gebhart/patrepeval huggingface dataset:
Bragg grating formation and germanosilicate fiber photosensitivity (1991)

The refractive index of germanosilicate and germano-aluminosilicate fiber can be increased by a few parts in 10<sup>5</sup> to upwards of five parts in 10<sup>4</sup> by photobleaching the oxygen vacancy defect band of germania. Typically, the fiber core is exposed through the side of the cladding to UV radiation at a wavelength from 240 - 250 nm. Permanent phase gratings are 'written' with a specified period by using a pair of intersecting coherent beams. We have investigated the fiber photosensitivity by monitoring the grating reflectivity and wavelength spectrum during the exposure. The Bragg wavelength shifts as the grating is 'written' due to a small increase in the average refractive index of the core. From these measurements, one can determine the growth and saturation characteristics of the photoinduced changes and study the effects of composition and high temperature hydrogen annealing. We have also measured the polarization sensitivity and thermal stability of gratings and the transient and permanent changes in fiber absorption.
Repair of Bone Tissue Affected by Osteoporosis with Hydroxyapatite-Poly-L-lactide (HAp-PLLA) With and Without Blood Plasma (2005)

The aim of this study is to examine the reparatory ability of the synthetic biomaterial hydroxyapatite-poly-L-lactide (HAp-PLLA), the replacement of alveolar ridge, and rehabilitation of bone defects caused by osteoporosis, in an experimental group of animals. The experiments are performed on syngeneic Sprague Dawley rats. Osteoporosis is induced by glucocorticoids in rats during a 12-week period. After this, the experimental group of animals is divided into five subgroups. An artificial defect is made in the alveolar bone on the left side of the mandible. In one group of animals, the defect is left to heal by itself, while in other groups, pure HAp-PLLA or one mixed with plasma is implanted. The best results are achieved by the implantation of the HAp-PLLA composite biomaterial mixed with autologous plasma. Formation of a new mandibular bone is seen, growing intensely, leading to rapid osteogenesis.
Cycloheximide increases glucocorticoid-stimulated α-ENaC mRNA in collecting duct cells by p38 MAPK-dependent pathway (2003)

Aldosterone and glucocorticoids (GCs) stimulate Na(+) reabsorption in the collecting ducts by increasing the activity of the epithelial Na(+) channel (ENaC). Our laboratory has used Madin-Darby canine kidney-C7 cells to demonstrate that this effect is associated with an increase in alpha-ENaC gene transcription (Mick VE, Itani OA, Loftus RW, Husted RF, Schmidt TJ, and Thomas CP, Mol Endocrinol 15: 575-588, 2001). Cycloheximide (CHX) superinduced the GC-stimulated alpha-ENaC expression in a dose-dependent manner, but had no effect on basal or aldosterone-stimulated alpha-ENaC expression, whereas anisomycin inhibited basal and corticosteroid-stimulated alpha-ENaC expression. The superinduction of alpha-ENaC expression was also seen with hypotonicity, was blocked by RU-38486, and was independent of protein synthesis. CHX had no effect on alpha-ENaC mRNA half-life, confirming that its effect was via an increase in alpha-ENaC transcription. The effect of CHX and hypotonicity on alpha-ENaC expression was abolished by SB-202190, indicating an effect mediated via p38 MAPK. Consistent with this scheme, CHX increased pp38 and MKK6, an upstream activator of p38, stimulated alpha-ENaC promoter activity. These data confirm a model in which CHX activates p38 in Madin-Darby canine kidney-C7 cells to increase alpha-ENaC gene transcription in a GC-dependent manner.
Light-switching excimer probes for rapid protein monitoring in complex biological fluids (2005)

