gebhart/patrepeval huggingface dataset:
Tumor-induced mechanical hyperalgesia involves CGRP receptors and altered innervation and vascularization of DsRed2 fluorescent hindpaw tumors (2005)

Functional and anatomical relationships among primary afferent fibers, blood vessels, and cancers are poorly understood. However, recent evidence suggests that physical and biochemical interactions between these peripheral components are important to both tumor biology and cancer-associated pain. To determine the role of these peripheral components in a mouse model of cancer pain, we quantified the change in nerve and blood vessel density within a fibrosarcoma tumor mass using stereological analysis of serial confocal optical sections of immunostained hind paw. To this end we introduced the Discoma coral-derived red fluorescent protein (DsRed2) into the NCTC 2472 fibrosarcoma line using the Sleeping Beauty transposon methodology, thus providing a unique opportunity to visualize tumor-nerve-vessel associations in context with behavioral assessment of tumor-associated hyperalgesia. Tumors from hyperalgesic mice are more densely innervated with calcitonin gene related peptide (CGRP)-immunoreactive nerve fibers and less densely vascularized than tumors from non-hyperalgesic mice. As hyperalgesia increased from Day 5 to 12 post-implantation, the density of protein gene product 9.5 (PGP9.5)-immunoreactive nerves and CD31-immunoreactive blood vessels in tumors decreased, whereas CGRP-immunoreactive nerve density remained unchanged. Importantly, intra-tumor injection of a CGRP1 receptor antagonist (CGRP 8-37) partially blocked the tumor-associated mechanical hyperalgesia, indicating that local production of CGRP may contribute to tumor-induced nociception through a receptor-mediated process. The results describe for the first time the interaction among sensory nerves, blood vessels and tumor cells in otherwise healthy tissue, and our assessment supports the hypothesis that direct tumor cell-axon communication may underlie, at least in part, the occurrence of cancer pain.
GaInNAsSb/GaAs vertical cavity surface-emitting lasers (VCSELs): current challenges and techniques to realize multiple-wavelength laser arrays at 1.55 μm (2008)

Multiple-wavelength laser arrays at 1.55 &mu;m are key components of wavelength division multiplexing (WDM) systems for increased bandwidth. Vertical cavity surface-emitting lasers (VCSELs) grown on GaAs substrates outperform their InP counterparts in several points. We summarize the current challenges to realize continuous-wave (CW) GaInNAsSb VCSELs on GaAs with 1.55 &mu;m emission wavelength and explain the work in progress to realize CW GaInNAsSb VCSELs. Finally, we detail two techniques to realize GaInNAsSb multiple-wavelength VCSEL arrays at 1.55 &mu;m. The first technique involves the incorporation of a photonic crystal into the upper mirror. Simulation results for GaAs-based VCSEL arrays at 1.55 &mu;m are shown. The second technique uses non-uniform molecular beam epitaxy (MBE). We have successfully demonstrated 1x6 resonant cavity light-emitting diode arrays at 850 nm using this technique, with wavelength spacing of 0.4 nm between devices and present these results.
Initiation of protein synthesis from a termination codon. (1990)

We show that the amber termination codon UAG can initiate protein synthesis in Escherichia coli. We mutated the initiation codon AUG of the chloramphenicol acetyltransferase (CAT) gene to UAG (CATam1) and translated mRNA derived from the mutant CAT gene in E. coli S-30 extracts. A full-length CAT polypeptide was synthesized in the presence of tRNA(fMetCUA), a mutant E. coli initiator tRNA which has a change in the anticodon sequence from CAU to CUA. Addition of purified E. coli glutaminyl-tRNA synthetase substantially stimulated synthesis of the CAT polypeptide. Thus, initiation of protein synthesis with UAG and tRNA(fMetCUA) most likely occurs with glutamine and not methionine. The UAG codon also initiates protein synthesis in vivo. To eliminate a weak secondary site of initiation from AUC, the fifth codon, we further mutagenized the CATam1 gene at codons 2 (GAG----GAC) and 5 (AUC----ACC). Transformation of E. coli with the resultant CATam1.2.5 gene yielded transformants that synthesized CAT polypeptide and were resistant to chloramphenicol only when they were also transformed with the mutant tRNA(fMetCUA) gene. Immunoblot analyses and assays for CAT enzyme activity in extracts from transformed cells indicate that initiation from UAG is efficient, 60-70% of that obtained from AUG. Initiation of protein synthesis from UAG using a mutant initiator tRNA allows tightly regulated expression of specific genes. This may be generally useful for overproduction in E. coli and other eubacteria of proteins which are toxic to these cells.
Percutaneous Drainage of Abdominal Abscesses in Pediatric Crohn's Disease (2007)

