gebhart/patrepeval huggingface dataset:
Molecular Follow-Up of Patients Treated with HSV-TK/ΔLNGFR Engineered Donor Lymphocytes after Allogeneic Stem Cell Transplantation. (2004)

Abstract Donor lymphocyte infusions (DLI) play a crucial role in promoting immune reconstitution and anti-tumor activity in patients treated with allogeneic hematopoietic stem cell transplantation (HSCT). The efficacy of DLI is, however, limited by the occurrence of graft-versus-host disease (GvHD). In three different clinical trials, we showed that the infusion of lymphocytes transduced by a retroviral vector expressing a suicide gene (HSV-TK) and a surface marker (ΔLNGFR) allows to control GvHD in 100% of cases, while preserving anti-tumor and antiviral activities. In &gt;40 patients treated with TK-cells in the context of HLA identical and haplo-identical HSCT, we observed consistent expansion (up to 40% of circulating cells) and long-term persistence (&gt;10 years) of transduced cells. No acute or chronic adverse or toxic effect due to the gene transfer procedure was observed in these patients, who were treated with a total of &gt;1011 cells generated by &gt;60 independent transductions. Analysis of vector integration sites was preformed by LM-PCR on lymphocytes obtained up to 10 years after treatment from 4 patients, and selected for ΔLNGFR expression. 60% of the sequences met our validity criteria and were unambiguously mapped onto the human genome by Ensembl BLAST analysis. Transduced T-cells were highly polyclonal, with vector integrations occurring preferentially within genes (52%), and particularly within the first intron (25%). Quantitative PCR analysis of selected integrations was performed to follow the dynamics of individual T-cell clones during time. Microchip analysis of the gene expression profile showed that &lt;200 out of &gt;22,000 genes (0.9%) were differentially expressed in ΔLNGFR+ vs. ΔLNGFR- T-cells from two different patients, suggesting that no significant perturbation was induced by retroviral transduction or HSV-TK/ΔLNGFR expression in human lymphocyte populations. Interestingly, these data also show the substantial biological identity of T-cell population generated by HSCT and those administered as DLI. Finally, the influence of proviral integration on the expression of targeted genes was studied in individual T-cell clones transduced in vitro or obtained ex vivo from treated patients by quantitative gene expression analysis.
GaN nanowire coated with atomic layer deposition of tungsten: a probe for near-field scanning microwave microscopy (2014)

GaN nanowires were coated with tungsten by means of atomic layer deposition. These structures were then adapted as probe tips for near-field scanning microwave microscopy. These probes displayed a capacitive resolution of ~0.03 fF, which surpasses that of a commercial Pt tip. Upon imaging of MoS₂ sheets with both the Pt and GaN nanowire tips, we found that the nanowire tips were comparatively immune to surface contamination and far more durable than their Pt counterparts.
Chemical inhibition of the RORγt-dependent transcriptional network in Th17 cells (P5163) (2013)

Abstract RORγt is a master transcription factor required for Th17 development. We identified two novel RORγt-specific inhibitors that suppress Th17 response and Th17-mediated autoimmune disease. To assess their mechanisms of action, we systemically characterize their function within the context of RORγt-directed transcriptional circuitry by integrating RORγt binding data in the presence and absence of drug with corresponding whole-transcriptome sequencing for wildtype and RORγt-deficient cells. RORγt is central in a densely interconnected regulatory network, acting both as a direct activator of genes important for Th17 differentiation and as a direct inhibitor of genes from other T-cell lineages. These inhibitors reversed both of these modes of action, but to varying extents and through distinct mechanisms. While one inhibitor displaced RORγt from its target-loci, the more potent inhibitor affected transcription predominantly without removing DNA-binding. Our work illustrates the power of a system-scale analysis of transcriptional regulation to characterize potential therapeutic compounds that inhibit pathogenic Th17 cells and suppress autoimmunity.
Reliable multicast with B.I.E.R. (2018)

