gebhart/patrepeval huggingface dataset:
Muscle- and fat-equivalent polyethylene-based phantom materials for X-ray dosimetry at tube voltages below 100 kV (1986)

In continuation of their development of the water-equivalent polyethylene-based phantom material RW-1 for X-rays in the tube voltage range 10-100 kV (see Hermann et al., ibid., vol.30, p.1195-200, 1985), the authors have developed a muscle-equivalent material, RM-1, and a fat-equivalent material, RF-1, for the same voltage range. The two substances have again been produced on a polyethylene basis, using CaCO3 and MgO as additives. The quality of these mixtures was tested by direct comparison with the attenuation and back-scattering data of porcine and human tissues. The authors' final results on RM-1 and RF-1 are summarised in this note.
Analysis of maxillopedia Expression Pattern and Larval Cuticular Phenotype in Wild-Type and Mutant Tribolium (2000)

The Tribolium castaneum homeotic gene maxillopedia (mxp) is the ortholog of Drosophila proboscipedia (pb). Here we describe and classify available mxp alleles. Larvae lacking all mxp function die soon after hatching, exhibiting strong transformations of maxillary and labial palps to legs. Hypomorphic mxp alleles produce less severe transformations to leg. RNA interference with maxillopedia double-stranded RNA results in phenocopies of mxp mutant phenotypes ranging from partial to complete transformations. A number of gain-of-function (GOF) mxp alleles have been isolated based on transformations of adult antennae and/or legs toward palps. Finally, we have characterized the mxp expression pattern in wild-type and mutant embryos. In normal embryos, mxp is expressed in the maxillary and labial segments, whereas ectopic expression is observed in some GOF variants. Although mxp and Pb display very similar expression patterns, pb null embryos develop normally. The mxp mutant larval phenotype in Tribolium is consistent with the hypothesis that an ancestral pb-like gene had an embryonic function that was lost in the lineage leading to Drosophila.
Multicluster tools scheduling: an integrated event graph and network model approach (2006)

Steady-state throughput and scheduling of a multicluster tool become complex as the number of modules and clusters grows. We propose a new methodology integrating event graph and network models to study the scheduling and throughput of multicluster tools. A symbolic decision-move-done graph modeling is developed to simplify discrete-event dynamics for the multicluster tool. This event graph is further used for searching feasible action sequences of the cluster tool. By representing sequences with networks, an extended critical path method is applied to calculate the corresponding cycle time. Grouping methods that are based on network are also introduced to reduce the searching complexity. Compared with optimization-based scheduling approaches, the proposed methodology can directly capture the cyclic characteristic of cluster tool schedules and be applied to analyze the impact of process and wafer flow variations on cycle time and robot schedules. We have successfully applied this new methodology to dozens of cluster tools at Intel Corporation. A chemical-mechanical planarization polisher is employed as an example to illustrate and validate the proposed methodology.
Electron Tunneling at the TiO2/Substrate Interface Can Determine Dye-Sensitized Solar Cell Performance (2004)

The electric potential distribution in dye-sensitized solar cells plays a major role in the operation of such cells. Models based on a built-in electric field which sets the upper limit for the open circuit voltage (Voc) and/or the possibility of a Schottky barrier at the interface between the mesoporous wide band gap semiconductor and the transparent conducting substrate have been presented. We show that I−V characteristics in the dark and upon illumination are very well explained by electron tunneling, rather than transport over a Schottky barrier, at this interface. Our calculations, based on tunnel currents, show that a discontinuity of the conduction band at the TiO2/FTO interface, rather than a built-in electric field, suffices for efficient electron transfer through this interface, and, thus, for efficient operation of this type of solar cell. Clearly, this will hold only if the photoinduced electrostatic potential barrier between the transparent conducting substrate and the mesoporous wide band gap semiconductor drops over a region that is sufficiently narrow to allow efficient tunneling through it.
One step beyond rows and columns flashes in the P300 speller: a theoretical description (2010)

