gebhart/patrepeval huggingface dataset:
Prophage Carriage and Diversity within Clinically Relevant Strains of Clostridium difficile (2012)

Prophages are encoded in most genomes of sequenced Clostridium difficile strains. They are key components of the mobile genetic elements and, as such, are likely to influence the biology of their host strains. The majority of these phages are not amenable to propagation, and therefore the development of a molecular marker is a useful tool with which to establish the extent and diversity of C. difficile prophage carriage within clinical strains. To design markers, several candidate genes were analyzed including structural and holin genes. The holin gene is the only gene present in all sequenced phage genomes, conserved at both terminals, with a variable mid-section. This allowed us to design two sets of degenerate PCR primers specific to C. difficile myoviruses and siphoviruses. Subsequent PCR analysis of 16 clinical C. difficile ribotypes showed that 15 of them are myovirus positive, and 2 of them are also siphovirus positive. Antibiotic induction and transmission electron microscope analysis confirmed the molecular prediction of myoviruses and/or siphovirus presence. Phylogenetic analysis of the holin sequences identified three groups of C. difficile phages, two within the myoviruses and a divergent siphovirus group. The marker also produced tight groups within temperate phages that infect other taxa, including Clostridium perfringens, Clostridium botulinum, and Bacillus spp., which suggests the potential application of the holin gene to study prophage carriage in other bacteria. This study reveals the high incidence of prophage carriage in clinically relevant strains of C. difficile and correlates the molecular data to the morphological observation.
Role of Hydrophilic Residues in Proton Transfer during Catalysis by Human Carbonic Anhydrase II (2008)

Catalysis by the zinc metalloenzyme human carbonic anhydrase II (HCA II) is limited in maximal velocity by proton transfer between His64 and the zinc-bound solvent molecule. Asn62 extends into the active site cavity of HCA II adjacent to His64 and has been shown to be one of several hydrophilic residues participating in a hydrogen-bonded solvent network within the active site. We compared several site-specific mutants of HCA II with replacements at position 62 (Ala, Val, Leu, Thr, and Asp). The efficiency of catalysis in the hydration of CO 2 for the resulting mutants has been characterized by (18)O exchange, and the structures of the mutants have been determined by X-ray crystallography to 1.5-1.7 A resolution. Each of these mutants maintained the ordered water structure observed by X-ray crystallography in the active site cavity of wild-type HCA II; hence, this water structure was not a variable in comparing with wild type the activities of mutants at residue 62. Crystal structures of wild-type and N62T HCA II showed both an inward and outward orientation of the side chain of His64; however, other mutants in this study showed predominantly inward (N62A, N62V, N62L) or predominantly outward (N62D) orientations of His64. A significant role of Asn62 in HCA II is to permit two conformations of the side chain of His64, the inward and outward, that contributes to maximal efficiency of proton transfer between the active site and solution. The site-specific mutant N62D had a mainly outward orientation of His64, yet the difference in p K a between the proton donor His64 and zinc-bound hydroxide was near zero, as in wild-type HCA II. The rate of proton transfer in catalysis by N62D HCA II was 5% that of wild type, showing that His64 mainly in the outward orientation is associated with inefficient proton transfer compared with His64 in wild type which shows both inward and outward orientations. These results emphasize the roles of the residues of the hydrophilic side of the active site cavity in maintaining efficient catalysis by carbonic anhydrase.
Mining program workflow from interleaved traces (2010)

