gebhart/patrepeval huggingface dataset:
Rab37 is a novel mast cell specific GTPase localized to secretory granules (2000)

GTPases regulate a myriad of cellular functions including signal transduction, cytoskeletal organization and membrane trafficking. Rab GTPases act to coordinate the membrane dynamics of cells by organizing and regulating the activity of effector proteins important in vesicle trafficking. Rab37 is a novel Rab GTPase specifically expressed in the MC-9 mast cell line and bone marrow mast cells. Rab37 is 74% identical to Rab26 and 47% identical to Rab8, a GTPase important in Golgi to plasma membrane vesicle trafficking in mammalian cells. When green fluorescent protein tagged Rab37 is expressed in bone marrow mast cells, the secretory granules are labeled. These data suggest that Rab37 may play an important role in mast cell degranulation making this protein a potentially important target for therapeutic intervention in the treatment of allergy.
Thread-Based Obfuscation through Control-Flow Mangling (2013)

The increasing use of cloud computing and remote execution have made program security especially important. Code obfuscation has been proposed to make the understanding of programs more complicated to attackers. In this paper, we exploit multi-core processing to substantially increase the complexity of programs, making reverse engineering more complicated. We propose a novel method that automatically partitions any serial thread into an arbitrary number of parallel threads, at the basic-block level. The method generates new control-flow graphs, preserving the blocks' serial successor relations and guaranteeing that one basic-block is active at a time using guards. The method generates m^n different combinations for m threads and n basic-blocks, significantly complicating the execution state. We provide a correctness proof for the algorithm and implement the algorithm in the LLVM compilation framework.
Mucus phospholipids are decreased in ulcerative colitis. A possible clue to pathogenesis? (2004)

Aims: A defective mucus composition represents a key pathogenetic factor for intestinal injury. Phosphatidylcholine (PC) is an essential component contributing to formation of a hydrophobic mucus layer. For evaluation of phosphatidylcholine in the pathogenesis of inflammatory bowel disease, the concentration and composition of PC in the rectal mucus of patients with ulcerative colitis was determined. Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) allows quantification of phosphatidylcholine species and enables us to analyze crude extracts. Methods: Lipid extracts of material obtained by light scrapings of the intestinal lumen were analyzed by nano-ESI MS/MS and with internal standardization quantified. PC and LPC species from rectoscopically acquired mucus aliquots of patients with ulcerative colitis (clinical remission) were compared to patients with Crohn's disease (clinical remission) and control subjects. Results: Patients with inactive ulcerative colitis showed significant less PC and LPC (median 346 [IQR: 230–405] pmol total PC/ mg dry weight) in rectal mucus compared to Crohn's disease (median 1126 [IQR: 465–1941] pmol total PC/ mg dry weight) and control subjects (median 1285 [IQR: 850–1639] pmol total PC/ mg dry weight) (p?<? 0.05). The molecular species of PC and LPC were not significant different in both groups. The most abundant species were PC 16: 0/18: 1; PC 16: 0/18: 2; PC 18: 0/18: 1; PC 18: 0/18: 2; LPC 16: 0; and LPC 18: 0. Conclusion: NanoESI MS/MS is a suitable tool to analyze and quantify small amounts of PC in human mucus. Patients with ulcerative colitis have significant less PC in their intestinal mucus despite a comparable PC molecular species composition pattern. This indicates that a low amount of protective mucus PC is a characteristic feature in ulcerative colitis and may predispose to an impaired mucosal barrier function facilitating inflammatory attacks by noxious colonic contents.
SURFACE TREATED NATURAL GRAPHITE AS ANODE MATERIAL FOR HIGH-POWER LI-ION BATTERY APPLICATIONS (2006)

High power application of Li-ion battery in hybrid electrical vehicles requires low cost and safe cell materials. Among the various carbon anode materials used in lithium-ion batteries, natural graphite shows the most promise with advantages in performance and cost. However, natural graphite is not compatible with propylene carbonate (PC)–based electrolytes, which have a lower melting point and improved safety characteristics. The problem with it is that the molecules of propylene carbonate intercalate with Li+ into graphite, and that frequently leads to the exfoliation of the graphite matrix.
iSHELL: a 1–5 micron R = 80,000 Immersion Grating Spectrograph for the NASA Infrared Telescope Facility (2022)

