gebhart/patrepeval huggingface dataset:
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale (2009)

Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R(2) = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
Controllable Synthesis of Fluorescent Carbon Dots and Their Detection Application as Nanoprobes (2013)

Abstract Carbon dots (CDs), as a new member of carbon nanomaterial family, have aroused great interest since their discovery in 2004. Because of their outstanding water solubility, high sensitivity and selectivity to target analytes, low toxicity, favorable biocompatibility, and excellent photostability, researchers from diverse disciplines have come together to further develop the fundamental properties of CDs. Many methods for the production of CDs have been reported, therein, hydrothermal and solvothermal technology needs simple equipments, and microwave synthesis needs less reaction time, hence these methods become current common synthesis methods, in which many precursors have been applied to produce CDs. Due to their excellent fluorescence, CDs have made impressive strides in sensitivity and selectivity to a diverse array of salt ions, organic/biological molecules and target gases. The development of CDs as nanoprobes is still in its infancy, but continued progress may lead to their integration into environmental and biological applications. Hydrothermal, solvothermal, and microwave synthesis of fluorescent carbon dots and their detection applications as nanoprobes in salt ions, organic/biological molecules, and target gases will be reviewed.
Tell Me More (2019)

In this study, we apply a "conversational search" to the design of the news service of smart speakers so that users can actively get richer information while listening to the news. We designed a research prototype called "Anchor," where a smart speaker news assistant provides users with news about specific keywords and responds to users' questions. We recruited 21 participants and conducted a user study where they consumed the news with Anchor, followed by post hoc interviews. The results of the qualitative analysis revealed the following. (1) People preferred interactive news to news briefings. (2) People found it useful to get answers on their questions by talking with the assistant. (3) Although users were allowed to ask questions anytime, they often hesitated, as they did not want to miss the whole flow of the news. (4) However, they had difficulty recalling the questions they had not asked. Based on these findings, we discuss the implications for news design in a voice-only user interface.
Imaging DNA synthesis in vivo with 18F-FMAU and PET. (2005)

The results showed that (18)F-FMAU was selectively retained in DNA of the proliferating tissues and was resistant to degradation. These features indicate that (18)F-FMAU might be an alternative to (11)C-thymidine for imaging DNA synthesis in normal tissues and tumors.
β-Alanine Betaine Synthesis in the Plumbaginaceae. Purification and Characterization of a Trifunctional,<i>S</i>-Adenosyl-<scp>l</scp>-Methionine-Dependent<i>N</i>-Methyltransferase from <i>Limonium latifolium</i>Leaves (2001)

beta-Alanine (beta-Ala) betaine is an osmoprotective compound accumulated by most members of the highly stress-tolerant family Plumbaginaceae. Its potential role in plant tolerance to salinity and hypoxia makes its synthetic pathway an interesting target for metabolic engineering. In the Plumbaginaceae, beta-Ala betaine is synthesized by S-adenosyl-L-methionine-dependent N-methylation of beta-Ala via N-methyl beta-Ala and N,N-dimethyl beta-Ala. It was not known how many N-methyltransferases (NMTases) participate in the three N-methylations of beta-Ala. An NMTase was purified about 1,890-fold, from Limonium latifolium leaves, using a protocol consisting of polyethylene glycol precipitation, heat treatment, anion-exchange chromatography, gel filtration, native polyacrylamide gel electrophoresis, and two substrate affinity chromatography steps. The purified NMTase was trifunctional, methylating beta-Ala, N-methyl beta-Ala, and N,N-dimethyl beta-Ala. Gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses indicated that the native NMTase is a dimer of 43-kD subunits. The NMTase had an apparent K(m) of 45 microM S-adenosyl-l-methionine and substrate inhibition was observed above 200 microM. The apparent K(m) values for the methyl acceptor substrates were 5.3, 5.7, and 5.9 mM for beta-Ala, N-methyl beta-Ala, and N,N-dimethyl beta-Ala, respectively. The NMTase had an isoelectric point of 5.15 and was reversibly inhibited by the thiol reagent p-hydroxymercuribenzoic acid.
Research on the safety evaluation index of urban rail transit network operation (2011)