Inter-network multicast protocols, which build and maintain multicast trees, incur both explicit protocol signalling, and maintenance of state in intermediate routers in the network. Bit-indexed explicit replication (B.I.E.R.) is a technique which can provide a multicast service yet removes such complexities: intermediate routers are unencumbered by group management, and no per-group state is to be maintained. This paper explores the use of B.I.E.R. as a basis for developing an efficient and reliable multicast mechanism, where redundant traffic is avoided, essential traffic is forwarded along shortest paths, and no per-flow state is required in intermediate routers. Evaluated by way of both an analytical model and network simulation both in generic and in real network topologies with varying background traffic loads, the proposed B.I.E.R.-based reliable multicast mechanism exhibits attractive performance attributes: It attains delivery success rates as high as any other reliable multicast service, but with significantly better link utilisation and no per-flow or per-group state in intermediate routers of the network.
Three-dimensional analysis and ultrastructural design of mitotic spindles from the cdc20 mutant of Saccharomyces cerevisiae. (1997)

The three-dimensional organization of mitotic microtubules in a mutant strain of Saccharomyces cerevisiae has been studied by computer-assisted serial reconstruction. At the nonpermissive temperature, cdc20 cells arrested with a spindle length of approximately 2.5 microns. These spindles contained a mean of 81 microtubules (range, 56-100) compared with 23 in wild-type spindles of comparable length. This increase in spindle microtubule number resulted in a total polymer length up to four times that of wild-type spindles. The spindle pole bodies in the cdc20 cells were approximately 2.3 times the size of wild-type, thereby accommodating the abnormally large number of spindle microtubules. The cdc20 spindles contained a large number of interpolar microtubules organized in a "core bundle." A neighbor density analysis of this bundle at the spindle midzone showed a preferred spacing of approximately 35 nm center-to-center between microtubules of opposite polarity. Although this is evidence of specific interaction between antiparallel microtubules, mutant spindles were less ordered than the spindle of wild-type cells. The number of noncore microtubules was significantly higher than that reported for wild-type, and these microtubules did not display a characteristic metaphase configuration. cdc20 spindles showed significantly more cross-bridges between spindle microtubules than were seen in the wild type. The cross-bridge density was highest between antiparallel microtubules. These data suggest that spindle microtubules are stabilized in cdc20 cells and that the CDC20 gene product may be involved in cell cycle processes that promote spindle microtubule disassembly.
Innentitelbild: Direct Light‐Driven Modulation of Luminescence from Mn‐Doped ZnSe Quantum Dots (Angew. Chem. 14/2008) (2008)

Die lichtgesteuerte Modulation der Fluoreszenz von Mn-dotierten ZnSe-Quantenpunkten wird von S. Hell et al. in ihrer Zuschrift auf S. 2725 ff. vorgestellt. Blaues Licht dient zur Anregung der Quanten-Nanokristalle, während ein zweiter, modulierter Strahl bei höherer Wellenlänge (rot) dazu verwendet werden kann, die Fluoreszenz der Quantenpunkte selektiv zu inhibieren. Der Einschub unten rechts im Bild veranschaulicht die Energieniveaus, die an der lichtgesteuerten Fluoreszenz von Mn-dotierten Quantenpunkten beteiligt sind.
2-D WDM optical interconnections for simultaneous and reconfigurable communication among many planes (1993)

The ability to efficiently connect many high-speed ports or 2-dimensional (2-D) sensor arrays is important for large-capacity data processing.
Gene Expression-Based Screen for Parkinson’s Disease Identifies GW8510 as a Neuroprotective Agent (2016)

We carried out a gene expression-based in silico screen in order to identify small molecules with gene-expression profiles that are anticorrelated with a gene-expression profile for Parkinson's disease (PD). We identified the cyclin-dependent kinase 2/5 (CDK2/5) inhibitor GW8510 as our most significant hit and characterized its effects in rodent MN9D cells and in human neuronal cells derived from induced pluripotent stem cells. GW8510 demonstrated neuroprotective ability in MN9D cells in the presence of 1-methyl-4-phenylpyridium (MPP(+)), a widely used neurotoxin model for Parkinson's disease. In order to delineate the nature and extent of GW8510's neuroprotective properties, we studied GW8510 in human neuronal cells in the context of various mechanisms of cellular stress. We found that GW8510 was protective against small-molecule mitochondrial and endoplasmic reticulum stressors. Our findings illustrate an approach to using small-molecule gene expression libraries to identify compounds with therapeutic potential in human diseases.
Resonant Operation of a Micro-Newton Thrust Stand (2002)

