gebhart/patrepeval huggingface dataset:
Vaccinia virus morphogenesis is blocked by a temperature-sensitive mutation in the I7 gene that encodes a virion component (1993)

The ts16 mutation of vaccinia virus WR (R. C. Condit, A. Motyczka, and G. Spizz, Virology 128:429-443, 1983) has been mapped by marker rescue to the I7L open reading frame located within the genomic HindIII I DNA fragment. The I7 gene encodes a 423-amino-acid polypeptide. Thermolabile growth was attributed to an amino acid substitution, Pro-344-->Leu, in the predicted I7 protein. A normal temporal pattern of viral protein synthesis was elicited in cells infected with ts16 at the nonpermissive temperature (40 degrees C). Electron microscopy revealed a defect in virion assembly at 40 degrees C. Morphogenesis was arrested at a stage subsequent to formation of spherical immature particles. Western immunoblot analysis with antiserum directed against the I7 polypeptide demonstrated an immunoreactive 47-kDa polypeptide accumulating during the late phase of synchronous vaccinia virus infection. Immunoblotting of extracts of wild-type virions showed that the I7 protein is encapsidated within the virus core. The I7 polypeptide displays amino acid sequence similarity to the type II DNA topoisomerase of Saccharomyces cerevisiae.
Following the south polar cap recession as viewed by OMEGA/MEX using automatic detection of H2O and CO2 ices (2006)

In order to understand Mars' current climate it is necessary to detect, characterize and monitor CO2 and H2O at the surface (permanent and seasonal icy deposits) and in the atmosphere (vapor and clouds). Here we will focus on the South Seasonal Polar Cap (SSPC) whose recession was previously observed with different techniques : from earth in the visible range with HST [James 1996], or from MGS spacecraft with MOC images [Benson 2005], in the thermal IR range by the TES [Kieffer 2000], in the near infrared by OMEGA/MEX [Langevin submitted]. The time and space evolutions of the SSPC is a major annual climatic signal both at the global and the regional scales. In particular the measurement of the temporal and spatial distributions of CO2 constrains exchange processes between both surface and atmosphere. This exchange may involve preponderant species : H2O, CO2 and dust. In this work we will apply a new detection technique : "wavanglet" in order to follow the recession of the SSPC thanks to OMEGA/MEX observations. This method was especially developed in the goal to classify a huge dataset, such OMEGA ones. We propose to use "wavanglet" as a supervised automatic classification method that identifies spectral features and classifies the image in spectrally homogeneous units. Additionally we will evaluate quantitative detection limits of "wavanglet" based on synthetic dataset simulating OMEGA spectra in typical situation of the SSPC. This detection limit will be discussed in terms of abundance for H2O and CO2 ices in order to improve the interpretation of the classification. Finally we will present the recession of the SSPC using "wavanglet" and we will compare the results with those of earlier investigation. An interpretation of the similarities and disagreements between those maps will be done.
Sub-ppt gas detection with pristine graphene (2012)

Graphene is widely regarded as one of the most promising materials for sensor applications. Here, we demonstrate that a pristine graphene can detect gas molecules at extremely low concentrations with detection limits as low as 158 parts-per-quadrillion (ppq) for a range of gas molecules at room temperature. The unprecedented sensitivity was achieved by applying our recently developed concept of continuous in situ cleaning of the sensing material with ultraviolet light. The simplicity of the concept, together with graphene’s flexibility to be used on various platforms, is expected to intrigue more investigations to develop ever more sensitive sensors.
JAK3 inhibition as a new concept for immune suppression. (2003)