International audience
Optimal activation of Fc-mediated effector functions by influenza virus hemagglutinin antibodies requires two points of contact (2016)

Influenza virus strain-specific monoclonal antibodies (mAbs) provide protection independent of Fc gamma receptor (FcγR) engagement. In contrast, optimal in vivo protection achieved by broadly reactive mAbs requires Fc-FcγR engagement. Most strain-specific mAbs target the head domain of the viral hemagglutinin (HA), whereas broadly reactive mAbs typically recognize epitopes within the HA stalk. This observation has led to questions regarding the mechanism regulating the activation of Fc-dependent effector functions by broadly reactive antibodies. To dissect the molecular mechanism responsible for this dichotomy, we inserted the FLAG epitope into discrete locations on HAs. By characterizing the interactions of several FLAG-tagged HAs with a FLAG-specific antibody, we show that in addition to Fc-FcγR engagement mediated by the FLAG-specific antibody, a second intermolecular bridge between the receptor-binding region of the HA and sialic acid on effector cells is required for optimal activation. Inhibition of this second molecular bridge, through the use of an F(ab')<sub>2</sub> or the mutation of the sialic acid-binding site, renders the Fc-FcγR interaction unable to optimally activate effector cells. Our findings indicate that broadly reactive mAbs require two molecular contacts to possibly stabilize the immunologic synapse and potently induce antibody-dependent cell-mediated antiviral responses: (i) the interaction between the Fc of a mAb bound to HA with the FcγR of the effector cell and (ii) the interaction between the HA and its sialic acid receptor on the effector cell. This concept might be broadly applicable for protective antibody responses to viral pathogens that have suitable receptors on effector cells.
Planning Ahead for Mars Sample Science in the Human Exploration Era (2015)

NASA recently requested that MEPAG evaluate the scientific objectives that could/should be carried out by a potential human mission to Mars that, for planning purposes, is assumed to launch in 2035. One of the key working conclusions is that sample-based science stands out as one of the more important aspects of a potential overall science package (recognizing that there would additionally be other scientific aspects of such a mission that would not be sample-based).
Induction of proliferation and Ig production in human B leukemic cells by anti-immunoglobulins and T cell factors. (1982)

The proliferation and differentiation of human leukemic B cells (B-CLL cells) with anti-Ig and T cell-derived helper factors are described. Stimulation of B-CLL cells with anti-Ig and T helper factors could induce proliferation as well as differentiation into IgM- and IgG-producing cells. Neither anti-Ig nor T helper factors alone could induce any proliferation and/or differentiation of B-CLL cells. Not only whole molecules of anti-Ig but also F(ab')2 fragments could induce proliferation and differentiation of B-CLL cells in the presence of T helper factors, but monovalent Fab' fragments were not effective. Induction of both IgM and IgG with the same idiotype was confirmed by immunofluorescent and SDS-PAGE analysis. By employing an IL 2-dependent cytotoxic T cell line and a TRF-responsive B cell line, T cell factors were separated into a fraction with IL2 activity but no TRF activity and a fraction with TRF activity but no IL 2 activity by chromatofocusing. Anti-Ig and IL 2 fraction could induce proliferation of B-CLL cells, but TRF fraction was not effective for the induction of proliferation in anti-IG-stimulated cells. For IgM and IgG production, anti-Ig and both IL 2 and TRF fractions were required. Depletion of IL 2 fraction in the first 2 days' culture inhibited Ig production, whereas the absence of TRF fraction in the first 2 days did not show any inhibitory effect on Ig production.
The novel object recognition memory: neurobiology, test procedure, and its modifications (2011)