Abstract iSHELL is a 1.06–5.3 μ m high spectral resolution spectrograph built for the 3.2 m NASA Infrared Telescope Facility (IRTF) on Maunakea, Hawaii. Dispersion is accomplished with a silicon immersion grating in order to keep the instrument small enough to be mounted at the Cassegrain focus of the telescope. The white pupil spectrograph produces resolving powers of up to about R ≡ λ / δλ = 80,000 (0.″375 slit). Cross-dispersing gratings mounted in a tiltable mechanism allow observers to select different wavelength ranges and, in combination with a slit wheel and Dekker mechanism, slit widths ranging from 0.″375 to 4.″0 and slit lengths ranging from 5″ to 25″. One Teledyne 2048 × 2048 HAWAII-2RG array is used in the spectrograph, and one Raytheon 512 × 512 Aladdin 2 array is used in a 1–5 μ m slit viewer for object acquisition, guiding, and scientific imaging. iSHELL has been in productive regular use on IRTF since first light in 2016 September. In this paper we discuss details of the science case, design, construction and astronomical use of iSHELL.
On the Growth of Stannic Oxide by Ion Beam Sputter Deposition (IBSD) (2017)

SnO 2 thin films were grown on (0001) ( c ‐plane), ( r ‐plane), ( a ‐plane) and ( m ‐plane) sapphire substrates using ion beam sputter deposition (IBSD) of a pure metallic Sn target at a constant gas mixture of 2.5 sccm argon and 15 sccm oxygen at 550 °C substrate temperature. X‐ray diffraction in Bragg–Brentano geometry revealed that SnO 2 film deposited on each substrate is grown with preferential out‐of‐plane orientation. The determined orientation relationships were SnO 2 Al 2 O 3 (0001) ( c ‐plane), SnO 2 Al 2 O 3 ( a ‐plane), SnO 2 Al 2 O 3 ( r ‐plane) and SnO 2 Al 2 O 3 ( m ‐plane). X‐ray diffraction (XRD) proved epitaxial growth, perceivable by very narrow full width at half maximum (FWHM) in rocking curves and Laue oscillations in standard Θ–2Θ Bragg–Brentano scans. X‐ray pole figures even revealed epitaxial in‐plane relationships.
Runx2 Transcriptional Activation of Indian Hedgehog and a Downstream Bone Metastatic Pathway in Breast Cancer Cells (2008)

Runx2, required for bone formation, is ectopically expressed in breast cancer cells. To address the mechanism by which Runx2 contributes to the osteolytic disease induced by MDA-MB-231 cells, we investigated the effect of Runx2 on key components of the "vicious cycle" of transforming growth factor beta (TGFbeta)-mediated tumor growth and osteolysis. We find that Runx2 directly up-regulates Indian Hedgehog (IHH) and colocalizes with Gli2, a Hedgehog signaling molecule. These events further activate parathyroid hormone-related protein (PTHrP). Furthermore, Runx2 directly regulates the TGFbeta-induced PTHrP levels. A subnuclear targeting deficient mutant Runx2, which disrupts TGFbeta-induced Runx2-Smad interactions, failed to induce IHH and downstream events. In addition, Runx2 knockdown in MDA-MB-231 inhibited IHH and PTHrP expression in the presence of TGFbeta. In vivo blockade of the Runx2-IHH pathway in MDA-MB-231 cells by Runx2 short hairpin RNA inhibition prevented the osteolytic disease. Thus, our studies define a novel role of Runx2 in up-regulating the vicious cycle of metastatic bone disease, in addition to Runx2 regulation of genes related to progression of tumor metastasis.
MIMO capacity dependence on realistic cross‐polarization and branch power ratios (2008)

Abstract The dependence of channel capacity on cross‐polarization and the branch power ratio is established over a wide range of both realistic and idealized values. An existing empirical model is adjusted to avoid self‐contradictory results for cross‐coupled, but uncorrelated energy. Typical ranges are highlighted for realistic channel measurements from the literature, and extreme cases are identified. The value of a peak capacity measure is established and compared with the outage and average capacities. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 1384–1388, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.23360
A genomic approach to the stability, elastic, and electronic properties of the MAX phases (Phys. Status Solidi B 8/2014) (2014)