Percutaneous abscess drainage is a valuable procedure in pediatric patients with Crohn's disease presenting with pelvic or abdominal abscesses (or both). It improves the general status of the patient and allows a less invasive and easier subsequent surgical procedure. Percutaneous abscess drainage should be performed before definitive treatment.
Experiences with a Lightweight Supercomputer Kernel: Lessons Learned from Blue Gene's CNK (2010)

The Petascale era has recently been ushered in and many researchers have already turned their attention to the challenges of exascale computing. To achieve petascale computing two broad approaches for kernels were taken, a lightweight approach embodied by IBM Blue Gene's CNK, and a more fullweight approach embodied by Cray's CNL. There are strengths and weaknesses to each approach. Examining the current generation can provide insight as to what mechanisms may be needed for the exascale generation. The contributions of this paper are the experiences we had with CNK on Blue Gene/P. We demonstrate it is possible to implement a small lightweight kernel that scales well but still provides a Linux environment and functionality desired by HPC programmers. Such an approach provides the values of reproducibility, low noise, high and stable performance, reliability, and ease of effectively exploiting unique hardware features. We describe the strengths and weaknesses of this approach.
Carotenoid Cation Formation and the Regulation of Photosynthetic Light Harvesting (2005)

Photosynthetic light harvesting in excess light is regulated by a process known as feedback deexcitation. Femtosecond transient absorption measurements on thylakoid membranes show selective formation of a carotenoid radical cation upon excitation of chlorophyll under conditions of maximum, steady-state feedback deexcitation. Studies on transgenic Arabidopsis thaliana plants confirmed that this carotenoid radical cation formation is correlated with feedback deexcitation and requires the presence of zeaxanthin, the specific carotenoid synthesized during high light exposure. These results indicate that energy transfer from chlorophyll molecules to a chlorophyllzeaxanthin heterodimer, which then undergoes charge separation, is the mechanism for excess energy dissipation during feedback deexcitation.
Transcriptional regulatory elements in the upstream and intron of the fibroin gene bind three specific factors POU-M1, Bm Fkh and FMBP-1 (1997)

The transcriptional modulator in the fibroin gene intron is composed of multiple octamer-like AT-rich elements, to which several specific DNA-binding proteins named fibroin-modulator-binding proteins (FMBPs) bind. Three major FMBPs in the silk gland were characterized. Two of them (FMBP-2 and -3) were identified as a Fork head homologue (Bm Fkh) and a POU-domain protein (POU-M1) respectively. These factors were expressed in the silk gland with distinct temporal- and spatial-specificities during late larval development as well as during embryogenesis, and did not correlate directly with fibroin gene expression. The other (FMBP-1) appeared to correlate with the expression of the fibroin gene for temporal- and spatial-specificity. These FMBPs also bind to the elements in the upstream modulator. Transcriptional enhancement by both modulators was inhibited by binding competition for these factors with oligonucleotides. These results suggest that expression of the fibroin gene is controlled by co-ordination of these factors with distinct specificities during silk-gland development.
Genetically modified adenoviruses against gliomas (2004)