Although current immunosuppressive drugs are effective, they have numerous severe side effects that mandate the search for new agents. Mutations in the gene for janus kinase (JAK)3 result in severe combined immune deficiency with severely impaired humoral and cellular immunity, an observation that has prompted the development of JAK3 inhibitors. Due to its central role in lymphocyte activation, proliferation and homeostasis, targeting the JAK/signal transducer and activator of transcription (STAT) pathway may provide the required efficacy, without the toxicities associated with current therapies. Several studies conducted in rodents have validated the proof-of-concept, with a variety of JAK3 inhibitors demonstrating efficacy for immune suppression. In addition, the selective JAK3 inhibitor CP-690550 (Pfizer Inc) significantly improved allograft survival in a stringent preclinical model in primates and exhibited a good safety profile in non-human primates. This, along with studies of protein kinase inhibitors for cancer treatment, could demonstrate that development of effective, safe and selective kinase inhibitors for immunosuppression is possible.
Functional differences between memory and naive CD8 T cells (1999)

To determine how murine memory and naive T cells differ, we generated large numbers of long-lived memory CD8(+) T cells and compared them to naive cells expressing the same antigen-specific receptor (T cell receptor; TCR). Although both populations expressed similar levels of TCR and CD8, on antigen stimulation in vitro memory T cells down-regulated their TCR faster and more extensively and secreted IFN-gamma and IL-2 faster than naive T cells. Memory cells were also larger, and when freshly isolated from mice they contained perforin and killed target cells without having to be restimulated. They further differed from naive cells in requiring IL-15 for proliferation and in having a greater tendency to undergo apoptosis in vitro. On antigen stimulation in vivo, however, they proliferated more rapidly than naive cells. These findings suggest that, unlike naive T cells, CD8 memory T cells are intrinsically programmed to rapidly express their effector functions in vivo without having to undergo clonal expansion and differentiation.
V 2 O 5 Xerogel Films as Intercalation Hosts for Lithium (1994)

Up to 3 moles of Li are inserted per mole of xerogel (XRG), as shown by concurrent charge and mass measurements with a quartz crystal microbalance. Further, it is demonstrated that only Li+ ions are intercalated from the electrolyte, without cointercalation by other species in solutions in propylene carbonate.
Inhibition of HIV-1 infection by lentiviral vectors expressing pol III-promoted anti-HIV RNAs (2003)

A primary advantage of lentiviral vectors is their ability to pass through the nuclear envelope into the cell nucleus thereby allowing transduction of nondividing cells. Using HIV-based lentiviral vectors, we delivered an anti-CCR5 ribozyme (CCR5RZ), a nucleolar localizing TAR RNA decoy, or Pol III-expressed siRNA genes into cultured and primary cells. The CCR5RZ is driven by the adenoviral VA1 Pol III promoter, while the human U6 snRNA Pol III-transcribed TAR decoy is embedded in a U16 snoRNA (designated U16TAR), and the siRNAs were expressed from the human U6 Pol III promoter. The transduction efficiencies of these vectors ranged from 96-98% in 293 cells to 15-20% in primary PBMCs. A combination of the CCR5RZ and U16TAR decoy in a single vector backbone gave enhanced protection against HIV-1 challenge in a selective survival assay in both primary T cells and CD34(+)-derived monocytes. The lentiviral vector backbone-expressed siRNAs also showed potent inhibition of p24 expression in PBMCs challenged with HIV-1. Overall our results demonstrate that the lentiviral-based vectors can efficiently deliver single constructs as well as combinations of Pol III therapeutic expression units into primary hematopoietic cells for anti-HIV gene therapy and hold promise for stem or T-cell-based gene therapy for HIV-1 infection.
Aspergillus nidulans VeA subcellular localization is dependent on the importin α carrier and on light (2006)

The veA gene is a light-dependent regulator governing development and secondary metabolism in Aspergillus nidulans. We have identified a putative bipartite nuclear localization signal (NLS) motif in the A. nidulans VeA amino acid sequence and demonstrated its functionality when expressed in yeast. Furthermore, migration of VeA to the nucleus was dependent on the importin alpha. This bipartite NLS is also functional when VeA is expressed in A. nidulans. Interestingly, we found that VeA migration to the nucleus is light-dependent. While in the dark VeA is located mainly in the nuclei, under light VeA is found abundantly in the cytoplasm. The VeA1 mutant protein (lacking the first 36 amino acids at the N-terminus) was found predominantly in the cytoplasm independent of illumination. This indicates that the truncated bipartite NLS in VeA1 is not functional and fails to respond to light. These results might explain the lack of the morphological light-dependent response in strains carrying the veA1 allele. We also evaluated the effect of light on production of the mycotoxin sterigmatocystin in a veA wild-type and the veA1 mutant strains and found that the highest amount of toxin was produced by the veA+ strain growing in the dark, condition favouring accumulation of VeA in the nucleus.
Preparation of Porous and Nonporous Silica Nanofilms from Aqueous Sodium Silicate (2003)

