gebhart/patrepeval huggingface dataset:
Modeling optical transitions of Er3+(4f11) in C2 and C3i sites in polycrystalline Y2O3 (2008)

The optical properties of Er3+ in polycrystalline (ceramic), and nanocrystalline forms of cubic (bixbyite) yttrium oxide are modeled based on the absorption spectra obtained between 400 and 1700 nm and the fluorescence spectra observed between 1500 and 1670 nm. Both spectra were obtained at 8 K. The observed crystal-field splitting and the measured intensities of transitions between Stark levels of the L2S+1J multiplet manifolds of Er3+(4f11) in both the C2 and C3i sites of Y2O3 are analyzed in terms of established models. The inversion symmetry of C3i sites limits the observed electronic transitions to magnetic dipole transitions between the I413/2 and I415/2 manifolds. There is no spectroscopic evidence for transitions involving other multiplet manifolds of Er3+ ions in C3i sites. For Er3+ ions in C2 sites, forced electric dipole transitions are allowed between the J+12 Stark levels associated with each manifold. With few exceptions, the crystal-field splitting and the intensities of the transitions between Stark levels are comparable between the nanocrystalline, polycrystalline, and the flame fusion grown crystals of cubic yttrium oxide containing trivalent erbium.
Profiling gene expression ratios of paired cancerous and normal tissue predicts relapse of esophageal squamous cell carcinoma. (2003)

Esophageal squamous cell carcinoma has heterogeneous clinical outcomes that cannot be predicted well using any existing clinical or molecular prognostic factors. Gene expression profiling may enable more precise prediction of the clinical outcome of these patients. We developed a new approach using gene expression ratios of paired cancerous and normal tissue specimens from the same patient to reduce the effects of variation among individuals. Using oligonucleotide microarrays, we analyzed total RNA expression levels corresponding to 12,600 transcript sequences in 24 paired cancerous and normal tissue operative specimens from 12 patients with esophageal squamous cell carcinoma. Hierarchical clustering analysis using gene expression ratios (cancer:normal) divided the 12 patients into two groups; all 7 patients in the first cluster survived without relapse (median follow-up, 483 days), whereas all 5 patients in the second cluster relapsed (median relapse-free survival time, 280 days; log-rank test, P = 0.006). In contrast, clustering either with cancerous tissue alone or with normal tissue alone did not show significant differences in the outcomes. The expressions of a variety of genes related with cell cycle, gene-repair, apoptosis and chemoradiotherpay resistance were up-regulated in the poor prognostic cluster. These results suggest that ratios of paired gene expression profiles may more efficiently predict relapse-free survival of esophageal squamous cell carcinoma than existing prognostic factors or than gene expression profiling with cancerous tissue alone.
A Proposed Standard Time and Control Code for Video-Tape Editing (1970)

A new proposal for an industry standard code for video-tape editing and control is needed to replace the various codes now used, not one of which is compatible with another. The code must contain sufficient information to unambiguously locate any desired video frame within a reel of tape, and should be self-contained on a single audio track. The method used is a biphase space modulation employing 16 bits of control data in each code frame. These control bits can consist of a single 16-bit binary number, two American National Standard Code for Information Interchange (ANSCII) standard alphanumeric characters, four binary-coded decimal (BCD) numbers, or some other arbitrary code combination. Since each code frame is uniquely identified, the control information can be compound coded using successive frames. The effect of changing to a standardized code and the feasibility of code conversion equipment are discussed.
Prolyl 4-hydroxylase is required for viability and morphogenesis in Caenorhabditis elegans (2000)

The genome of Caenorhabditis elegans possesses two genes, dpy-18 and phy-2, that encode α subunits of the enzyme prolyl 4-hydroxylase. We have generated deletions within each gene to eliminate prolyl 4-hydroxylase activity from the animal. The dpy-18 mutant has an aberrant body morphology, consistent with a role of prolyl 4-hydroxylase in formation of the body cuticle. The phy-2 mutant is phenotypically wild type. However, the dpy-18; phy-2 double mutant is not viable, suggesting an essential role for prolyl 4-hydroxylase that is normally accomplished by either dpy-18 or phy-2 . The effects of the double mutation were mimicked by small-molecule inhibitors of prolyl 4-hydroxylase, validating the genetic results and suggesting that C. elegans can serve as a model system for the discovery of new inhibitors.
Neuromuscular Blockade in the Management of Cerebral Palsy (1996)

