gebhart/patrepeval huggingface dataset:
SAP1 is a critical post‐transcriptional regulator of infectivity in malaria parasite sporozoite stages (2010)

Plasmodium salivary gland sporozoites upregulate expression of a unique subset of genes, collectively called the UIS (upregulated in infectious sporozoites). Many UIS were shown to be essential for early liver stage development, although little is known about their regulation. We previously identified a conserved sporozoite-specific protein, SAP1, which has an essential role in Plasmodium liver infection. Targeted deletion of SAP1 in Plasmodium yoelii caused the depletion of a number of selectively tested UIS transcripts in sporozoites, resulting in a complete early liver stage arrest. Here, we use a global gene expression survey to more comprehensively identify transcripts that are affected by SAP1 deletion. We find an effect upon both the transcript abundance of UIS genes, as well as of select genes previously not grouped as UIS. Importantly, we show that the lack of SAP1 causes the specific degradation of these transcripts. Collectively, our data suggest that SAP1 is involved in a selective post-transcriptional mechanism to regulate the abundance of transcripts critical to the infectivity of sporozoites. Although Pysap1(-) sporozoites are depleted of many of these important transcripts, they confer long-lasting sterile protection against wild-type sporozoite challenge in mice. SAP1 is therefore an appealing candidate locus for attenuation of Plasmodium falciparum.
In vivo pathways of degradation and strategies for protein stabilization (1992)

Improper Glycosylation and the Cellular Editing of Nascent Proteins D.A. Cumming. Protein Aggregation In Vivo R. Wetzel. Pathways of Intracellular Protein Degradation in Eukaryotic Cells T.S. Olson, et al. Effects of Aging on Proteins R.W. Gracy. Engineering Dramatic Increases in the Stability of Subtilisin P.N. Bryan. Increased Stability of Mutant Forms of Yeast Cytochrome c D.R. Hickey, et al. Introduction to Formulation of Protein Pharmaceuticals M.A. Hanson, S.K.E. Rouan. PEG Modified Proteins G.E. Francis, et al. Stabilization of Protein Structure by Solvent Additives S.N. Timasheff. Heat-Shock Proteins and their Potential Uses for Pharmaceutical Protein Production in Microorganisms J.M. McCoy. Index.
Drotrecogin Alfa (Activated) in Adults with Septic Shock (2012)

DrotAA did not significantly reduce mortality at 28 or 90 days, as compared with placebo, in patients with septic shock. (Funded by Eli Lilly; PROWESS-SHOCK ClinicalTrials.gov number, NCT00604214.).
Protective murine monoclonal antibodies to Cryptococcus neoformans (1992)

Several murine monoclonal antibodies (MAbs) specific for the capsular glucuronoxylomannan of Cryptococcus neoformans were studied for their capacity to confer protection when passively administered to lethally infected mice. The MAb group studied recognized at least three distinct epitopes and included immunoglobulin M (IgM), IgG3, IgG1, and IgA isotypes. The protection model used A/J and BALB/c mice infected intraperitoneally with 10(8) cryptococci. The MAbs were administered either immediately preceding or, in one experiment, 24 to 48 h prior to infection. Protective efficacy was assessed by the ability of passively administered MAbs to prolong the survival of lethally infected mice. Three IgM MAbs, each of which recognized a distinct epitope, were able to prolong survival of lethally infected mice to different extents. A set of IgM, IgG3, IgG1 and IgA MAbs which utilize the same immunoglobulin gene elements and were derived from the same B-cell clone exhibited significant class differences in protective efficacy with IgA, IgG1 > IgM > IgG3. The results confirm that protective MAbs against C. neoformans capsular polysaccharide exist and strongly suggest that both epitope specificity and isotype are important determinants of protective efficacy.
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy (2017)

Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalized. In particular, sequencing errors in the UMI sequence are often ignored or else resolved in an ad hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single-cell RNA-seq data sets. Reproducibility between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package.
Characterization of the interface between Ge+-implanted crystalline silicon and its thermally grown oxide by spectroscopic ellipsometry (1990)

Using spectroscopic ellipsometry we have studied a series of virgin and germanium-implanted crystalline silicon samples oxidized at 900 and 1000 °C. The thickness of the oxide in the virgin and implanted sample was accurately determined and found to be in agreement with the results previously obtained by single-wavelength ellipsometry. The interface structure between the silicon substrate and the oxide layer of all the samples was investigated in detail. We find that the interposing layer between the oxide and the silicon substrate is composed of a thin layer of crystalline germanium-silicon alloy. A brief discussion on the strain and quantum confinement of the interface that may affect the calculated composition is also presented. The interface thickness was found to be slightly larger to that obtained by high-resolution transmission electron microscopy measurement for samples implanted at higher doses. A plausible explanation for the discrepancy is provided.
A unified gate oxide reliability model (2003)