Successful software maintenance is becoming increasingly critical due to the increasing dependence of our society and economy on software systems. One key problem of software maintenance is the difficulty in understanding the evolving software systems. Program workflows can help system operators and administrators to understand system behaviors and verify system executions so as to greatly facilitate system maintenance. In this paper, we propose an algorithm to automatically discover program workflows from event traces that record system events during system execution. Different from existing workflow mining algorithms, our approach can construct concurrent workflows from traces of interleaved events. Our workflow mining approach is a three-step coarse-to-fine algorithm. At first, we mine temporal dependencies for each pair of events. Then, based on the mined pair-wise tem-poral dependencies, we construct a basic workflow model by a breadth-first path pruning algorithm. After that, we refine the workflow by verifying it with all training event traces. The re-finement algorithm tries to find out a workflow that can interpret all event traces with minimal state transitions and threads. The results of both simulation data and real program data show that our algorithm is highly effective.
BARD1 is necessary for ubiquitylation of nucleosomal histone H2A and for transcriptional regulation of estrogen metabolism genes (2018)

Missense mutations that disrupt the RING domain of the tumor suppressor gene <i>BRCA1</i> lead to increased risk of breast and ovarian cancer. The BRCA1 RING domain is a ubiquitin ligase, whose structure and function rely critically on forming a heterodimer with BARD1, which also harbors a RING domain. The function of the BARD1 RING domain is unknown. In families severely affected with breast cancer, we identified inherited BARD1 missense mutations Cys53Trp, Cys71Tyr, and Cys83Arg that alter three zinc-binding residues of the BARD1 RING domain. Each of these mutant BARD1 proteins retained the ability to form heterodimeric complexes with BRCA1 to make an active ubiquitin ligase, but the mutant BRCA1/BARD1 complexes were deficient in binding to nucleosomes and in ubiquitylating histone H2A. The BARD1 mutations also caused loss of transcriptional repression of BRCA1-regulated estrogen metabolism genes <i>CYP1A1</i> and <i>CYP3A4</i>; breast epithelial cells edited to create heterozygous loss of <i>BARD1</i> showed significantly higher expression of <i>CYP1A1</i> and <i>CYP3A4</i> Reintroduction of wild-type <i>BARD1</i> into these cells restored <i>CYP1A1</i> and <i>CYP3A4</i> transcription to normal levels, but introduction of the cancer-predisposing <i>BARD1</i> RING mutants failed to do so. These results indicate that an intact BARD1 RING domain is critical to BRCA1/BARD1 binding to nucleosomes and hence to ubiquitylation of histone H2A and also critical to transcriptional repression of BRCA1-regulated genes active in estrogen metabolism.
The Utilization of Academic Policy Research Assistance: The University and State Government (1995)

補正完畢
Development of a duplex one-step RT-qPCR assay for the simultaneous detection of Apple scar skin viroid and plant RNA internal control (2015)

Apple scar skin viroid (ASSVd) is an important quarantine pathogen for international movement of pome germplasm as it can cause significant damage to pip fruit. A one-step real-time RT-PCR assay was developed for the rapid and sensitive detection of ASSVd. The assay was able to detect a wide range of ASSVd isolates and was highly specific compared to a published conventional RT-PCR. The detection limit of the new assay was estimated to be about 100 copies of the ASSVd target. The assay can be run as a duplex with the nad5 internal control primers and probe to simultaneously check the PCR competency of the samples therefore reducing the risk of false negatives. It is expected that this real-time RT-PCR assay will facilitate efficient testing for ASSVd by regulatory services, and will also have a wider use for the general detection of ASSVd in a range of pip fruit.
CO Impact on the Stability Properties of PtxCoy Nanoparticles in PEM Fuel Cell Anodes: Mechanistic Insights (2011)

ENERGIE+KIC:PGE
Real time monitoring of the chemistry of hydroxylamine nitrate and iron as surrogates for nuclear materials processing (2019)

