gebhart/patrepeval huggingface dataset:
MethyLight (2008)

MethyLight is a sodium-bisulfite-dependent, quantitative, fluorescence-based, real-time PCR method to sensitively detect and quantify DNA methylation in genomic DNA. MethyLight relies on methylation-specific priming combined with methylation-specific fluorescent probing. This combination of methylation-specific detection principles results in a highly methylation-specific detection technology, with an accompanying ability to sensitively detect very low frequencies of hypermethylated alleles. The high sensitivity and specificity of MethyLight make it uniquely well suited for detection of low-frequency DNA methylation biomarkers as evidence of disease. At the same time, the quantitative accuracy of real-time PCR and the flexibility to design bisulfite-dependent, methylation-independent control reactions allows for a quantitative assessment of these low-frequency methylation events. We describe the experimental steps of MethyLight analysis in detail. Furthermore, we present here principles and design examples for three types of quality-control reactions. QC-1 reactions are methylation-independent reactions to monitor sample quantity and integrity. QC-2 reactions are bisulfite-independent reactions to monitor recovery efficiencies of the bisulfite-conversion methodology used. QC-3 reactions are bisulfite-independent primed reactions with variable bisulfite-dependent probing to monitor completeness of the sodium bisulfite treatment. We show that these control reactions perform as expected in a time-course experiment interrupting sodium bisulfite conversion at various timepoints.
Glycosylation defining cancer malignancy: New wine in an old bottle (2002)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Effects of Capillary Forces on a Hydrogel Sphere Pressed against a Surface (2015)

A theoretical treatment is provided for effects of capillary forces on a hemispherically shaped hydrogel sample pressed against a solid hydrophilic surface. It is pointed out that the adhesion of a hydrogel to a surface resulting from capillary forces is different from that of a nonporous solid because of the porous nature of the hydrogel. Because of this, the Laplace pressure subtracts from the osmotic pressure inside the gel. For neutral gels, it can exceed the osmotic pressure, causing the gel to deswell. For charged gels, since the counterions inside the gel generally provide much higher osmotic pressure than that due to monomers alone (which is the only source of osmotic pressure in neutral hydrogels), the Laplace pressure is less likely to make the gel deswell. The Laplace pressure can, however, be large enough to deswell asperities (due to surface roughness) on the gel surface, increasing the contact area. This could result in an increase in the friction and ionic electrical conductivity between the gel and the surface (if the surface is an electrical conductor).
A novel dual-channel 3D NAND flash featuring both N-channel and P-channel NAND characteristics for bit-alterable Flash memory and a new opportunity in sensing the stored charge in the WL space (2013)

This work proposes a novel dual-channel 3D NAND Flash that exhibits both n-channel and p-channel NAND characteristics. The NAND is junction-free without dopant inside the array. Unlike the conventional 3D NAND, the drain side near SSL is N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> doped junction, while source side near GSL is P <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> junction. A positive pass-gate read voltage (Vpass, r) induces n-type virtual source/drain for the center WL's, giving an n-channel behavior. On the other hand, a negative Vpass, r induces p-type virtual source/drain, giving the p-channel behavior. Both n- and p-channel reads produce excellent Id-Vg characteristics with very small leakage current. The advantage of this device is that the carrier source of both +FN programming and -FN erasing can be readily provided by either N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> drain or P <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> source, respectively, without waiting for the GIDL generated minority carrier for the floating-body 3D NAND. This gives a much faster +/- FN speed than conventional 3D NAND. Moreover, both +FN and -FN can find suitable inhibit method, enabling a novel bit-alterable Flash memory. We have successfully compared, for the first time, two sensing methods (n- and p-channel read) and identified the trapped charge in the space between WL's. This not only provides characterization of charge lateral profile but also a new opportunity to create another storage node (in WL space) inside the array.
Repair of Scleral Perforation With Preserved Scleral and Amniotic Membrane in Marian's Syndrome (1999)

