gebhart/patrepeval huggingface dataset:
A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing (2011)

We have developed an integrated strategy for targeted resequencing and analysis of gene subsets from the human exome for variants. Our capture technology is geared towards resequencing gene subsets substantially larger than can be done efficiently with simplex or multiplex PCR but smaller in scale than exome sequencing. We describe all the steps from the initial capture assay to single nucleotide variant (SNV) discovery. The capture methodology uses in-solution 80-mer oligonucleotides. To provide optimal flexibility in choosing human gene targets, we designed an in silico set of oligonucleotides, the Human OligoExome, that covers the gene exons annotated by the Consensus Coding Sequencing Project (CCDS). This resource is openly available as an Internet accessible database where one can download capture oligonucleotides sequences for any CCDS gene and design custom capture assays. Using this resource, we demonstrated the flexibility of this assay by custom designing capture assays ranging from 10 to over 100 gene targets with total capture sizes from over 100 Kilobases to nearly one Megabase. We established a method to reduce capture variability and incorporated indexing schemes to increase sample throughput. Our approach has multiple applications that include but are not limited to population targeted resequencing studies of specific gene subsets, validation of variants discovered in whole genome sequencing surveys and possible diagnostic analysis of disease gene subsets. We also present a cost analysis demonstrating its cost-effectiveness for large population studies.
Germanium nanowires sheathed with an oxide layer (2000)

We report how the structural arrangement of germanium nanowires optimizes surface stability and enables the formation of very thin free-standing crystalline wires. Ge nanowires consisting of a crystalline Ge core and an amorphous ${\mathrm{GeO}}_{2}$ sheath have been formed by laser ablation of a mixture of Ge and ${\mathrm{GeO}}_{2}.$ The crystalline Ge core lies in the axial [211] direction and is terminated by the {111} facets on the surface. The ${\mathrm{GeO}}_{2}$ sheath saturates the surface bonds of the core, adapts to the core surface roughness, and prohibits the growth of the nanowire in the lateral direction. With such a core and sheath, the surface energy of the nanowire is reduced and the formation of very thin nanowires is thereby permitted. Phonon confinement in the Ge nanowires has been observed by Raman scattering.
Vitamin E Succinate Induces Ceramide-Mediated Apoptosis in Head and Neck Squamous Cell Carcinoma In vitro and In vivo (2008)

Alpha-TOS showed promising anticancer effects to inhibit HNSCC growth and viability in vivo and in vitro. The induction of enzymes involved in ceramide metabolism by alpha-TOS suggests that ceramide-mediated apoptosis may expand therapeutic strategies in the treatment of carcinoma.
Differential Role of CTLA-4 in Regulation of Resting Memory Versus Naive CD4 T Cell Activation (1998)

Regulation of peripheral T cell responses is critical for preserving self tolerance. Memory T cells have a lower threshold for activation through the TCR and are thought to be less dependent on costimulation than naive T cells, suggesting a requirement for more stringent regulation of memory T cells. We have recently shown that CD4 engagement apart from the TCR results in the inactivation of memory, but not naive, CD4 T cells. We show here that this inhibition requires ligation of CTLA-4, in that blocking CTLA-4-B7 interactions restores memory CD4 T cell responsiveness. Early signaling through CTLA-4 is possible because resting memory, but not naive, CD4 T cells contain intracellular stores of CTLA-4 that are continuously recycled between the cytoplasm and the cell surface. This mechanism ensures that low intensity TCR engagements, which are thought to be important for peripheral T cell longevity, do not cause memory T cell activation but instead raise their threshold for costimulatory signals. This may give memory T cells an extended lifespan with a reduced risk of inappropriate activation.
High minority-carrier lifetimes in GaAs grown on low-defect-density Ge/GeSi/Si substrates (1998)

