gebhart/patrepeval huggingface dataset:
The Role of the CD8‐Positive Subset of T Cells in Proliferative Responses to Soluble Antigens (1986)

Using magnetic monosized polymer particles (M 450) coated with a monoclonal mouse IgM anti-CD8 (ITI 5C2) antibody, we were able to selectively remove and isolate functionally active CD8+ T cells from human peripheral blood mononuclear cells. Isolated CD8+ cells did not respond by proliferation to soluble antigens, but proliferated in response to phytohaemagglutinin. However, in the presence of CD4+ T cells, CD8+ cells were able to mount a substantial proliferation when stimulated with soluble antigens. Depletion of CD8+ cells decreased rather than increased the T-cell responses to the antigens glyc-gli, Coxsackie B4, and mumps in healthy individuals. We therefore found no indication of involvement of functionally-active CD8+ suppressor cells in vitro. The T-cell responsiveness to these antigens has previously been shown to be influenced by HLA-DR-associated restriction elements, but the tendency for decreased responsiveness to these antigens by CD8 depletion seemed independent of the DR type of the cell donors. As in healthy subjects, CD8 depletion resulted in a decreased responsiveness to the gluten antigen glyc-gli in untreated and treated coeliac disease patients and to Coxsackie B4 and mumps antigens in Type 1 diabetics.
Fully Integrated Self-Powered Electrical Stimulation Cell Culture Dish for Noncontact High-Efficiency Plasmid Transfection (2021)

Plasmid DNA transfection of mammalian cells is widely used in biomedical research and genetic drug delivery, but low transfection efficiency, especially in the context of the primary cells, limits its application. To improve the efficiency of plasmid transfection, a fully integrated self-powered electrical stimulation cell culture dish (SESD) has been developed to provide self-powered electrical stimulation (ES) of adherent cells, significantly improving the efficiency of plasmid transfection into mammalian cells and cell survival by the standard lipofectamine transfection method. Mechanistically, ES can safely increase the intracellular calcium concentration by opening calcium-ion channels, leading to a higher efficiency of plasmid transfection. Therefore, SESD has the potential to become an effective platform for high-efficiency plasmid DNA transfection in biomedical research and drug delivery.
Preliminary Co-Design of L and X-band Stacked Arrays with Scanning Capabilities (2020)

International audience
Visual discovery and model-driven explanation of time series patterns (2016)

Gatherminer is an interactive visual tool for analysing time series data with two key strengths. First, it facilitates bottom-up analysis, i.e., the detection of trends and patterns whose shapes are not known beforehand. Second, it integrates data mining algorithms to explain such patterns in terms of the time series' metadata attributes - an extremely difficult task if the space of attribute-value combinations is large. To accomplish these aims, Gatherminer automatically rearranges the data to visually expose patterns and clusters, whereupon users can select those groups they deem `interesting.' To explain the selected patterns, the visualisation is tightly coupled with automated classification techniques, such as decision tree learning. We present a brief evaluation with telecommunications experts comparing our tool against their current commercial solution, and conclude that Gatherminer significantly improves both the completeness of analyses as well as analysts' confidence therein.
Genetic, Functional, and Phenotypic Diversity in TAS2R38-Mediated Bitter Taste Perception (2013)

Mutational polymorphism in the TAS2R38 bitter taste receptor is a key determinant of threshold taste detection of isolated compounds, such as phenylthiocarbamide (PTC) and propylthiouracil (PROP), as well as complex orosensation-mediated traits such as diet choice and smoking habits. These relationships are accounted for, in part, by 2 common alleles differing in functionality, TAS2R38-PAV and TAS2R38-AVI. However, TAS2R38 harbors extensive additional polymorphism whose functional significance remains unknown. To examine this variation, we ascertained genetic diversity in 56 Caucasian subjects via whole-gene sequencing, analyzed allele-specific responses to 5 TAS2R38 agonists (PTC, PROP, goitrin, methimazole, and sinigrin) using in vitro assays, and assessed genotypic associations with threshold detection phenotypes. Sequencing identified 3 single-nucleotide substitutions encoding 3 amino acid changes (C145G/P49A, C785T/A262V, and A886G/I296V), which combined to form 6 haplotypes in our sample. In vitro assays revealed a continuous range of response across alleles, and associations with threshold were significant for all single nucleotide polymorphisms (P < 0.002) and PAV/AVI haplotypes (P < 0.001). Haplotypes other than PAV and AVI did not exhibit phenotypic associations in our sample, possibly as a result of their low frequencies. However, prior studies have indicated that these alleles are common in some global regions, suggesting that alleles rare in our sample may be phenotypically relevant in other populations.
Mechanical and fracture performance of carbon fibre reinforced composites with nanoparticle modified matrices (2016)