Animal models of memory have been considered as the subject of many scientific publications at least since the beginning of the twentieth century. In humans, memory is often accessed through spoken or written language, while in animals, cognitive functions must be accessed through different kind of behaviors in many specific, experimental models of memory and learning. Among them, the novel object recognition test can be evaluated by the differences in the exploration time of novel and familiar objects. Its application is not limited to a field of research and enables that various issues can be studied, such as the memory and learning, the preference for novelty, the influence of different brain regions in the process of recognition, and even the study of different drugs and their effects. This paper describes the novel object recognition paradigms in animals, as a valuable measure of cognition. The purpose of this work was to review the neurobiology and methodological modifications of the test commonly used in behavioral pharmacology.
Induction of CREB activity via the surface Ig receptor of B cells. (1993)

The regulation and function of CREB was examined in B cells to begin to elucidate the role of cAMP-derived signals in B cell activation. CRE-binding activity detected by the electrophoretic mobility shift assay was found to be constitutively expressed in nuclear extracts of primary murine splenic B cells and was unchanged in nuclear extracts obtained from B cells stimulated in a variety of ways. This activity was shown to be specific by competition analysis and to represent CREB or a closely related molecule on the basis of a "supershift" in the mobility of the nucleoprotein complex induced by anti-CREB antiserum. The function of B cell CREB was assessed by transient transfection of the murine B lymphoma cell line, BAL-17, with a CRE-dependent chloramphenicol acetyl-transferase (CAT) construct that contains a portion of the somatostatin promoter. Cross-linking of the surface Ig receptors of transfected BAL-17 B cells produced a threefold induction of CAT activity. Forskolin, which markedly induced CAT expression in PC12 cells transfected with the CRE-dependent construct, failed to stimulate CAT activity in transfected BAL-17 B cells despite an increase in cAMP. However, anti-Ig was found to act in synergy with forskolin to produce enhanced CAT activity. A phosphoprotein of appropriate molecular size for CREB was immunoprecipitated from anti-Ig plus forskolin treated BAL-17 B cells. These results suggest that CREB is present in primary B cells and that CRE-dependent gene expression is regulated by surface Ig either alone or in synergy with cAMP; the latter implies cross-talk between intracellular signaling pathways acting at the level of CREB.
An oral preparation to release drugs in the human colon. (1982)

1 A colonic delivery system is described to deliver orally ingested drugs to the colon and release them at that site by coating with an acrylic based resin (Eudragit S). The technique is validated using X-ray evidence and serum levels of a convenient marker, sulphapyridine. 2 This colonic delivery system is particularly suitable for drugs such as 5-amino salicylic acid or steroids in the management of patients with colitis.
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques (2011)

The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus macaque. Comparison with the previously sequenced Indian rhesus macaque reveals that all three macaques maintain abundant genetic heterogeneity, including millions of single-nucleotide substitutions and many insertions, deletions and gross chromosomal rearrangements. By assessing genetic regions with reduced variability, we identify genes in each macaque species that may have experienced positive selection. Genetic divergence patterns suggest that the cynomolgus macaque genome has been shaped by introgression after hybridization with the Chinese rhesus macaque. Macaque genes display a high degree of sequence similarity with human disease gene orthologs and drug targets. However, we identify several putatively dysfunctional genetic differences between the three macaque species, which may explain functional differences between them previously observed in clinical studies.
Annealing characteristics of Si-rich SiO2 films (1985)

