gebhart/patrepeval huggingface dataset:
Cell-surface expression of a mutated Epstein–Barr virus glycoprotein B allows fusion independent of other viral proteins (2004)

Epstein-Barr virus (EBV) infects human B lymphocytes and epithelial cells. We have compared the requirements for EBV glycoprotein-induced cell fusion between Chinese hamster ovary effecter cells and human B lymphoblasts or epithelial cells by using a virus-free cell fusion assay. EBV-encoded gB, gH, gL, and gp42 glycoproteins were required for efficient B cell fusion, whereas EBV gB, gH, and gL glycoproteins were required for Chinese hamster ovary effecter cell fusion with epithelial cell lines (AGS and SCC68) or the human embryonic kidney cell line 293-P. Fusion with human embryonic kidney 293-P cells was greater than fusion observed with B cells, indicative of an important role for cell contact. An antibody directed against the gH and gL complex inhibited epithelial cell fusion. Increased surface expression of gB alone as a result of truncations or point mutants in the carboxyl-terminal tail allowed gB-mediated fusion with epithelial cells, albeit at a lower level than with coexpression of gB, gH, and gL. Overall, gB appears to be the critical component for EBV glycoprotein-mediated cell fusion.
Mechanism of Thermal Al<sub>2</sub>O<sub>3</sub> Atomic Layer Etching Using Sequential Reactions with Sn(acac)<sub>2</sub> and HF (2015)

Thermal Al2O3 atomic layer etching (ALE) can be performed using sequential, self-limiting reactions with tin(II) acetylacetonate (Sn(acac)2) and HF as the reactants. To understand the reaction mechanism, in situ quartz crystal microbalance (QCM) and Fourier transform infrared (FTIR) measurements were conducted versus temperature. The mass change per cycle (MCPC) increased with temperature from −4.1 ng/(cm2 cycle) at 150 °C to −18.3 ng/(cm2 cycle) at 250 °C. Arrhenius analysis of the temperature-dependent MCPC values yielded an activation barrier for Al2O3 ALE of E = 6.6 ± 0.4 kcal/mol. The mass changes after the individual Sn(acac)2 and HF exposures also varied with temperature. The mass changes after the Sn(acac)2 exposures were consistent with more Sn(acac)2 surface reaction products remaining at lower temperatures. The mass changes after the HF exposures were consistent with more AlF3 species remaining at higher temperatures. The FTIR spectroscopic analysis observed Al2O3 etching by measuring the loss of absorbance of Al–O stretching vibrations in the Al2O3 film. The infrared absorbance of the acetylacetonate vibrational features from Sn(acac)2 surface reaction products was also smaller at higher temperatures. The correlation between the MCPC values and the acetylacetonate infrared absorbance suggested that the Al2O3 ALE rate is inversely dependent on the acetylacetonate surface coverage. In addition, the QCM and FTIR measurements explored the nucleation of the Al2O3 ALE. A large mass gain and loss of infrared absorbance of Al–O stretching vibrations after the initial HF exposure on the Al2O3 film was consistent with the conversion of Al2O3 to AlF3. FTIR experiments also observed the formation of AlF3 after the initial HF exposure and the presence of AlF3 on the surface after each HF exposure during Al2O3 ALE. In the proposed reaction mechanism, AlF3 is the key reaction intermediate during Al2O3 ALE. HF converts Al2O3 to AlF3 prior to removal of AlF3 by Sn(acac)2.
Synthesis of Fluoro Organic Compounds, (1974)

Detailed descriptions of syntheses of fluoro organic compounds are presented. Attention is paid primarily to the methods of synthesizing polyfluorinated compounds, since it is namely these substances that are of greatest interest, both from the procedural and practical point of view. In selecting methods, the authors strove, on the one hand, to offer descriptions for the derivation of such compounds, that can serve as initial products for further syntheses, and, on the other, illustrate as completely as possible the main procedures in fluoro organic chemistry. This report deals with aliphatic fluoro compounds. The description of synthesis for each compound is preceded by an enumeration of its physical characteristics and other methods of its derivation.
Avian cecal microanatomy: A morphometric comparison of two species (1989)