Oncolytic or tumor-selective adenoviruses are constructed as novel antiglioma therapies. After infection, the invading genetic adenoviral material is activated within the host cell. E1A and E1B adenoviral proteins are expressed immediately. E1A protein interacts with cell cycle regulatory proteins, such as retinoblastoma (Rb), driving the cell into the S phase and ensuing viral replication. The action of E1A stimulates the cellular p53 tumor suppressor system, which results in growth arrest or apoptosis, and halts adenovirus replication. However, adenoviral E1B interacts with p53 protein, preventing the DNA replication process from being abrogated by the induction of p53-mediated apoptosis. It was subsequently hypothesized that mutant adenoviruses that were unable to express wild-type E1A or E1B proteins could not replicate in normal cells with functional Rb or p53 pathways but instead would replicate and kill glioma cells that had defects in the regulation of these tumor suppressor pathways. Mutant E1B adenoviruses have already entered the clinical setting as an experimental treatment for patients with malignant gliomas. Mutant E1A adenoviruses are now in preclinical development as antiglioma therapy. In this review, the authors describe the mechanisms underlying the production of oncolytic adenoviruses, preclinical and clinical experiences with specific oncolytic adenoviruses, and the possibilities of combining mutant oncolytic adenoviruses with gene therapy or conventional therapies for managing malignant gliomas.
Effects of magnesium infusions on magnesium and nitrogen balance during parenteral nutrition. (1982)

The effects of magnesium infusions on urinary and fecal magnesium excretion, serum magnesium and nitrogen balance were examined in seven well-nourished and three nutritionally depleted adult surgical patients receiving total parenteral nutrition. They were maintained on constant nitrogen and caloric intake for 14 +/- 2 days. Magnesium doses ranged from 0 to 664 mg/d and were given in varying crossover patterns. In both groups, urinary magnesium excretion increased as the amount of magnesium infused increased but, at comparable magnesium infusions, depleted patients excreted significantly less magnesium. Renal conservation was most pronounced in well-nourished patients on magnesium-free intake and in depleted patients given 70 mg magnesium daily. Urinary magnesium losses were 40 +/- 5 mg/d and 33 +/- 8 mg/d, respectively, in these two groups. Endogenous fecal magnesium excretion was minimal and ranged from 2 to 38 mg/d. At each level of magnesium intake, serum levels of well-nourished patients were normal. With infusions of less than 200 mg/d, serum magnesium concentrations in depleted subjects averaged 1.6 mg/dl. Reduced urinary magnesium excretion as well as borderline serum levels measured in depleted adults suggest that the magnesium dosage should be higher than that usually recommended during total parenteral nutrition. In both groups a positive correlation between magnesium and nitrogen balance was noted.
Study on the Lane Mark Identification Method in Intelligent Vehicle Navigation (2008)

The intelligent vehicle navigation based on machine vision is the important part to realize Intelligent Transportation System (ITS), and it includes road detection, obstacle detection and motion control. Combining with foreign and domestic latest research trends, in this article, we mainly study the typical method of road detection, and point out the research and development tendency of intelligent vehicle navigation of technology based on the machine vision.
Formation of Alkenes via Degradation of tert -Alkyl Ethers and Alcohols by Aquincola tertiaricarbonis L108 and Methylibium spp (2011)

Bacterial degradation pathways of fuel oxygenates such as methyl tert-butyl and tert-amyl methyl ether (MTBE and TAME, respectively) have already been studied in some detail. However, many of the involved enzymes are still unknown, and possible side reactions have not yet been considered. In Aquincola tertiaricarbonis L108, Methylibium petroleiphilum PM1, and Methylibium sp. strain R8, we have now detected volatile hydrocarbons as by-products of the degradation of the tert-alkyl ether metabolites tert-butyl and tert-amyl alcohol (TBA and TAA, respectively). The alkene isobutene was formed only during TBA catabolism, while the beta and gamma isomers of isoamylene were produced only during TAA conversion. Both tert-alkyl alcohol degradation and alkene production were strictly oxygen dependent. However, the relative contribution of the dehydration reaction to total alcohol conversion increased with decreasing oxygen concentrations. In resting-cell experiments where the headspace oxygen content was adjusted to less than 2%, more than 50% of the TAA was converted to isoamylene. Isobutene formation from TBA was about 20-fold lower, reaching up to 4% alcohol turnover at low oxygen concentrations. It is likely that the putative tert-alkyl alcohol monooxygenase MdpJ, belonging to the Rieske nonheme mononuclear iron enzymes and found in all three strains tested, or an associated enzymatic step catalyzed the unusual elimination reaction. This was also supported by the detection of mdpJK genes in MTBE-degrading and isobutene-emitting enrichment cultures obtained from two treatment ponds operating at Leuna, Germany. The possible use of alkene formation as an easy-to-measure indicator of aerobic fuel oxygenate biodegradation in contaminated aquifers is discussed.
Molecular Evolution of the Human Enteroviruses: Correlation of Serotype with VP1 Sequence and Application to Picornavirus Classification (1999)