Silicon-rich SiO2 films of various compositions were deposited by atmospheric or plasma-enhanced chemical vapor deposition (CVD) techniques. These films were annealed at various temperatures between 700 and 1100 °C. The growth and crystallinity of the silicon clusters were monitored by transmission electron microscopy. The growth of the silicon clusters was found to be diffusion controlled with an activation energy measured to a first approximation at 1.9 eV/atom for both atmospheric and plasma-enhanced CVD films. A minimum annealing temperature of between 800 and 950 °C and a minimum amount of excess Si above SiO2 are required to form crystalline silicon particles in the films. The minimum silicon crystal diameter was measured at 2.5 nm.
Tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) and paclitaxel have cooperative in vivo effects against glioblastoma multiforme cells (2009)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) in conjunction with microtubule-targeting agents may be a promising novel anticancer treatment strategy. In vitro studies have suggested that relatively low concentrations of TRAIL enhance the lethality of paclitaxel (Taxol) against human cancer cells. The increased efficacy may be due to the triggering of caspase activation, resulting in mitotic checkpoint abrogation and catastrophe. We show here that wild-type p53 protects cells from caspase-dependent death induced by this therapeutic combination in vitro. We have now also developed an imaging-based model system to test the in vivo efficacy of combined TRAIL and Taxol, in which tumor growth and treatment response can be monitored noninvasively and in real-time. We further utilize bioluminescence, F18-fluorodeoxyglucose-positron emission tomography, and microscale computed tomography imaging to confirm the effects of combined treatment on tumors. These studies together provide the first in vivo confirmation that combined TRAIL plus paclitaxel results in better tumor control compared with either TRAIL or paclitaxel alone, and with no discernable increased normal tissue toxicity in the mouse. Interestingly, the in vivo antitumor response elicited by combined treatment was not affected by the p53 status of the tumor cells. These preclinical observations together suggest the therapeutic potential of combining TRAIL plus paclitaxel in cancer treatment, and support further preclinical and future clinical testing.
Crystal Structure of the Human Natural Killer Cell Activating Receptor KIR2DS2 (CD158j) (2003)

Killer cell Ig-like receptors (KIRs) regulate the function of human natural killer and T cell subsets. A feature of the KIR locus is the clustering of homologous genes encoding for inhibitory and activating KIR. Inhibitory and activating KIR differ for ligand specificities and/or affinities. In particular, we show here with KIR tetramers that activating KIR2DS2 does not bind HLA-Cw3 molecules recognized by inhibitory KIR2DL2, despite 99% extracellular amino acid identity. We also report the 2.3-A structure of KIR2DS2, which reveals subtle displacements of two residues (Tyr45 and Gln71) involved in the interaction of KIR2DL2 with HLA-Cw3. These results show that KIR molecules cannot tolerate any variability in their three-dimensional structure without altering their MHC class I recognition capacities. Therefore, the mode of recognition used by KIR largely differs from the conformational changes that characterize T cell receptor or NKG2D interaction with their respective ligands.
Dynamic O-GlcNAc Modification of Nucleocytoplasmic Proteins in Response to Stress (2004)

Cellular response to environmental, physiological, or chemical stress is key to survival following injury or disease. Here we describe a unique signaling mechanism by which cells detect and respond to stress in order to survive. A wide variety of stress stimuli rapidly increase nucleocytoplasmic protein modification by O-linked beta-N-acetylglucosamine (O-GlcNAc), an essential post-translational modification of Ser and Thr residues of metazoans. Blocking this post-translational modification, or reducing it, renders cells more sensitive to stress and results in decreased cell survival; and increasing O-GlcNAc levels protects cells. O-GlcNAc regulates both the rates and extent of the stress-induced induction of heat shock proteins, providing a molecular basis for these findings.
Tracing Transduced Cells in Osteochondral Defects (2003)

In this study the authors explored the feasibility of using transduced cells for gene therapy to induce healing of osteochondral defects. Both a mouse mesenchymal cell line and mixed rabbit adherent stromal cells were transduced with either liposomal transfection or retroviral transduction using a traceable gene. Transduction efficiency was more than 95% with the retroviral construct and expression was maintained for over 6 months of passage. The liposomal transfection led to a transient expression with an efficiency of 50%. The expression of osteochondral genes was diminished but preserved after transduction in vitro. Transduced rabbit cells were transplanted into osteochondral defects in rabbit femoral condyles. Cells transplanted in vivo could be detected for 4 weeks in the repair tissue. The authors' data demonstrate that mesenchymal cells from bone marrow, stably transduced with a traceable gene product, retain the bone and cartilage phenotype and can be followed in vivo after transplantation into cartilage defects.
Optimization of photosynthetic light energy utilization by microalgae (2012)