A large database on the elastic and electronic properties of 665 MAX (Mn+1AXn) phases with n = 1 to 4 using ab initio methods has been established (see the article by S. Aryal et al., pp. 1480–1497). Various correlations among and between them are fully explored. The key elements in the interdependence between the elastic properties, mechanical parameters (bulk modulus, shear modulus, Young's modulus and Poisson's ratio), electronic structure and interatomic bonding are identified. The detailed analysis of various correlation plots shows that there is a clear correspondence between bulk modulus K and total bond order density. The special role played by the A element in MAX is emphasized. These calculations also show a marked difference between the carbides and nitrides. The database is used to test and demonstrate the efficacy of data mining algorithms for materials genome. The complete data base on the elastic and electronic structure together with the mechanical parameters for these 665 MAX phase compounds is fully accessible.
Greedy feature selection for subspace clustering (2013)

Unions of subspaces provide a powerful generalization of single subspace models for collections of high-dimensional data; however, learning multiple subspaces from data is challenging due to the fact that segmentation--the identification of points that live in the same subspace--and subspace estimation must be performed simultaneously. Recently, sparse recovery methods were shown to provide a provable and robust strategy for exact feature selection (EFS)--recovering subsets of points from the ensemble that live in the same subspace. In parallel with recent studies of EFS with l1-minimization, in this paper, we develop sufficient conditions for EFS with a greedy method for sparse signal recovery known as orthogonal matching pursuit (OMP). Following our analysis, we provide an empirical study of feature selection strategies for signals living on unions of subspaces and characterize the gap between sparse recovery methods and nearest neighbor (NN)-based approaches. In particular, we demonstrate that sparse recovery methods provide significant advantages over NN methods and that the gap between the two approaches is particularly pronounced when the sampling of subspaces in the data set is sparse. Our results suggest that OMP may be employed to reliably recover exact feature sets in a number of regimes where NN approaches fail to reveal the subspace membership of points in the ensemble.
Guided optimization of fluid status in haemodialysis patients (2009)

The BCM provides an objective assessment of normohydration that is clinically applicable. Guiding the patients towards this target of normohydration leads to better control of hypertension in hyperhydrated patients, less intradialytic adverse events and improved cardiac function.
Quality evaluation of full color hologram (2007)

The quality of a hologram depends on many factors including its resolution, brightness and color reproduction. In a holographic image, good resolution entails that overt and covert images are clearly visible. However, the effects of using the H1H2 method to construct holograms, on the resolution of holographic images have not been investigated to date. In this study, the resolution of images reconstructed from mass-produced color Lippmann holograms using the H1H2 method was evaluated. Silver halide (H1, master hologram) and photopolymer (H2, intermediate and H3 mass-produced holograms) were used as recording materials. Results indicated that the resolution of H3 images decreased progressively as noise in H1 images increased. The noise in H1 images was dependent on conditions related to developing the silver halide and factors related to producing H1. Optimizing the process of creating H1 images was effective in creating high quality H1H2 holograms.
Transcription Factor Binding Sites Are Genetic Determinant of Retroviral Integration in the Human Genome (2008)