The microstructure and fracture performance of carbon-fibre reinforced polymer (CFRP) composites with an epoxy resin cured with an anhydride hardener containing silica nanoparticles and/or polysiloxane core-shell rubber (CSR) particles were investigated in the current work. Double cantilever beam tests were performed in order to evaluate the fracture energy of the CFRP composites, while the single edge notched bend (SENB) specimen was employed to evaluate the fracture energy of the bulk polymers. Tests were conducted at room temperature and at -80°C. The transferability of the toughness from the bulk polymers to the fibre-composite systems is discussed, with an emphasis on the toughening mechanisms.
Dual-Porosity Hollow Nanoparticles for the Immunoprotection and Delivery of Nonhuman Enzymes (2014)

Although enzymes of nonhuman origin have been studied for a variety of therapeutic and diagnostic applications, their use has been limited by the immune responses generated against them. The described dual-porosity hollow nanoparticle platform obviates immune attack on nonhuman enzymes paving the way to in vivo applications including enzyme-prodrug therapies and enzymatic depletion of tumor nutrients. This platform is manufactured with a versatile, scalable, and robust fabrication method. It efficiently encapsulates macromolecular cargos filled through mesopores into a hollow interior, shielding them from antibodies and proteases once the mesopores are sealed with nanoporous material. The nanoporous shell allows small molecule diffusion allowing interaction with the large macromolecular payload in the hollow center. The approach has been validated in vivo using l-asparaginase to achieve l-asparagine depletion in the presence of neutralizing antibodies.
Convenient, Scalable and Flexible Method for the Preparation of Imidazolium Salts with Previously Inaccessible Substitution Patterns. (2006)

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, please click on HTML or PDF.
Self-Assembly of Alkylammonium Chains on Montmorillonite:  Effect of Chain Length, Head Group Structure, and Cation Exchange Capacity (2006)

The structure and dynamics of alkylammonium-modified montmorillonites with different cation exchange capacity (CEC), ammonium head groups, and chain length is investigated by molecular dynamics simulation for a large set of structures and compared to a wide array of experimental data. In the 44 systems, the relationship between computational (molecular dynamics) and experimental data (X-ray, IR, NMR, and DSC) was found to be very complementary. Much of the properties appear to be dictated through the inorganic−organic interface, which in addition to electrostatic interactions involves hydrogen bonds between primary ammonium head groups (NH3+−R) and oxygen on the silicate surface (O···H distance ∼150 pm) or flexibly attached quaternary ammonium head groups (NMe3+−R) of higher lateral mobility (O···H distance ∼290 pm). The gauche content is a function of the packing density of the head groups on the surface, the preferred orientation of the head groups, and the interlayer density of the alkyl chains. These effects cause up to 45% gauche conformations as compared to only 5% gauche conformations in chains with crystalline order. A low CEC leads to stepwise increases of the basal plane spacing with increasing chain length, corresponding to the subsequent formation of alkyl monolayers, bilayers, trilayers, etc., while a high CEC leads to a continuous increase in basal plane spacing with increasing chain length. The density of the organic interlayer space between two silicate layers shows minima for emerging new layers of alkyl chains and maxima for densely packed layers. These fluctuations decrease as the number of layers increases. On an isolated clay mineral surface, layer formation of the surfactants is also found and lateral 2D diffusion constants range from 5 × 10-6 cm2/s to <10-9 cm2/s depending on the structure of the surfactant.
Measurement of $$\psi {(2S)} $$ ψ ( 2 S ) polarisation in $$pp$$ p p collisions at $$\sqrt{s}$$ s = 7 TeV (2014)

The polarisation of prompt [Formula: see text] mesons is measured by performing an angular analysis of [Formula: see text] decays using proton-proton collision data, corresponding to an integrated luminosity of 1.0[Formula: see text], collected by the LHCb detector at a centre-of-mass energy of 7 TeV. The polarisation is measured in bins of transverse momentum [Formula: see text] and rapidity [Formula: see text] in the kinematic region [Formula: see text] and [Formula: see text], and is compared to theoretical models. No significant polarisation is observed.
Sub- μ m features patterned with laser interference lithography for the epitaxial lateral overgrowth of α-Ga2O3 via mist chemical vapor deposition (2021)