Sixty-six human enterovirus serotypes have been identified by serum neutralization, but the molecular determinants of the serotypes are unknown. Since the picornavirus VP1 protein contains a number of neutralization domains, we hypothesized that the VP1 sequence should correspond with neutralization (serotype) and, hence, with phylogenetic lineage. To test this hypothesis and to analyze the phylogenetic relationships among the human enteroviruses, we determined the complete VP1 sequences of the prototype strains of 47 human enterovirus serotypes and 10 antigenic variants. Our sequences, together with those available from GenBank, comprise a database of complete VP1 sequences for all 66 human enterovirus serotypes plus additional strains of seven serotypes. Phylogenetic trees constructed from complete VP1 sequences produced the same four major clusters as published trees based on partial VP2 sequences; in contrast to the VP2 trees, however, in the VP1 trees strains of the same serotype were always monophyletic. In pairwise comparisons of complete VP1 sequences, enteroviruses of the same serotype were clearly distinguished from those of heterologous serotypes, and the limits of intraserotypic divergence appeared to be about 25% nucleotide sequence difference or 12% amino acid sequence difference. Pairwise comparisons suggested that coxsackie A11 and A15 viruses should be classified as strains of the same serotype, as should coxsackie A13 and A18 viruses. Pairwise identity scores also distinguished between enteroviruses of different clusters and enteroviruses from picornaviruses of different genera. The data suggest that VP1 sequence comparisons may be valuable in enterovirus typing and in picornavirus taxonomy by assisting in the genus assignment of unclassified picornaviruses.
EFNS guideline on mild traumatic brain injury: report of an EFNS task force (2002)

In 1999, a Task Force on Mild Traumatic Brain Injury (MTBI) was set up under the auspices of the European Federation of Neurological Societies. Its aim was to propose an acceptable uniform nomenclature for MTBI and definition of MTBI, and to develop a set of rules to guide initial management with respect to ancillary investigations, hospital admission, observation and follow-up.
The Impact of Fatty Acid Oxidation on Energy Utilization: Targets and Therapy (2002)

Utilization of fat as a long-term energy storage vehicle is crucial for the maintenance of cellular metabolism and is under intricate and many times redundant control mechanisms. Aberrations in the control of energy metabolism is apparent in diseases such as diabetes and obesity and is evident early on in patients with impaired glucose tolerance. Insulin resistance has been observed at the level of muscle, liver and adipose tissue. Hyperglycemia is the hallmark of diabetes and is characterized by decreased glucose disposal and increased glucose production, driven by enhanced and uncontrolled fatty acid oxidation (FAO). Mechanisms aimed at limiting the availability of substrates or the activity of processes involved in FAO should provide an immediate reduction in undesired glucose production in these individuals. Numerous targets are available which influence directly the metabolism of fat, including limiting availability of substrate to FAO, inhibiting oxidation of the fatty acid per se, and uncoupling the energy obtained during the oxidation of the fatty acid. These include antilipolytic agents which limit the availability of substrate, FAO inhibitors which limit fatty acid transport (carnitine palmitoyl transferase, CoA sequestration), FAO per se (beta oxidation), and agents which uncouple the energy of FAO (uncoupling proteins, beta3 agonists). These other targets which affect fatty acid metabolism indirectly will be discussed in this review with 184 references.
An electrostatically-actuated MEMS switch for power applications (2002)

