable to virtually every soluble or fusible polymer. The polymers can be chemically modified and can also be tailored with additives ranging from simple carbon-black particles to complex species such as enzymes, viruses, and bacteria. Electrospinning appears to be straightforward, but is a rather intricate process that depends on a multitude of molecular, process, and technical parameters. The method provides access to entirely new materials, which may have complex chemical structures. Electrospinning is not only a focus of intense academic investigation; the technique is already being applied in many technological areas.
Dynein and dynein-related genes (1998)

Dyneins are large, multisubunit ATPases that interact with microtubules to generate force. Dyneins move eukaryotic cilia and flagella and are in the cytoplasm, where they are involved in the transport of particles and organelles along microtubules and in the transport of condensed chromosomes during mitosis [reviewed in Holzbaur et al., 1994; Gibbons, 1996]. Defects in human axonemal dynein complexes have been shown to be associated with Kartagener's syndrome, which is characterized by recurrent respiratory tract infections, immotile sperm and situs inversus. Cytoplasmic and axonemal dyneins are composed of heavy, intermediate, and light chains. The best characterised groups of dynein genes so far are those encoding cytoplasmic heavy chains and heavy chains from the outer arms from axonemes. These share extensive sequence similarity and are conserved throughout species. Recently, several genes encoding intermediate and light chains have been identified; these have encoded a remarkable diversity of products, which also seem to be highly conserved between species, although they fall into several complex groups. The structure of dynein heavy chain genes, the emerging knowledge on intermediate and light chain genes and their products, and the possible involvement of dyneins in disease are discussed.
Engineered E. coli as Vehicles for Targeted Therapeutics (2010)

Improving the means of drug delivery has become an important field of pharmaceutical research. The development of safe and advanced vectors for gene therapy and other novel therapies will allow for targeted delivery of pharmaceutically active agents and carries promise to improve therapies both through increased efficiency (e.g. improved cellular uptake of the active drug) as well as lower toxicity (e.g. through targeted delivery only to the cells requiring treatment) for a large number of pharmaceutical agents. Here we are reviewing the nascent field using live bacteria as vectors for therapeutic and preventive agents in a wide range of areas, from vaccine purposes to gene therapy and delivery of therapeutic RNA interference. This review focuses particularly on the use of E. coli derived strains for therapeutic delivery.
Effects of Cell Density on Lipids of Human Glioma and Fetal Neural Cells (1981)

Abstract: Gangliosides, phospholipids, and cholesterol of human glioma (12‐18) and fetal neural cells (CH) were analyzed at specified cell densities, from sparse to confluent. Total ganglioside sialic acid, phospholipid phosphorus, and cholesterol increased in the glioma cells on a per cell, mg protein, or mg total lipid basis two‐ to threefold as cell density increased 25‐fold. These same three constituents in the fetal cells increased with cell density on a per cell and mg protein basis but not on a per mg total lipid basis. In glioma cells, the di‐ and trisialogangliosides (GD 2 + GD lb + GT 1 ) increased from 1–2% of total ganglioside sialic acid at sparse densities to 7–8% at intermediate (logarithmic phase) densities to 10–13% at confluent densities. The set of simpler gangliosides (GM 4 + GM 3 + GM 2 ) decreased from 50% of total ganglioside sialic acid at sparse glioma cell densities, to 36% at intermediate and 30% at confluent densities. In the fetal neural cells, the set of gangliosides (GM 4 + GM 3 + GM 2 ) had about 48% of total ganglioside sialic acid in both sparse and confluent preparations. The fetal cells were twofold higher in GM 3 (32.4 ± 2.1%) than the glioma cells (16.8 ± 1.6%), but lower in GM t (9.1 ± 0.9% versus 18.2 ± 1.8%), cell densities notwithstanding. Confluent cell preparations of both cell lines were consistently higher in ethanolamine plasmalogen than sparse cells. We conclude that in these two neural cell lines quantitative changes in ganglioside and phospholipid species occurred correlatively as cell densities increased. Higher glioma cell densities were associated with greater proportions of complex ganglioside species. These changes in cell membrane constituents during growth may result from cell contact and may indicate a role for them in cell growth regulation and/or differentiation.
Efficient simulation of large-scale Spiking Neural Networks using CUDA graphics processors (2009)