Ultrathin SiO2 films in the range of 2−50-nm thickness were readily fabricated from inexpensive sodium silicate as starting material by its alternate adsorption with cationic polymer and subsequent treatment with O2 plasma and calcination. Film thickness can be controlled by adjusting the number of adsorption cycles and the pH value of silicate solution. Film surface is generally smooth (small roughness) and remains unchanged after O2 plasma treatment or calcination. Whereas a nanoporous thin film is obtained by O2 plasma treatment, a dense silica film is produced through calcination at 450 °C. These preparative methods prove that inexpensive sodium silicates are converted to advanced silica-based materials, such as functional ultrathin films, coatings, capsules, and catalysts, by simple procedures.
Molecular therapy via transcriptional regulation with double-stranded oligodeoxynucleotides as decoys. (2002)

The number of reports on in vivo gene therapies with decoy ODNs complexed with HVJ liposomes has recently increased. Diligent efforts to improve HVJ vectors as gene carriers and to expand the therapeutic applications of NFkB and E2F decoy ODNs will be important for the improved treatment of many genetic diseases.
Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins (1995)

Abstract We present the derivation of charges of ribo‐ and deoxynucleosides, nucleotides, and peptide fragments using electrostatic potentials obtained from ab initio calculations with the 6‐31G* basis set. For the nucleic acid fragments, we used electrostatic potentials of the four deoxyribonucleosides (A, G, C, T) and four ribonucleosides (A, G, C, U) and dimethylphosphate. The charges for the deoxyribose nucleosides and nucleotides are derived using multiple‐molecule fitting and restrained electrostatic potential (RESP) fits, 1,2 with Lagrangian multipliers ensuring a net charge of 0 or ± 1. We suggest that the preferred approach for deriving charges for nucleosides and nucleotides involves allowing only C1′ and H1′ of the sugar to vary as the nucleic acid base, with the remainder of sugar and backbone atoms forced to be equivalent. For peptide fragments, we have combined multiple conformation fitting, previously employed by Williams 3 and Reynolds et al., 4 with the RESP approach 1,2 to derive charges for blocked dipeptides appropriate for each of the 20 naturally occuring amino acids. Based on our results for propyl amine, 1,2 we suggest that two conformations for each peptide suffice to give charges that represent well the conformationally dependent electrostatic properties of molecules, provided that these two conformations contain different values of the dihedral angles that terminate in heteroatoms or hydrogens attached to heteroatoms. In these blocked dipeptide models, it is useful to require equivalent N—H and CO charges for all amino acids with a given net charge (except proline), and this is accomplished in a straightforward fashion with multiple‐molecule fitting. Finally, the application of multiple Lagrangian constraints allows for the derivation of monomeric residues with the appropriate net charge from a chemically blocked version of the residue. The multiple Lagrange constraints also enable charges from two or more molecules to be spliced together in a well‐defined fashion. Thus, the combined use of multiple molecules, multiple conformations, multiple Lagrangian constraints, and RESP fitting is shown to be a powerful approach to deriving electrostatic charges for biopolymers. © 1995 John Wiley &amp; Sons, Inc.
Capacity of human serum to depolymerize actin filaments (1987)