The low growth rate of mist chemical vapor deposition normally requires a long growth time to achieve coalescence in the epitaxial lateral overgrowth of α-Ga2O3 thin films on sapphire substrates. To address this issue, sub-μm features were patterned using laser interference lithography. Periodical stripes with a ∼590-nm pitch allowed the overgrowth of crack-free, void-free, and continuous thin films, while typical growth conditions using a low carrier gas flow rate and a low Ga precursor concentration were maintained. Coalescence was achieved even with a short growth time of &amp;lt;30 min and a low film thickness of &amp;lt;500 nm. Transmittance and x-ray diffraction spectra show that the film was predominantly in α-phase. Transmission electron microscopy (TEM) images reveal cup-top-like α-Ga2O3 regions of low dislocation density on the SiOx mask. Selected area electron diffraction and high-resolution TEM analyses confirm that an α-Ga2O3 layer was formed even on the top of the SiOx mask. Interestingly, the dislocations formed on the window areas did not bend toward the center of the masks; rather, a dislocation bending outward from the center was observed. This suggests the occurrence of early coalescence and/or atomic rearrangement.
IgA and IgG Hypogammaglobulinemia Persists in Most Patients with Waldenstrom’s Macroglobulinemia Despite Therapeutic Responses, Including Complete Remissions. (2004)

Abstract Recurrent infections are common in pts with Waldenstrom’s macroglobulinemia (WM) and may be related to IgA and IgG hypogammaglobulinemia. The impact of therapy and therapeutic responses on humoral immunity in WM is therefore of clinical interest. We examined IgA and IgG levels before and after therapy in 92 serially treated and responding WM patients. Their median age was 59 yrs and 70/92 (76.1%) were previously untreated. Median follow-up for all patients was 11 (range 3-134) months. Pre-therapy, 72/92 (78.2%) and 70/92 (76.1%), and post-therapy 82/92 (89.1%) and 80/92 (86.9%) pts demonstrated IgG (&amp;lt;700 mg/dL) and IgA (&amp;lt;70 mg/dL) hypogammaglobulinemia, respectively. Changes in median IgG and IgA levels by therapy were as follows: N= Pre-IgG Post-IgG T-Test Pre-IgA Post-IgA T-Test Nucleoside analogue 5 438 399 0.63 32 38 0.35 Rituximab 17 455 358 0.29 35 29 0.43 Rituximab/Thalidomide 19 388 374 0.3 28 24 0.32 Rituximab/Nucleoside 21 571 423 0.006 55 29 0.05 CHOP 3 702 568 0.62 48 30 0.82 CHOP/Rituximab 14 537 383 0.1 61 36 0.21 Chlorambucil ± steroids 5 837 659 0.57 129 66 0.52 Campath-1H 7 521 444 0.62 28 27 0.61 HD Dexamethasone 1 269 173 NA 27 28 NA All therapies 92 480 398 0.008 38 28 0.01 Changes in median IgG and IgA levels by response category were as follows: N= Pre-IgG Post-IgG T-Test Pre-IgA Post-IgA T-Test CR 8 644 472 0.05 75 37 0.08 PR 70 415 349 0.09 27 28 0.91 MR 14 474 394 0.01 38 26 0.02 These studies demonstrate that IgA and IgG hypogammaglobulinemia persists despite therapeutic responses, including complete remissions in patients with WM. Futhermore, the therapeutic regimen employed may aggravate persistent IgA and IgG hypogammaglobulinemia.
Vortex fluidic mediated synthesis of polysulfone (2020)