Neural network simulators that take into account the spiking behavior of neurons are useful for studying brain mechanisms and for engineering applications. Spiking neural network (SNN) simulators have been traditionally simulated on large-scale clusters, super-computers, or on dedicated hardware architectures. Alternatively, graphics processing units (GPUs) can provide a low-cost, programmable, and high-performance computing platform for simulation of SNNs. In this paper we demonstrate an efficient, Izhikevich neuron based large-scale SNN simulator that runs on a single GPU. The GPU-SNN model (running on an NVIDIA GTX-280 with 1 GB of memory), is up to 26 times faster than a CPU version for the simulation of 100 K neurons with 50 million synaptic connections, firing at an average rate of 7 Hz. For simulation of 100 K neurons with 10 million synaptic connections, the GPU-SNN model is only 1.5 times slower than real-time. Further, we present a collection of new techniques related to parallelism extraction, mapping of irregular communication, and compact network representation for effective simulation of SNNs on GPUs. The fidelity of the simulation results were validated against CPU simulations using firing rate, synaptic weight distribution, and inter-spike interval analysis. We intend to make our simulator available to the modeling community so that researchers will have easy access to large-scale SNN simulations.
Phenotypical and functional properties of human bone marrow mesenchymal progenitor cells (1999)

Bone marrow stroma provides the microenvironment for hematopoiesis and is also the source of mesenchymal progenitors (mesenchymal or marrow stromal cells [MSC]) that may serve as long-lasting precursors for bone, cartilage, lung, and muscle. While several studies have indicated the differentiation potential of MSC, few studies have been performed on the cells themselves. In an attempt to further expand our knowledge on these cells, we have performed studies on their cell cycle, immuno- and adhesive-phenotype, ex vivo expansion, and differentiation properties. MSC cultures have been initiated from human bone marrow low-density mononuclear cells and maintained in the absence of differentiation stimuli and hematopoietic cells. The homogenous layer of adherent cells thus formed exhibits a typical fibroblastlike morphology, a population doubling time of 33 h, a large expansive potential, and cell cycle characteristics including a subset (20%) of quiescent cells. The antigenic phenotype of MSC is not unique, borrowing features of mesenchymal, endothelial, and epithelial cells. Together, MSC express several adhesion-related antigens, like the integrin subunits alpha4, alpha5, beta1, integrins alphavbeta3 and alphavbeta5, ICAM-1, and CD44H. MSC produce and functionally adhere to extracellular matrix molecules. When incubated under proper stimuli, MSC differentiate into osteoblasts or adipocytes. Taken together, these results demonstrate that adherent marrow-derived cells cultured in the absence of hematopoietic cells and differentiation stimulus give rise to a population of cells with phenotypical and functional features of mesenchymal progenitors. The existence of a subset of quiescent cells in MSC cultures seems to be extremely significant, since their number and properties should be enough to sustain a steady supply of cells that upon proliferation and commitment may serve as precursors for a number of nonhematopoietic tissues.
Synthesis and characterization of CsSnI3 thin films (2010)

We report on the synthesis and characterization of CsSnI3 perovskite semiconductor thin films deposited on inexpensive substrates such as glass and ceramics. These films contained polycrystalline domains with typical size of 300 nm. It is confirmed experimentally that CsSnI3 compound in its black phase is a direct band-gap semiconductor, consistent with the calculated band structure from the first principles. The band gap is determined to be ∼1.3 eV at Γ point at room temperature.
Nonstandard symmetry classes in mesoscopic normal-superconducting hybrid structures (1997)