Quantitative protein bioanalysis in complex biological fluids presents considerable challenges in biological studies and disease diagnosis. The major obstacles are the background signals from both the probe and the biological fluids where the proteins reside. We have molecularly engineered light-switching excimer aptamer probes for rapid and sensitive detection of a biomarker protein, platelet-derived growth factor (PDGF). Labeled with one pyrene at each end, the aptamer switches its fluorescence emission from approximately 400 nm (pyrene monomer) to 485 nm (pyrene excimer) upon PDGF binding. This fluorescence wavelength change from monomer to excimer emission is a result of aptamer conformation rearrangement induced by target binding. The excimer probe is able to effectively detect picomolar PDGF in homogeneous solutions. Because the excimer has a much longer fluorescence lifetime (approximately 40 ns) than that of the background (approximately 5 ns), time-resolved measurements were used to eliminate the biological background. We thus were able to detect PDGF in a cell sample quantitatively without any sample pretreatment. This molecular engineering strategy can be used to develop other aptamer probes for protein monitoring. Combined with lifetime-based measurements and molecular engineering, light-switching excimer aptamer probes hold great potential in protein analysis for biomedical studies.
MPW: the Metabolic Pathways Database (1998)

The Metabolic Pathwasy Database (MPW) (www.biobase.com/emphome.html/homepage. html.pags/pathways.html) a derivative of EMP (www.biobase.com/EMP) plays a fundamental role in the technology of metabolic reconstructions from sequenced genomes under the PUMA (www.mcs.anl.gov/home/compbio/PUMA/Production/ ReconstructedMetabolism/reconstruction.html), WIT (www.mcs.anl.gov/home/compbio/WIT/wit.html ) and WIT2 (beauty.isdn.msc.anl.gov/WIT2.pub/CGI/user.cgi) systems. In October 1997, it included some 2800 pathway diagrams covering primary and secondary metabolism, membrane transport, signal transduction pathways, intracellular traffic, translation and transcription. In the current public release of MPW (beauty.isdn.mcs.anl.gov/MPW), the encoding is based on the logical structure of the pathways and is represented by the objects commonly used in electronic circuit design. This facilitates drawing and editing the diagrams and makes possible automation of the basic simulation operations such as deriving stoichiometric matrices, rate laws, and, ultimately, dynamic models of metabolic pathways. Individual pathway diagrams, automatically derived from the original ASCII records, are stored as SGML instances supplemented by relational indices. An auxiliary database of compound names and structures, encoded in the SMILES format, is maintained to unambiguously connect the pathways to the chemical structures of their intermediates.
A usable real-time 3D hand tracker (2002)

This paper presents a computer vision system for tracking human hands. The algorithms used to extract the 3D position, and planar orientation of the hand, and the joint angles of the fingers are described. The combined system is able to track a natural hand at 30 frames per second on a standard workstation with no special image processing hardware other than a frame grabber. The tracker has been used as an interface for navigating around virtual worlds.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Genomic Analysis ofClostridium perfringensBacteriophage φ3626, Which Integrates intoguaAand Possibly Affects Sporulation (2002)

Two temperate viruses, phi3626 and phi8533, have been isolated from lysogenic Clostridium perfringens strains. Phage phi3626 was chosen for detailed analysis and was inspected by electron microscopy, protein profiling, and host range determination. For the first time, the nucleotide sequence of a bacteriophage infecting Clostridium species was determined. The virus belongs to the Siphoviridae family of the tailed phages, the order Caudovirales. Its genome consists of a linear double-stranded DNA molecule of 33,507 nucleotides, with invariable 3'-protruding cohesive ends of nine residues. Fifty open reading frames were identified, which are organized in three major life cycle-specific gene clusters. The genes required for lytic development show an opposite orientation and arrangement compared to the lysogeny control region. A function could be assigned to 19 gene products, based upon bioinformatic analyses, N-terminal amino acid sequencing, or experimental evidence. These include DNA-packaging proteins, structural components, a dual lysis system, a putative lysogeny switch, and proteins that are involved in replication, recombination, and modification of phage DNA. The presence of genes encoding a putative sigma factor related to sporulation-dependent sigma factors and a putative sporulation-dependent transcription regulator suggests a possible interaction of phi3626 with onset of sporulation in C. perfringens. We found that the phi3626 attachment site attP lies in a noncoding region immediately downstream of int. Integration of the viral genome occurs into the bacterial attachment site attB, which is located within the 3' end of a guaA homologue. This essential housekeeping gene is functionally independent of the integration status, due to reconstitution of its terminal codons by phage sequence.
<title>High-density two-dimensional barcode</title> (1991)

