gebhart/patrepeval huggingface dataset:
Light chain replacement: a new model for antibody gene rearrangement. (1995)

A functional B cell antigen receptor is thought to regulate antibody gene rearrangement either by stopping further rearrangement (exclusion) or by promoting additional rearrangement (editing). We have developed a new model to study the regulation of antibody gene rearrangement. In this model, we used gene targeting to replace the J kappa region with a functional V kappa-J kappa light chain gene. Two different strains of mice were created; one, V kappa 4R, has a V kappa 4-J kappa 4 rearrangement followed by a downstream J kappa 5 segment, while the other, V kappa 8R, has a V kappa 8-J kappa 5 light chain. Here, we analyze the influence of these functional light chains on light chain rearrangement. We show that some V kappa 4R and V kappa 8R B cells only have the V kappa R light chain rearrangement, whereas others undergo additional rearrangements. Additional rearrangement can occur not only at the other kappa allele or isotype (lambda), but also at the targeted locus in both V kappa 4R and V kappa 8R. Rearrangement to the downstream J kappa 5 segment is observed in V kappa 4R, as is deletion of the targeted locus in both V kappa 4R and V kappa 8R. The V kappa R models illustrate that a productively rearranged light chain can either terminate further rearrangement or allow further rearrangement. We attribute the latter to editing of autoantibodies and to corrections of dysfunctional receptors.
Distribution power flow for smart grid technologies (2009)

Smart Grid technologies hold the promise of being able to solve many of the problems currently facing in the electric power industry. However, the large scale deployment of these new technologies has been limited due to an inability to accurately model their effects or to quantify their potential benefits. GridLAB-D is a new open source power system modeling and simulation environment developed by the United States Department of Energy specifically to integrate detailed power systems and end-use models. In order to effectively model the vast array of possible smart grid technologies GridLAB-D was developed as a general simulation environment. This paper describes the basic design concept, the power flow solutions implemented, and a detailed example of the type of analysis that can be performed within the simulation environment in order to support the evaluation of smart grid technologies.
Interaction of alcohol with phospholipid membrane: NMR and XRD investigations on DPPC–hexanol system (2010)

The investigations of the interaction between phospholipid bilayer and short-chain alcohols are relevant for the potential of lipid bilayer membranes to serve as model systems for studies of various biological processes including permeability of the plasma membrane and molecular mechanisms of anesthesia. Because the hydrophobic portion of an alcohol favorably interacts with lipid hydrocarbon chains, the polar hydroxyl group remains free to form hydrogen bonds with polar lipid atoms that are located near the water/lipid interface. Experiments on phospholipid membranes have shown that alcohols can induce an interdigitated phase and at high concentration even promote the assembly of some lipids into non-bilayer structures within the membrane interior. In this paper we have investigated the DPPC:hexanol system at high alcohol concentration (two molecules per phospholipid) by means of calorimetric, Nuclear Magnetic Resonance, X-ray diffraction and density measurements. We have found that the presence of a high alcohol concentration shifts the membrane transition temperature to lower values, and has a disordering effect on the phospholipid acyl chains in the gel phase. The bilayer spacing and the area of polar head have been also derived for the liquid phase.
ER stress and its regulator X‐box‐binding protein‐1 enhance polyIC‐induced innate immune response in dendritic cells (2011)

Multiple physiological and pathological conditions interfere with the function of the endoplasmic reticulum (ER). However, much remains unknown regarding the impact of ER stress on inflammatory responses in dendritic cells (DCs) upon the recognition of pathogen molecules. We show that ER stress greatly potentiates the expression of inflammatory cytokines and IFN-β in murine DCs stimulated by polyIC, a synthetic mimic of virus dsRNA. Both toll-like receptor 3 and melanoma differentiation-associated gene-5 are involved in the enhanced IFN-β production, which is associated with increased activation of NF-κB and IRF3 signaling as well as the splicing of X-box-binding protein-1 (XBP-1), an important regulator involved in ER stress response. Surprisingly, silencing of XBP-1 reduces polyIC-stimulated IFN-β expression in the presence or absence of ER stress, indicating that XBP-1 may be essential for polyIC signaling and ER stress-amplified IFN-β production. Overexpression of a spliced form of XBP-1 (XBP-1s) synergistically augments polyIC-induced inflammatory response. For the first time, we show that XBP-1s overexpression-enhanced IFN-β production in DCs markedly suppresses vesicular stomatitis virus infection, revealing a previously unrecognized role for XBP-1 in an antiviral response. Our findings suggest that evolutionarily conserved ER stress response and XBP-1 may function collaboratively with innate immunity to maintain cellular homeostasis.
Activation of Epstein-Barr Virus by 5-Bromodeoxyuridine in “Virus-Free” Human Cells (1972)

