gebhart/patrepeval huggingface dataset:
Mammalian X ray sensitive mutants: a tool for the elucidation of the cellular response to ionizing radiation. (1996)

The complexity of the cellular response to ionizing radiation is indicated by many complementation groups identified among mammalian cells sensitive to ionizing radiation. Genetic complementation analysis of these mutants has been based on cell fusion and complementation of cell killing by X ray, whereas complementation of RDS after gamma rays has led to false results among AT cell lines and could not also be used in rodent cells. Studies on the relationship between cell killing and RDS following gamma irradiation have indicated that (a) RDS is not responsible for cell killing and (b) DNA replication in response to gamma rays is controlled by several genes. Complementation groups established in rodent cell mutants have led to the identification of the gene function in several mutants, and remarkable progress has been made in the understanding of DSB repair and its involvement in V(D)J recombination. The remaining complementation groups of X ray sensitive mutants await the determination of the role of the defective genes in the pathways operating in mammalian cells against ionizing radiation. One group of rodent mutants seems to be defective in the gene homologous to the ATM gene, and so far no more human counterparts have been found among rodent mutants. Newly characterized mutants, V-C8 and UV40, showed combined features of several human disorders, suggesting that their defective gene products could be involved in several pathways handling the response to DNA damage.
Energy-Efficient Resource Allocation With Hybrid TDMA–NOMA for Cellular-Enabled Machine-to-Machine Communications (2019)

Machine-to-machine (M2M) communications, which are considered as an integral part of the Internet of Things (IoT), are being more and more ubiquitous. Meanwhile, due to the advantages of cellular networks (e.g., excellent coverage and mobility/roaming support), cellular-enabled M2M communication is a promising solution for M2M-based applications. However, there are significant challenges in cellular-enabled M2M communications due to the special features of M2M-based applications [e.g., massive concurrent uplink transmissions, small bursty traffic, and the high requirements of energy efficiency (EE)]. On the other hand, non-orthogonal multiple access (NOMA) can simultaneously serve multiple users at the same frequency and time by splitting different users in the power domain and thus increase the number of concurrent connections. In this paper, we propose an energy-efficient resource allocation scheme with hybrid time division multiple access (TDMA)-non-orthogonal multiple access (NOMA) for cellular-enabled M2M networks. First, we configure the user equipments (UEs) as the machine type communication gateways (MTCGs). Then, we propose our time sharing scheme. Next, we formulate the resource allocation problems as a noncooperative game. Finally, in order to obtain the optimal EE of machine type communication devices (MTCDs) and UEs in the game to confirm the power allocation, we transform each non-convex optimization problem into the convex form by using nonlinear fractional programming and solve the transformed problem by Dinkelbach's method and Lagrangian duality theory. The simulation results show that our scheme can dramatically shorten the total transmission time at the cost of a little more total energy when compared to the existing works.
Microfluidic Generation of Acoustically Active Nanodroplets (2012)

A microfluidic approach for the generation of perfluorocarbon nanodroplets as the primary emulsion with diameters as small as 300-400 nm is described. The system uses a pressure-controlled delivery of all reagents and increased viscosity in the continuous phase to drive the device into an advanced tip-streaming regime, which results in generation of droplets in the sub-micrometer range. Such nanodroplets may be appropriate for emerging biomedical applications.
In vivo Probabilistic Structural Atlas of the Inferior and Superior Colliculi, Medial and Lateral Geniculate Nuclei and Superior Olivary Complex in Humans Based on 7 Tesla MRI (2019)