A high bulk minority-carrier lifetime in GaAs grown on Si-based substrates is demonstrated. This was achieved by utilizing a step-graded Ge/GeSi buffer (threading dislocation density 2×106 cm−2) grown on an offcut (001) Si wafer, coupled with monolayer-scale control of the GaAs nucleation to suppress antiphase domains. Bulk minority-carrier lifetimes (τp) were measured using room-temperature time-resolved photoluminescence applied to a series of Al0.3Ga0.7As/GaAs/Al0.3Ga0.7As double-heterojunction structures doped n=1.1×1017 cm−3 with GaAs thicknesses of 0.5, 1.0, and 1.5 μm. A lifetime τp=7.7 ns was determined for GaAs grown on Si. The extracted interface recombination velocity of 3.9×103 cm/s is comparable to recombination velocities found for Al0.3Ga0.7As/GaAs interfaces grown on both GaAs and Ge wafers, indicating that the crosshatch surface morphology characteristic of strain-relaxed Ge/GeSi surfaces does not impede the formation of high-electronic-quality interfaces. These results hold great promise for future integration of III–V minority-carrier devices with Si wafer technologies.
On the Use of Carbon Cables from Plastic Solvent Combinations of Polystyrene and Toluene in Carbon Nanotube Synthesis (2021)

For every three people on the planet, there are approximately two Tonnes (Te) of plastic waste. We show that carbon recovery from polystyrene (PS) plastic is enhanced by the coaddition of solvents to grow carbon nanotubes (CNTs) by liquid injection chemical vapour deposition. Polystyrene was loaded up to 4 wt% in toluene and heated to 780 °C in the presence of a ferrocene catalyst and a hydrogen/argon carrier gas at a 1:19 ratio. High resolution transmission electron microscopy (HRTEM), scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and Raman spectroscopy were used to identify multiwalled carbon nanotubes (MWCNTs). The PS addition in the range from 0 to 4 wt% showed improved quality and CNT homogeneity; Raman "Graphitic/Defective" (G/D) values increased from 1.9 to 2.3; mean CNT diameters increased from 43.0 to 49.2 nm; and maximum CNT yield increased from 11.37% to 14.31%. Since both the CNT diameters and the percentage yield increased following the addition of polystyrene, we conclude that carbon from PS contributes to the carbon within the MWCNTs. The electrical contact resistance of acid-washed Bucky papers produced from each loading ranged from 2.2 to 4.4 Ohm, with no direct correlation to PS loading. Due to this narrow range, materials with different loadings were mixed to create the six wires of an Ethernet cable and tested using iPerf3; the cable achieved up- and down- link speeds of ~99.5 Mbps, i.e., comparable to Cu wire with the same dimensions (~99.5 Mbps). The lifecycle assessment (LCA) of CNT wire production was compared to copper wire production for a use case in a Boeing 747-400 over the lifespan of the aircraft. Due to their lightweight nature, the CNT wires decreased the CO<sub>2</sub> footprint by 21 kTonnes (kTe) over the aircraft's lifespan.
Unbiased and Automated Identification of a Circulating Tumour Cell Definition That Associates with Overall Survival (2011)

Circulating tumour cells (CTC) in patients with metastatic carcinomas are associated with poor survival and can be used to guide therapy. Classification of CTC however remains subjective, as they are morphologically heterogeneous. We acquired digital images, using the CellSearch TM system, from blood of 185 castration resistant prostate cancer (CRPC) patients and 68 healthy subjects to define CTC by computer algorithms. Patient survival data was used as the training parameter for the computer to define CTC. The computer-generated CTC definition was validated on a separate CRPC dataset comprising 100 patients. The optimal definition of the computer defined CTC (aCTC) was stricter as compared to the manual CellSearch CTC (mCTC) definition and as a consequence aCTC were less frequent. The computer-generated CTC definition resulted in hazard ratios (HRs) of 2.8 for baseline and 3.9 for follow-up samples, which is comparable to the mCTC definition (baseline HR 2.9, follow-up HR 4.5). Validation resulted in HRs at baseline/follow-up of 3.9/5.4 for computer and 4.8/5.8 for manual definitions. In conclusion, we have defined and validated CTC by clinical outcome using a perfectly reproducing automated algorithm.
Growth of thin films of molybdenum oxide by atomic layer deposition (2010)