Tissues from the proximal, middle, and distal regions of the ceca of Gambel's quail and domestic fowl were examined by scanning and transmission electron microscopy for ultrastructural detail. Cellular aad subcellular structures, including epithelial cell height, mitochondrial volume fraction, microvillar surface area, and junctional complex characteristics, were quantified by stereologic procedures. The mucosal surface of the quail ceca shows a more highly developed pattern of ridges and flat areas than that of the fowl. The fowl has significantly greater cell heights than the quail in all cecal regions. The mitochondrial volume fraction does not differ significantly with species or region, but the mitochondria in all samples tend to be concentrated on the apical side of the nucleus. In both species, the proximal cecal region has the greatest microvillar surface area. In the fowl cecum, the zona occludens and macula adherans heights are significantly less in the proximal than in the middle or distal regions. In the quail cecum, the zona adherans height is least is the distal region. The zona occludens height in the fowl middle and distal regions is significantly greater than those for the quail. The middle region of the quail cecum has the lowest proportions of cell boundaries with zona adherans and macula adherans in the junctional complexes. When all factors are considered, the quail ceca appear to have morphological characteristics consistent with a greater potential capacity for absorption by passive diffusion than the fowl ceca.
A potent KRAS macromolecule degrader specifically targeting tumours with mutant KRAS (2020)

Tumour-associated KRAS mutations are the most prevalent in the three RAS-family isoforms and involve many different amino-acids. Therefore, molecules able to interfere with mutant KRAS protein are potentially important for wide-ranging tumour therapy. We describe the engineering of two RAS degraders based on protein macromolecules (macrodrugs) fused to specific E3 ligases. A KRAS-specific DARPin fused to the VHL E3 ligase is compared to a pan-RAS intracellular single domain antibody (iDAb) fused to the UBOX domain of the CHIP E3 ligase. We demonstrate that while the KRAS-specific DARPin degrader induces specific proteolysis of both mutant and wild type KRAS, it only inhibits proliferation of cancer cells expressing mutant KRAS in vitro and in vivo. Pan-RAS protein degradation, however, affects proliferation irrespective of the RAS mutation. These data show that specific KRAS degradation is an important therapeutic strategy to affect tumours expressing any of the range of KRAS mutations.
Downstream Signaling Molecules Bind to Different Phosphorylated Immunoreceptor Tyrosine-based Activation Motif (ITAM) Peptides of the High Affinity IgE Receptor (1996)

The cytoplasmic tails of both the beta and gamma subunits of the high affinity IgE receptor (FcepsilonRI) contain a consensus sequence termed the immunoreceptor tyrosine-based activation motif (ITAM). This motif plays a critical role in receptor-mediated signal transduction. Synthetic peptides based on the ITAM sequences of the beta and gamma subunits of FcepsilonRI were used to investigate which proteins associate with these motifs. Tyrosine-phosphorylated beta and gamma ITAM peptides immobilized on beads precipitated Syk, Lyn, Shc, Grb2, and phospholipase C-gamma1 from lysates of rat basophilic leukemia RBL-2H3 cells. Syk was precipitated predominantly by the tyrosine-diphosphorylated gamma ITAM peptide, but much less by the diphosphorylated beta ITAM peptide or by the monophosphorylated peptides. Phospholipase C-gamma1, Shc, and Grb2 were precipitated only by the diphosphorylated beta ITAM peptide. Non-phosphorylated ITAM peptides did not precipitate these proteins. In membrane binding assays, fusion proteins containing the Src homology 2 domains of phospholipase C-gamma1, Shc, Syk, and Lyn directly bound the tyrosine-phosphorylated ITAM peptides. Although the ITAM sequences of the beta and gamma subunits of FcepsilonRI are similar, once they are tyrosine-phosphorylated they preferentially bind different downstream signaling molecules. Tyrosine phosphorylation of the ITAM of the gamma subunit recruits and activates Syk, whereas the beta subunit may be important for the Ras signaling pathway.
ChemInform Abstract: Spectral Characterization and Antifungal Activity of Some Newly Synthesized Sulfur Containing Triorganotin(IV) Derivatives. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Sequence-Specific 2-Cyanobenzothiazole Ligation (2016)

