gebhart/patrepeval huggingface dataset:
Comparative toxicity and virulence of Escherichia coli clones expressing variant and chimeric Shiga-like toxin type II operons (1995)

Shiga-like toxin (SLT)-producing strains of Escherichia coli are known to cause diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome in humans. The SLTs, particularly those related to type II (SLT-II), are a diverse family of toxins which may have differing in vitro or in vivo properties. To examine the impact of naturally occurring SLT-II sequence variation on the capacity of a given E. coli strain to cause disease, operons encoding four different SLT-II-related toxins, designated SLT-II/O111, SLT-II/OX3a, SLT-II/OX3b, and SLT-II/O48, were cloned in the same orientation in pBluescript. French pressure cell lysates of E. coli DH5 alpha derivatives carrying these plasmids differed markedly in cytotoxicity for Vero cells, with 50% cytotoxic doses ranging from 20 to 328,000/ml. The strains also differed in oral virulence for streptomycin-treated mice, as judged by survival rate and/or median survival time, but virulence did not necessarily correlate with in vitro cytotoxicity. The SLT-II type associated with the lowest oral virulence was SLT-II/O111. Both the overall survival rate and the median survival time of mice challenged with clones producing this toxin were significantly greater than that for mice challenged with a clone producing the closely related SLT-II/OX3a. Experiments with clones carrying chimeric O111/OX3a SLT-II operons indicated that the reduced virulence was associated with an Arg-176-->Gly substitution in the mature A subunit. Clones producing SLT-II/O48 and SLT-II/OX3b had similarly high cytotoxicities for Vero cells, but the latter was more virulent when fed to streptomycin-treated mice, as judged by median survival time. Experiments with clones carrying chimeric O48/OX3b SLT-II operons indicated that the increased virulence was a function of the A subunit of SLT-II/OX3b, which differs from the A subunit of SLT-II/O48 by only two amino acids (Met-4-->Thr and Gly-102-->Asp, respectively). These findings raise the possibility that naturally occurring SLT-II sequence variations may impact directly on the capacity of a given SLT-producing E. coli strain to cause disease.
Articulating a metaphor through user-centered design (1995)

Article Free Access Share on Articulating a metaphor through user-centered design Authors: Hector J. Moll-Carrillo IDEO Product Development, 1527 Stockton Street, San Francisco, CA IDEO Product Development, 1527 Stockton Street, San Francisco, CAView Profile , Gitta Salomon IDEO Product Development, 1527 Stockton Street, San Francisco, CA IDEO Product Development, 1527 Stockton Street, San Francisco, CAView Profile , Matthew Marsh IDEO Product Development, 1527 Stockton Street, San Francisco, CA IDEO Product Development, 1527 Stockton Street, San Francisco, CAView Profile , Jane Fulton Suri IDEO Product Development, 1527 Stockton Street, San Francisco, CA IDEO Product Development, 1527 Stockton Street, San Francisco, CAView Profile , Peter Spreenberg IDEO Product Development, 1527 Stockton Street, San Francisco, CA IDEO Product Development, 1527 Stockton Street, San Francisco, CAView Profile Authors Info & Claims CHI '95: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsMay 1995 Pages 566–572https://doi.org/10.1145/223904.223981Online:01 May 1995Publication History 9citation750DownloadsMetricsTotal Citations9Total Downloads750Last 12 Months36Last 6 weeks4 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 SiteView all FormatsPDF
The Disintegrin Kistrin Inhibits Neurite Extension from Spiral Ganglion Explants Cultured on Laminin (2001)

The influence of laminin-1 (LN) and tenascin-C (TN), extracellular matrix molecules expressed spatially and temporally along the neural growth route from spiral ganglion (SG) neurons to the cochlear sensory cells, was evaluated in cultured SG explants from postnatal day 4 rats. Increasing concentrations of LN resulted in a strong, dose-dependent increase in the length of neurites and in a higher number of neural processes, while varying TN concentrations had relatively minor effects on both parameters. The results suggest differential receptor activation by LN and TN. When explants grown on LN were treated with Kistrin, an inhibitor of the alphavbeta3 integrin, the LN-induced increase in neurite length was reduced in a dose-dependent manner. However, the number of extending neurites was not affected, indicating that different receptors mediate this response, perhaps by increasing neuronal survival.
Risk factors associated with the classification of unspecified and/or unexplained causes of death in an occupational cohort. (1992)