The separation of actinides in aqueous solution often involves changes in redox chemistry achieved by reagents such as hydroxylamine nitrate (HAN). Thus, in situ monitoring of the chemistry of HAN in contact with plutonium and neptunium in concentrated nitric acid at 35°C is important for the efficacy of Pu-238 extraction. A spectroscopic method of following the chemistry of HAN in contact with iron (as a simulant for plutonium) was developed, using a quantum cascade laser-attenuated total reflectance (QCL-ATR) system. The mid-infrared (3.67–12.5 μm) was chosen for its ability to distinguish the molecular vibrations of analytes and exclude the background absorption of the concentrated HNO3 matrix. The concentrations of chemical species found in the reaction were drawn from the collected QCL power data using Beer’s law after a baseline correction. These data were qualitatively compared to a kinetic rate model based on a simplified reaction mechanism. The QCL-ATR method can help determine the areas of stability of HAN, nitrate/nitrite interactions, and assist process control of actinide separations.
ZOOM Lite: next-generation sequencing data mapping and visualization software (2010)

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/.
Highly Concentrated Graphene Solutions via Polymer Enhanced Solvent Exfoliation and Iterative Solvent Exchange (2010)

Efficient graphene exfoliation in a nontraditional solvent, ethanol, is achieved through the addition of a stabilizing polymer, ethyl cellulose. Iterative solvent exchange is further demonstrated as a rapid, room-temperature, ultracentrifugation-free approach to concentrate the graphene solution to a level exceeding 1 mg/mL. The outstanding processability and electrical properties of these graphene inks are verified through the realization of aligned graphene-polymer nanocomposites and transparent conductive graphene thin films.
Development of emotional tremor-based vision system (2009)

We aim to investigate biological function of emotional bodily movements while building a robot in the sense of survival. In this particular paper, we build a novel active vision system which detects weak signals by generating tremor actively. Proposed active vision system consists of a noise generator and a neural system. As a noise generator, we use motors with a decentered weight. And as a neural system in order to detect visual signals, we use ensemble of FitzHugh-Nagumo neurons. We first show that our robotic platform can generate several kinds of tremors; tremor around 40 Hz, 50 Hz, and tremor which does not involve specific peak in its power spectrum. And, in order to evaluate the effect of tremor, we prepare clear-films as visual stimuli which move aperiodically in a dark environment. We show that as a result of sensory noise induced by tremor, and as a result of stochastic resonance, neural system successfully detects movements of clear films.
Nodular defect planarization for improved multilayer mirror laser resistance (2013)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text C. J. Stolz, J. E. Wolfe, P. B. Mirkarimi, J. A. Folta, J. J. Adams, M. G. Menor, N. E. Teslich, R. Soufli, C. Menoni, and D. Patel, "Nodular defect planarization for improved multilayer mirror laser resistance," in Optical Interference Coatings, M. Tilsch and D. Ristau, eds., OSA Technical Digest (online) (Optica Publishing Group, 2013), paper FA.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Effect of yoghurt containing Bifidobacterium lactis Bb12®on faecal excretion of secretory immunoglobulin A and human beta-defensin 2 in healthy adult volunteers (2011)

Bifidobacterium lactis Bb12® increased secretory IgA output in faeces. This property may explain the ability of probiotics to prevent gastrointestinal and lower respiratory tract infections.
Ultrasonic Flaw Detection of Special Composite Squeeze Castings (1972)

The special composite squeeze castings, being develped under Daido's research, for punching dies and cutters are those things having chiefly tool steel of mother material on which a tungsten carbide hardened layer of from 1 to 5mm is squeeze cast on its one side.The harmful flaws are inclined to grow in the said layer and the boundry layer between mother material and the former layer.The thickness of hardened layer is necessary to be cast as thick as appointed thickness.And these are important tasks to detect flaws and to measure the thickness of the hardened layer under non-destructive method.For these, it is now possible to detect flaws in the layer and in the boundry layer by ultrasonic wave double crystal probe method. Furthermore, a new technique which enables us to detect the thickness of the hardened layer was invented using the same method.After repetition of various checking experiments of detecting flaws and thickness we were able to confirm that the practical use is high enough with precise flaws detecting conditions and therefore, the report is described hereunder.
Subunit composition and quantitative importance of GABAAreceptor subtypes in the cerebellum of mouse and rat (2003)