The use of small, natural chemical reporters in conjunction with catalyst-free bioorthogonal reactions will greatly streamline protein labeling in a cellular environment with minimum perturbation to their function. Here we report the discovery of a 2-cyanobenzothiazole (CBT)-reactive peptide tag, CX10R7, from a cysteine-encoded peptide phage library using the phage-assisted interrogation of reactivity method. Fusion of CX10R7 with a protein of interest allows site-specific labeling of the protein with CBT both in vitro and on the surface of E. coli cells. Mutagenesis studies indicated that the reactivity and specificity of CX10R7 are attributed to the sequence environment, in which the residues surrounding cysteine help to stabilize the ligation product.
A Monte Carlo dose calculation tool for radiotherapy treatment planning (2002)

A Monte Carlo user code, MCDOSE, has been developed for radiotherapy treatment planning (RTP) dose calculations. MCDOSE is designed as a dose calculation module suitable for adaptation to host RTP systems. MCDOSE can be used for both conventional photon/electron beam calculation and intensity modulated radiotherapy (IMRT) treatment planning. MCDOSE uses a multiple-source model to reconstruct the treatment beam phase space. Based on Monte Carlo simulated or measured beam data acquired during commissioning, source-model parameters are adjusted through an automated procedure. Beam modifiers such as jaws, physical and dynamic wedges, compensators, blocks, electron cut-outs and bolus are simulated by MCDOSE together with a 3D rectilinear patient geometry model built from CT data. Dose distributions calculated using MCDOSE agreed well with those calculated by the EGS4/DOSXYZ code using different beam set-ups and beam modifiers. Heterogeneity correction factors for layered-lung or layered-bone phantoms as calculated by both codes were consistent with measured data to within 1%. The effect of energy cut-offs for particle transport was investigated. Variance reduction techniques were implemented in MCDOSE to achieve a speedup factor of 10-30 compared to DOSXYZ.
Immunization with a Lentivector That Targets Tumor Antigen Expression to Dendritic Cells Induces Potent CD8 <sup>+</sup> and CD4 <sup>+</sup> T-Cell Responses (2007)

Lentivectors stimulate potent immune responses to antigen transgenes and are being developed as novel genetic vaccines. To improve safety while retaining efficacy, we constructed a lentivector in which transgene expression was restricted to antigen-presenting cells using the mouse dectin-2 gene promoter. This lentivector expressed a green fluorescent protein (GFP) transgene in mouse bone marrow-derived dendritic cell cultures and in human skin-derived Langerhans and dermal dendritic cells. In mice GFP expression was detected in splenic dectin-2(+) cells after intravenous injection and in CD11c(+) dendritic cells in the draining lymph node after subcutaneous injection. A dectin-2 lentivector encoding the human melanoma antigen NY-ESO-1 primed an NY-ESO-1-specific CD8(+) T-cell response in HLA-A2 transgenic mice and stimulated a CD4(+) T-cell response to a newly identified NY-ESO-1 epitope presented by H2 I-A(b). As immunization with the optimal dose of the dectin-2 lentivector was similar to that stimulated by a lentivector containing a strong constitutive viral promoter, targeting antigen expression to dendritic cells can provide a safe and effective vaccine.
Photonic Flash Soldering of Thin Chips and SMD Components on Foils for Flexible Electronics (2014)