Thin films of MoO3 have been obtained by the atomic layer deposition (ALD) technique using molybdenum hexacarbonyl (Mo(CO)6), ozone, and water as precursors. A window for ALD growth was found in the temperature range 152 to 172 °C. Self-limiting growth was verified at a deposition temperature of 163 °C. The upper temperature range is determined by the thermal stability of the Mo(CO)6 precursor. The growth dynamics was further investigated by quartz crystal microbalance to determine the effect of ozone and water on the deposition process. Growth using only water as oxygen source is hardly detectable. The growth rate increases to 0.75 Å per cycle when ozone is introduced. X-ray diffraction analysis indicates that the films are amorphous as deposited, but crystallise into the α- and β-MoO3 phases during annealing in air at 500 °C and to phase-pure, highly oriented α-MoO3 at 600 °C. Analysis by X-ray photoelectron spectroscopy shows that both as-deposited and annealed films contain Mo(VI). Atomic force microscopy proves a very low surface roughness for as-deposited films, which becomes rather rough for annealed films. This investigation has clearly proven the capability of carbonyls as useful precursors for ALD growth of oxides.
The Total Synthesis of a Natural Cardenolide:  (+)-Digitoxigenin (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTThe Total Synthesis of a Natural Cardenolide: (+)-DigitoxigeninGilbert Stork, Fred West, Hee Yoon Lee, Richard C. A. Isaacs, and Shino ManabeView Author Information Department of Chemistry, Columbia University New York, New York 10027 Cite this: J. Am. Chem. Soc. 1996, 118, 43, 10660–10661Publication Date (Web):October 30, 1996Publication History Received26 June 1996Published online30 October 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja962163mhttps://doi.org/10.1021/ja962163mrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views4129Altmetric-Citations86LEARN 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:Aldehydes,Chemical synthesis,Cyclization,Organic synthesis,Substituents Get e-Alerts
Identification of murine homologues of the Drosophila son of sevenless gene: potential activators of ras. (1992)

Several findings suggest that signals from tyrosine kinases are transduced, at least in part, through ras proteins. These findings include (i) blockage of the transforming activity of constitutively active tyrosine kinases by inhibiting ras function and (ii) genetic screens in Caenorhabditis elegans and in Drosophila that identified ras genes as downstream effectors of tyrosine kinases. The recently isolated Drosophila gene Son of sevenless (Sos) is postulated to act as a positive regulatory link between tyrosine kinase and ras proteins by catalyzing exchange of GDP for GTP on ras protein. Such exchange proteins have been reported in extracts of mammalian cells but have not been previously characterized at a molecular level. As Sos appears to function in this role in Drosophila, we sought to isolate a vertebrate counterpart(s). We have characterized two widely expressed murine genes with a high degree of homology to Sos. Hybridization with human DNA and RNA indicates a high degree of conservation of these genes in other vertebrates.
Gene Conversion in Salt-Losing Congenital Adrenal Hyperplasia with Absent Complement C4B Protein* (1986)

Two of four siblings expressed the salt-losing form of congenital adrenal hyperplasia due to 21-hydroxylase deficiency (CAH) and had identical human lymphocyte antigen (HLA) and complement C4 (fourth component of complement) types (HLA-A3,C4,B35,C4A3,C4BQO,DR1/A2,C-,B18,C4A3, C4BQO,DR6). The father and one unaffected sibling were heterozygous carriers of CAH, as determined by a 30-min iv ACTH stimulation test and HLA typing. In addition, the iv ACTH stimulation test revealed that the mother and the other unaffected sibling also carried an allele for an attenuated form of CAH. Restriction endonuclease digests of genomic DNA obtained from members of this family and from normal unrelated subjects were hybridized with cDNA probes encoding human 21-hydroxylase and C4. With the 21-hydroxylase probe, Southern blots prepared from control DNA samples revealed two major restriction fragments in each of four restriction endonuclease digests; TaqI produced major bands at 3.7 and 3.2 kilobases (kb), KpnI at 4.0 and 2.9 kb, EcoRI at 18 and 13 kb, and BglII at 15 and 12.5 kb. Southern blots prepared from DNA of the two patients lacked the 3.7-kb TaqI and 2.9-kb KpnI fragments, but had increased hybridization intensity (relative to control DNA samples) in the 3.2-kb TaqI and 4.0-kb KpnI fragments. By contrast, blots with EcoRI or BglII had two large hybridization fragments not different from control DNA samples. These data indicate the presence of two different 21-hydroxylase genes. Additional mapping studies revealed that the two genes had the restriction pattern of the inactive 21-hydroxylase gene. When genomic DNA that had been isolated from all members of this family and from normal subjects was hybridized with the human C4 cDNA probe, the restriction fragment hybridization patterns for all four endonuclease digests were similar in the two groups. Hence, our results suggest that the 21-hydroxylase deficiency of our patients is due to conversion of the active 21-hydroxylase gene to the inactive gene. This gene conversion was associated with absence of functional C4B protein, without any detectable alterations in the restriction fragment pattern of the C4 genes.
Distance-constrained molecular docking by simulated annealing (1990)