In cerebellum, 13 different GABA(A) receptor subunits are expressed. The number of different receptor subtypes formed in this tissue, their subunit composition and their quantitative importance so far has not been determined. In the present study, immunodepletion by immunoaffinity chromatography, as well as immunoprecipitation and western blot analysis was performed using 13 different subunit-specific antibodies to provide an overview on the subunit composition and abundance of GABA(A) receptor subtypes in mouse and rat cerebellum. Results obtained indicate that alpha1betaxgamma2, alpha1alpha6betaxgamma2, alpha6betaxgamma2, alpha6betaxdelta and alpha1alpha6betaxdelta are the major GABA(A) receptor subtypes present in the cerebellum. In addition, small amounts of alpha1betaxdelta receptors and a series of minor receptor subtypes containing alpha2, alpha3, alpha4, alpha5, gamma1 or gamma3 subunits are also present in the cerebellum. Whereas the abundance of alpha1alpha6betaxgamma2, alpha6betaxdelta and alpha1alpha6betaxdelta receptors is different in mouse and rat cerebellum, that of other receptors is quite similar in these tissues. Data obtained for the first time provide an overview on the GABA(A) receptor subtypes present in the cerebellum and represent the basis for further studies investigating changes in receptor expression and composition under pathological conditions.
ChemInform Abstract: HOMOLYTISCHE AROMATISCHE SUBSTITUTION HETEROCYCLISCHER VERBINDUNGEN 1. MITT. ABBAU VON PHENYLAZOTRIPHENYLMETHAN IN THIOPHEN (1970)

Abstract Bei der Reaktion der Azoverbindung (I) mit Thiophen (II) entstanden die Verbindungen (III) bis (VIII).
Change of ultrasonic attenuation and microstructure evolution during creep of nickel base superalloy (2003)

Electromagnetic acoustic resonance (EMAR) is a contactless resonant method with an electromagnetic acoustic transducer (EMAT). This method is free from extra energy losses, resulting in the measurement of intrinsic ultrasonic attenuation in solids. In this study, the EMAR was applied to detect the creep damage of a Ni base superalloy (Waspaloy). The material was exposed to the temperature of 1073K at various stresses. We measured ultrasonic attenuation for 1-6-MHz frequency range as the creep advanced. The attenuation coefficient exhibits much larger sensitivity to the damage accumulation than the velocity. It shows a maximum around 35% of the whole life, which is interpreted as resulting from microstructural changes, especially, dislocation mobility. This is supported by TEM observations for dislocation structure. This technique has a potential to assess the damage advance and to predict the creep life of metals.
Stochastic queueing-theory approach to human dynamics (2012)

Recently, numerous studies have shown that human dynamics cannot be described accurately by exponential laws. For instance, Barabási [Nature (London) 435, 207 (2005)] demonstrates that waiting times of tasks to be performed by a human are more suitably modeled by power laws. He presumes that these power laws are caused by a priority selection mechanism among the tasks. Priority models are well-developed in queueing theory (e.g., for telecommunication applications), and this paper demonstrates the (quasi-)immediate applicability of such a stochastic priority model to human dynamics. By calculating generating functions and by studying them in their dominant singularity, we prove that nonexponential tails result naturally. Contrary to popular belief, however, these are not necessarily triggered by the priority selection mechanism.
Local recovery of a piecewise constant anisotropic conductivity in EIT on domains with exposed corners (2022)