Despite extensive neuroimaging research of primary sensory cortices involved in auditory and visual functions, subcortical structures within these domains, such as the inferior and superior colliculi, the medial and lateral geniculate nuclei and the superior olivary complex, are currently understudied with magnetic resonance imaging (MRI) in living humans. This is because a precise localization of these nuclei is hampered by the limited contrast and sensitivity of conventional neuroimaging methods for deep brain nuclei. In this work, we used 7 Tesla multi-modal (T<sub>2</sub>-weighted and diffusion fractional anisotropy) 1.1 mm isotropic resolution MRI to achieve high sensitivity and contrast for single-subject brainstem and thalamic nuclei delineation. After precise coregistration to stereotactic space, we generated an <i>in vivo</i> human probabilistic atlas of auditory (medial geniculate nucleus, inferior colliculus, and superior olivary complex) and visual (lateral geniculate nucleus and superior colliculus) subcortical nuclei. We foresee the use of this atlas as a tool to precisely identify the location and shape of auditory/visual deep nuclei in research as well as clinical human studies.
Dual roles of the 90-kDa heat shock protein hsp90 in modulating functional activities of the dioxin receptor. Evidence that the dioxin receptor functionally belongs to a subclass of nuclear receptors which require hsp90 both for ligand binding activity and repression of intrinsic DNA binding activity. (1992)

Signal transduction by dioxin (2,3,7,8-tetrachloro-dibenzo-p-dioxin) is mediated by the intracellular dioxin receptor which, in its dioxin-activated state, regulates transcription of target genes encoding drug metabolizing enzymes such as cytochrome P-450IA1 and glutathione S-transferase Ya. Upon binding of dioxin the receptor translocates from the cytoplasm to the nucleus in vivo and is converted from a latent non-DNA binding form to a species which binds to dioxin-responsive positive control elements in vitro. The latent receptor form is associated with an inhibitory protein (the 90-kDa heat shock protein, hsp90), the release of which is necessary to unmask the DNA binding activity of the receptor. Here we have established a protocol to disrupt the hsp90-receptor complex in the absence of ligand. We show that it was possible to covalently cross-link with dioxin only the hsp90-associated form of dioxin receptor. In contrast, the disrupted hsp90-free form of receptor did not form a stable complex with dioxin but bound DNA constitutively. Moreover, we could partially reconstitute the ligand binding activity of the salt-disrupted hsp90-free dioxin receptor by incubation with hsp90-containing reticulocyte lysate but not by incubation with wheat germ lysate which lacks immuno-detectable levels of hsp90. Thus, we demonstrate that the dioxin receptor loses its high affinity ligand binding activity following release of hsp90 and that it is possible to reverse this process. In conclusion, hsp90 appears to play dual roles in the modulation of functional activities of the dioxin receptor: (i) it represses the intrinsic DNA binding activity of the receptor and (ii) it appears to determine the ability of the receptor to assume and/or maintain a ligand binding conformation.
Issues in a submicron Cu interconnect system using liftoff patterning (2002)

A liftoff process has been used to study integration issues associated with submicron copper interconnects. Copper interconnects clad with upper and lower layers of chromium have been patterned at 0.8 and 0.5 mu m dimensions using a silicon template-based tri-layer resist stack. Reliability studies have been performed which indicate that complete cladding of copper lines is necessary in integrated systems. To protect the interconnect sidewalls, blanket PECVD SiON films have been deposited over the lifted-off Cr/Cu/Cr structures. This type of sidewall cladding procedure has been found to be effective even when the lines are entrenched in polyimide layers. Based on these findings, 0.8 mu m double level metal chains have been constructed with entrenched features, fully clad Cr/Cu/Cr interconnects, and lifted-off Ti/AlCu/Ti plugs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biliary transport of glutathione S-conjugate by rat liver canalicular membrane vesicles. (1984)