Treatment of three human lymphoid cell lines, free of detectable Epstein-Barr virus, with 5-bromodeoxyuridine resulted in activation of virus synthesis in up to 8% of the cells. The induction of infectious virus could be demonstrated by cocultivation experiments with peripheral leukocytes. These studies demonstrated that the entire viral genome may persist in at least a portion of the lymphoid cells.
MECHANISM AND CONTROL OF V(D)J RECOMBINATION AT THE IMMUNOGLOBULIN HEAVY CHAIN LOCUS (2006)

V(D)J recombination assembles antigen receptor variable region genes from component germline variable (V), diversity (D), and joining (J) gene segments. For B cells, such rearrangements lead to the production of immunoglobulin (Ig) proteins composed of heavy and light chains. V(D)J is tightly controlled at the Ig heavy chain locus (IgH) at several different levels, including cell-type specificity, intra- and interlocus ordering, and allelic exclusion. Such controls are mediated at the level of gene segment accessibility to V(D)J recombinase activity. Although much has been learned, many long-standing questions regarding the regulation of IgH locus rearrangements remain to be elucidated. In this review, we summarize advances that have been made in understanding how V(D)J recombination at the IgH locus is controlled and discuss important areas for future investigation.
The Cysteine-Rich Domain of Human Adam 12 Supports Cell Adhesion through Syndecans and Triggers Signaling Events That Lead to β1 Integrin–Dependent Cell Spreading (2000)

The ADAMs (a disintegrin and metalloprotease) family of proteins is involved in a variety of cellular interactions, including cell adhesion and ecto- domain shedding. Here we show that ADAM 12 binds to cell surface syndecans. Three forms of recombinant ADAM 12 were used in these experiments: the cys-teine-rich domain made in Escherichia coli (rADAM 12-cys), the disintegrin-like and cysteine-rich domain made in insect cells (rADAM 12-DC), and full-length human ADAM 12-S tagged with green fluorescent protein made in mammalian cells (rADAM 12-GFP). Mesenchymal cells specifically and in a dose-dependent manner attach to ADAM 12 via members of the syndecan family. After binding to syndecans, mesenchymal cells spread and form focal adhesions and actin stress fibers. Integrin beta1 was responsible for cell spreading because function-blocking monoclonal antibodies completely inhibited cell spreading, and chondroblasts lacking beta1 integrin attached but did not spread. These data suggest that mesenchymal cells use syndecans as the initial receptor for the ADAM 12 cysteine-rich domain-mediated cell adhesion, and then the beta1 integrin to induce cell spreading. Interestingly, carcinoma cells attached but did not spread on ADAM 12. However, spreading could be efficiently induced by the addition of either 1 mM Mn(2+) or the beta1 integrin-activating monoclonal antibody 12G10, suggesting that in these carcinoma cells, the ADAM 12-syndecan complex fails to modulate the function of beta1 integrin.
Time‐resolved fluorescence studies on the dihydrolipoyl transacetylase (E2) component of the pyruvate dehydrogenase complex from Azotobacter vinelandii (1988)

The dihydrolipoyl transacetylase (E 2 ) component of A. vinelandii PDC and its lipoyl domain shows similar dynamic properties as revealed with fluorescence anisotropy decay of lipoyl‐bound IAANS. The lipoyl domain (32.6 kDa), containing three almost identical subdomains shows a mode of rotation characteristic for a protein of about 30 kDa. A similar rotation is found in E 2 , indicating an independent rotational mobility of the whole domain in the multimeric E 2 core (1.6MDa). No independent rotation of a single lipoyl subdomain (10 kDa) is observed. The E 1 component, in contrast to the E 3 component, shows interaction with the lipoyl domain.
N-Acetyl-Seryl-Aspartyl-Lysyl-Proline Prevents Renal Insufficiency and Mesangial Matrix Expansion in Diabetic db/db Mice (2005)