Neuromuscular blocking agents-45% alcohol, 4% to 6% aqueous phenol, local anesthetics, and botulinum A toxin-have been used for many years in the evaluation and management of spasticity and movement disorders in children with cerebral palsy. Recent reports suggest that longer-acting neuromuscular blocking agents may impact positively on the natural history of dynamic deformity and improve health-related quality of life. This review includes the mechanism of action, techniques, indications, complications, and clinical outcomes associated with these agents.
Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays (2003)

Microarray analysis is a critically important technology for genome-enabled biology, therefore it is essential that the data obtained be reliable. Current software and normalization techniques for microarray analysis rely on the assumption that fluorescent background within spots is essentially the same throughout the glass slide and can be measured by fluorescence surrounding the spots. This assumption is not valid if background fluorescence is spot-localized. Inaccurate estimates of background fluorescence under the spot create a source of error, especially for low expressed genes. We have identified spot-localized, contaminating fluorescence in the Cy3 channel on several commercial and in-house printed microarray slides. We determined through mock hybridizations (without labeled target) that pre-hybridization scans could not be used to predict the contribution of this contaminating fluorescence after hybridization because the change in spot-to-spot fluorescence after hybridization was too variable. Two solutions to this problem were identified. First, allowing 4 h of exposure to air prior to printing on to Corning UltraGAPS slides significantly reduced contaminating fluorescence intensities to approximately the value of the surrounding glass. Alternatively, application of a novel, hyperspectral imaging scanner and multivariate curve resolution algorithms, allowed the spectral contributions of Cy3 signal, glass, and contaminating fluorescence to be distinguished and quantified after hybridization.
PYY in developing murine islet cells: comparisons to development of islet hormones, NPY, and BrdU incorporation. (1996)

Exhaustive characterizations of antisera to the structurally related peptides pancreatic polypeptide (PP), neuropeptide Y (NPY), and peptide YY (PYY) enabled us to establish the developmental pattern of these peptides in rat and mouse pancreas. PYY was the earliest detectable peptide and was present in all early appearing endocrine cell types. NPY appeared later and occurred exclusively in a subpopulation of insulin cells, whereas PP cells arose latest. At the earliest stage studied, all endocrine cells stored PYY. Most of these cells also contained glucagon. Subsequently, the endocrine cells comprised glucagon+PYY cells and glucagon+PYY+insulin cells. Later, cells storing either only insulin or insulin+PYY appeared. Quantitations of the relative numbers of these cell populations during development were consistent with a precursor role of triple-positive (insulin+glucagon+PYY) cells. Moreover, bromodeoxyuridine (BrdU) injections at E15.5 showed that a large percentage of triple-positive cells were in S-phase and therefore were actively dividing, whereas almost no pure insulin cells or insulin+PYY cells synthesized DNA at this time. These results suggest that PYY-positive endocrine cells may represent precursors for mature islet cells.
Glycosylphosphatidylinositol-modified murine B7-1 and B7-2 retain costimulator function (1995)

Glycosylphosphatidylinositol (GPI)-modified variants of murine B7-1 and B7-2 cell surface costimulators were produced via chimerization with alternative GPI-modification signal sequences from decay-accelerating factor (DAF). GPI anchorage was verified by demonstrating phosphatidylinositol-specific phospholipase C (PI-PLC) sensitivity of the chimeric polypeptides in both immunofluorescence/flow-cytometric and immunoprecipitation analyses. The various GPI-modified chimeric B7-1:DAF and B7-2:DAF polypeptides were shown to retain costimulator function, in both an in vitro proliferation assay and an in vivo triggering of cytotoxicity assay. The findings indicate that costimulator function for both B7-1 and B7-2 is not dependent upon native hydrophobic transmembrane anchorage. Moreover, the functionality of the GPI-modified variants in enhancing the immunogenicity of the murine T lymphoma line EL-4 suggests a novel route for generating APC-centered immunotherapeutics, including cellular cancer vaccines, that is based upon protein transfer of GPI-modified costimulators.
A data distributed, parallel algorithm for ray-traced volume rendering (1993)