Abstract Human blood depolymerizes filamentous (F-)actin. The interaction of actin filaments and monomers with human serum was studied by following the kinetics and extent of the depolymerization of pyrene-labeled F- actin and by analysis of serum proteins adhering to immobilized actin monomers. In physiologic Ca2+ concentrations, the depolymerization of F- actin proceeds in two stages: a rapid phase, attributed to direct severing of filaments by plasma gelsolin, and a slow phase attributed to the binding of actin monomers to vitamin D-binding protein (DBP). Without Ca2+, only the slow phase is observed. Human serum can completely depolymerize 10 to 18 mumol/L of actin, of which approximately 5 mumol/L occurs rapidly. Depolymerization can be accounted for by the normal serum concentrations of gelsolin and DBP. Fibrin(ogen) and fibronectin, which bind actin in vitro, do not contribute to the kinetics or extent of its depolymerization. Affinity chromatography and functional assays for the presence of gelsolin-actin complexes show that addition of G-actin to serum results in preferential formation of actin-DBP complexes, but that addition of F- actin to serum produces both gelsolin-actin complexes and DBP-actin complexes. The distinctive binding of actin monomers and polymers to these two serum proteins suggests a means by which their coordinated actions are maximized in vivo, from the standpoint of depolymerizing filaments and clearing monomers from the circulation.
Single crystal silver nanowires prepared by the metal amplification method (2002)

We present a method of fabricating single crystal silver nanowires based on the electroless deposition of silver into the pores of the polycarbonate membranes by the metal amplification process. A gold film on one side of the nanoporous membrane is used as the initiation layer for the silver crystal growth, while the pores of the membrane are used for guiding the growth of the silver crystal into a cylindrical nanostructure. Optical microscopy and spectroscopy of individual nanowires, transmission electron microscopy (TEM), and TEM diffraction crystallography were used to characterize the silver nanostructures. The metal amplification technique presents an electroless, simple, and inexpensive solution to the challenge of fabricating silver nanowires for electronic, optical, and biological applications.
Comparison of the Inhibition Mechanisms of Adalimumab and Infliximab in Treating Tumor Necrosis Factor α-Associated Diseases from a Molecular View (2013)

TNFα-targeting therapy with the use of the drugs Etanercept, Infliximab, and Adalimumab is used in the clinical treatment of various inflammatory and immune diseases. Although all of these reagents function to disrupt the interaction between TNFα and its receptors, clinical investigations showed the advantages of Adalimumab treatment compared with Etanercept and Infliximab. However, the underlying molecular mechanism of action of Adalimumab remains unclear. In our previous work, we presented structural data on how Infliximab binds with the E-F loop of TNFα and functions as a TNFα receptor-binding blocker. To further elucidate the variations between TNFα inhibitors, we solved the crystal structure of TNFα in complex with Adalimumab Fab. The structural observation and the mutagenesis analysis provided direct evidence for identifying the Adalimumab epitope on TNFα and revealed the mechanism of Adalimumab inhibition of TNFα by occupying the TNFα receptor-binding site. The larger antigen-antibody interface in TNFα Adalimumab also provided information at a molecular level for further understanding the clinical advantages of Adalimumab therapy compared with Infliximab.
Antitumor Activity of the Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor Gefitinib (ZD1839, Iressa) in Non–Small Cell Lung Cancer Cell Lines Correlates with Gene Copy Number and EGFR Mutations but not EGFR Protein Levels (2006)

This panel of NSCLC lines characterized for gefitinib response was used to identify predictive molecular markers of response to gefitinib. Several of these have subsequently been shown to identify NSCLC patients likely to benefit from gefitinib therapy.
FIP1L1/RARA with breakpoint at FIP1L1 intron 13: a variant translocation in acute promyelocytic leukemia (2011)

Acute promyelocytic leukemia (APL) is a distinct subtype of acute myeloid leukemia that is characterized by three distinct features: i) accumulation in the bone marrow (BM) of tumor cells with promyelocytic phenotype; ii) association with specific translocations which involve chromosome 17 at the
Berberine, a Natural Plant Product, Activates AMP-Activated Protein Kinase With Beneficial Metabolic Effects in Diabetic and Insulin-Resistant States (2006)