We have previously reported that N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP), which is a tetrapeptide hydrolyzed by ACE, inhibits the transforming growth factor-beta (TGF-beta)-induced expression of extracellular matrix proteins via inhibition of the Smad signaling in human mesangial cells. To test in vivo the antifibrotic efficacy of Ac-SDKP, we examined whether long-term Ac-SDKP treatment can prevent renal insufficiency and glomerulosclerosis in diabetic db/db mice. Diabetic db/db mice or nondiabetic db/m mice were treated with Ac-SDKP for 8 weeks using osmotic minipumps. The treatment with Ac-SDKP increased plasma Ac-SDKP concentrations by approximately threefold in both groups but did not affect the blood glucose levels. Histologically, the increased glomerular surface area, mesangial matrix expansion, and overproduction of extracellular matrix proteins in db/db mice were significantly inhibited by Ac-SDKP. Furthermore, Ac-SDKP treatment normalized the increased plasma creatinine value in db/db mice, whereas the albuminuria in Ac-SDKP-treated db/db mice was somewhat decreased as compared with nontreated db/db mice, although the difference was not statistically significant. In addition, the nuclear translocation of Smad3 was inhibited by Ac-SDKP. These results demonstrate that long-term Ac-SDKP treatment ameliorates renal insufficiency and glomerulosclerosis in db/db mice via inhibition of TGF-beta/Smad pathway, suggesting that Ac-SDKP could be useful in the treatment of diabetic nephropathy.
Highly resolved chemical imaging of living cells by using synchrotron infrared microspectrometry (1998)

Using synchrotron radiation as an ultra-bright infrared source, we have been able to map the distributions of functional groups such as proteins, lipids, and nucleic acids inside a single living cell with a spatial resolution of a few microns. In particular, we have mapped the changes in the lipid and protein distributions in both the final stages of cell division and also during necrosis.
Janick AUBERGER, Ctésias. Histoires de l'Orient. Introduction, traduction et notes par J. A. Paris, Les belles Lettres, 1991. 1 vol. 13,5 x 21 cm, XXI-190 p., 2 pl., 2 cartes. (LA ROUE A LIVRES). Prix : 115 FF. ISBN 2-251-33910-3 (1993)

info:eu-repo/semantics/published
Identification and localization of an iron-regulated 35 kDa protein of Pasteurella haemolytica serotype A2 (1991)

Iodination of intact Pasteurella haemolytica serotype A2 cells labelled a sub-set of total cellular proteins. Comparison of the autoradiographic patterns obtained from iodinated cells grown on complete medium and on iron-depleted medium showed that expression of three proteins, of 100, 70 and 35 kDa, respectively, was increased by growth under iron-depleted conditions. Of these proteins, that of 35 kDa had not been reported previously. Like the 100 and 70 kDa proteins, the 35 kDa protein was expressed in natural infections, since it was recognized by antiserum from sheep that had recovered from an experimental infection with P. haemolytica A2. The 35 kDa protein was partially purified by reverse-phase HPLC and was found to be antigenic in both sheep and mice. A monoclonal antibody that was specific for the 35 kDa protein was used to identify the cellular location of the protein by immunoblotting of cell fractions enriched for particular cellular components. This demonstrated that the 35 kDa protein was located mainly in the periplasm.
Dispersion compensation in Fourier domain optical coherence tomography using the fractional Fourier transform (2012)

We address numerical dispersion compensation based on the use of the fractional Fourier transform (FrFT). The FrFT provides a new fundamental perspective on the nature and role of group-velocity dispersion in Fourier domain OCT. The dispersion induced by a 26 mm long water cell was compensated for a spectral bandwidth of 110 nm, allowing the theoretical axial resolution in air of 3.6 μm to be recovered from the dispersion degraded point spread function. Additionally, we present a new approach for depth dependent dispersion compensation based on numerical simulations. Finally, we show how the optimized fractional Fourier transform order parameter can be used to extract the group velocity dispersion coefficient of a material.
Sharing data and work across concurrent analytical queries (2013)