Normal-conducting mesoscopic systems in contact with a superconductor are classified by the symmetry operations of time reversal and rotation of the electron's spin. Four symmetry classes are identified, which correspond to Cartan's symmetric spaces of type C, CI, D, and DIII. A detailed study is made of the systems where the phase shift due to Andreev reflection averages to zero along a typical semiclassical single-electron trajectory. Such systems are particularly interesting because they do not have a genuine excitation gap but support quasiparticle states close to the chemical potential. Disorder or dynamically generated chaos mixes the states and produces forms of universal level statistics different from Wigner-Dyson. For two of the four universality classes, the n-level correlation functions are calculated by the mapping on a free one-dimensional Fermi gas with a boundary. The remaining two classes are related to the Laguerre orthogonal and symplectic random-matrix ensembles. For a quantum dot with a normal-metal--superconducting geometry, the weak-localization correction to the conductance is calculated as a function of sticking probability and two perturbations breaking time-reversal symmetry and spin-rotation invariance. The universal conductance fluctuations are computed from a maximum-entropy S-matrix ensemble. They are larger by a factor of 2 than what is naively expected from the analogy with normal-conducting systems. This enhancement is explained by the doubling of the number of slow modes: owing to the coupling of particles and holes by the proximity to the superconductor, every cooperon and diffusion mode in the advanced-retarded channel entails a corresponding mode in the advanced-advanced (or retarded-retarded) channel.
Metabolism of 20-hydroxyeicosatetraenoic acid by cyclooxygenase (1989)

We recently demonstrated that 20-hydroxyeicosatetraenoic acid (20-HETE) constricts rat aortic rings. The contractile response was partially dependent on the presence of endothelium and was abolished by pretreatment of the rings with either indomethacin or the endoperoxide/thromboxane receptor antagonist, SQ29548. Addition of GSH or SnCl2 to the organ bath diminished the contractile response of 20-HETE, whereas preincubation of the rings with a thromboxane synthase inhibitor did not affect the 20-HETE induced contractions. Short time incubation (2 min) of 20-HETE with ram seminal vesicle microsomes in the presence of p-hydroxymercurybenzoate yielded metabolites which migrated similarly on thin layer chromatography to the known arachidonate endoperoxides prostaglandin (PG) G2 and PGH2 and possess vasoconstrictory properties. The vasoconstriction was dose-dependent with a half-life of approximately 6.3 +/- 0.6 min. Addition of SQ29548 to the aortic ring bath 1 min after metabolite elicited vasoconstriction produced immediate relaxation. Furthermore, pretreatment of the rings with SQ29548 totally abolished the contraction. SnCl2 reduction of the metabolites produced in incubation of rat seminal vesicles with 20-HETE and p-hydroxymercurybenzoate resulted in a single radioactive peak which was further identified by gas chromatography/mass spectrometry as 20-hydroxy-PGF2 alpha. The inhibitory effect of SQ29548, the appearance of labile metabolites with a half-life of approximately 6 min and the production of 20-hydroxy-PGF2 alpha by SnCl2 reduction clearly indicate that the vasoconstrictor metabolites of 20-HETE are the labile endoperoxides of 20-HETE, 20-hydroxy-PGG2, and 20-hydroxy-PGH2.
Synthesis and Structure-Activity Relationships in a Series of Ethenesulfonamide Derivatives, a Novel Class of Endothelin Receptor Antagonists. (2001)

In the previous paper, we described a series of the 2-arylethenesulfonamide derivatives, a novel class of ETA-selective endothelin (ET) receptor antagonists, including the compounds 1a, b. Compound 1a showed excellent oral antagonistic activities and pharmacokinetic profiles, and the monopotassium salt of 1 (YM-598 monopotassium) is in clinical trials. In this paper, we wish to report the investigation of the further details of structure-activity relationships (SARs) of the 2-phenylethenesulfonamide region in 1a. It was found that methyl substitutions at the 2-, 4- and 6-positions of the phenyl group in 1a led to the discovery of the ET(A)/ET(B) mixed antagonist (6s) with an IC50 of 2.2 nM for the ET(A) receptor. We also found that introduction of an ethyl group to the 1-position of the ethenyl group in 1a gave the ET(A) selective antagonist (6u) with an oral endothelin antagonistic activity in rats.
Retinitis pigmentosa: understanding the clinical presentation, mechanisms and treatment options (2004)