Ultrathin bare die chips and small-size surface mount device components were successfully soldered using a novel roll-to-roll compatible soldering technology. A high-power xenon light flash was used to successfully solder the components to copper tracks on polyimide (PI) and polyethylene terephthalate (PET) flex foils by using a lead-free solder paste. Results are compared with oven-reflowed solder joints on PI substrates. The delicate PET foil substrates were not damaged owing to the selectivity of light absorption, leading to a limited temperature increase in the PET foil while the chip and copper tracks were heated to a temperature high enough to initiate soldering. The microstructure of the soldered joints was investigated and found to be dependent on the photonic flash intensity. Reliability of the photonically soldered joints during damp heat testing and dynamic flexing testing was comparable with the reflowed benchmark and showed increased reliability compared with anisotropic conductive adhesives bonded on PET foils.
An Integrated Human Mammary Epithelial Cell Culture System for Studying Carcinogenesis and Aging (2013)

Experimental examination of the agents and processes that may propel or prevent human breast carcinogenesis can be facilitated by in vitro model systems of transformation, starting with normal cells, that accurately reflect the in vivo biology. Model systems that can replicate the types of alterations seen during in vivo progression offer the potential to understand the mechanisms underlying progression and to examine possible means of individualized prevention and treatment. To this end, we have developed an experimentally tractable human mammary epithelial cell (HMEC) culture system that has been used to examine the normal processes governing HMEC growth, differentiation, aging, and senescence and how these normal processes are altered during immortal and malignant transformation. Isogenic cells at different stages of multistep carcinogenesis were generated by exposing normal finite lifespan HMEC to a variety of oncogenic agents that may play an etiologic role in breast cancer. Examination of the molecular alterations present at each stage has indicated that this model is consistent with observed multistep carcinogenesis in vivo. We have seen that varying target cell type, and oncogenic agents used, can lead to multiple distinct molecular pathways of transformation, although the full diversity of human breast cancer cell types has not yet been generated in culture models. Using this integrated system, we have formulated a comprehensive model of the proliferative barriers normal HMEC must overcome to gain immortality and malignancy. Our data provide insights on acquisition of cancer-associated properties and suggest that the most crucial step in breast cancer progression involves the transition from a finite to an indefinite lifespan. For example, we see that genomic instability originates in finite lifespan HMEC when telomeres become critically short and engage in telomeric associations and is then maintained in resultant immortalized and malignant lines. Direct genomic targeting of the tumor-suppressive senescence barriers can produce lines lacking gross genomic errors, supporting the hypothesis that genomic instability is a mechanism to generate cancer-causing errors, but is not necessary per se. Immortalization through telomerase reactivation was also associated with acquisition of resistance to TGFβ growth inhibition and to oncogene-induced senescence (OIS) and with large-scale changes in gene expression and epigenetic marks. Being able to examine the progressive changes that fuel malignancy, starting with normal cells, provides an integrated perspective that can reveal novel information on the origins and consequences of individual cancer-associated aberrations.
Time-dependent transport through scattering media: from radiative transfer to diffusion (2002)

International audience
Efficient selection of informative and diverse training samples with applications in scene classification (2016)

The huge amount of time required to construct a set of labeled images to train a classifier has led researchers to develop algorithms which can identify the most informative training images, such that labelling those will be sufficient to achieve a considerable classification accuracy. In this paper we focus on choosing a subset of the most informative and diverse images based on which the classification model can be learned efficiently. The size of the subset to be chosen is determined by the available budget for manual labeling. Although the problem of identifying the informative images can be solved by active learning algorithms, it will require a set of labeled images for initial model construction, which is not required in our method as we identify the best samples at one shot. We incorporate the concepts of strong and weak teacher to help the learner to learn the model efficiently with limited budget for manual labeling. We perform rigorous experiments on two challenging scene classification datasets to demonstrate the effectiveness of our algorithm.
DinofelisAR demo augmented reality based on natural features (2017)

Augmented reality has seen a fast-growing gain of interest in the last few decades. Due to technological advances, smartphones are now devices that allow to experience augmented reality systems, anytime and anywhere. Although its emerging success among users, some problems AR have been reported inhibiting its full acceptance in our digital society. The aim of this paper is to present a study about techniques to implement augmented reality systems in the cultural heritage context, including a prototype to test the technology which, based on physical objects that belong to the landscape, present an effective and accurate augmented reality approach, overlaying 3D virtual models aligned over the real images, using a smartphone's camera.
Progress in culture and subculture of spheroplasts and fastidious acid-fast bacilli isolated from intestinal tissues (1988)