Today's data deluge enables organizations to collect massive data, and analyze it with an ever-increasing number of concurrent queries. Traditional data warehouses (DW) face a challenging problem in executing this task, due to their query-centric model: each query is optimized and executed independently. This model results in high contention for resources. Thus, modern DW depart from the query-centric model to execution models involving sharing of common data and work. Our goal is to show when and how a DW should employ sharing. We evaluate experimentally two sharing methodologies, based on their original prototype systems, that exploit work sharing opportunities among concurrent queries at run-time: Simultaneous Pipelining (SP), which shares intermediate results of common sub-plans, and Global Query Plans (GQP), which build and evaluate a single query plan with shared operators. First, after a short review of sharing methodologies, we show that SP and GQP are orthogonal techniques. SP can be applied to shared operators of a GQP, reducing response times by 20%-48% in workloads with numerous common sub-plans. Second, we corroborate previous results on the negative impact of SP on performance for cases of low concurrency. We attribute this behavior to a bottleneck caused by the push-based communication model of SP. We show that pull-based communication for SP eliminates the overhead of sharing altogether for low concurrency, and scales better on multi-core machines than push-based SP, further reducing response times by 82%-86% for high concurrency. Third, we perform an experimental analysis of SP, GQP and their combination, and show when each one is beneficial. We identify a trade-off between low and high concurrency. In the former case, traditional query-centric operators with SP perform better, while in the latter case, GQP with shared operators enhanced by SP give the best results.
Inhibition of Akt by the alkylphospholipid perifosine does not enhance the radiosensitivity of human glioma cells (2006)

Akt has been implicated as a molecular determinant of cellular radiosensitivity. Because it is often constitutively activated or overexpressed in malignant gliomas, it has been suggested as a target for brain tumor radiosensitization. To evaluate the role of Akt in glioma radioresponse, we have determined the effects of perifosine, a clinically relevant alkylphospholipid that inhibits Akt activation, on the radiosensitivity of three human glioma cell lines (U87, U251, and LN229). Each of the glioma cell lines expressed clearly detectable levels of phosphorylated Akt indicative of constitutive Akt activity. Exposure to a perifosine concentration that reduced survival by approximately 50% significantly reduced the level of phosphorylated Akt as well as Akt activity. Cell survival analysis using a clonogenic assay, however, revealed that this Akt-inhibiting perifosine treatment did not enhance the radiosensitivity of the glioma cell lines. This evaluation was then extended to an in vivo model using U251 xenografts. Perifosine delivered to mice bearing U251 xenografts substantially reduced tumor phosphorylated Akt levels and inhibited tumor growth rate. However, the combination of perifosine and radiation resulted in a less than additive increase in tumor growth delay. Thus, in vitro and in vivo data indicate that the perifosine-mediated decrease in Akt activity does not enhance the radiosensitivity of three genetically disparate glioma cell lines. These results suggest that, although Akt may influence the radiosensitivity of other tumor types, it does not seem to be a target for glioma cell radiosensitization.
Two novel HTRA1 mutations in a European CARASIL patient (2014)

Two patients with low random serum vitamin K1 concentrations but with normal prothrombin times and normal biological assays of the vitamin K dependent coagulation proteins were treated with an N-methyl-thiotetrazole cephalosporin (cefotetan) postoperatively. Four to six days later both patients developed a prolonged prothrombin time and a noticeable and specific lowering of the clotting activities of factors II, VII, IX and X, though the serum vitamin K1 concentrations remained unchanged. Crossed immunoelectrophoresis of prothrombin showed the appearance of a second peak corresponding to descarboxyprothrombin (PIVKA II). These abnormalities corrected after vitamin K administration. These data are consistent with the hypothesis that cephalosporins with an N-methyl-thiotetrazole side chain inhibit the hepatic utilisation of vitamin K but that this only causes hypoprothrombinaemia when liver reserves of vitamin K are low.
Oxidative Stress, Glutamate, and Neurodegenerative Disorders (1993)