We describe a method for encoding information on stacked rows of bar codes. Each row uses one of three sets of codewords. When a single scan crosses data rows the difference in codewords can be used to organize the collected data correctly. The code provides for error detection and error correction both at the level of the codewords and at the whole message level.
Systematic Review of Discography as aDiagnostic Test for Spinal Pain: An Update (2007)

Discography is a useful imaging and pain evaluation tool in identifying a subset of patients with chronic spinal pain secondary to intervertebral disc disorders.
Critical Enhancements of MRI Contrast and Hyperthermic Effects by Dopant‐Controlled Magnetic Nanoparticles (2009)

Doped up: The incorporation of Zn(2+) dopants in tetrahedral sites leads to the successful magnetism tuning of spinel metal ferrite nanoparticles (see picture). (Zn(0.4)Mn(0.6))Fe(2)O(4) nanoparticles exhibit the highest magnetization value among the metal ferrite nanoparticles. Such high magnetism results in the largest MRI contrast effects (r2=860 mm(-1) s(-1)) reported to date and also huge hyperthermic effects.
Molecular Biology of Mammalian Plasma Membrane Amino Acid Transporters (1998)

Molecular biology entered the field of mammalian amino acid transporters in 1990-1991 with the cloning of the first GABA and cationic amino acid transporters. Since then, cDNA have been isolated for more than 20 mammalian amino acid transporters. All of them belong to four protein families. Here we describe the tissue expression, transport characteristics, structure-function relationship, and the putative physiological roles of these transporters. Wherever possible, the ascription of these transporters to known amino acid transport systems is suggested. Significant contributions have been made to the molecular biology of amino acid transport in mammals in the last 3 years, such as the construction of knockouts for the CAT-1 cationic amino acid transporter and the EAAT2 and EAAT3 glutamate transporters, as well as a growing number of studies aimed to elucidate the structure-function relationship of the amino acid transporter. In addition, the first gene (rBAT) responsible for an inherited disease of amino acid transport (cystinuria) has been identified. Identifying the molecular structure of amino acid transport systems of high physiological relevance (e.g., system A, L, N, and x(c)- and of the genes responsible for other aminoacidurias as well as revealing the key molecular mechanisms of the amino acid transporters are the main challenges of the future in this field.
A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species (2008)

ETR-D sequencing allowed accurate, single-step identification of the MTC at the species level. It circumvented the current expensive, time-consuming polyphasic approach. It could be used to depict epidemiology of zoonotic and human tuberculosis, especially in African countries where several MTC species are emerging.
DIETARY INDOLE-3-CARBINOL ALTERS IMMUNE FUNCTIONS IN RATS (2000)

To further elucidate the physiological mechanisms that may contribute to the dichotomy of effect of indole-3-carbinol (I3C) on cancer development, we examined immune functions representative of the three major branches of the immune system in rats fed either a high (150 mg/kg) or low (50 mg/kg) dose of I3C. Animals fed the high dose of I3C daily for 7 wk had significantly reduced natural killer cell activity. In contrast, T-cell-mediated delayed-type hypersensitivity was significantly elevated. Antibody production in response to the antigen keyhole limpet hemocyanin was not significantly altered compared to controls. These results indicate that exposure to I3C may have differential effects on major immune responses. The significance of these immune function alterations in tumor development will require additional investigation of the effects of dietary I3C on immune functions in appropriate tumor models.
Targeting the Human Genome–Microbiome Axis for Drug Discovery: Inspirations from Global Systems Biology and Traditional Chinese Medicine (2012)

Most chronic diseases impairing current human public health involve not only the human genome but also gene-environment interactions, and in the latter case the gut microbiome is an important factor. This makes the classical single drug-receptor target drug discovery paradigm much less applicable. There is widespread and increasing international interest in understanding the properties of traditional Chinese medicines (TCMs) for their potential utilization as a source of new drugs for Western markets as emerging evidence indicates that most TCM drugs are actually targeting both the host and its symbiotic microbes. In this review, we explore the challenges of and opportunities for harmonizing Eastern-Western drug discovery paradigms by focusing on emergent functions at the whole body level of humans as superorganisms. This could lead to new drug candidate compounds for chronic diseases targeting receptors outside the currently accepted "druggable genome" and shed light on current high interest issues in Western medicine such as drug-drug and drug-diet-gut microbial interactions that will be crucial in the development and delivery of future therapeutic regimes optimized for the individual patient.
Insulin-like Growth Factor I Receptor Activated by a Transmembrane Mutation (1995)