In a matched case-control study of an occupational cohort in East Tennessee, data from the death certificates of 608 cases and controls were abstracted and analyzed in order to investigate possible risk factors associated with the certification on the death certificate of an ill-defined cause of death. There was a very strong association between the ill-defined classification and the certifier, especially if the certifier was a medical examiner (OR = 10.4, 95% CI: 6.0, 18.0).
A Study of Applying Gaze-Tracking Control to Motorized Assistive Devices (2010)

One of the most difficult barriers to alleviating the effects of degenerative diseases is the severe retrogression they cause not only in communication, but also in the ability to manipulate devices designed to restore agency.This project aims to reproduce the muscle control that people with ALS (PALS) have lost, using a lowcost gaze tracker as the input device for a motorized headrest.  Eye movement is often the last remaining method of control in a number of progressive neurodegenerative diseases, and harnessing it as an input device allows a broad range of applications that can benefit users of this technology.The tracker and associated electronics are connected to a motorized headrest, the first of its kind, developed on campus at the University of British Columbia (UBC).  This system uses the Mirametrix S1 eye-gaze tracking device to take a user’s commands and translate them into head movement, which allows for communication through predefined nods or shakes, the ability to self-direct an otherwise immobile individual’s head position, and comfortable selection of a resting head position.The development of our novel user interface demonstrates the utility of eye-gaze tracking as a functional and promising method to restore control to immobilized persons.
Two ParaHox genes,SpLoxandSpCdx, interact to partition the posterior endoderm in the formation of a functional gut (2009)

We report the characterization of the ortholog of the Xenopus XlHbox8 ParaHox gene from the sea urchin Strongylocentrotus purpuratus, SpLox. It is expressed during embryogenesis, first appearing at late gastrulation in the posterior-most region of the endodermal tube, becoming progressively restricted to the constriction between the mid- and hindgut. The physiological effects of the absence of the activity of this gene have been analyzed through knockdown experiments using gene-specific morpholino antisense oligonucleotides. We show that blocking the translation of the SpLox mRNA reduces the capacity of the digestive tract to process food, as well as eliminating the morphological constriction normally present between the mid- and hindgut. Genetic interactions of the SpLox gene are revealed by the analysis of the expression of a set of genes involved in endoderm specification. Two such interactions have been analyzed in more detail: one involving the midgut marker gene Endo16, and another involving the other endodermally expressed ParaHox gene, SpCdx. We find that SpLox is able to bind Endo16 cis-regulatory DNA, suggesting direct repression of Endo16 expression in presumptive hindgut territories. More significantly, we provide the first evidence of interaction between ParaHox genes in establishing hindgut identity, and present a model of gene regulation involving a negative-feedback loop.
Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators (2009)

Genetically encoded calcium indicators (GECIs) can be used to image activity in defined neuronal populations. However, current GECIs produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. We developed a single-wavelength GCaMP2-based GECI (GCaMP3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected GCaMP3 fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of GCaMP2, D3cpVenus and TN-XXL. In Caenorhabditis elegans chemosensory neurons and the Drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with GCaMP3 (4-6-fold). In somatosensory and motor cortical neurons in the intact mouse, GCaMP3 detected calcium transients with amplitudes linearly dependent on action potential number. Long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.
Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPβ (1998)