To describe the surgical technique used in the repair of a large scleral perforation in a patient with Marfan's syndrome and a past history of various surgical interventions in both eyes. Scleral homograft and amniotic membrane transplant were used to reconstruct the large scleral defect present in his left eye. One month after surgical intervention, the patient showed excellent restoration of the scleral perforation without signs of inflammation or infection. The combination of scleral homograft and amniotic membrane transplant constitute an effective alternative to autologous scleral and conjunctival grafts when these cannot be used.
Efficient GaInAsSb/AlGaAsSb diode lasers emitting at 2.29 μm (1990)

Diode lasers emitting at 2.29 μm have been fabricated from lattice-matched double heterostructures having a GaInAsSb active layer and AlGaAsSb confining layers grown by molecular beam epitaxy on GaSb substrates. For pulsed room-temperature operation these devices have exhibited threshold current densities as low as 1.7 kA/cm2 and differential quantum efficiencies as high as 18% per facet, the highest room-temperature efficiency reported for any semiconductor diode laser emitting beyond 2 μm.
Introduction of interleukin-3 gene into stromal cells from the bone marrow alters hemopoietic differentiation but does not modify stem cell renewal (1988)

Cloned endothelial-adipocytes from the stroma of mouse bone marrow (designated 14F1.1) induced growth of stem cells in vitro, accompanied by either pre-B lymphopoiesis or myelopoiesis. We examined the contribution of colony stimulating factors (CSF) to the process. mRNA for GM-CSF, interleukin 3 (IL3), G-CSF, and IL4 could not be detected in the stromal cells. Expression of IL3 gene, achieved by transfection of 14F1.1 cells with a plasmid carrying an IL3 cDNA, shifted the direction of differentiation but did not improve stem cell maintenance. It is proposed that novel stromal cell factors, distinct from known CSFs, regulate stem cell renewal.
Model-based 3-D pose estimation and feature tracking for robot assisted surgery with medical imaging (2007)

Abstract — In this paper we address the problem of the pose estimation based on multiple geometrical features for monocular endoscopic vision with laparoscopes and for stereotaxy with CT scanners. Partial and full pose estimation (6 dofs) are considered with applications to minimally invasive surgery. At the University of Strasbourg, we have been developing a set of techniques for assisting surgeons in navigating and manipulating the three-dimensional space within the human body. In order to develop such systems, a variety of challenging visual tracking and registration problems with pre-operative and/or intra-operative images must be solved. This paper integrates several issues where computational vision can play a role. Depth recovery (from the tip of a surgical instrument w.r.t. living tissue), the Plücker coordinates (4 dofs) of a markerless cylindrical instrument, the 6 dofs of a needle-holder with an heterogeneous set of features and stereotaxy are the examples we describe. Projective invariants with perspective projection, quadrics of revolution and stereotactic markers are features which are useful to achieve the registration with uncalibrated or calibrated devices. Visual servoing-based tracking methods have been developed for image-guided robotic systems, for assisting surgeons in laparoscopic surgery and in interventional radiology. Real-time endoscopic vision and single-slice stereotactic registration has been proposed to retrieve the out-of-field of view instruments, to position a needle and to compensate small displacements like those due to patient breathing or any small disturbances which may occur during an image-guided surgical procedure. I.
Total Synthesis of (+)-Neocarzinostatin Chromophore (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTotal Synthesis of (+)-Neocarzinostatin ChromophoreAndrew G. Myers, Jun Liang, Marlys Hammond, Philip M. Harrington, Yusheng Wu, and Elaine Y. KuoView Author Information Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Cite this: J. Am. Chem. Soc. 1998, 120, 21, 5319–5320Publication Date (Web):May 14, 1998Publication History Received20 February 1998Published online14 May 1998Published inissue 1 June 1998https://pubs.acs.org/doi/10.1021/ja980588yhttps://doi.org/10.1021/ja980588yrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views1334Altmetric-Citations59LEARN 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:Chromophores,Free radicals,Ions,Post-translational modification,Purification Get e-Alerts
The Anisotropic Hydraulic Permeability of Human Lumbar Anulus Fibrosus (1999)