We constructed mutant receptors by mutating transmembrane Val922 of the human insulin-like growth factor I receptor (IGF-IR). Assays of receptor kinase and autophosphorylation revealed constitutively augmented tyrosine kinase activity of V922E IGF-IR in both transient and stable expression. The constitutively active tyrosine kinase of this mutant was verified by promoted tyrosine phosphorylation of insulin receptor substrate-1 (IRS-1) in the absence of IGF-I. In CHO cells stably increasing V922E IGF-IR, both IRS-1 phosphorylation and the IRS-1 associated phosphoinositide 3-kinase activity were stimulated in the absence of IGF-I to the level attained by 1 nM IGF-I stimulation of wild-type IGF-IR, whereas the Ras-mitogen-activated protein kinase pathway was not activated under the same condition. In these CHO cells, V922E IGF-IR significantly stimulated glucose uptake but did not promote mitogenesis in the absence of IGF-I. We thus conclude that the V922E mutation of IGF-IR switches on the intrinsic tyrosine kinase and differentially activates the downstream pathways. This mutant is extremely useful in clarifying the turning-on mechanism of IGF-IR as well as the differential roles of individual downstream pathways of receptor tyrosine kinases.
Rapid synthesis of oligosaccharides using an anomeric fluorous silyl protecting groupElectronic supplementary information (ESI) available: experimental data. See http://www.rsc.org/suppdata/cc/b3/b311448a/ (2003)

A fluorous silyl ether tag as protecting group at the anomeric position of sugar acceptors allows rapid synthesis of oligosaccharides by reducing the purification procedures to a simple and fast fluorous solid-phase extraction.
The expression in Saccharomyces cerevisiae of a glucose/xylose symporter from Candida intermedia is affected by the presence of a glucose/xylose facilitator (2008)

Two glucose/xylose transporter genes from Candida intermedia were recently cloned and characterized: GXF1, which encodes a glucose/xylose facilitator; and GXS1, which encodes a glucose/xylose proton symporter. Here we report the functional expression of these transporters in Saccharomyces cerevisiae. While Gxf1p seems to be fully functional in S. cerevisiae, the symporter Gxs1p exhibits very low glucose/xylose transport activity, which could not be ascribed to insufficient production of the protein or incorrect subcellular localization. In addition, co-expression of glucose/xylose facilitators with Gxs1p strongly reduced GXS1 mRNA levels, and consequently symport activity, in glucose-grown, but not in ethanol-grown, cells. The observed decrease in GXS1 transcript levels seems to be related to an enhanced glucose influx mediated by glucose facilitator protein(s), and not to a specific interaction between Gxs1p and other transporters. We found GXS1 mRNA levels to be severely reduced as a result of glucose addition, and we show that this effect takes place at the level of GXS1 mRNA stability. Our results suggest that a decrease in mRNAs encoding high-affinity/active sugar transport systems may be a widespread and conserved mechanism in yeasts, limiting expression of these proteins whenever their activity is dispensable.
Recombinant adenovirus induces antibody response to hepatitis B virus surface antigen in hamsters. (1987)

Recombinant adenoviruses carrying the hepatitis B virus surface antigen coding sequence in the adenovirus E3 region were constructed using DNA from either adenovirus type 5 or an adenovirus type 5 E3-region deletion mutant. Both of these recombinant adenoviruses replicated as efficiently as wild-type adenovirus in all human cells tested, including the human diploid cell strain WI-38. This indicates that insertion of the hepatitis B virus surface antigen gene into the E3 region does not significantly affect viral replication. Human cells infected with these recombinant adenoviruses secreted immunoreactive hepatitis B virus surface antigen. Since a practical small animal model for human adenoviruses was lacking, a hamster model was developed to evaluate the immunogenic potential of these recombinant adenoviruses. Upon intranasal inoculation, both wild-type adenovirus and the adenovirus E3-region deletion mutant replicated in the lungs of these animals and induced an antibody response against adenovirus. Hamsters similarly immunized with the live recombinant adenoviruses produced antibody against both adenovirus and hepatitis B virus surface antigen.
Query-Adaptive Fusion for Multimodal Search (2008)