The two putative ribonucleotide reductase subunits of the Bacillus subtilis bacteriophage SPbeta are encoded by the bnrdE and bnrdF genes that are highly similar to corresponding host paralogs, located on the opposite replication arm. In contrast to their bacterial counterparts, bnrdE and bnrdF each are interrupted by a group I intron, efficiently removed in vivo by mRNA processing. The bnrdF intron contains an ORF encoding a polypeptide similar to homing endonucleases responsible for intron mobility, whereas the bnrdE intron has no obvious trace of coding sequence. The downstream bnrdE exon harbors an intervening sequence not excised at the level of the primary transcript, which encodes an in-frame polypeptide displaying all the features of an intein. Presently, this is the only intein identified in bacteriophages. In addition, bnrdE provides an example of a group I intron and an intein coding sequence within the same gene.
A Simple Technique for Converting CO2 to AMS Target Graphite (1992)

I describe a simple, rapid and inexpensive method for converting CO 2 samples into AMS target graphite. The technique is applicable for both small- and large-scale production facilities. With some modification, the method is suitable for use with very small samples.
Effect of Weight Loss on Upper Airway Collapsibility in Obstructive Sleep Apnea (1991)

Previous investigators have demonstrated in patients with obstructive sleep apnea that weight reduction results in a decrease in apnea severity. Although the mechanism for this decrease is not clear, we hypothesize that decreases in upper airway collapsibility account for decreases in apnea severity with weight loss. To determine whether weight loss causes decreases in collapsibility, we measured the upper airway critical pressure (Pcrit) before and after a 17.4 +/- 3.4% (mean +/- SD) reduction in body mass index in 13 patients with obstructive sleep apnea. Thirteen weight-stable control subjects matched for age, body mass index, gender (all men), and non-REM disordered breathing rate (DBR) also were studied before and after usual care intervention. During non-REM sleep, maximal inspiratory airflow was measured by varying the level of nasal pressure and Pcrit was determined by the level of nasal pressure below which maximal inspiratory airflow ceased. In the weight loss group, a significant decrease in DBR from 83.3 +/- 31.0 to 32.5 +/- 35.9 episodes/h and in Pcrit from 3.1 +/- 4.2 to -2.4 +/- 4.4 cm H2O (p less than 0.00001) was demonstrated. Moreover, decreases in Pcrit were associated with nearly complete elimination of apnea in each patient whose Pcrit fell below -4 cm H2O. In contrast, no significant change in DBR and a minimal reduction in Pcrit from 5.2 +/- 2.3 to 4.2 +/- 1.8 cm H2O (p = 0.031) was observed in the "usual care" group. We conclude that (1) weight loss is associated with decreases in upper airway collapsibility in obstructive sleep apnea, and that (2) the resolution of sleep apnea depends on the absolute level to which Pcrit falls.
Optical performance of holographic kinoforms (1989)

The optical properties of holographic kinoforms are described. It is shown that paraxial designs are not adequate for f/Nos. less than F/10. A nonparaxial design is introduced that retains the high diffraction efficiency of the paraxial designs, yet also produces an unaberrated diffracted wavefront for the design wavelength. Aberration calculations and computer calculations, based on the Huygens-Fresnel principle, of the point spread functions for these elements show the necessity of using the nonparaxial design. Specifications for a surface profile that takes account of the finite thickness of the diffracting surface are given. A model for kinoforms which can be used in optical design programs is proposed.
Prognostic and predictive value of EGFR in head and neck squamous cell carcinoma (2016)

EGFR is an extensively studied biomarker in head and neck squamous cell carcinoma (HNSCC). In this review, we discuss the prognostic and predictive role of EGFR in HNSCC, focusing on the different molecular alterations in specific treatment modalities such as radiotherapy alone (RT), combination of surgery, RT and chemotherapy (CT), EGFR inhibitors. We considered EGFR at different molecular levels: protein expression, protein activation, gene copy number, polymorphisms, mutation, EGFRvIII expression and EGFR ligand expression.Considering RT alone, evidence supports the predictive and prognostic role of high EGFR expression only when evaluated by quantitative assays: this may help select the patients who can mostly benefit from accelerated treatment. Conversely, no predictive biomarkers are available when treatment is a combination of surgery, CT and RT. For this combined treatment, several studies indicate that EGFR expression represents a good prognostic parameter only when measured by a "quantitative" or at least semi-quantitative method. With respect to EGFR inhibitors, neither EGFR expression nor increased gene copy number represent prognostic/predictive factors.If validated, nuclear EGFR, TGFα levels, EGFR phopshorylation and polymorphisms could represent additional prognostic factors in relation to combination of surgery, CT and RT, while EGFR polymorphisms and high amphiregulin levels could have prognostic value in patients treated with EGFR inhibitors.
Changes in the structural complexity of the aged brain (2007)