Existing literature indicates that there are two major mechanisms involved in the time dependent dielectric breakdown (TDDB) of silicon dioxide, and each mechanism dominates under different stress conditions. We suggest that the thermochemical (linear E) model and the hole-induced (1/E) model can be unified in one model. Based on the unified model, a wide range of TDDB data from different sources were examined and shown to behave consistently. Temperature and stress field dependencies are treated together in the model so that the lifetime is a single-valued function of temperature and field. The criterion for screen/ramp breakdown test is also discussed with the model. Furthermore, the unified model accounts for the effect of gross defects, which limit the oxide reliability in real ICs. The model is be used to predict the 10-year lifetime breakdown field or acceptable oxide thickness for a given voltage, and results suggest that further refinements for thin oxide (<5 nm) are necessary.
Macromolecular stereochemistry: the out-of-proportion influence of optically active comonomers on the conformational characteristics of polyisocyanates. The sergeants and soldiers experiment (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMacromolecular stereochemistry: the out-of-proportion influence of optically active comonomers on the conformational characteristics of polyisocyanates. The sergeants and soldiers experimentMark M. Green, Michael P. Reidy, Robert D. Johnson, Graham Darling, Daniel J. O'Leary, and Grant WillsonCite this: J. Am. Chem. Soc. 1989, 111, 16, 6452–6454Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://pubs.acs.org/doi/10.1021/ja00198a084https://doi.org/10.1021/ja00198a084research-articleACS PublicationsRequest reuse permissionsArticle Views3093Altmetric-Citations605LEARN 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 Get e-Alerts
Continuous Electrospinning of Aligned Polymer Nanofibers onto a Wire Drum Collector (2004)

The process of electrospinning produces polymeric fibers with diameters ranging from the micrometer to the nanometer scale. As the fibers are produced, they are usually spun and collected in a random mat lacking structural orientation. In some applications there is interest in parallel alignment of nanofibers to produce structures with unique electrical, optical, and mechanical properties. A simple and successful method for spinning sheets with one centimeter wide strips of aligned nanofibers is presented. The technique uses copper wires spaced evenly in the form of a circular drum as a collector of the electrospun nanofibers. Aligned nanofiber sheets can be collected easily without disturbing the aligned structure, and the method is robust.
Structural Basis for Antioxidant Activity of trans-Resveratrol:  Ab Initio Calculations and Crystal and Molecular Structure (2004)

From the experimental crystal structure and ab initio calculations on resveratrol and its derivatives, structural features of mechanistic importance are described. The molecular structure reveals the relative coplanarity of the trans-stilbene skeleton, and the molecular packing in the solid state shows an extensive hydrogen bond network that elucidates the flip-flop motion of the three hydroxyl groups that alternately form and break H bonds with each of the neighboring phenolic oxygens. The dynamic behavior provoked by the alternation of hydrogen bond formation and breaking can result in the ready mobility of up to three hydrogen atoms per resveratrol molecule that can be transferred to reactive oxidants that are rich in electron density. In addition, theoretical studies confirm the planarity of resveratrol as well as for half of the molecule of a condensation dimeric derivative of resveratrol, trans-sigma-viniferin. Furthermore, these studies show the p-4'-OH group to be more acidic compared to the other two m-OH groups. These features correlate with the biological activity of resveratrol as an antioxidant and support earlier studies showing H-atom transfer to be the dominant mechanism by which phenolic antioxidants intercept free radicals.
Diaryliodonium Salts. A New Class of Photoinitiators for Cationic Polymerization (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiaryliodonium Salts. A New Class of Photoinitiators for Cationic PolymerizationJ. V. Crivello and J. H. W. LamCite this: Macromolecules 1977, 10, 6, 1307–1315Publication Date (Print):November 1, 1977Publication History Published online1 May 2002Published inissue 1 November 1977https://pubs.acs.org/doi/10.1021/ma60060a028https://doi.org/10.1021/ma60060a028research-articleACS PublicationsRequest reuse permissionsArticle Views3161Altmetric-Citations577LEARN 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-Alertsclose Get e-Alerts
Detection threshold of single SPIO‐labeled cells with FIESTA (2005)