We conduct a broad survey of query-adaptive search strategies in a variety of application domains, where the internal retrieval mechanisms used for search are adapted in response to the anticipated needs for each individual query experienced by the system. While these query-adaptive approaches can range from meta-search over text collections to multimodal search over video databases, we propose that all such systems can be framed and discussed in the context of a single, unified framework. In our paper, we keep an eye towards the domain of video search, where search cues are available from a rich set of modalities, including textual speech transcripts, low-level visual features, and high-level semantic concept detectors. The relative efficacy of each of the modalities is highly variant between many types of queries. We observe that the state of the art in query-adaptive retrieval frameworks for video collections is highly dependent upon the definition of classes of queries, which are groups of queries that share similar optimal search strategies, while many applications in text and Web retrieval have included many advanced strategies, such as direct prediction of search method performance and inclusion of contextual cues from the searcher. We conclude that such advanced strategies previously developed for text retrieval have a broad range of possible applications in future research in multimodal video search.
Indium nitride (InN): A review on growth, characterization, and properties (2003)

During the last few years the interest in the indium nitride (InN) semiconductor has been remarkable. There have been significant improvements in the growth of InN films. High quality single crystalline InN film with two-dimensional growth and high growth rate are now routinely obtained. The background carrier concentration and Hall mobility have also improved. Observation of strong photoluminescence near the band edge is reported very recently, leading to conflicts concerning the exact band gap of InN. Attempts have also been made on the deposition of InN based heterostructures for the fabrication of InN based electronic devices. Preliminary evidence of two-dimensional electron gas accumulation in the InN and studies on InN-based field-effect transistor structure are reported. In this article, the work accomplished in the InN research, from its evolution to till now, is reviewed. The In containing alloys or other nitrides (AlGaInN, GaN, AlN) are not discussed here. We mainly concentrate on the growth, characterization, and recent developments in InN research. The most popular growth techniques, metalorganic vapor phase epitaxy and molecular beam epitaxy, are discussed in detail with their recent progress. Important phenomena in the epitaxial growth of InN as well as the problems remaining for future study are also discussed.
Src family‐selective tyrosine kinase inhibitor, PP1, inhibits both FcεRI‐ and Thy‐1‐mediated activation of rat basophilic leukemia cells (1997)

Cross-linking of the surface receptor with high affinity for IgE (Fc epsilonRI) by multivalent antigen/immunoglobulin E complexes, as well as aggregation of Thy-1 glycoprotein by monoclonal antibodies lead in rat basophilic leukemia cells, clone RBL-2H3, to tyrosine phosphorylation of several cellular proteins, followed by a release of secretory components. To investigate the molecular mechanisms of Fc epsilonRI- and Thy-1-mediated transmembrane signaling and to map a step at which they converge into a common secretory pathway, we used a novel Src family-selective tyrosine kinase inhibitor, 4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1), and analyzed its inhibitory activity on cell activation. Here we show that in RBL-2H3 cells PP1 demonstrates substrate specificity for a Src family kinase Lyn. In immunocomplex kinase assays in vitro, PP1 inhibited the Lyn kinase activity at nanomolar levels without any effect on Syk kinase activity. However, in RBL cells activated via aggregation of Fc epsilonRI, phosphorylation of both Syk and Lyn kinases was inhibited. Fc epsilonRI- and Thy-1-mediated early (protein-tyrosine phosphorylation) and late (release of beta-hexosaminidase) activation events were similarly affected by PP1. The inhibition was specific for membrane receptor-mediated signaling and was not observed in cells activated by an exposure to pervanadate. The combined data suggest that activation of Lyn is the early activation step at which the Fc epsilonRI- and Thy-1-mediated activation pathways of mast cells and basophils may converge.