Article A data distributed, parallel algorithm for ray-traced volume rendering Share on Authors: Kwan Liu Ma View Profile , James S. Painter View Profile , Charles D. Hansen View Profile , Michael F. Krogh View Profile Authors Info & Claims PRS '93: Proceedings of the 1993 symposium on Parallel renderingNovember 1993 Pages 15–22https://doi.org/10.1145/166181.166183Online:01 November 1993Publication History 36citation297DownloadsMetricsTotal Citations36Total Downloads297Last 12 Months4Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
A 27-Amino-Acid Synthetic Peptide Corresponding to the NH2-Terminal Zinc-Binding Domain of Endostatin Is Responsible for Its Antitumor Activity (2005)

The first recombinant endostatin that elicited strong antitumor activity was expressed in Escherichia coli and administered as a suspension. Under these conditions, the protein retained its full antiangiogenic activity. Lack of requirement for a folded structure prompted us to investigate antitumor properties of synthetic peptides corresponding to different regions of endostatin. Here, we show that the entire antitumor, antimigration, and antipermeability activities of endostatin are mimicked by a 27-amino-acid peptide corresponding to the NH2-terminal domain of endostatin. This peptide contains three histidines that are responsible for zinc binding. Mutations of the zinc-binding histidines abolished its antitumor and antimigration activities, but not antipermeability properties.
High-Content Microscopy Identifies New Neurite Outgrowth Regulators (2006)

Neurons, with their long axons and elaborate dendritic arbour, establish the complex circuitry that is essential for the proper functioning of the nervous system. Whereas a catalogue of structural, molecular, and functional differences between axons and dendrites is accumulating, the mechanisms involved in early events of neuronal differentiation, such as neurite initiation and elongation, are less well understood, mainly because the key molecules involved remain elusive. Here we describe the establishment and application of a microscopy-based approach designed to identify novel proteins involved in neurite initiation and/or elongation. We identified 21 proteins that affected neurite outgrowth when ectopically expressed in cells. Complementary time-lapse microscopy allowed us to discriminate between early and late effector proteins. Localization experiments with GFP-tagged proteins in fixed and living cells revealed a further 14 proteins that associated with neurite tips either early or late during neurite outgrowth. Coexpression experiments of the new effector proteins provide a first glimpse on a possible functional relationship of these proteins during neurite outgrowth. Altogether, we demonstrate the potential of the systematic microscope-based screening approaches described here to tackle the complex biological process of neurite outgrowth regulation.
Numerical analysis of sound propagation in rooms using the finite difference time domain method (2006)

Impulse response is an important quantity for room acoustics. To predict the impulse response, several types of calculation methods based on wave theory, such as the boundary element method (BEM), finite element method (FEM) and finite difference method (FDM), are being investigated. Among them, the authors are exploring application of the finite difference time domain (FDTD) method to calculate room sound fields. Using the method, by which the acoustical quantities at discrete grid points of a closed field are successively solved step-by-step according to vector operations, the impulse responses can be obtained directly in a time domain using little computer memory storage. Furthermore, changes of spatial distributions of room sound fields in time can be obtained easily by storing the sound pressure at grid points and displaying them by animation. In this presentation, several examples of the FDTD analyses of room impulse responses are reported and computer animation of their room sound fields is introduced. In addition, examination of the applicability of prediction of the impulse responses by comparison with in situ measurement of a small hall is discussed.
Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria (2001)