The efficiency of culture media was compared for the culture and subculture of very slowly growing acid-fast bacilli and spheroplast forms obtained from intestinal tissues of patients with Crohn's disease and ulcerative colitis and from controls without inflammatory bowel disease. Media were developed by modifying a nutrient broth medium based on veal infusion broth and yeast extract. We evaluated the effects of pH and the addition of Tween 80, Dubo oleic albumin complex, an extract from intestinal tissue from a patient with Crohn's disease, horse serum, sucrose, magnesium sulfate, ferrous ammonium sulfate, and sodium citrate. All media contained mycobactin J (2 micrograms/ml). We developed a medium (MG3) which was highly successful in promoting the growth of very fastidious organisms and promoted reversion of spheroplasts to acid-fast rods. MG3 contained veal infusion broth, 1% yeast extract, 10% horse serum, 0.3 M sucrose, 0.2% MgSO4, 0.1% ferrous ammonium sulfate, 0.1% sodium citrate, and 2 mg of mycobactin J per liter. We were able to obtain quantities of organisms sufficient for examination of the organisms by molecular techniques. Successful cultivation of all isolates and reversion of spheroplasts to acid-fast forms encourage further studies of the possibility of a complex association of mycobacteria and Crohn's disease.
Tri-state map for the minimisation of exclusive-OR switching functions (1989)

A tri-state map is developed as a general format for Karnaugh maps, Reed-Muller coefficient maps and transition (partially polarised) maps. The polarisation statuses of the variables in transition maps and Reed-Muller coefficient maps are indicated by the labels on the tri-state maps. A variable in a tri-state map can exist in two of three different states: true, complemented or nonexistent. Karnaugh maps and positive-polarity or negative-polarity Reed-Muller coefficient maps are special cases, in which there are only two states. Minimisation of exclusive-OR switching functions can be carried out, not only on Reed-Muller coefficient maps, but also on Karnaugh maps or any of the transition maps.
Mice Lacking G-Protein Receptor Kinase 1 Have Profoundly Slowed Recovery of Cone-Driven Retinal Responses (2000)

G-Protein receptor kinase 1 (GRK1) ("rhodopsin kinase") is necessary for the inactivation of photoactivated rhodopsin, the light receptor of the G-protein transduction cascade of rod photoreceptors. GRK1 has also been reported to be present in retinal cones in which its function is unknown. To examine the role of GRK1 in retinal cone signaling pathways, we measured in mice having null mutations of GRK1 (GRK1 -/-) cone-driven electroretinographic (ERG) responses, including an a-wave component identified as the field potential generated by suppression of the circulating current of the cone photoreceptors. Dark-adapted GRK1 -/- animals generated cone-driven ERGs having saturating amplitudes and sensitivities in both visible and UV spectral regions similar to those of wild-type (WT) mice. However, after exposure to a bright conditioning flash, the cone-driven ERGs of GRK1 -/- animals recovered 30-50 times more slowly than those of WT mice and similarly slower than the cone-driven ERGs of mice homozygously null for arrestin (Arrestin -/-), whose cone (but not rod) response recoveries were found to be as rapid as those of WT. Our observations argue that GRK1 is essential for normal deactivation of murine cone phototransduction and provide the first functional evidence for a major role of a specific GRK in the inactivation of vertebrate cone phototransduction.
THE DIRECTED ISOLATION OF MUTANTS PRODUCING INCREASED AMOUNTS OF METABOLITES (1962)

A method is described whereby mutants having a directed increased yield of a metabolite may readily be isolated. A culture of bacterial cells is exposed to a gradient concentration of an antimetabolite that is inhibitory to the growth of the organism and mutants are isolated which survive because of an increased yield of the metabolite. This increased yield may be several times that formed by the parent culture. Techniques and results for increasing the yields of pyridoxine, nicotinic acid and thiamine are described.