Transport of S-dinitrophenyl glutathione, a model compound of glutathione S-conjugates, was studied in isolated rat liver canalicular membrane vesicles by a rapid filtration technique. The membrane vesicles exhibited time-dependent uptake of [2-3H]glycine-glutathione conjugate into an osmotically sensitive intravesicular space. Inactivation of vesicle-associated gamma-glutamyltransferase by affinity labeling with L-(alpha-S,5S)-alpha-amino-3-chloro-4,5-dihydro-5-isoxazole-acetic acid had no effect on the initial rate of transport. Chemical analysis revealed that the intact glutathione conjugate accounted for most vesicle-associated radioactivity, reflecting the low transferase activity in the liver and membrane vesicles. The initial rate of transport followed saturation kinetics with respect to conjugate concentrations; an apparent Km of 1.0 mM and Vmax of 1.7 nmol/mg of protein X 20 s were calculated. These results indicate that transport of the glutathione S-conjugate across the canalicular membranes is a carrier-mediated process. Sodium chloride in the transport medium could be replaced by KCl, LiCl, or choline chloride without any changes in transport activity. The rate of conjugate transport was enhanced by a valinomycin-induced K+ diffusion potential (vesicle-inside-positive). The rate of conjugate uptake was enhanced by replacing KCl in the transport medium with K gluconate, providing a less permeant anion, and was reduced by replacing KCl with KSCN, providing a more permeant anion. These data indicate that conjugate transport is electrogenic and involves the transfer of negative charge. Transport of S-dinitrophenyl glutathione was inhibited by S-benzyl glutathione, oxidized glutathione, or reduced glutathione. This transport system in canalicular membranes may function in biliary secretion of glutathione S-conjugates of xenobiotics whose synthesis in hepatocytes requires glutathione S-transferases.
ChemInform Abstract: SYNTHESIS OF (S)‐1‐BENZYLGLYCEROL AND (R)‐BENZYL 2,3‐EPOXYPROPYL ETHER FROM (R)‐1‐BENZYLGLYCEROL (1983)

Abstract (R)‐Glycerin‐1‐benzylether (I) wird über die Stufe des Sulfonats (II) unter Inversion in das Diacetat (III) und dieses nach Methanolyse in den (S)‐Glycerin‐1‐benzylether (I) übergeführt.
Extracellular acidosis elevates carbonic anhydrase IX in human glioblastoma cells via transcriptional modulation that does not depend on hypoxia (2006)

Most solid tumors display extracellular acidosis, which only partially overlaps with hypoxia and induces distinct adaptive changes leading to aggressive phenotype. Although acidosis is mainly attributable to excessive production of lactic acid, it also involves carbonic anhydrase (CA) IX-mediated conversion of CO(2) to an extracellular proton and a bicarbonate ion transported to cytoplasm. CA IX is pre-dominantly expressed in tumors with poor prognosis and its transcription and activity are induced by hypoxia. Here we investigated whether low extracellular pH in absence of hypoxia can influence CA IX expression in cell lines derived from glioblastoma, a tumor type particularly linked with acidosis. Our data show that extracellular acidosis increased the level of CA IX protein, mRNA and the activity of minimal CA9 promoter that contains binding sites for HIF-1 and SP-1 transcription factors. Mutation within each of these two biding sites reduced the promoter activity, but did not eliminate the increase by acidosis. Transfection of HIF-1alpha cDNA produced additive inducing effect with acidosis. Normoxic acidosis was accompanied by HIF-1alpha protein accumulation and transiently increased phosphorylation of ERK1/2. Expression of a dominant-negative mutant of ERK2 reduced the CA9 promoter activity in both standard and acidic conditions. Similar result was obtained by inhibitors of MAPK and PI3K pathways, whose combination completely suppressed CA IX expression and abolished induction by acidosis. Altogether, our results suggest that acidosis increases the CA IX expression via a hypoxia-independent mechanism that operates through modulation of the basic CA9 transcriptional machinery.
Metabolic engineering and classical selection of the methylotrophic thermotolerant yeast Hansenula polymorpha for improvement of high-temperature xylose alcoholic fermentation (2014)

Our results indicate that xylose conversion to ethanol at elevated temperature can be significantly improved in H. polymorpha by combining methods of metabolic engineering and classical selection.
An Empirical Investigation of Trusting Bases in Intitial Trust Formation with National Identity Systems (2005)