The hydraulic permeability of human nondegenerate anulus fibrosus is direction-dependent (i.e., anisotropic), with the greatest permeability in the radial direction. With disc degeneration, the radial permeability of anulus fibrosus decreases, mainly because of decreased water content, and the axial and circumferential permeability coefficients increase, mainly because of structural change, leading to more isotropic permeability behavior for Grade III discs.
A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension (2000)

A rapid, high throughput readout for single-nucleotide polymorphism (SNP) analysis was developed employing single base chain extension and cytometric analysis of an array of fluorescent microspheres. An array of fluorescent microspheres was coupled with uniquely identifying sequences, termed complementary ZipCodes (cZipCodes), which allowed for multiplexing possibilities. For a given assay, querying a polymorphic base involved extending an oligonucleotide containing both a ZipCode and a SNP-specific sequence with a DNA polymerase and a pair of fluoresceinated dideoxynucleotides. To capture the reaction products for analysis, the ZipCode portion of the oligonucleotide was hybridized with its cZipCodes on the microsphere. Flow cytometry was used for microsphere decoding and SNP typing by detecting the fluorescein label captured on the microspheres. In addition to multiplexing capability, the ZipCode system allows multiple sets of SNPs to be analyzed by a limited set of cZipCode-attached microspheres. A standard set of non-cross reactive ZipCodes was established experimentally and the accuracy of the system was validated by comparison with genotypes determined by other technologies. From a total of 58 SNPs, 55 SNPs were successfully analyzed in the first pass using this assay format and all 181 genotypes across the 55 SNPs were correct. These data demonstrate that the microsphere-based single base chain extension (SBCE) method is a sensitive and reliable assay. It can be readily adapted to an automated, high-throughput genotyping system. [Primer sequences used in this study are available as online supplementary materials at www.genome.org.]
In Situ Li3PS4 Solid‐State Electrolyte Protection Layers for Superior Long‐Life and High‐Rate Lithium‐Metal Anodes (2018)

A thin and adjustable Li<sub>3</sub> PS<sub>4</sub> (LPS) solid-state electrolyte protection layer on the surface of Li is proposed to address the dynamic plating/stripping process of Li metal. The LPS interlayer is formed by an in situ and self-limiting reaction between P<sub>4</sub> S<sub>16</sub> and Li in N-methyl-2-pyrrolidone. By increasing the concentration of P<sub>4</sub> S<sub>16</sub> , the thickness of the LPS layer can be adjusted up to 60 nm. Due to the high ionic conductivity and low electrochemical activity of Li<sub>3</sub> PS<sub>4</sub> , the intimate protection layer of LPS can not only prevent the formation of Li dendrites, but also reduces parasitic side reactions and improves the electrochemical performance. As a result, symmetric cells with the LPS protection layer can deliver stable Li plating/stripping for 2000 h. Full cells assembled with the LPS-protected Li exhibit two times higher capacity retention in Li-S batteries (≈800 mAh g<sup>-1</sup> ) at 5 A g<sup>-1</sup> for over 400 cycles compared to their bare Li counterparts. Furthermore, high rate performances can be achieved with Li-LPS/LiCoO<sub>2</sub> cells, which are capable of cycling at rates as high as 20 C. This innovative and scalable approach to stabilizing the Li anode can serve as a basis for the development of next-generation high-performance lithium-metal batteries.
Anti‐tau antibody reduces insoluble tau and decreases brain atrophy (2015)

Our results indicate that systemically administered anti-tau antibody HJ8.5 significantly decreases insoluble tau, decreases brain atrophy, and improves motor/sensorimotor function in a mouse model of tauopathy. These data further support the idea that anti-tau antibodies should be further assessed as a potential treatment for tauopathies.
Immunologic Purging of Marrow Assessed by PCR before Autologous Bone Marrow Transplantation for B-Cell Lymphoma (1991)