Retinitis pigmentosa (RP) is a leading cause of human blindness due to degeneration of retinal photoreceptor cells. Causes of retinal degeneration include defects in the visual pigment, defects in the proteins important for photoreceptor function or in enzymes involved in initiating visual transduction. Despite the diversity of genetic mutations identified in inherited forms of retinal dystrophy, there is a common end result of photoreceptor death and functional blindness. In this review, pertinent anatomical and physiological pathways involved in RP and the underlying genetic mutations are outlined, including a discussion on the inheritance patterns revealed by advances in molecular biological techniques. Characteristics of progression rates of visual field loss and current management options will provide useful clinical guidelines for the management of patients with RP.
Mevalonate and Nonmevalonate Pathways for the Biosynthesis of Isoprene Units (2002)

Isoprenoids are synthesized by consecutive condensations of their five-carbon precursor, isopentenyl diphosphate, to its isomer, dimethylallyl diphosphate. Two pathways for these precursors are known. One is the mevalonate pathway, which operates in eucaryotes, archaebacteria, and cytosols of higher plants. The other is a recently discovered pathway, the nonmevalonate pathway, which is used by many eubacteria, green algae, and chloroplasts of higher plants. To date, five reaction steps in this new pathway and their corresponding enzymes have been identified. EC numbers of these enzymes have been assigned by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and are available at http://www.chem.qmw.ac.uk/iubmb/enzyme/reaction/terp/nonMVA.html.
Poly-lactic-glycolic-acid surface nanotopographies selectively decrease breast adenocarcinoma cell functions (2012)

The ability of poly(lactic-co-glycolic acid) (PLGA, 50:50 PLG/PGA, wt%) nanotopographies to decrease lung epithelial carcinoma cell functions (including adhesion, proliferation, apoptosis and vascular endothelial growth factor (VEGF) secretion) has been previously reported. Specifically, results demonstrated decreased lung epithelial carcinoma cell VEGF synthesis on 23 nm surface-featured PLGA compared to traditional nanosmooth PLGA. However, clearly, different cell lines could have different behaviors on similar biomaterials. Thus, to investigate the universality of nanopatterned PLGA substrates to inhibit numerous cancer cell functions, here, breast epithelial adenocarcinoma cell (MCF-7) adhesion, proliferation, apoptosis and VEGF secretion were determined on different PLGA nanometer surface topographies. To isolate surface nanotopographical effects from all other surface properties, PLGA surfaces with various nanotopographies but similar chemistry and hydrophobicity were fabricated here. Atomic force microscopy (AFM) verified the varied nanotopographies on the PLGA surfaces prepared in this study. Importantly, results demonstrated for the first time significantly decreased breast adenocarcinoma cell functions (including decreased proliferation rate, increased apoptosis and decreased VEGF synthesis) on 23 nm featured PLGA surfaces compared to all other PLGA surface topographies fabricated (specifically, nanosmooth, 300 and 400 nm surface-featured PLGA surfaces). In contrast, healthy breast epithelial cells proliferated more (24%) on the 23 nm featured PLGA surfaces compared to all other PLGA samples. In summary, these results provided further insights into understanding the role PLGA surface nanotopographies can have on cancer cell functions and, more importantly, open the possibility of using polymer nanotopographies for a wide range of anticancer regenerative medicine applications (without resorting to the use of chemotherapeutics).
The Factors Affecting Successful Implementation of ERP in Nanjing Manufacturing SMEs (2011)

Enterprise Resource Planning (ERP) system in companies can be implemented to Multi National Corporation (MNC), Larger Enterprise, and Small & Medium-sized Enterprises (SMEs). In China, 99% of all companies can be categorized as SMEs. With a decade of high-speed economy development after entering the 21st century, traditional Chinese SMEs want to find a new management model to improve work efficiency and increase business opportunities. This study finds the factors affecting the diffusion and successful implementation of ERP in Chinese Nanjing manufacturing SMEs. It will lead to the conclusion that ERP investment and implementation, which could be used as project guideline by the management of SMEs or companies that adopt ERP in intend to implement them. The objective is to provide Nanjing’s SMEs implementing ERP with knowledge about ERP implementation factors.Request access from your librarian to read this article's full text.