Structural changes of neurons in the brain during aging are complex and not well understood. Neurons have significant homeostatic control of essential brain functions, including synaptic excitability, gene expression, and metabolic regulation. Any deviations from the norm can have severe consequences as seen in aging and injury. In this review, we present some of the structural adaptations that neurons undergo throughout normal and pathological aging and discuss their effects on electrophysiological properties and cognition. During aging, it is evident that neurons undergo morphological changes such as a reduction in the complexity of dendrite arborization and dendritic length. Spine numbers are also decreased, and because spines are the major sites for excitatory synapses, changes in their numbers could reflect a change in synaptic densities. This idea has been supported by studies that demonstrate a decrease in the overall frequency of spontaneous glutamate receptor-mediated excitatory responses, as well as a decrease in the levels of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid and N-methyl-d-aspartate receptor expression. Other properties such as gamma-aminobutyric acid A receptor-mediated inhibitory responses and action potential firing rates are both significantly increased with age. These findings suggest that age-related neuronal dysfunction, which must underlie observed decline in cognitive function, probably involves a host of other subtle changes within the cortex that could include alterations in receptors, loss of dendrites, and spines and myelin dystrophy, as well as the alterations in synaptic transmission. Together these multiple alterations in the brain may constitute the substrate for age-related loss of cognitive function.
Freeze‐dried platelet‐rich plasma shows beneficial healing properties in chronic wounds (2006)

Fresh platelet concentrates are used in many centers to treat recalcitrant wounds. To extend the therapeutic shelf-life of platelets, we analyzed the wound-healing effects of fresh-frozen and freeze-dried (FD) platelet-rich plasma (PRP) using a diabetic mouse model. Db/db mice with 1.0 cm2 dorsal excisional wounds (n = 15/group) were treated with a single application of FD PRP (1.2 x 10(6) platelets/microL) with or without a stabilization solution, and compared with wounds treated with fresh-frozen, sonicated PRP, and untreated wounds. Granulation tissue area, thickness, and wound size were analyzed 9 days posttreatment. Immunostained sections were quantified for vascularity and proliferation using antiplatelet endothelial cell adhesion molecule I and antiproliferating cell nuclear antigen antibodies. The results showed that all PRP preparations increased granulation tissue formation as assessed by surface coverage, thickness, and angiogenic response, when compared with untreated wounds. In addition, wounds treated with FD PRP, and biochemically stabilized FD PRP, exhibited higher proliferative levels. The possibility to deliver growth factors using platelets, and the potential to extend the shelf-life of platelet concentrates makes freeze-drying methods particularly suitable for enhanced wound care.
Acceptor-bound exciton recombination dynamics in p-type GaN (1995)

Dynamics of the neutral-acceptor-bound exciton transition (the I1 line) in a Mg doped p-type GaN epitaxial layer grown by metalorganic chemical vapor deposition (MOCVD) have been studied by time-resolved photoluminescence emission spectroscopy. Two emission lines in the I1 transition region have been resolved in the time-resolved spectra, possibly due to the existence of two energy states of the Mg impurities after postgrowth thermal annealing. The recombination lifetimes of the acceptor-bound exciton transition have been measured under different conditions including temperature, excitation intensity, and emission energy. From these measurements, a value of about 450 ps for the radiative recombination lifetime has been obtained, which is an important physical quantity for optoelectronic device applications based on GaN.
The Neutrophil: The Unnoticed Threat in Xenotransplantation? (2004)

On the basis of these observations, we should consider the potential for neutrophil-mediated low-grade damage to xenografts emerging as a significant problem when others have been circumvented.
Site‐specific interplay between O‐GlcNAcylation and phosphorylation in cellular regulation (2010)