Clean, high-yielding routes are described to ruthenium-diiodide catalysts that were recently shown to enable high productivity in olefin metathesis. For the second-generation Grubbs and Hoveyda catalysts (<b>GII</b>: RuCl<sub>2</sub>(H<sub>2</sub>IMes)(PCy<sub>3</sub>)(=CHPh); <b>HII</b>: RuCl<sub>2</sub>(H<sub>2</sub>IMes)(=CHAr), Ar = C<sub>6</sub>H<sub>4</sub>-2-O <i><sup>i</sup></i> Pr), slow salt metathesis is shown to arise from the low lability of the ancillary PCy<sub>3</sub> or ether ligands, which retards access to the four-coordinate intermediate required for efficient halide exchange. To exploit the lability of the first-generation catalysts, the diiodide complex RuI<sub>2</sub>(PCy<sub>3</sub>)(=CHAr) <b>HI-I</b> <sub><b>2</b></sub> was prepared by treating "Grubbs I" (RuCl<sub>2</sub>(PCy<sub>3</sub>)<sub>2</sub>(=CHPh), <b>GI</b>) with NaI, H<sub>2</sub>C=CHAr (<b>1a</b>), and a phosphine-scavenging Merrifield iodide (<b>MF-I</b>) resin. Subsequent installation of H<sub>2</sub>IMes or cyclic (alkyl)(amino)carbene (CAAC) ligands afforded the second-generation iodide catalysts in good to excellent yields. Given the incompatibility of the nitro group with a free carbene, the iodo-Grela catalyst RuI<sub>2</sub>(H<sub>2</sub>IMes)(=CHAr') (<b>nG-I</b> <sub><b>2</b></sub> : Ar' = C<sub>6</sub>H<sub>3</sub>-2-O <i><sup>i</sup></i> Pr-4-NO<sub>2</sub>) was instead accessed by sequential salt metathesis of <b>GI</b> with NaI, installation of H<sub>2</sub>IMes, and finally cross-metathesis with the nitrostyrenyl ether H<sub>2</sub>C=CHAr' (<b>1b</b>), with <b>MF-I</b> as the phosphine scavenger. The bulky iodide ligands improve the selectivity for macrocyclization in ring-closing metathesis.
Comparison of Glycosyltransferase Families Using the Profile Hidden Markov Model (2004)

糖転移酵素ファミリー間の関係とそれらのモチーフについて調べるため、我々はプロファイルHMM法を用いCAZyデータベースの47糖転移酵素ツァミリーを4つのスーパーファミリー (GTS-A、B、C、D) に分類した。その結果得られた分類および、GTS-Aと糖ヌクレオチド合成を触媒する nucleotidylyltransferase ファミリーとの配列類似性から、我々は古代の糖鎖はGTS-Bの祖先型により合成され、GTS-Aは基質である糖ヌクレオチドを合成する遺伝子であったという仮説を提唱した。その後、GTS-Aの祖先型は糖転移酵素へと進化し、それに伴い糖鎖構造の多様性が増していったと考えられる。また、スーパーファミリーはそれぞれ固有の細胞内局在部位で進化し、それにより糖鎖構造の多様性が増していったということが示唆される。
Specific requirement for translation initiation factor 4E or its isoform drives plant host susceptibility to Tobacco etch virus (2014)

We report here a complementation system in Arabidopsis that makes it possible to assess the role of pepper pvr2-eIF4E alleles in susceptibility to TEV. Heterologous complementation experiments showed that the idiosyncratic properties of the 4E and iso4E proteins create a major checkpoint for viral infection of different hosts. This system could be used to screen natural or induced eIF4E alleles to find and study alleles of interest for plant breeding.
InSilico Proteomics System: Integration and Application of Protein and Protein-Protein Interaction Data using Microsoft .NET (2006)

Summary In the last decades, biological databases became the major knowledge resource for researchers in the field of molecular biology. The distribution of information among these databases is one of the major problems. An overview about the subject area of data access and representation of protein and protein-protein interaction data within public biological databases is described. For a comprehensive and consistent way of searching and analysing integrated protein and protein-protein interaction data, the InSilico Proteomics (ISP) project has been initiated. Its three main objectives are (1) to provide an integrated knowledge pool for data investigation and global network analysis functions for a better understanding of a cell’s interactome, (2) employment of public data for plausibility analysis and validation of in-house experimental data and (3) testing the applicability of Microsoft’s .NET architecture for bioinformatics applications. Data integrated into the ISP database can be queried through the Web portal PRIMOS (PRotein Interaction and MOlecule Search) which is freely available at http://biomis.fh-hagenberg.at/isp/primos.
Enhanced histogram normalization in the acoustic feature space (2002)