A computer automated technique suitable for evaluating micro pulsed plasma thruster (micro PPT) performance has been constructed and validated in the micro-Newton (micro N) force range. A swinging gate pendulum architecture oscillates with an 8 second period. Force is applied resonantly with oscillation each half period. The calibration method utilizes an electromagnet to pick up and drop masses to apply a known force in the same resonant fashion as thruster operation. The resulting equilibrium amplitudes are linearly proportional to the applied force with an intercept near zero. Thrust measurements are insensitive to short term random vibrational noise because of the resonant operation and are insensitive to long term drift because the amplitude measurements are relative, rather than absolute. The system is capable of resolving 0.5 micro N over the range of 1 to 100 micro N.
Multiple roles of the candidate oncogene ZNF217 in ovarian epithelial neoplastic progression (2007)

The transcription factor ZNF217 is often amplified in ovarian cancer, but its role in neoplastic progression is unknown. We introduced ZNF217-HA by adenoviral and retroviral infection into normal human ovarian surface epithelial cells (OSE), i.e., the source of ovarian cancer, and into SV40 Tag/tag expressing, p53/pRB-deficient OSE with extended but finite life spans (IOSE). In OSE, ZNF217-HA reduced cell-substratum adhesion and accelerated loss of senescent cells, but caused no obvious proneoplastic changes. In contrast, ZNF217-HA transduction into IOSE yielded two permanent lines, I-80RZ and I-144RZ, which exhibited telomerase activity, stable telomere lengths, anchorage independence and reduced serum dependence, but were not tumorigenic in SCID mice. This immortalization required short-term EGF treatment near the time of crisis. The permanent lines were EGF-independent, but ZNF217-dependent since siRNA to ZNF217 inhibited anchorage independence and arrested growth. Array CGH revealed genomic changes resembling those of ovarian carcinomas, such as amplicons at 3q and 20q, and deletions at 4q and 18, associated with underexpressed annexin A10, N-cadherin, desmocollin 3 and PAI-2, which have been reported as tumor suppressors. The lines overexpressed EEF1A2, SMARA3 and STAT1 and underexpressed other oncogenes, tumor suppressors and extracellular matrix/adhesion genes. The results implicate ZNF217 as an ovarian oncogene, which is detrimental to senescing normal OSE cells but contributes to neoplastic progression in OSE with inactivated p53/RB. The resemblance of the genomic changes in the ZNF217-overexpressing lines to ovarian carcinomas provides a unique model to investigate interrelationships between these changes and ovarian neoplastic phenotypes.
Exercise does not enhance short-term deprivation-induced ocular dominance plasticity: evidence from dichoptic surround suppression (2020)

A bstract The input from the two eyes is combined in the brain. In this combination, the relative strength of the input from each eye is determined by the ocular dominance. Recent work has shown that this dominance can be temporarily shifted. Covering one eye with an eye patch for a few hours makes its contribution stronger. It has been proposed that this shift can be enhanced by exercise. Here, we test this hypothesis using a dichoptic surround suppression task, and with exercise performed according to American College of Sport Medicine guidelines. We measured detection thresholds for patches of sinusoidal grating shown to one eye. When an annular mask grating was shown simultaneously to the other eye, thresholds were elevated. The difference in the elevation found in each eye is our measure of relative eye dominance. We made these measurements before and after 120 minutes of monocular deprivation (with an eye patch). In the control condition, subjects rested during this time. For the exercise condition, 30 minutes of exercise were performed at the beginning of the patching period. This was followed by 90 minutes of rest. We find that patching results in a shift in ocular dominance that can be measured using dichoptic surround suppression. However, we find no effect of exercise on the magnitude of this shift. We further performed a meta-analysis on the four studies that have examined the effects of exercise on the dominance shift. Looking across these studies, we find no evidence for such an effect.
An Integrated Approach to Fragment-Based Lead Generation:Philosophy, Strategy and Case Studies from AstraZenecas Drug Discovery Programmes (2007)