Polysulfone (PSF) was prepared under high shear in a vortex fluidic device (VFD) operating in confined mode, and its properties compared with that prepared using batch processing. This involved reacting the pre-prepared disodium salt of bisphenol A (BPA) with a 4,4'-dihalodiphenylsulfone under anhydrous conditions. Scanning electron microscopy (SEM) established that in the thin film microfluidic platform, the PSF particles are sheet-like, for short reaction times, and fibrous for long reaction times, in contrast to spherical like particles for the polymer prepared using the conventional batch synthesis. The operating parameters of the VFD (rotational speed of the glass tube, its tilt angle and temperature) were systematically varied for establishing their effect on the molecular weight (<i>M</i> <sub>w</sub>), glass transition temperature (<i>T</i> <sub>g</sub>) and decomposition temperature, featuring gel permeation chromatography (GPC), differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) respectively. The optimal VFD prepared PSF was obtained at 6000 rpm rotational speed, 45° tilt angle and 160 °C, for 1 h of processing with <i>M</i> <sub>w</sub> ∼10 000 g mol<sup>-1</sup>, <i>T</i> <sub>g</sub> ∼158 °C and decomposition temperature ∼530 °C, which is comparable to the conventionally prepared PSF.
Convergence of integrin and growth factor receptor signaling pathways within the focal adhesion complex. (1995)

Extracellular matrix controls capillary endothelial cell sensitivity to soluble mitogens by binding integrin receptors and thereby activating a chemical signaling response that rapidly integrates with growth factor-induced signaling mechanisms. Here we report that in addition to integrins, growth factor receptors and multiple molecules that transduce signals conveyed by both types of receptors are immobilized on the cytoskeleton (CSK) and spatially integrated within the focal adhesion complex (FAC) at the site of integrin binding. FACs were rapidly induced in round cells and physically isolated from the remainder of the CSK after detergent-extraction using magnetic microbeads coated with fibronectin or a synthetic RGD-containing peptide. Immunofluorescence microscopy revealed that multiple signaling molecules (e.g., pp60c-src, pp125FAK, phosphatidylinositol-3-kinase, phospholipase C-gamma, and Na+/H+ antiporter) involved in both integrin and growth factor receptor signaling pathways became associated with the CSK framework of the FAC within 15 min after binding to beads coated with integrin ligands. Recruitment of tyrosine kinases to the FAC was also accompanied by a local increase in tyrosine phosphorylation, as indicated by enhanced phosphotyrosine staining at the site of integrin binding. In contrast, neither recruitment of signaling molecules nor increased phosphotyrosine staining was observed when cells bound to beads coated with a control ligand (acetylated low density lipoprotein) that ligates transmembrane scavenger receptors, but does not induce FAC formation. Western blot analysis confirmed that FACs isolated using RGD-beads were enriched for pp60c-src, pp125FAK, phospholipase C-gamma, and the Na+/H+ antiporter when compared with intact CSK or basal cell surface preparations that retained lipid bilayer. Isolated FACs were also greatly enriched for the high affinity fibroblast growth factor receptor flg. Most importantly, isolated FACs continued to exhibit multiple chemical signaling activities in vitro, including protein tyrosine kinase activities (pp60c-src and pp125FAK) as well as the ability to undergo multiple sequential steps in the inositol lipid synthesis cascade. These data suggest that many of the chemical signaling events that are induced by integrins and growth factor receptors in capillary cells may effectively function in a "solid-state" on insoluble CSK scaffolds within the FAC and that the FAC may represent a major site for signal integration between these two regulatory pathways. Future investigations into the biochemical and biophysical basis of signal transduction may be facilitated by this method, which results in isolation of FACs that retain the CSK framework as well as multiple associated chemical signaling activities.
Cloning of a Schizosaccharomyces pombe homologue of elongation factor 1 alpha by two-hybrid selection of calmodulin-binding proteins (1999)

This study reports the cloning and characterization of a cDNA encoding elongation factor 1-alpha (EF1alpha) from the yeast Schizosaccharomyces pombe. The cDNA was cloned from an Schizosaccharomyces pombe expression library by a two-hybrid selection for clones encoding calmodulin (CaM)-binding proteins. The predicted protein is highly homologous to mammalian EF1alpha, indicating a strong tendency towards conservation of the primary amino acid sequence. The protein was expressed as a glutathione S-transferase fusion in both bacteria and in Schizosaccharomyces pombe. The bacterial protein was shown by solution assay to compete with CaM kinase II for CaM. The CaM binding domain was localized to the C-terminus of the protein by this method. Expression of full-length EF1alpha in vivo caused an increase in cell cycle length and a decreased rate of growth as evidenced by a lack of elongated cells in slowly dividing cultures. This effect appears to involve CaM binding because a truncation mutant version of EF1alpha lacking the CaM binding domain did not cause cell cycle delay.Key words: calmodulin, two-hybrid selection, calmodulin-binding protein, yeast, cell proliferation.
ThroughputScheduler: Learning to Schedule on Heterogeneous Hadoop Clusters (2013)