We describe two methods that aim at normalizing acoustic vectors at the filterbank level such that the test data distribution matches the training data distribution. They enhance the histogram normalization technique proposed earlier by taking care of the variable silence fraction for each speaker, and by rotating the feature space. We report a number of recognition tests under minor (different microphones in training and test, telephone data) and major (office vs. car recordings) mismatch conditions. Both methods give superior performance to the basic histogram normalization approach. The overall improvements in word error rate (WER) range between 6% and 85% relative.
Preparation of Human Immunoglobulin by Caprylic Acid Precipitation (1984)

Caprylic acid was used to precipitate nonimmunoglobulin proteins from human plasma. The crude IgG present in the supernatant (which contained 26-29% of the total protein in terms of absorbance units or 78-87% of IgG by weight) was fractionated on DEAE-cellulose, to yield pure IgG as shown by disc electrophoresis, immunoelectrophoresis and gel filtration. Pure IgG was free of plasmin and plasminogen and did not exhibit any fragmentation or aggregation during storage for periods up to 4 weeks at 40 degrees C, and its anticomplementary activity was low. Antibodies to viral agents were recovered unchanged.
A Tunable Narrow-Band Optical Filter (1947)

Polarization interference filters are described which can have a pass band ranging from a fraction of an angstrom to several hundred angstroms in width. The pass band can be shifted to any desired region of the spectrum. These tunable filters are based on the fixed filters discussed by Lyot and Evans. The transmission band is formed by the superposition of the polarized channel spectra, produced by x-cut plates of quartz or other birefringent media placed between parallel polarizers. The birefringent plates have thicknesses in the ratio 1:2:4 etc. The tuning is accomplished by changing the retardation of successive elements so that transmission maxima in the various channel spectra coincide at the desired wave-length. The retardation change can be made mechanically, for example, by stretching supplemental plastic sheets in series with the filter elements, or can be made electrically by using Kerr cells or crystals with high electro-optic coefficients, such as ammonium dihydrogen phosphate. The additional retardation never has to exceed a full wave at the wave-length of peak transmission. The measured transmission of an experimental filter is shown. The electrical tuning method is particularly adapted to cathode-ray oscillograph presentation of spectra. The filter also has possible application in color reproduction and colorimetry. With a pass band of a half-angstrom line of sight motion of solar prominences could be determined by the use of the Doppler shift of the prominence radiation.
Detection of Parkinson's tremor from EMG signals; a singular spectrum analysis approach (2015)

A robust constrained complex singular spectrum analysis approach for the assessment of Parkinson's tremor by separation of electromyograms (EMGs) is presented in this paper. This approach exploits the expected EMG characteristics of tremor within a subspace of the single channel surface EMG signal measured during the prescribed hand movement including flexion and extension and decomposed using singular spectrum analysis. The results are validated using the tremor signals simultaneously recorded using motion sensors.
Quantifying the spatial pattern of dialect words spreading from a central population (2020)

Some dialect words are shared among geographically distant groups of people without close interaction. Such a pattern may indicate the current or past presence of a cultural centre exerting a strong influence on peripheries. For example, concentric distributions of dialect variants in Japan may be explicable by repeated inventions of new variants at Kyoto, the ancient capital, with subsequent outward diffusion. Here we develop a model of linguistic diffusion within a population network to quantify the distribution of variants created at the central population. Equilibrium distributions of word ages are obtained for idealized networks and for a realistic network of Japanese prefectures. Our model successfully replicates the observed pattern, supporting the notion that a centre-periphery social structure underlies the emergence of concentric patterns. Unlike what has previously been claimed, our model indicates that a novelty bias in linguistic transmission is not always necessary to account for the concentric pattern, whereas some bias in the direction of transmission between populations is needed to be consistent with the observed absence of old words near the central population. Our analysis on the realistic network also suggests that the process of linguistic transmission was not much affected by between-prefecture differences in population size.
Commonwealth legal framework for grants (2012)

No matter what type of grant is being considered, for agencies subject to the Financial Management and Accountability Act 1997 (FMA Act), the FMA Act provides a framework for the proper management of public money and public property (the term 'public money' is defined to mean, among other things, money in the custody or under the control of the Commonwealth: FMA Act, s 5). However, most of the detailed procedures for the management of public money are contained in the FMA Regulations. Grants can also be affected by an agency's Chief Executive's Instructions made under the FMA Act.