Abstract Gamma-retroviruses and lentiviruses integrate non-randomly in mammalian genomes, with specific preferences for active chromatin, promoters and regulatory regions. Gamma-retroviral gene transfer vectors show a high frequency of insertional gene activation, and may induce neoplastic or pre-neoplastic clonal expansions in patients treated with genetically modified cells. An analysis of &gt;10,000 integration sites of a Moloney leukemia virus (MLV)-derived vector in human CD34+ hematopoietic progenitors showed that genes involved the control of growth, differentiation and development of the hematopoietic and immune system are targeted at high frequency and enriched in integration hot spots, suggesting that the cell gene expression program is instrumental in directing MLV integration. To investigate the role of transcriptional regulatory networks in retroviral target site selection, we analyzed the distribution of transcription factor binding sites (TFBSs) flanking &gt;4,000 MLV- and HIV-derived proviruses in human hematopoietic and non-hematopoietic cells. We show that MLV vectors integrate in genomic regions enriched in cell-type specific subsets of TFBSs, independently from their relative position with respect to genes and transcription start sites. Conversely, HIV vectors appear to avoid TFBS-rich genomic regions. Hierarchical clustering and a principal component analysis of TFBSs flanking retroviral integration sites in CD34+ and HeLa cells showed that TFBS subsets are vector- and cell type-specific. Analysis of sequences flanking the integration sites of vectors carrying mutations in their long terminal repeats (LTRs), and of HIV vectors packaged with a MLV integrase, indicates that the MLV integrase and LTR enhancer are the viral determinants of the selection of TFBS-rich regions in the genome. Chromatin immunoprecipitation analysis shows that transcription factors bind the LTR enhancers in the cell nucleus before integration, and may therefore synergize with the integrase in tethering retroviral pre-integration complexes to transcriptionally active regulatory regions. This study identifies TFBSs as differential genomic determinants of retroviral target site selection in the human genome, and indicates that gamma-retroviruses and lentiviruses have evolved dramatically different strategies to interact with the host cell chromatin. These differences predict a higher risk in using gamma-retroviral vs. lentiviral vectors for human gene therapy applications, independently from the design of the vector and the transgene expression cassette.
ChemInform Abstract: Improved Procedure for the Detritylation of DMT‐Oligonucleotides: Use of Dowex. (1996)

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.
Implications on design of rapid manufacturing (2003)

During the last few decades, designers have been educated to develop designs with restricted geometry so that parts can be made easily. The revolutionary aspect of rapid manufacturing will be that geometry will no longer be a limiting factor. The introduction of rapid manufacturing will have a number of effects on design. It will be possible to have re-entrant shapes without complicating manufacturing, no draft angles, variable wall thickness, no split lines and fewer parts, leading to easier assembly and lower stock. The individual designer's method of working will change with the introduction of rapid manufacturing and also there will be changes to the overall design process.
Visibility of solid and liquid fiducial markers used for image-guided radiation therapy on optical coherence tomography: an esophageal phantom study (Conference Presentation) (2017)

Radiation therapy (RT) is used in operable and inoperable esophageal cancer patients. Endoscopic ultrasound-guided fiducial marker placement allows improved translation of the disease extent on endoscopy to computed tomography (CT) images used for RT planning and enables image-guided RT. However, microscopic tumor extent at the time of RT planning is unknown. Endoscopic optical coherence tomography (OCT) is a high-resolution (10-30µm) imaging modality with the potential for accurately determining the longitudinal disease extent. Visibility of fiducial markers on OCT is crucial for integrating OCT findings with the RT planning CT. We investigated the visibility on OCT (NinePoint Medical, Inc.) of 13 commercially available solid (Visicoil, Gold Anchor, Flexicoil, Polymark, and QLRAD) and liquid (BioXmark, Lipiodol, and Hydrogel) fiducial markers of different diameter. We designed and manufactured a set of dedicated Silicone-based esophageal phantoms to perform imaging in a controlled environment. The esophageal phantoms consist of several layers with different TiO2 concentrations to simulate the scattering properties of a typical healthy human esophagus. Markers were placed at various depths (0.5, 1.1, 2.0, and 3.0mm). OCT imaging allowed detection of all fiducial markers and phantom layers. The signal to background ratio was 6-fold higher for the solid fiducial markers than the liquid fiducial markers, yet OCT was capable of visualizing all 13 fiducial markers at all investigated depths. We conclude that RT fiducial markers can be visualized with OCT. This allows integration of OCT findings with CT for image-guided RT.
Fabrication of SOI Substrates with Buried Silicide Layers for BICMOS-applications (2006)