Ser(Thr)-O-linked beta-N-acetylglucosamine (O-GlcNAc) is a ubiquitous modification of nucleocytoplasmic proteins. Extensive crosstalk exists between O-GlcNAcylation and phosphorylation, which regulates signaling in response to nutrients/stress. The development of novel O-GlcNAc detection and enrichment methods has improved our understanding of O-GlcNAc functions. Mass spectrometry has revealed O-GlcNAc's many interactions with phosphorylation-mediated signaling. However, mechanisms regulating O-GlcNAcylation and phosphorylation are quite different. Phosphorylation is catalyzed by hundreds of distinct kinases. In contrast, in mammals, uridine diphospho-N-acetylglucosamine:polypeptide beta-N-acetylglucosaminyl transferase (OGT) and beta-D-N-acetylglucosaminidase (OGA) are encoded by single highly conserved genes. Both OGT's and OGA's specificities are determined by their transient associations with many other proteins to create a multitude of specific holoenzymes. The extensive crosstalk between O-GlcNAcylation and phosphorylation represents a new paradigm for cellular signaling.
Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast (2007)

Splicing of pre-mRNA is a critical step in mRNA maturation and disturbances cause several genetic disorders. We apply the synthetic tetracycline (tc)-binding riboswitch to establish a gene expression system for conditional tc-dependent control of pre-mRNA splicing in yeast. Efficient regulation is obtained when the aptamer is inserted close to the 5'splice site (SS) with the consensus sequence of the SS located within the aptamer stem. Structural probing indicates limited spontaneous cleavage within this stem in the absence of the ligand. Addition of tc leads to tightening of the stem and the whole aptamer structure which probably prevents recognition of the 5'SS. Combination of more then one aptamer-regulated intron increases the extent of regulation leading to highly efficient conditional gene expression systems. Our findings highlight the potential of direct RNA-ligand interaction for regulation of gene expression.
Interleukin-6 in autoimmune disorders. (1992)

Interleukin-6, a pleiotropic cytokine, appears to play a key role as a physiologically functioning molecule in host defense mechanisms. Previous reports have suggested that dysregulated interleukin-6 production may be involved in lymph node hyperplasia, plasmacytosis, immunoglobulin hyperproduction, thrombocytosis, mesangial cell proliferation and acute phase response, all of which are frequently observed in autoimmune disorders. In this report, we discuss the possible involvement of interleukin-6 in the pathogenesis of a variety of autoimmune diseases and the regulatory mechanism of expression of the interleukin-6 gene.
The VW Scandal and Evolving Emissions Regulations (2016)

In September 2015, Volkswagen (VW) admitted to having programmed nearly 11 million of its diesel vehicles to cheat on tailpipe emissions tests. To put VW?s emissions rigging into a broader context, the authors review the different approaches that the U.S. and Europe have historically taken in regulating automotive emissions and fuel economy. Moreover, they discuss the scandal?s implications for regulatory changes in both regions.
Fast source-level data assignment to dual memory banks (2008)

Due to their streaming nature memory bandwidth is critical for most digital signal processing applications. To accommodate for these bandwidth requirements digital signal processors are typically equipped with dual memory banks that enable simultaneous access to two operands if the data is partitioned appropriately. Fully automated and compiler integrated approaches to data partitioning and memory bank assignment, however, have found little acceptance by DSP software developers. This is partly due to their inflexibility and inability to cope with certain manual data pre-assignments, e.g. due to I/O constraints. In this paper we present a different and more flexible approach, namely source-level dual memory assignment where code generation targets DSP-C, a standardised C language extension widely supported by industrial C compilers for DSPs. Additionally, we present a novel partitioning algorithm based on soft colouring that is more efficient and scalable than the currently known best integer linear programming algorithm, whilst achieving competitive code quality. We have evaluated our scheme on an Analog Devices TigerSHARC DSP and achieved speedups of up to 1.57 on 13 UTDSP benchmarks.