This paper presents the design, analysis, fabrication, and testing of an electrostatically-actuated MEMS power switch. The device can be switched electrostatically (20 V), pneumatically (1200 Pa), or through combined actuation. Prototype switches carry currents in excess of 400 mA in either current direction with a contact resistance as low as 14 m/spl Omega/. Their off-state resistance is higher than the 30 M/spl Omega/ limit of the test equipment. Breakdown voltages of 300 V have been achieved across their small air gaps. Their nominal switching time is 20 ms. Extended lifetime testing has not been carried out but our tests to date show that the prototype switches operate more than 4000 cycles without significant degradation in their contact resistance. Finally, a protective switching scheme is proposed to minimize contact wear due to arcing during switch opening and closing.
gprMax: Open source software to simulate electromagnetic wave propagation for Ground Penetrating Radar (2016)

gprMax is open source software that simulates electromagnetic wave propagation, using the Finite-Difference Time-Domain (FDTD) method, for the numerical modelling of Ground Penetrating Radar (GPR). gprMax was originally developed in 1996 when numerical modelling using the FDTD method and, in general, the numerical modelling of GPR were in their infancy. Current computing resources offer the opportunity to build detailed and complex FDTD models of GPR to an extent that was not previously possible. To enable these types of simulations to be more easily realised, and also to facilitate the addition of more advanced features, gprMax has been redeveloped and significantly modernised. The original C-based code has been completely rewritten using a combination of Python and Cython programming languages. Standard and robust file formats have been chosen for geometry and field output files. New advanced modelling features have been added including: an unsplit implementation of higher order Perfectly Matched Layers (PMLs) using a recursive integration approach; diagonally anisotropic materials; dispersive media using multi-pole Debye, Drude or Lorenz expressions; soil modelling using a semi-empirical formulation for dielectric properties and fractals for geometric characteristics; rough surface generation; and the ability to embed complex transducers and targets. Program title: gprMax Catalogue identifier: AFBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFBG_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU GPL v3 No. of lines in distributed program, including test data, etc.: 627180 No. of bytes in distributed program, including test data, etc.: 26762280 Distribution format: tar.gz Programming language: Python. Computer: Any computer with a Python interpreter and a C compiler. Operating system: Microsoft Windows, Mac OS X, and Linux. RAM: Problem dependent Classification: 10. External routines: Cython[1], h5py[2], matplotlib[3], NumPy[4], mpi4py[5] Nature of problem: Classical electrodynamics Solution method: Finite-Difference Time-Domain (FDTD) Running time: Problem dependent References: Cython, http://www.cython.org h5py, http://www.h5py.org matplotlib, http://www.matplotlib.org NumPy, http://www.numpy.org mpi4py, http://mpi4py.scipy.org
Xylose Monomer and Oligomer Yields for Uncatalyzed Hydrolysis of Sugarcane Bagasse Hemicellulose at Varying Solids Concentration (2002)

Pretreatment is an essential, but expensive, step in biologically converting biomass to fuels and chemicals, and acids added or released during the reaction hydrolyze hemicellulose to sugars and expose cellulose for enzymatic digestion with good yields. Pretreatment by liquid flow past solids increases hemicellulose removal yields particularly at higher flow rates, but current first-order homogeneous kinetic models indicate that the amount of water should not be important. However, these models suffer from inconsistencies, and the effect of varying sugarcane bagasse concentrations on xylose monomer and oligomer yields was experimentally measured in a batch reactor without adding acids or other chemicals at 200 °C. A greater drop in pH was observed at higher solids concentrations, as anticipated. Furthermore, only about 7−13% of the total xylose recovered in solution was as monomers at the maximum total xylose yield point, with the rest being oligomers, and although monomer yields could be increased at longer hold times, overall yields declined. These results and the general yield versus time profiles are consistent with the predictions of first-order models. However, a possible trend toward greater yields was observed at lower solids concentrations, but a paired difference test showed that these yield differences were only statistically significant between the extremes in biomass concentrations.