Berberine has been shown to have antidiabetic properties, although its mode of action is not known. Here, we have investigated the metabolic effects of berberine in two animal models of insulin resistance and in insulin-responsive cell lines. Berberine reduced body weight and caused a significant improvement in glucose tolerance without altering food intake in db/db mice. Similarly, berberine reduced body weight and plasma triglycerides and improved insulin action in high-fat-fed Wistar rats. Berberine downregulated the expression of genes involved in lipogenesis and upregulated those involved in energy expenditure in adipose tissue and muscle. Berberine treatment resulted in increased AMP-activated protein kinase (AMPK) activity in 3T3-L1 adipocytes and L6 myotubes, increased GLUT4 translocation in L6 cells in a phosphatidylinositol 3' kinase-independent manner, and reduced lipid accumulation in 3T3-L1 adipocytes. These findings suggest that berberine displays beneficial effects in the treatment of diabetes and obesity at least in part via stimulation of AMPK activity.
Unsupervised Speaker Identification in TV Broadcast Based on Written Names (2014)

Identifying speakers in TV broadcast in an unsupervised way (i.e., without biometric models) is a solution for avoiding costly annotations. Existing methods usually use pronounced names, as a source of names, for identifying speech clusters provided by a diarization step but this source is too imprecise for having sufficient confidence. To overcome this issue, another source of names can be used: the names written in a title block in the image track. We first compared these two sources of names on their abilities to provide the name of the speakers in TV broadcast. This study shows that it is more interesting to use written names for their high precision for identifying the current speaker. We also propose two approaches for finding speaker identity based only on names written in the image track. With the “late naming” approach, we propose different propagations of written names onto clusters. Our second proposition, “Early naming,” modifies the speaker diarization module (agglomerative clustering) by adding constraints preventing two clusters with different associated written names to be merged together. These methods were tested on the REPERE corpus phase 1, containing 3 hours of annotated videos. Our best “late naming” system reaches an F-measure of 73.1%. “early naming” improves over this result both in terms of identification error rate and of stability of the clustering stopping criterion. By comparison, a mono-modal, supervised speaker identification system with 535 speaker models trained on matching development data and additional TV and radio data only provided a 57.2% F-measure.
Crystal to Non-Equilibrium Phase Transition Induced by Ball-Milling (1992)

International audience
Hardware Trojan: Threats and emerging solutions (2009)

Malicious modification of hardware during design or fabrication has emerged as a major security concern. Such tampering (also referred to as Hardware Trojan) causes an integrated circuit (IC) to have altered functional behavior, potentially with disastrous consequences in safety-critical applications. Conventional design-time verification and post-manufacturing testing cannot be readily extended to detect hardware Trojans due to their stealthy nature, inordinately large number of possible instances and large variety in structure and operating mode. In this paper, we analyze the threat posed by hardware Trojans and the methods of deterring them. We present a Trojan taxonomy, models of Trojan operations and a review of the state-of-the-art Trojan prevention and detection techniques. Next, we discuss the major challenges associated with this security concern and future research needs to address them.
The burn edema process: current concepts. (2005)

Massive tissue edema after thermal injury is a well-recognized entity. Although this process is responsible for the patient's large fluid needs during resuscitation and also for local problems, such as a compartment syndrome, there have been no effective treatment modalities introduced into clinical care to control the degree of edema. A review of what is now known about the edema process is presented here, including attempted prevention and treatment modalities. The pathogenesis involves changes in most of the physical forces controlling fluid flux across the capillary and also how fluid accumulates in the interstitium. Increased capillary permeability to protein is but one of these changes. The presence of an initial profound negative interstitial pressure "sucking" fluid into the tissues and a marked increase in interstitial space compliance are equally important components. A host of mediators, especially oxidants, have been reported to cause these physical changes, and some mediator inhibitors appear to be of benefit, especially antioxidants. However, few clinical trials, aimed at decreasing edema, have been performed. With these new insights into the edema process, future prevention and treatment modalities can be developed.