An optimized method based on the principle of simulated annealing is presented for determining the relative position and orientation of interacting molecules. The spatial relationships of these molecules are described by intermolecular distance constraints between specific pairs of atoms, such as found in hydrogen bonds or from experimentally determined data. The method makes use of a random walk through six rotational and translational degrees of freedom where the constituent molecules are treated as rigid bodies. Van der Waals repulsions are used only to define a lower bound on distances between constrained atom pairs within the docking procedure. A cost function comprised of purely geometric constraints is optimized via simulated annealing, in order to search for the best orientation and position of the two molecules. Our docking procedure is applied to eight serine proteinase complexes from the Brookhaven Protein Data Bank. For each simulation 100 computations were performed. A typical docking computation requires only a few seconds of CPU time on a VAXserver 3500. The influence of the number of constraints on the final docked positions was studied. The sensitivity of the docking procedure to a ligand structure which is not well defined is also addressed. Possible applications of this method include using approximate distances incorporating complete energy functions.
Soluble derivatives of feather keratin. 1. Isolation, fractionation and amino acid composition (1964)

2. There is a lag in growth and oxygen uptake on transferring cells from growth on glucose to an amino acid medium during which the enzymes for amino acid catabolism are formed.
Lyme borreliosis research (1995)

Borrelia burgdorferi The etiological agent of Lyme disease has been the object of intensive molecular analysis. Animal models have been developed to study the pathogenesis of the disease. Early diagnosis is being improved by using appropriate antigens for antibody detection and polymerase chain reaction for detection of Borrelia DNA. However, even using better diagnostic tools, many cases, especially those seen early in the development of the disease, can only be diagnosed clinically. Intensive research is also in progress to develop a Borrelia vaccine. The outer surface proteins have been efficacious in animal models. Vaccine development appears difficult, however, because of the antigenic heterogeneity of strains, especially those isolated in Europe.
Lymphohematopoietic progenitors immortalized by a retroviral vector harboring a dominant-negative retinoic acid receptor can recapitulate lymphoid, myeloid, and erythroid development. (1994)

The lymphohematopoietic progenitors represent < 0.01% of nucleated marrow cells. Here, we describe the immortalization of the murine lymphohematopoietic progenitors by a retroviral vector harboring a dominant-negative retinoic acid receptor. The immortalized progenitors proliferate as a stem-cell-factor-dependent clonal line EML that spontaneously generates pre-pro-B lymphocytes and erythroid and myeloid progenitors. Upon stimulation with interleukin-7 and stromal cells, the pre-pro-B lymphocytes express RAG-1 and undergo D-J rearrangements of the immunoglobulin heavy-chain genes. With erythropoietin the erythroid progenitors proliferate and differentiate into red cells. Generation of the common progenitors for neutrophils and macrophages is suppressed in EML but is inducible by high concentrations of retinoic acid. An additional block in neutrophil differentiation occurs at the promyelocyte stage but can also be overcome by high concentrations of retinoic acid. These studies demonstrate a reproducible way to immortalize lymphohematopoietic progenitors and implicate specific roles for retinoic acid receptors at two distinct stages of hematopoiesis.
Reducing DNA context dependence in bacterial promoters (2017)