We study the local recovery of an unknown piecewise constant anisotropic conductivity in EIT (electric impedance tomography) on certain bounded Lipschitz domains $Ω$ in $\mathbb{R}^2$ with corners. The measurement is conducted on a connected open subset of the boundary $\partialΩ$ of $Ω$ containing corners and is given as a localized Neumann-to-Dirichlet map. The above unknown conductivity is defined via a decomposition of $Ω$ into polygonal cells. Specifically, we consider a parallelogram-based decomposition and a trapezoid-based decomposition. We assume that the decomposition is known, but the conductivity on each cell is unknown. We prove that the local recovery is almost surely true near a known piecewise constant anisotropic conductivity $γ_0$. We do so by proving that the injectivity of the Fréchet derivative $F'(γ_0)$ of the forward map $F$, say, at $γ_0$ is almost surely true. The proof presented, here, involves defining different classes of decompositions for $γ_0$ and a perturbation or contrast $H$ in a proper way so that we can find in the interior of a cell for $γ_0$ exposed single or double corners of a cell of $\mbox{supp}H$ for the former decomposition and latter decomposition, respectively. Then, by adapting the usual proof near such corners, we establish the aforementioned injectivity.
ChemInform Abstract: STEP TELOMERIZATION OF VINYLCHLORIDE BY METHYLBROMOACETATE (1975)

Abstract Dibro‐messigsäure‐methylester (I) reagiert mit Vinylchlorid (II) in Gegenwart von Eisenpentacarbonyl bei 100‐150°C je nach Mengenverhältnis zum α‐Brom‐γ‐chlorbuttersäure‐methylester (III) oder zum Telomeren (IV).
Pharmacodynamic effects of daclizumab in the intrathecal compartment (2017)

These observations confirm daclizumab's direct pharmacodynamics effects on immune cells within central nervous system tissues and identify inhibition of CSF biomarkers of myeloid lineage as a stronger determinant of reduction in clinical MS activity than inhibition of biomarkers of adaptive immunity.
Ambulatory Blood Pressure Monitoring During Pregnancy (1994)

Ambulatory blood pressure monitoring (ABPM) was used as an effective methodology by a primary care physician to assess normalcy of blood pressure (BP) and heart rate during pregnancy. One hundred fifty pregnant women in one of three periods (18 to 22, 30 to 32, and 36 to 38 weeks) of gestation and 30 age-matched nonpregnant women participated in this study. The study was designed to establish ABPM standards of normalcy during critical times of gestation. Twenty-four-hour BP (systolic and diastolic BP) values monitored during gestational weeks 18 to 22 and 30 to 32 were similar to each other and lower than the same values recorded in nonpregnant women. Blood pressures monitored during gestational weeks 36 to 38 were significantly higher than similar values observed during the two earlier gestational periods but not significantly higher than nonpregnancy BP values. Heart rates were significantly elevated during all gestational periods when compared with nonpregnancy heart rates. The results of this study established normalcy BP curves during three different gestational periods. Mean 24-h, daytime, and nighttime BPs were significantly elevated during weeks 36 to 38 when compared with BPs recorded during gestational weeks 18 to 22 and 30 to 32. Ambulatory blood pressure monitoring is a useful tool for the measurement and treatment of BP abnormalities during pregnancy.
"Só ponho bebop no meu samba...": intercambios culturales y formación de los compositores en la formulación de la MPB en las décadas de 1960 y 1970 (2017)

My objective is to discuss cultural exchange seeking to find, on the one hand, the general lines associated to the subject of national identity in the production of Brazilian popular music (MPB) and, on the other, the particular features of the choices made by some of the creators of such music. The approach I propose takes as a reference the studies of popular music which have reflected on local, regional and global dimensions, and the contemporary debates over cultural exchanges which have made use of the concepts of hybridization or transculturalization. I discuss the question of cultural exchanges in Brazilian popular music in two stages. In the first one, I deal with the debate over the existence of a particular national identity –a brazilianness– present in the discussions on the history of Brazilian popular music. In the second one, in turn, I refer to the musical background of the principal members of the generation of the central names in Brazilian popular music between 1960 and 1970. On focusing on the testimonies of those musicians and their aesthetic choices, I try to demonstrate that they were more worried about thinking of ways of hybridizating than purely accepting or reflecting on the elements considered alien, which was decisive in the composition of what today we designate as Brazilian popular music.