Over 50% of the energy losses associated with the conversion of solar energy into chemical energy during photosynthesis are attributed to kinetic constraints between the fast rate of photon capture by the light harvesting apparatus and the slower downstream rate of photosynthetic electron transfer. At full sunlight intensities, energy flux from the light harvesting antennae to the reaction centers may be 100-folds greater than the overall linear electron flow resulting in the dissipation of up to 75% of the captured energy as heat or fluorescence. One possible means to couple energy capture and photosynthetic electron transfer more efficiently is to reduce the optical cross-section of the light harvesting antennae. We show that by partially reducing chlorophyll b levels in the green alga, Chlamydomonas reinhardtii, we can tune the peripheral light harvesting antennae size for increased photosynthetic efficiency resulting in more than a two-fold increase in photosynthetic rate at high light intensities and a 30% increase in growth rate at saturating light intensities. Unlike chlorophyll b-less mutants which lack the peripheral light harvesting antennae; transgenics with intermediate sized peripheral antennae have the advantage that they can carry out state transitions facilitating enhanced cyclic ATP synthesis and have robust zeaxanthin–violaxanthin cycles providing protection from high light levels. It is hypothesized that the large antennae size of wild-type algae and land plants offers a competitive advantage in mixed cultures due to the ability of photosynthetic organisms with large light harvesting antennae to shade competing species and to harvest light at low flux densities.
TrustCloud: A Framework for Accountability and Trust in Cloud Computing (2011)

The key barrier to widespread uptake of cloud computing is the lack of trust in clouds by potential customers. While preventive controls for security and privacy are actively researched, there is still little focus on detective controls related to cloud accountability and audit ability. The complexity resulting from large-scale virtualization and data distribution carried out in current clouds has revealed an urgent research agenda for cloud accountability, as has the shift in focus of customer concerns from servers to data. This paper discusses key issues and challenges in achieving a trusted cloud through the use of detective controls, and presents the Trust Cloud framework, which addresses accountability in cloud computing via technical and policy-based approaches.
Glucagon-Like Peptide-1 Promotes Islet Cell Growth and Inhibits Apoptosis in Zucker Diabetic Rats (2002)

A constant remodeling of islet cell mass mediated by proliferative and apoptotic stimuli ensures a dynamic response to a changing demand for insulin. In this study, we investigated the effect of glucagon-like peptide-1 (GLP-1) in Zucker diabetic rats, an animal model in which the onset of diabetes occurs when the proliferative potential and the rate of beta-cell apoptosis no longer compensate for the increased demand for insulin. We subjected diabetic rats to a 2-d infusion of GLP-1 and tested their response to an ip glucose tolerance test. GLP-1 produced a significant increase of insulin secretion, which was paralleled by a decrease in plasma glucose levels (P < 0.001 and P < 0.01, respectively). Four days after the removal of the infusion pumps, rats were killed and the pancreas harvested to study the mechanism by which GLP-1 ameliorated glucose tolerance. Ex vivo immunostaining with the marker of cell proliferation, Ki-67, showed that the metabolic changes observed in rats treated with GLP-1 were associated with an increase in cell proliferation of the endocrine and exocrine component of the pancreas. Terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling staining, a marker of cellular apoptosis, indicated a reduction of apoptotic cells within the islet as well in the exocrine pancreas in GLP-1-treated rats. Double immunostaining for the apoptotic marker caspase-3 and for insulin showed a significant reduction of caspase-3 expression and an increase in insulin content in GLP-1-treated animals. Finally, staining of pancreatic sections with the nuclear dye 4,6-Diaminidino-2-phenyl-dihydrochloride demonstrated a marked reduction of fragmented nuclei in the islet cells of rats treated with GLP-1. Our findings provide evidence that the beneficial effects of GLP-1 in Zucker diabetic rats is mediated by an increase in islet cell proliferation and a decrease of cellular apoptosis.