The traditional safety evaluation of urban rail transit operation was limited to the station or line, not from the perspective of the whole network operation safety. Specific to the characteristics of the urban rail transit network operation in the new situation, based on complex network theory, the urban rail transit network model was established, and the formalized description of the network model was given. Based on above, from the passenger traffic, environment and other aspects, the safety evaluation index of urban rail transit network operation was established, which included hidden trouble indexes, accident indexes and safety economic index, aiming at to provide support for overall safety evaluation.
DNA polymerase chain reaction: A model of error frequencies and extension rates (2005)

Abstract The polymerase chain reaction (PCR) is one of the most important reactions in molecular biology. The detailed mechanistic studies of the polymerase chain reaction have revealed a complex sequence of reversible reactions that involve intermediaries and activated complexes. The DNA polymerase does not merely facilitate the insertion of dNMP (deoxynucleotide monophosphates), but it also performs rapid screening of substrates to ensure a high degree of fidelity. The main result of this study is an expression for the average extension rate of the enzyme. The model is versatile and additional complexities, such as the type of nucleotide to be inserted, the GC content of the sequence in the vicinity of the insertion site, and the topology of the template, such as kinks and hairpins, are easy to incorporate. The insertion of incorrect nucleotides into the sequence is also addressed. Expressions to predict error frequencies are presented. It is shown that a relation exists between error frequency and extension rate: the error frequency is a minimum when the extension rate is optimal. © 2005 American Institute of Chemical Engineers AIChE J, 2006
The Emerging Role of Nuclear Viral DNA Sensors (2015)

Detecting pathogenic DNA by intracellular receptors termed "sensors" is critical toward galvanizing host immune responses and eliminating microbial infections. Emerging evidence has challenged the dogma that sensing of viral DNA occurs exclusively in sub-cellular compartments normally devoid of cellular DNA. The interferon-inducible protein IFI16 was shown to bind nuclear viral DNA and initiate immune signaling, culminating in antiviral cytokine secretion. Here, we review the newly characterized nucleus-originating immune signaling pathways, their links to other crucial host defenses, and unique mechanisms by which viruses suppress their functions. We frame these findings in the context of human pathologies associated with nuclear replicating DNA viruses.
The effect of pH on the growth and carbohydrate metabolism of a lymphoblastoid cell line. (1980)

Glucose limited the maximum population density of the cell line Bri 8 over a wide range of pH values. Efficiency of glucose utilisation varied with pH and hence pH influenced maximum population density. Surprisingly the ratio of glucose consumed to lactic acid produced was not greatly influenced by pH.
OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action (2014)

Supplementary data are available at Bioinformatics online.
Predicting Clinical Events by Combining Static and Dynamic Information Using Recurrent Neural Networks (2016)

In clinical data sets we often find static information (e.g. patient gender, blood type, etc.) combined with sequences of data that are recorded during multiple hospital visits (e.g. medications prescribed, tests performed, etc.). Recurrent Neural Networks (RNNs) have proven to be very successful for modelling sequences of data in many areas of Machine Learning. In this work we present an approach based on RNNs, specifically designed for the clinical domain, that combines static and dynamic information in order to predict future events. We work with a database collected in the Charité Hospital in Berlin that contains complete information concerning patients that underwent a kidney transplantation. After the transplantation three main endpoints can occur: rejection of the kidney, loss of the kidney and death of the patient. Our goal is to predict, based on information recorded in the Electronic Health Record of each patient, whether any of those endpoints will occur within the next six or twelve months after each visit to the clinic. We compared different types of RNNs that we developed for this work, with a model based on a Feedforward Neural Network and a Logistic Regression model. We found that the RNN that we developed based on Gated Recurrent Units provides the best performance for this task. We also used the same models for a second task, i.e., next event prediction, and found that here the model based on a Feedforward Neural Network outperformed the other models. Our hypothesis is that long-term dependencies are not as relevant in this task.
Essential roles of the Fas-Fas ligand pathway in the development of pulmonary fibrosis (1999)