In Bacillus subtilis, utilisation of xylose, arabinose and ribose is controlled by the transcriptional factors XylR, AraR and RbsR, respectively. Here we apply the comparative approach to the analysis of these regulons in the Bacillus/Clostridium group. Evolutionary variability of operon structures is demonstrated and operator sites for the main transcription factors are predicted. The consensus sequences for the XylR and RbsR binding sites vary in different subgroups of genomes. The functional coupling of gene clusters and the conservation of regulatory sites allow for detection of non-orthologous gene displacement of ribulose kinase in Enterococcus faecium and Clostridium acetobutylicum. Moreover, candidate catabolite responsive elements found upstream of most pentose-utilising genes suggest CcpA-mediated catabolite repression.
Elliptic Airfoil Stall Analysis With Trailing Edge Slots (2010)

Circulation control (CC) is a high-lift methodology that can be used on a variety of aerodynamic applications. This technology has been in the research and development phase for over sixty years primarily for fixed wing aircraft where the early models were referred to as “blown flaps”. Circulation control works by increasing the near surface velocity of the airflow over the leading edge and/or trailing edge of a lifting surface This phenomenon keeps the boundary layer jet attached to the wing surface thus increasing the lift generated on the surface. The circulation control airflow adds energy to the lift force through conventional airfoil lift production and by altering the circulation of stream lines around the airfoil. For this study, a 10:1 aspect ratio elliptical airfoil with a chord length of 11.8 inches and a span of 31.5 inches was inserted into the West Virginia University Closed Loop Wind Tunnel and was tested at varying wind speeds (80, 100, and 120 feet per second), angle of attack (zero to sixteen degrees), and blowing coefficients, ranging from 0.0006 to 0.0127 depending on plenum pressure. By comparing the non-circulation controlled wing with the active circulation control data, a trend was found as to the influence of circulation control on the stall characteristics of the wing for trailing edge active control. For this specific case, when the circulation control is in use on the 10:1 elliptical airfoil, the stall angle decreased, from eight degrees to six degrees, while providing a 70% increase in lift coefficient. It should be noted that due to the trailing edge location of the circulation control exit jet, a “virtual” camber is created with the free stream air adding length to the overall airfoil. Due to this phenomena, the actual stall angle measured increased from eight degrees on the un-augmented airfoil, to a maximum of twelve degrees.
Interleukins and Contrasuppression Induce Immune Regression of Head and Neck Cancer (1994)

Metastatic squamous cell head and neck cancer was treated in four patients with low-dose cyclophosphamide (to reduce suppressor T-cell activity), indomethacin (to reduce prostaglandins that mediate macrophage-induced immune suppression), zinc (to augment T-cell function via thymulin), and mixed natural interleukins perilymphatically in the neck (as adjuvant for tumor antigen in the region). Three patients responded within 7 days with major tumor regressions progressive during the period of treatment and associated with increased infiltration with lymphocytes and tumor cell lysis. Two showed histologic features of intense delayed hypersensitivity with granulomatous changes. The fourth patient was anergic and failed to respond clinically. Tumor-specific immune response, despite preexisting immunodeficiency, is postulated as the mechanism of the responses in these patients.
Real Time Monitoring of Sickle Cell Hemoglobin Fiber Formation by UV Resonance Raman Spectroscopy (2009)

In sickle cell hemoglobin, individual tetramers associate into long fibers as a consequence of the mutation at the beta6 position. In this study UV resonance Raman spectroscopy is used to monitor the formation of Hb S fibers in real time through aromatic amino acid vibrational modes. The intermolecular contact formed by the mutation site ((1)beta(1)6 Glu-->Val) of one tetramer and the (2)beta(2)85 Phe-(2)beta(2)88 Leu hydrophobic pocket on a different tetramer is observed by monitoring the increase in signal intensity of Phe vibrational modes as a function of time, yielding kinetic progress curves similar to those obtained by turbidity measurements. Comparison of individual spectra collected at early time points (<1000 s) show small Phe intensity changes, which are attributed to weak transient associations of Hb S tetramers during the initial stages of the polymerization process. At later times (1000-2000 s) Phe signal intensity steadily increases because of increasing hydrophobicity of local Phe environment, a consequence of forming more stable (1)beta(1)-(2)beta(2) contacts. Tyr and Trp vibrational modes monitor H-bond strength between critical residues at the alpha(1)beta(2) interface of individual tetramers. Kinetic progress curves generated from these signals exhibit two distinct transitions at 2040 and 7340 s. These transitions, which occur later in time than those detected either by turbidity (1560 s) or by Phe signal intensity (1680 s), are attributed to initial fiber formation and subsequent formation of larger assemblies, such as macrofibers or gels. These results provide molecular insight into the interactions governing Hb S fiber formation.
Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform (2011)