Variation in the DNA sequence upstream of bacterial promoters is known to affect the expression levels of the products they regulate, sometimes dramatically. While neutral synthetic insulator sequences have been found to buffer promoters from upstream DNA context, there are no established methods for designing effective insulator sequences with predictable effects on expression levels. We address this problem with Degenerate Insulation Screening (DIS), a novel method based on a randomized 36-nucleotide insulator library and a simple, high-throughput, flow-cytometry-based screen that randomly samples from a library of 436 potential insulated promoters. The results of this screen can then be compared against a reference uninsulated device to select a set of insulated promoters providing a precise level of expression. We verify this method by insulating the constitutive, inducible, and repressible promotors of a four transcriptional-unit inverter (NOT-gate) circuit, finding both that order dependence is largely eliminated by insulation and that circuit performance is also significantly improved, with a 5.8-fold mean improvement in on/off ratio.
Real-time 3D light field transmission (2010)

Although capturing and displaying stereo 3D content is now commonplace, information-rich light-field video content capture, transmission and display are much more challenging, resulting in at least one order of magnitude increase in complexity even in the simplest cases. We present an end-to-end system capable of capturing and real-time displaying of high-quality light-field video content on various HoloVizio light-field displays, providing very high 3D image quality and continuous motion parallax. The system is compact in terms of number of computers, and provides superior image quality, resolution and frame rate compared to other published systems. To generate light-field content, we have built a camera system with a large number of cameras and connected them to PC computers. The cameras were in an evenly spaced linear arrangement. The capture PC was directly connected through a single gigabit Ethernet connection to the demonstration 3D display, supported by a PC computation cluster. For the task of dense light field displaying massively parallel reordering and filtering of the original camera images is required. We were utilizing both CPU and GPU threads for this task. On the GPU we do the light-field conversion and reordering, filtering and the YUV-RGB conversion. We use OpenGL 3.0 shaders and 2D texture arrays to have easy access to individual camera images. A network-based synchronization scheme is used to present the final rendered images.
Photoaffinity labeling of tubulin with (2-nitro-4-azidophenyl)deacetylcolchicine: direct evidence for two colchicine binding sites (1989)

A new photoaffinity analogue of colchicine, (2-nitro-4-azidophenyl)deacetylcolchicine (NAPDAC), bound to two classes of sites on bovine renal tubulin and photolabeled both the alpha- and beta-subunits. The apparent Ki for the photoaffinity analogue was 1.40 +/- 0.17 microM (mean +/- SD, n = 3) as measured by competition with [3H] colchicine. Values of the apparent KdS for the two sites, as measured by the direct binding of the [3H]NAPDAC to tubulin, were 0.48 +/- 0.11 microM and 11.6 +/- 3.5 microM (mean +/- SD, n = 6), and the corresponding stoichiometries of binding of the two sites were 0.25 +/- 0.06 and 1.3 +/- 0.4 mol/mol of tubulin (mean +/- SD, n = 6). NAPDAC was a potent inhibitor of microtubule formation as detected by electron microscopy. When tubulin was photolabeled with NAPDAC at 25 degrees C, 15 +/- 3 mol % (mean +/- SD, n = 6) of the [3H]NAPDAC was covalently bound to the alpha-subunit, and 67 +/- 9 mol % (mean +/- SD, n = 6) was covalently bound to the beta-subunit. Since NAPDAC is a mixture of two interconvertible diastereomers, the photoincorporation of each was also examined. One diastereomer photolabeled both alpha- and beta-tubulin; however, the other did not significantly photolabel either subunit. Tubulin photolabeled with NAPDAC (1:1 mole ratio) exhibited a 23% decrease in colchicine binding. Preblocking and prephotolysis experiments with colchicine, NAPDAC, or ANPAH-CLC [Williams et al. (1985) J. Biol. Chem. 260, 13794-13802] provided evidence for conformational changes in tubulin upon colchicine binding. Peptide maps of [3H]NAPDAC-labeled alpha- and beta-tubulin, using Staphylococcus aureus V8 protease, demonstrated the presence of NAPDAC in one peptide of the alpha-subunit and in five peptides of the beta-subunit as detected by autoradiography. NAPDAC provides the first direct evidence for two colchicine binding sites on tubulin.