The Fas ligand is predominantly expressed in activated T lymphocytes and is one of the major effector molecules of cytotoxic T lymphocytes and natural killer cells. Previously, we found excessive apoptosis of epithelial cells and infiltrating lymphocytes expressing Fas ligand mRNA in the lung tissue of bleomycin-induced pulmonary fibrosis in mice. Here we demonstrated that the administration of a soluble form of Fas antigen or anti-Fas ligand antibody prevented the development of this model and that lpr and gld mice were resistant against the induction of pneumopathy. These results suggest that the Fas-Fas ligand pathway plays an essential role in the development of pulmonary fibrosis and that preventing this pathway could have therapeutic value in lung injury and fibrosis.
A mapping approach for designing neural sub-nets (2002)

Summary form only given. Several investigators have constructed backpropagation (BP) neural networks by assembling smaller, pretrained building blocks. This approach leads to faster training and provides a known topology for the network. The authors have carried this process down one additional level by describing methods for mapping given functions to subblocks. First, polynomial, approximations to the desired function were found. Then the polynomial was mapped to a BP network, using an extension of a constructive proof to universal approximation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Automatic and Online Pollen Monitoring (2015)

The BAA500 is a functional automated pollen counter. Its software can be upgraded, and so we expected its performance to improve upon training. Automated pollen counting has great potential for workload reduction and rapid online pollen reporting.
A Miniaturized Two Axis Sun Sensor for Attitude Control of Nano-Satellites (2010)

This paper describes the design, fabrication, characterization, and satellite integration of a miniaturized two axis sun sensor which has been used in the attitude control system of the Spanish nano-satellite NANOSAT-1B. This device is made of four silicon photodiodes monolithically integrated in a crystalline silicon substrate, protected by a transparent cover glass assembled on the same silicon die against space radiation damage. The sensor fabrication combines standard silicon processing technology with a high performance solar cell fabrication process. The sensor, including electronics and mechanical and electrical interfacing with the satellite, has a small size (3 cm × 3 cm) and low weight (24 gr.), with a sun field-of-view greater than ±60° with an angle accuracy better than 0.15°. Three of these sensors have already been integrated in the NANOSAT-1B platform that has been successfully launched in July 2009.
Measurement of Differences in pO 2 in Response to Perfluorocarbon/Carbogen in FSa and NFSa Murine Fibrosarcomas with Low-Frequency Electron Paramagnetic Resonance Oximetry (1996)

We have used very low-frequency electron paramagnetic resonance (EPR) oximetry to measure the change in oxygen concentration (delta pO2) due to change in breathing atmosphere in FSa and NFSa fibrosarcomas implanted in the legs of C3H mice infused with perfluoro-octylbromine (PFOB). Measurements in each tumor were made before and after the administration of the high-density (47% v/v) perfluorocarbon PFOB, perflubron (Alliance Pharmaceutical Corporation, San Diego, CA). Measurements in each tumor were also made, after the administration of the PFOB, both before (PFOB/air) and after the administration of carbogen (95% O2 + 5% CO2, PFOB/carbogen). Large changes (delta p02) relative to PFOB/air oxygenation were seen with the administration of PFOB/carbogen. No significant difference in oxygen concentration was seen between air-breathing mice with and without PFOB. The mean delta pO2 for FSa tumors was 13 +/- 6 torr, while the mean for NFSa fibrosarcomas was 28 +/- 7 torr. There were such large intertumor differences that the trend toward a smaller change in the more hypoxic FSa tumors was not significant (P = 0.13). This paper describes a novel method of measuring differences in oxygenation in tumor tissues. The results of such measurements indicate large differences in pO2 response to different breathing atmospheres in PFOB-infused tumors of similar histology. The intertumor delta pO2 differences may correlate with differences in radiation response.
Joint source/channel coding of statistically multiplexed real-time services on packet networks (1993)

The interaction of congestion control with the partitioning of source information into components of varying importance for variable-bit-rate packet voice and packet video is investigated. High-priority transport for the more important signal components results in substantially increased objective service quality. Using a Markov chain voice source model with simple PCM speech encoding and a priority queue, simulation results show a signal-to-noise ratio improvement of 45 dB with two priorities over an unprioritized system. Performance is sensitive to the fraction of traffic placed in each priority, and the optimal partition depends on network loss conditions. When this partition is optimized dynamically, quality degrades gracefully over a wide range of load values. Results with DCT encoded speech and video samples show similar behavior. Variations are investigated such as further partition of low-priority information into multiple priorities. A simulation with delay added to represent other network nodes shows general insensitivity to delay of network feedback information. A comparison is made between dropping packets on buffer overflow and timeout based on service requirements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Physical layer network coding for two-way relaying with QAM and Latin Squares (2012)