A new approach for a BiCMOS technology based on Silicon on Metal on Insulator (SOMI) technology will be presented. The SOMI technology includes cobalt silicidation, wafer bonding and CMP processes. CoSi2 is used to form the SOMI substrate, because CoSi2 has a high thermal stability, a low resistivity, and is relatively easy to fabricate. Two different process flows to prepare a SOMI substrate with thin silicon layers on a buried CoSi2 layer are shown. The first process is a modified BESOI method and the second uses a H+ Implanted Layer Splitting (HILS) regime combined with wafer bonding. Both process flows could be realized successfully. The paper describes the cobalt film deposition, the silicidation, the implantation, the wafer bonding process and the CMP to planarize the silicon film roughness as well as some special effects observed during the fabrication process.
Reaction analysis of the formation of CuInSe2 films in a physical vapor deposition reactor (1998)

The reaction kinetics for the formation of CuInSe2 films by reacting Cu/In layers with elemental selenium are compared with those for H2Se. The species mole fractions as a function of time in a single Se-source physical vapor deposition (PVD) reactor are found to be essentially the same as those obtained in a chemical vapor deposition (CVD) reactor with flowing H2Se, indicating that the same chemical equation representation can be used in both cases. The chemical engineering reaction analysis model developed previously by us is shown to predict adequately the experimental data in both reactors. The model is employed to predict three-source behavior. The effects of rate of species delivery and substrate temperature on the time to make CuInSe2 is presented quantitatively. © 1998 John Wiley & Sons, Ltd.
In Colorectal Cancer Cells With Mutant KRAS, SLC25A22-Mediated Glutaminolysis Reduces DNA Demethylation to Increase WNT Signaling, Stemness, and Drug Resistance (2020)

In CRC cells that express activated KRAS, SLC25A22 promotes accumulation of succinate, resulting in increased DNA methylation, activation of WNT signaling to β-catenin, increased expression of LGR5, proliferation, stem cell features, and resistance to 5-fluorouacil. Strategies to disrupt this pathway might be developed for treatment of CRC.
Both LFA‐1‐positive and ‐deficient T cell clones require the CD2/LFA‐3 interaction for specific cytolytic activation (1992)

We investigated the capacity of T lymphocytes from a leukocyte adhesion-deficient (LAD) patient to respond to alloantigen. Leukocytes of this patient completely lacked LFA-1 surface expression due to the absence of mRNA coding for the LFA-1 beta chain. Despite the absence of LFA-1, T lymphocytes obtained from this patient, cultured with allogeneic stimulator cells (lymphoblastoid B cells JY), were capable of lysing JY cells. Furthermore, two T cell clones (one CD4+ and one CD8+), generated from this lymphocyte culture, specifically lysed the allogeneic lymphoblastoid JY cells. The cytolytic capacity of LFA-1-negative T lymphocytes and T cell clones was comparable to that of control LFA-1-positive T cells with allospecificity against JY. Detailed analysis of the CD4 positive and LFA-1-negative T cell clone demonstrated that it specifically recognized HLA-DQ. Antibody inhibition studies showed that the CTL/target cell interaction was mediated through the CD2/LFA-3 adhesion pathway. LFA-1 expressed by the target cells did not participate in the CTL/target cell conjugate formation and contributed only minimally to the cytotoxic activity. Moreover, when allogeneic LFA-1-deficient B cells, bearing the appropriate HLA-DQ alloantigen, were used as target cells, significant levels of specific cytotoxicity were measured, further excluding a role for LFA-1 in this interaction. The adhesion molecules, VLA-4, CD44 and L-selectin (LECAM1) were not involved. These results demonstrate that LFA-1-negative T lymphocytes can exert allospecific cytotoxicity and that CTL/target cell contact is mediated through the CD2/LFA-3 route. This observation may explain in part why in LAD patients viral infections, cleared largely by T cells, are less frequently observed than bacterial infections, in which phagocytic cells play a major role.
Syntheses of C12,N13 Heterocyclic Bridged Fused Indenopyrrolocarbazoles (2002)

Tandem alkylation/cyclization of indenopyrrolocarbazole 4a, a C12 carbon analogue of indolocarbazole K252c, was carried out by general solid-phase and solution-phase methods. Alkylation of fused pyrroloindenylcarbazole 4a derivatives with appropriate monoacetals of diketones afforded the corresponding C12-substituted acetal alcohols. Acid-catalyzed cyclization of these adducts yielded C12,N13-bridged tetrahydrofuran, pyran, and dioxane compounds 10-13.