MRI of superparamagnetic iron oxide (SPIO)-labeled cells has become a valuable tool for studying the in vivo trafficking of transplanted cells. Cellular detection with MRI is generally considered to be orders of magnitude less sensitive than other techniques, such as positron emission tomography (PET), single photon emission-computed tomography (SPECT), or optical fluorescence microscopy. However, an analytic description of the detection threshold for single SPIO-labeled cells and the parameters that govern detection has not been adequately provided. In the present work, the detection threshold for single SPIO-labeled cells and the effect of resolution and SNR were studied for a balanced steady-state free precession (SSFP) sequence (3D-FIESTA). Based on the results from both theoretical and experimental analyses, an expression that predicts the minimum detectable mass of SPIO (m(c)) required to detect a single cell against a uniform signal background was derived: m(c) = 5v/(K(fsl) x SNR), where v is the voxel volume, SNR is the image signal-to-noise ratio, and K(fsl) is an empirical constant measured to be 6.2 +/- 0.5 x 10(-5) microl/pgFe. Using this expression, it was shown that the sensitivity of MRI is not very different from that of PET, requiring femtomole quantities of SPIO iron for detection under typical micro-imaging conditions (100 microm isotropic resolution, SNR = 60). The results of this work will aid in the design of cellular imaging experiments by defining the lower limit of SPIO labeling required for single cell detection at any given resolution and SNR.
[Ulcerative colitis--colon delivery of 5-aminosalicylic acid]. (1998)

Ulcerative colitis, Crohn's disease and hemorrhage colitis are typical example of colon specific diseases. The targeting of the drugs for these colon specific diseases was attempted by a new technology, where ethylcellulose (EC) was used as pharmaceutical material. Especially, pressure-controlled colon delivery capsule (PCDC) made of EC is a unique system. PCDC was prepared by coating the inner surface of gelatin capsule with water-insoluble polymer, EC. By adjusting the coating thickness of EC membrane to be approximately 40 microns, colon delivery of dug were obtained both in beagle dogs and human volunteers. PCDC containing 5-ASA was prepared and was administered orally to beagle dogs. After administration, 5-ASA appeared into the systemic circulation at 3-5 h which corresponds to the colon arrival time confirmed with sulfasalazine.
Pulmonary CT image registration and warping for tracking tissue deformation during the respiratory cycle through 3D consistent image registration (2008)

Tracking lung tissues during the respiratory cycle has been a challenging task for diagnostic CT and CT-guided radiotherapy. We propose an intensity- and landmark-based image registration algorithm to perform image registration and warping of 3D pulmonary CT image data sets, based on consistency constraints and matching corresponding airway branchpoints. In this paper, we demonstrate the effectivenss and accuracy of this algorithm in tracking lung tissues by both animal and human data sets. In the animal study, the result showed a tracking accuracy of 1.9 mm between 50% functional residual capacity (FRC) and 85% total lung capacity (TLC) for 12 metal seeds implanted in the lungs of a breathing sheep under precise volume control using a pulmonary ventilator. Visual inspection of the human subject results revealed the algorithm's potential not only in matching the global shapes, but also in registering the internal structures (e.g., oblique lobe fissures, pulmonary artery branches, etc.). These results suggest that our algorithm has significant potential for warping and tracking lung tissue deformation with applications in diagnostic CT, CT-guided radiotherapy treatment planning, and therapeutic effect evaluation.
Sketch-Based 3D-Shape Creation for Industrial Styling Design (2007)

While recent decades have seen significant progress in CAD software, current state of the art still appears insufficient when it comes to the styling design of products. This is evidenced by the fact that a-significant portion of early design activities such as concept development and style generation occurs almost exclusively in 2D environments - be it the traditional pen-and-paper environment or its digital equivalents. The authors describe a pen-based modeling system for the styling design of 3D objects. Their system is tailored toward the rapid and intuitive design of styling features such as free-form curves and surfaces. Basic wireframe and surfaces are constructed and modified using the strategy of curve creation, curve modification, surface creation, and finally surface modification
Induction of Autologous Tumor-Specific Cytotoxic T-Lymphocyte Activity Against a Human Renal Carcinoma Cell Line by B7–1 (CD80) Costimulation (1996)