Fragment-based lead generation (FBLG) has recently emerged as an alternative to traditional high throughput screening (HTS) to identify initial chemistry starting points for drug discovery programs. In comparison to HTS screening libraries, the screening sets for FBLG tend to contain orders of magnitude fewer compounds, and the compounds themselves are less structurally complex and have lower molecular weight. This report summarises the advent of FBLG within the industry and then describes the FBLG experience at AstraZeneca. We discuss (1) optimising the design of screening libraries, (2) hit detection methodologies, (3) evaluation of hit quality and use of ligand efficiency calculations, and (4) approaches to evolve fragment-based, low complexity hits towards drug-like leads. Furthermore, we exemplify our use of FBLG with case studies in the following drug discovery areas: antibacterial enzyme targets, GPCRs (melanocortin 4 receptor modulators), prostaglandin D2 synthase inhibitors, phosphatase inhibitors (protein tyrosine phosphotase 1B), and protease inhibitors (b-secretase).
Measurement ofCPViolation in the Phase Space ofB±→K±π+π−andB±→K±K+K−Decays (2013)

The charmless decays ${B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}{K}^{\ifmmode\pm\else\textpm\fi{}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ and ${B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}{K}^{\ifmmode\pm\else\textpm\fi{}}{K}^{+}{K}^{\ensuremath{-}}$ are reconstructed using data, corresponding to an integrated luminosity of $1.0\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$, collected by LHCb in 2011. The inclusive charge asymmetries of these modes are measured as ${A}_{CP}({B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}{K}^{\ifmmode\pm\else\textpm\fi{}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}})=0.032\ifmmode\pm\else\textpm\fi{}0.008\text{ }(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.004\text{ }(\mathrm{syst})\ifmmode\pm\else\textpm\fi{}0.007(J/\ensuremath{\psi}{K}^{\ifmmode\pm\else\textpm\fi{}})$ and ${A}_{CP}({B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}{K}^{\ifmmode\pm\else\textpm\fi{}}{K}^{+}{K}^{\ensuremath{-}})=\ensuremath{-}0.043\ifmmode\pm\else\textpm\fi{}0.009\text{ }(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.003\text{ }(\mathrm{syst})\ifmmode\pm\else\textpm\fi{}0.007(J/\ensuremath{\psi}{K}^{\ifmmode\pm\else\textpm\fi{}})$, where the third uncertainty is due to the $CP$ asymmetry of the ${B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}J/\ensuremath{\psi}{K}^{\ifmmode\pm\else\textpm\fi{}}$ reference mode. The significance of ${A}_{CP}({B}^{\ifmmode\pm\else\textpm\fi{}}\ensuremath{\rightarrow}{K}^{\ifmmode\pm\else\textpm\fi{}}{K}^{+}{K}^{\ensuremath{-}})$ exceeds three standard deviations and is the first evidence of an inclusive $CP$ asymmetry in charmless three-body $B$ decays. In addition to the inclusive $CP$ asymmetries, larger asymmetries are observed in localized regions of phase space.
Cover Feature: Isomerization of Allylic Alcohols to Ketones Catalyzed by Well‐Defined Iron PNP Pincer Catalysts (Chem. Eur. J. 16/2018) (2018)

A well-defined iron pincer complex has been successfully applied for the isomerization of allylic and homo-allylic alcohols to the corresponding ketones. A range of differently substituted aromatic as well as aliphatic allylic alcohols are suitable candidates. The addition of KOtBu leads to the formation of the active catalyst, which performs the isomerization by a two-step self-hydrogen-borrowing process. The mechanism was verified using DFT calculations. More information can be found in the Full Paper by J. G. de Vries, et al. on page 4043.
Experimentally induced changes in the endocytic traffic of P-glycoprotein alter drug resistance of cancer cells (1997)