Hadoop is the de-facto standard for big data analytics applications. Presently available schedulers for Hadoop clusters assign tasks to nodes without regard to the capability of the nodes. We propose ThroughputScheduler, which reduces the overall job completion time on a clusters of heterogeneous nodes by actively scheduling tasks on nodes based on optimally matching job requirements to node capabilities. Node capabilities are learned by running probe jobs on the cluster. ThroughputScheduler uses a Bayesian, active learning scheme to learn the resource requirements of jobs on-the-fly. An empirical evaluation on a set of sample problems demonstrates that ThroughputScheduler can reduce total job completion time by almost 20 % compared to the Hadoop FairScheduler and 40 % compared to FIFOScheduler. ThroughputScheduler also reduces average mapping time by 33 % compared to either of these schedulers. 1
Neighbor Discovery Using Galois Fields and Its Hardware Implementation (2013)

Neighbor discovery is essential in all channel access protocols based on transmission scheduling, whether such protocols are topology-dependent or topology-independent. We propose a novel approach to neighbor discovery based on relative GPS coordinates (RGPS), extending the work by Chlamtac and Farago on topology-transparent transmission scheduling. The proposed approach attains neighbor discovery with timing guarantees, which yields greater scalability and requires smaller transmission compared to neighbor discovery mechanisms based on probabilistic methods. We further present the design and implementation of a hardware accelerator for evaluating the Galois field polynomials used in the proposed neighbor-discovery scheme.
Energy/Area/Delay Tradeoffs in the Physical Design of On-Chip Segmented Bus Architecture (2007)

The increasing gap between design productivity and chip complexity and the emerging systems-on-chip (SoCs) architectural template have led to the wide utilization of reusable hard intellectual property (IP) cores. Macro block-based physical design implementation needs to find a well-balanced solution among chip area, on-chip communication energy, and critical communication path delay. We present in this paper an automated way to implement an energy optimal netlist interconnecting the hard macro blocks using a heavily segmented communication architecture. We explore the entire tradeoff curve among the network energy, chip area, and critical communication path delay at the floorplanning stage based on two real-life application drivers. Large energy gains with small area overheads are illustrated during the floorplanning stage. This tradeoff profile is a good guideline for the SOC designers to choose the optimal solution for their specific systems.
The abp locus of Streptococcus uberis encodes a protein homologous to polar amino acid and opine binding proteins of Gram-negative bacteria (1998)

A gene locus abp was identified immediately upstream of the CAMP factor gene cfu in Streptococcus uberis. An open reading frame capable of coding for a 277-residue protein was identified. On the basis of sequence characteristics, the abp gene product is potentially a polar amino acid and opine binding component of an ATP-binding cassette type (ABC-type) transport system similar to those of Gram-negative bacteria. This membrane protein is likely lipid modified at its amino terminus and was present in five S. uberis strains and one Streptococcus parauberis strain examined.Key words: bovine mastitis, Streptococcus uberis, amino acid transport.
The fluorine atom as a halogen bond donor, viz. a positive site (2011)

When bound to residues which can work as particularly strong electron withdrawing groups, fluorine can display a region of positive electrostatic potential (positive σ-hole). Fluorine can thus function as a halogen bond donor and form complexes with lone-pair-containing neutral atoms and anions. Examples in the gas, liquid, and solid phases are discussed.
Real-Time Universal Synthetic Transmit Aperture Beamforming with Retrospective Encoding for Conventional Ultrasound Sequences (REFoCUS) (2021)

Retrospective transmit beamforming can be achieved by modeling a set of steered focused, diverging, or plane wave transmissions as virtual sources. These virtual sources are time-delayed and apodized so as to form a synthetic transmit aperture (STA) with dynamic focusing in retrospect. However, a separate time-delay algorithm and geometric model is needed for each case, and the virtual source model limits the granularity with which delays and apodizations can be applied. Multistatic STA has fine granularity due to the use of single element transmits, but suffers from poor electronic signal-to-noise ratio (SNR). Retrospective encoding for conventional ultrasound sequences (REFoCUS) has recently been proposed as a technique to recover the multistatic dataset from ordinary ultrasound sequences with high SNR. REFoCUS treats all transmit sequences as multiplicative frequency-domain encodings that can be (pseudo-)inverted to recover multistatic data. Here, we demonstrate a prototype imaging system capable of real-time frame rates using GPU-based processing.