Recently mouse models have shown that expression of costimulatory molecules such as B7–1 on tumor cells can induce tumor-specific immunity, suggesting that tumor cells modified to express costimulatory molecules can be a potential tumor vaccine. To investigate the importance of B7–1 co-stimulation in induction of autologous tumor immunity in humans, we established a renal carcinoma cell line, RCC-1, from a tumor resection and studied the patient's antitumor immune responses in vitro. The RCC-1 cell line con-stitutively expressed major histocompatibility complex (MHC) class I, intercellular adhesion molecule (ICAM)-1, and leukocyte function-associated antigen (LFA)-3 molecules, and MHC class II molecules were induced by interferon-γ (IFN-γ) treatment in vitro. However, neither RCC-1− nor IFN-γ-treated RCC-1 cells expressed B7–1, and both failed to induce T-cell proliferative responses in mixed lymphocyte and tumor cell reaction (MLTR) assays, suggesting that the costimulatory signals provided by cell adhesion molecules such as ICAM-1 and LFA-3 were not sufficient to elicit an antitumor immune response. However, on transfection of the human B7–1 into RCC-1, these cells were able to induce a significant T-cell proliferation in MLTR assays. This T-cell response could be blocked by anti-B7 mAb treatment of the tumor cells. RCC-1B7 cells also induced the generation of tumor-specific cytolytic T lymphocytes to the parent RCC-1 cells in vitro, with little nonspecific cytolysis of an unrelated RCC line, A498, or autologous phytohemagglutinin (PHA) blasts. This specific cytotoxicity could be abrogated by anti-CD8 mAb and complement treatment. In summary, our study indicates that B7–1-CD28 interaction plays a critical role in induction of autologous tumor-specific cytotoxic T lymphocytes (CTLs) in humans, suggesting that the costimulatory molecule-transfected tumor cells could be useful in expanding tumor-specific autologous CTL in vitro for adoptive tumor immunotherapy.
Anatomic Changes in Schlemm's Canal and Collector Channels in Normal and Primary Open-Angle Glaucoma Eyes Using Low and High Perfusion Pressures (2014)

Compensatory mechanisms for transient and short periods of increased pressure appear to be diminished in POAG eyes. Variable response to pressure change in SC and CCs may be a contributing factor to outflow facility change in POAG eyes.
Sorting Nexins – Unifying Trends and New Perspectives (2004)

The sorting nexins (SNXs) are a family of PX domain-containing proteins found in yeast and mammalian cells that have been proposed to regulate intracellular trafficking. Mammalian SNXs have been suggested to function variously in pro-degradative sorting, internalization, endosomal recycling, or simply in endosomal sorting. In yeast, the defining function for these proteins is a regulation of cargo retrieval. Here we examine recent data on the SNX family of proteins and attempt to draw out unifying themes between the work performed in yeast and mammalian systems.
Monocyte chemoattractant protein 1 acts as a T-lymphocyte chemoattractant. (1994)

We have utilized a transendothelial lymphocyte chemotaxis assay to identify and purify a lymphocyte chemoattractant in supernatants of mitogen-stimulated peripheral blood mononuclear cells. Amino acid sequence analysis revealed identity with monocyte chemoattractant protein 1 (MCP-1), a chemoattractant previously thought to be specific for monocytes. Recombinant MCP-1 is chemoattractive for purified T lymphocytes and for CD3+ lymphocytes in peripheral blood lymphocyte preparations. The T-cell response to MCP-1 is dose-dependent and chemotactic, rather than chemokinetic. Phenotyping of chemoattracted T lymphocytes shows they are an activated memory subset. The response to MCP-1 by T lymphocytes can be duplicated in the absence of an endothelial monolayer and the majority of T-lymphocyte chemotactic activity in mitogen-stimulated peripheral blood mononuclear cell supernatants can be neutralized by antibody to MCP-1. Thus, MCP-1 is the major lymphocyte chemoattractant secreted by mitogen-stimulated peripheral blood mononuclear cells and is capable of acting as a potent T-lymphocyte, as well as monocyte, chemoattractant. This may help explain why monocytes and T lymphocytes of the memory subset are always found together at sites of antigen-induced inflammation.
Omeprazole inhibits proliferation and modulates autophagy in pancreatic cancer cells (2011)

Einleitung: Der weltweit zur Behandlung der gastrischen Hyperazidität etablierte Protonenpumpeninhibitor Omeprazol (OMP) wurde kürzlich als Resistenzmodulator für Tumorzellen beschrieben, die molekularen Mechanismen dafür sind jedoch nach wie vor nicht eindeutig bekannt.
Molecular Biomimetics: Building Materials Nature's Way, One Molecule at a Time (2005)

Introduction Inorganic Binding Peptides via Combinatorial Biology Physical Specificity and Molecular Modeling Applications of Engineered Polypeptides as Molecular Erectors Self-Assembly of Inorganic-Binding Polypeptides as Monolayers Morphogenesis of Inorganic Nanoparticles via GEPIs Assembly of Inorganic Nanoparticles via GEPIs Future Prospects and Potential Applications in Nanotechnology
Integration of triple-band GSM antenna switch module using SOI CMOS (2004)

An integrated triple-band GSM antenna switch module, fabricated in RF CMOS on a sapphire substrate, is presented in this paper. The low cost and compact size requirements in wireless and mobile communication systems motivate the continuing integration of the analog portions of the design. The antenna switch die incorporates a FET switch, transmit path filters, and all bias and control circuitry on the same substrate using a 0.5 /spl mu/m CMOS process. A revised version of the die is also proposed, which makes use of an additional copper interconnect layer to reduce die area.