The inability to purge residual lymphoma cells was the most important prognostic indicator in predicting relapse. These results provide evidence of the clinical usefulness of ex vivo purging of autologous bone marrow in the treatment of patients with lymphoma and suggest that the reinfusion of malignant cells in autologous marrow contributes to relapse
Ranibizumab (Lucentis) in neovascular age-related macular degeneration: evidence from clinical trials (2009)

Evidence-based guidelines will help to optimise treatment outcomes with ranibizumab in neovascular AMD.
The role of disulfide bonds in the assembly and function of MD-2 (2003)

MD-2 is a secreted glycoprotein that binds to the extracellular domain of Toll-like receptor 4 (TLR4) and is required for the activation of TLR4 by lipopolysaccharide (LPS). The protein contains seven Cys residues and consists of a heterogeneous collection of disulfide-linked oligomers. To investigate the role of sulfhydryls in MD-2 structure and function, we created 17 single and multiple Cys substitution mutants. All of the MD-2 mutant proteins, including one totally lacking Cys residues, were secreted and stable. SDSPAGE analyses indicated that most Cys residues could participate in oligomer formation and that no single Cys residue was required for oligomerization. Of the single Cys substitutions, only C95S and C105S failed to confer LPS responsiveness on TLR4 when mutant and TLR4 were cotransfected into cells expressing an NF-kappaB reporter plasmid. Surprisingly, substitution of both C95 and C105 partially restored activity. Structural analyses revealed that C95 and C105 formed an intrachain disulfide bond, whereas C95 by itself produced an inactive dimer. In contrast to the cotransfection experiments, only WT MD-2 conferred responsiveness to LPS when secreted proteins were added directly to TLR4 reporter cells. Our data are consistent with a model in which most, possibly all sulfhydryls lie on the surface of a stable MD-2 core structure where they form both intra- and interchain disulfide bridges. These disulfide bonds produce a heterogeneous array of oligomers, including some species that can form an active complex with TLR4.
Modification of rhodamine staining allows identification of hematopoietic stem cells with preferential short-term or long-term bone marrow-repopulating ability. (1995)

We have developed a modified rhodamine (Rho) staining procedure to study uptake and efflux in murine hematopoietic stem cells. Distinct populations of Rho++ (bright), Rho+ (dull), and Rho- (negative) cells could be discriminated. Sorted Rho- cells were subjected to a second Rho staining procedure with the P-glycoprotein blocking agent verapamil (VP). Most cells became Rho positive [Rho-/Rho(VP)+ cells] and some remained Rho negative [Rho-/Rho(VP)- cells]. These cell fractions were characterized by their marrow-repopulating ability in a syngeneic, sex-mismatch transplantation model. Short-term repopulating ability was determined by recipient survival for at least 6 weeks after lethal irradiation and transplantation--i.e., radioprotection. Long-term repopulating ability at 6 months after transplantation was measured by fluorescence in situ hybridization with a Y-chromosome-specific probe, by graft function and recipient survival. Marrow-repopulating cells were mainly present in the small Rho- cell fraction. Transplantation of 30 Rho- cells resulted in 50% radioprotection and > 80% donor repopulation in marrow, spleen, and thymus 6 months after transplantation. Cotransplantation of cells from both fractions in individual mice directly showed that within this Rho- cell fraction, the Rho-/Rho(VP)+ cells exhibited mainly short-term and the Rho-/Rho(VP)- cells exhibited mainly long-term repopulating ability. Our results indicate that hematopoietic stem cells have relatively high P-glycoprotein expression and that the cells responsible for long-term repopulating ability can be separated from cells exhibiting short-term repopulating ability, probably by a reduced mitochondrial Rho-binding capacity.
RBF Neural Network Based SLM Peak-to-Average Power Ratio Reduction in OFDM Systems (2007)