There is an increasing amount of experimental evidence that oxidative stress is a causal, or at least an ancillary, factor in the neuropathology of several adult neurodegenerative disorders, as well as in stroke, trauma, and seizures. At the same time, excessive or persistent activation of glutamate-gated ion channels may cause neuronal degeneration in these same conditions. Glutamate and related acidic amino acids are thought to be the major excitatory neurotransmitters in brain and may be utilized by 40 percent of the synapses. Thus, two broad mechanisms--oxidative stress and excessive activation of glutamate receptors--are converging and represent sequential as well as interacting processes that provide a final common pathway for cell vulnerability in the brain. The broad distribution in brain of the processes regulating oxidative stress and mediating glutamatergic neurotransmission may explain the wide range of disorders in which both have been implicated. Yet differential expression of components of the processes in particular neuronal systems may account for selective neurodegeneration in certain disorders.
Metal–organic framework materials as catalysts (2009)

A critical review of the emerging field of MOF-based catalysis is presented. Discussed are examples of: (a) opportunistic catalysis with metal nodes, (b) designed catalysis with framework nodes, (c) catalysis by homogeneous catalysts incorporated as framework struts, (d) catalysis by MOF-encapsulated molecular species, (e) catalysis by metal-free organic struts or cavity modifiers, and (f) catalysis by MOF-encapsulated clusters (66 references).
Automated Detection of Motion Artefacts in MR Imaging Using Decision Forests (2017)

The acquisition of a Magnetic Resonance (MR) scan usually takes longer than subjects can remain still. Movement of the subject such as bulk patient motion or respiratory motion degrades the image quality and its diagnostic value by producing image artefacts like ghosting, blurring, and smearing. This work focuses on the effect of motion on the reconstructed slices and the detection of motion artefacts in the reconstruction by using a supervised learning approach based on random decision forests. Both the effects of bulk patient motion occurring at various time points in the acquisition on head scans and the effects of respiratory motion on cardiac scans are studied. Evaluation is performed on synthetic images where motion artefacts have been introduced by altering the <i>k</i>-space data according to a motion trajectory, using the three common <i>k</i>-space sampling patterns: Cartesian, radial, and spiral. The results suggest that a machine learning approach is well capable of learning the characteristics of motion artefacts and subsequently detecting motion artefacts with a confidence that depends on the sampling pattern.
Toxicity of Luminescent Silica Nanoparticles to Living Cells (2007)

Luminescent nanomaterials can provide high-intensity and photostable luminescent signals when used as labeling materials for the determination of trace amounts of analytes. However, a major concern that has arisen is whether the nanomaterials cause toxic effects in living systems. Here, we address this problem through a systematic investigation of the cytotoxicity and genotoxicity of luminescent silica nanoparticles. These nanoparticles are intensely luminescent labeling materials for ultrasensitive determination of biological samples. The investigation of genotoxicity of the nanomaterials was carried out from two perspectives. First, the integrity of the DNA was examined by detecting DNA base modification, strand breaks, and increased DNA repair activity to recover the damage. Second, different sets of cellular DNAs, including nuclear DNA extracts and the whole genomic DNAs, were examined. Furthermore, to fully assess DNA damage by the nanoparticles, isolated genomic DNAs were directly exposed to the nanoparticles. The cytotoxicity of the nanoparticle was detected by measuring the cell proliferation rate, cell death, and death patterns (necrosis and apoptosis) after the nanoparticle treatments. Results show no significant toxic effects due to the luminescent nanoparticles at the molecular and cellular levels below a concentration of 0.1 mg/mL. Our study indicates that the luminescent silica nanoparticle is a promising labeling reagent for various biomedical applications.
Simple, rapid and sensitive determination of epinephrine and norepinephrine in urine and plasma by non-competitive enzyme immunoassay, compared with HPLC method. (2002)

The CatCombi ELISA kit as an alternative to HPLC methods is very useful for clinical applications as well as for basic research where a simple, rapid, accurate and reproducible assay for epinephrine and norepinephrine determinations is required.
Planar lipid bilayer reconstitution with a micro-fluidic system (2004)

A planar lipid bilayer which is widely used for the electrophysiological study of membrane proteins in laboratories is reconstituted using a micro-fluidic system, in a manner that is suitable for automated processing. We fabricated micro-channels on both sides of the substrate, which are connected through a 100-200 microm aperture, and showed that the bilayer can be formed at the aperture by flowing the lipid solution and buffer, alternately. Parylene coating is found to be suitable for both bilayer formation and electric noise reduction. Future applications include a high-sensitivity ion sensor chip and a high-throughput drug screening device.