Despite the ever-increasing throughput and steadily decreasing cost of next generation sequencing (NGS), whole genome sequencing of humans is still not a viable option for the majority of genetics laboratories. This is particularly true in the case of complex disease studies, where large sample sets are often required to achieve adequate statistical power. To fully leverage the potential of NGS technology on large sample sets, several methods have been developed to selectively enrich for regions of interest. Enrichment reduces both monetary and computational costs compared to whole genome sequencing, while allowing researchers to take advantage of NGS throughput. Several targeted enrichment approaches are currently available, including molecular inversion probe ligation sequencing (MIPS), oligonucleotide hybridization based approaches, and PCR-based strategies. To assess how these methods performed when used in conjunction with the ABI SOLID3+, we investigated three enrichment techniques: Nimblegen oligonucleotide hybridization array-based capture; Agilent SureSelect oligonucleotide hybridization solution-based capture; and Raindance Technologies' multiplexed PCR-based approach. Target regions were selected from exons and evolutionarily conserved areas throughout the human genome. Probe and primer pair design was carried out for all three methods using their respective informatics pipelines. In all, approximately 0.8 Mb of target space was identical for all 3 methods. SOLiD sequencing results were analyzed for several metrics, including consistency of coverage depth across samples, on-target versus off-target efficiency, allelic bias, and genotype concordance with array-based genotyping data. Agilent SureSelect exhibited superior on-target efficiency and correlation of read depths across samples. Nimblegen performance was similar at read depths at 20× and below. Both Raindance and Nimblegen SeqCap exhibited tighter distributions of read depth around the mean, but both suffered from lower on-target efficiency in our experiments. Raindance demonstrated the highest versatility in assay design.
Quantitative determination of lysozyme‐ligand binding in the solution and gas phases by electrospray ionisation mass spectrometry (2007)

Affinity constants for the binding of a range of substrate and non-substrate oligosaccharides to hen egg white lysozyme were determined by direct observation of the protein.ligand complexes using electrospray ionisation mass spectrometry (ESI-MS) with a chip-based nano-ESI source. The values obtained for a series of beta-1,4-N-acetylglucosamine oligomers (NAGn) were found to be in good agreement with those determined by fluorescence measurement. Oligomers of alpha-1,4-glucose (Glcn), which are believed to bind to lysozyme non-specifically, exhibited a 10(6)- to 10(8)-fold lower affinity for the enzyme. Lysozyme.NAGn complexes displayed an increase in Ka from n=2 to n=4, but then reached a plateau. In contrast non-specific lysozyme.Glcn complexes showed no such trend. Determination of gas-phase complex stability was achieved by quantitative collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) measurements. The collision energy (Ec50) or laser power (IRMPD50) required to dissociate precursor ions to 50% of their original intensity was determined for lysozyme.NAGn and Glcn complexes using the [M+8H]8+ charge state. An excellent correlation between trends in Ka and gas-phase stability was seen for NAGn oligomers bound to lysozyme, whereas no such relationship was observed with the non-specific, weaker lysozyme.Glcn complexes. These results illustrate that ESI-MS can be used to quantify the interactions between lysozyme and oligosaccharides in both the solution and gas phase and that measurement of gas-phase complex stability by CID or IRMPD can provide information about specific solution binding events.