ABSTRACTOne of the major disadvantages of the orthogonal frequency division multiplexing system is high peak-to-average power ratio (PAPR). Selected mapping (SLM) is an efficient distortionless PAPR reduction scheme which selects the minimum PAPR sequence from a group of independent phase rotated sequences. However, the SLM requires explicit side information and a large number of IFFT operations. In this letter we investigate a novel PAPR reduction method based on the radial basis function network and SLM.
Parallel Synthesis of Potent, Pyrazole-Based Inhibitors of Helicobacter pylori Dihydroorotate Dehydrogenase (2002)

The identification of several potent pyrazole-based inhibitors of bacterial dihydroorotate dehydrogenase (DHODase) via a directed parallel synthetic approach is described below. The initial pyrazole-containing lead compounds were optimized for potency against Helicobacter pylori DHODase. Using three successive focused libraries, inhibitors were rapidly identified with the following characteristics: K(i) < 10 nM against H. pylori DHODase, sub-microg/mL H. pylori minimum inhibitory concentration activity, low molecular weight, and >10 000-fold selectivity over human DHODase.
Mice lacking inducible nitric oxide synthase are not resistant to lipopolysaccharide-induced death. (1995)

Nitric oxide produced by cytokine-inducible nitric oxide synthase (iNOS) is thought to be important in the pathogenesis of septic shock. To further our understanding of the role of iNOS in normal biology and in a variety of inflammatory disorders, including septic shock, we have used gene targeting to generate a mouse strain that lacks iNOS. Mice lacking iNOS were indistinguishable from wild-type mice in appearance and histology. Upon treatment with lipopolysaccharide and interferon gamma, peritoneal macrophages from the mutant mice did not produce nitric oxide measured as nitrite in the culture medium. In addition, lysates of these cells did not contain iNOS protein by immunoblot analysis or iNOS enzyme activity. In a Northern analysis of total RNA, no iNOS transcript of the correct size was detected. No increases in serum nitrite plus nitrate levels were observed in homozygous mutant mice treated with a lethal dose of lipopolysaccharide, but the mutant mice exhibited no significant survival advantage over wild-type mice. These results show that lack of iNOS activity does not prevent mortality in this murine model for septic shock.
Lyn Kinase Mediates Cell Motility and Tumor Growth in EGFRvIII-Expressing Head and Neck Cancer (2012)

These findings show that Lyn mediates tumor progression of EGFRvIII-expressing HNSCCs in which strategies to inhibit SFK may represent an effective therapeutic strategy.
Genetics and Assembly Line Enzymology of Siderophore Biosynthesis in Bacteria (2002)

The regulatory logic of siderophore biosynthetic genes in bacteria involves the universal repressor Fur, which acts together with iron as a negative regulator. However in other bacteria, in addition to the Fur-mediated mechanism of regulation, there is a concurrent positive regulation of iron transport and siderophore biosynthetic genes that occurs under conditions of iron deprivation. Despite these regulatory differences the mechanisms of siderophore biosynthesis follow the same fundamental enzymatic logic, which involves a series of elongating acyl-S-enzyme intermediates on multimodular protein assembly lines: nonribosomal peptide synthetases (NRPS). A substantial variety of siderophore structures are produced from similar NRPS assembly lines, and variation can come in the choice of the phenolic acid selected as the N-cap, the tailoring of amino acid residues during chain elongation, the mode of chain termination, and the nature of the capturing nucleophile of the siderophore acyl chain being released. Of course the specific parts that get assembled in a given bacterium may reflect a combination of the inventory of biosynthetic and tailoring gene clusters available. This modular assembly logic can account for all known siderophores. The ability to mix and match domains within modules and to swap modules themselves is likely to be an ongoing process in combinatorial biosynthesis. NRPS evolution will try out new combinations of chain initiation, elongation and tailoring, and termination steps, possibly by genetic exchange with other microorganisms and/or within the same bacterium, to create new variants of iron-chelating siderophores that can fit a particular niche for the producer bacterium.