The MDR-1 gene product, plasma membrane glycoprotein or P-glycoprotein (PGP), has been shown to confer drug resistance to cancer cells by acting as an energy-dependent drug-efflux pump. We have examined the endocytic traffic of PGP in human multidrug-resistant cells and tested whether the traffic and the steady-state intracellular localization of PGP can be experimentally modulated. Here we show that 1) under steady state approximately 70% of cellular PGP is on the surface whereas approximately 30% is intracellular, 2) surface PGP undergoes constitutive endocytosis and recycling, 3) endocytosis of PGP involves clathrin and adaptin complex 2-dependent mechanism, and 4) PGP cycles through a Rab5-responsive endosomal compartment. Biochemical (such as antibody crosslinking of PGP or treatment of cells with chloroquine) and molecular (such as overexpression of Rab5) treatments were used to modulate the endocytic/ recycling traffic of PGP. Such treatments resulted in the redistribution of PGP from the cell surface to intracellular compartments. Cells with such "mislocalized" PGP showed a decrease in multidrug resistance, suggesting that clinically relevant strategies can be attempted by modulating PGP's temporal and spatial distribution within cancer cells.
Defect engineering of silicon with ion pulses from laser acceleration (2023)

Abstract Defect engineering is foundational to classical electronic device development and for emerging quantum devices. Here, we report on defect engineering of silicon with ion pulses from a laser accelerator in the laser intensity range of 10 19 W cm −2 and ion flux levels of up to 10 22 ions cm −2 s −1 , about five orders of magnitude higher than conventional ion implanters. Low energy ions from plasma expansion of the laser-foil target are implanted near the surface and then diffuse into silicon samples locally pre-heated by high energy ions from the same laser-ion pulse. Silicon crystals exfoliate in the areas of highest energy deposition. Color centers, predominantly W and G-centers, form directly in response to ion pulses without a subsequent annealing step. We find that the linewidth of G-centers increases with high ion flux faster than the linewidth of W-centers, consistent with density functional theory calculations of their electronic structure. Intense ion pulses from a laser-accelerator drive materials far from equilibrium and enable direct local defect engineering and high flux doping of semiconductors.
High-Pressure Torsion for Ring Samples in Different Thicknesses (2010)

High-pressure torsion (HPT) was conducted with ring samples of pure Al (99.99%) having different thicknesses. They were cut from an Al plate with 10 mm thickness to dimensions having inner and outer diameters of 23 and 30 mm with thicknesses of 2 mm or 4 mm. HPT was conducted at room temperature under a pressure of 1 GPa at a rotation speed of 1 rpm. It is shown that the strain was introduced more intensely in the mid part on the cross section. This strained region extended with increasing number of revolution and covered throughout the cross section in the 2 mm thickness ring after 30 revolutions. The intense-strained region extended to ~3 mm in the 4 mm thickness ring after 30 revolutions but remains almost the same even after 100 revolutions. The thickness of ~3 mm may be an upper limit to achieve homogeneous introduction of the strained region throughout the cross section.
One-Pot Synthesis of Substituted 2-Aminobenzo[b]thiophenes (2007)

Reaction of 1-(2-chloro-5-nitrophenyl)ethanone 1, via Willgerodt-Kindler routes, using the primary and secondary amines 2a-k resulted in a simple, efficient three-component one-pot synthesis of 2-aminobenzo[b]thiophenes 3a-k.
Fully Convolutional Neural Networks For Remote Sensing Image Classification (2016)

International audience
Diffusive Transport of Micelles and Monomeric Solutes in Supercritical CO2 (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDiffusive Transport of Micelles and Monomeric Solutes in Supercritical CO2Dongil Lee, John C. Hutchison, Joseph M. DeSimone, and Royce W. MurrayView Author Information Kenan Laboratories of Chemistry and NSF Center for Environmentally Responsible Solvents and Processes University of North Carolina Chapel Hill, North Carolina 27599 Cite this: J. Am. Chem. Soc. 2001, 123, 34, 8406–8407Publication Date (Web):August 2, 2001Publication History Received25 May 2001Revised9 July 2001Published online2 August 2001Published inissue 1 August 2001https://pubs.acs.org/doi/10.1021/ja0162818https://doi.org/10.1021/ja0162818rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views290Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Diffusion,Emulsions,Micelles,Probes,Surfactants Get e-Alerts