In the design of modulation schemes for the physical layer network-coded two way relaying scenario with two phases (Multiple access (MA) Phase and Broadcast (BC) Phase), it was observed by Koike-Akino et al. that adaptively changing the network coding map used at the relay according to the channel conditions greatly reduces the impact of multiple access interference and all these network coding maps should satisfy a requirement called the exclusive law. In [11] the case in which the end nodes use M-PSK signal sets is extensively studied using Latin Squares. This paper deals with the case in which the end nodes use square M-QAM signal sets. In a fading scenario, for certain channel conditions, termed singular fade states, the MA phase performance is greatly reduced. We show that the square QAM signal sets lead to lesser number of singular fade states compared to PSK signal sets. Because of this, the complexity at the relay is enormously reduced. Moreover lesser number of overhead bits are required in the BC phase. We find the number of singular fade states for PAM and QAM signal sets used at the end nodes. The fade state γℯ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">jθ</sup> = 1 is a singular fade state for M-QAM for all values of M and it is shown that certain block circulant Latin Squares remove this singular fade state. Simulation results are presented to show that QAM signal set perform better than PSK.
Glycine metabolism by Pseudomonas aeruginosa: hydrogen cyanide biosynthesis (1977)

Hydrogen cyanide (HCN) production by Pseudomonas aeruginosa in a synthetic medium is stimulated by the presence of glycine. Methionine enhances this stimulation but will not substitute for glycine as a stimulator of cyanogenesis. Threonine and phenylalanine are effective substitutes for glycine in the stimulation of HCN production. Glycine, threonine, and serine are good radioisotope precursors of HCN, but methionine and phenylalanine are not. Cell extracts of P. aeruginosa convert [14C]threonine to [14C]glycine. H14CN is produced with low dilution of label from either [1-14C]glycine or [2-14C]glycine, indicating a randomization of label either in the primary or secondary metabolism of glycine. When whole cells were fed [1,2-14C]glycine, cyanide and bicarbonate were the only radioactive extracellular products observed.
Engineering the performance of metal/insulator/metal devices with ALD nanolaminate insulators (2015)

Thin film metal-insulator-metal (MIM) devices find application not only as back-end-of-line (BEOL) capacitors (MIMCAPs), but also as tunnel diodes for optical rectenna based IR energy harvesting, IR detectors, large area macroelectronics, hot electron transistors, and as selector devices to avoid sneak leakage in resistive memory (RRAM) crossbar arrays. This invited talk will highlight how nanolaminate combinations of insulators deposited via atomic layer deposition (ALD) can be used to enhance the performance of MIIM diodes and MIIM capacitors as well as discuss reliability issues.
Higher oxidation state iron and cobalt phthalocyanine derivatives. Phthalocyanine radical cation complexes (1973)

Reaction of cobalt(II) phthalocyanine (CoPc) with thionyl chloride and with bromine leads to the formation of CoPcCl2 and CoPcBr2, respectively; magnetic i.r., oxidative titration, and e.s.r. data indicate these complexes to contain a phchalocyanine radical species, characterised in the solid state for the first time.
RHOA mutation in diffuse-type gastric cancer: a comparative clinicopathology analysis of 87 cases (2015)

These observations suggest that RHOA mutation may be associated with the growth patterns of diffuse-type gastric cancer but have a limited prognostic impact in isolation. Further studies, including analyses of the other alterations involving the RhoA pathways, such as CLDN18-ARHGAP fusion, as well as functional studies of mutant RhoA, are necessary to clarify the significance of alterations in the RhoA-signaling pathway in diffuse-type gastric cancers.
Precise lattice location of substitutional and interstitial Mg in AlN (2013)

The lattice site location of radioactive 27Mg implanted in AlN was determined by means of emission channeling. The majority of the 27Mg was found to substitute for Al, yet significant fractions (up to 33%) were also identified close to the octahedral interstitial site. The activation energy for interstitial Mg diffusion is estimated to be between 1.1 eV and 1.7 eV. Substitutional Mg is shown to occupy ideal Al sites within a 0.1 Å experimental uncertainty. We discuss the absence of significant displacements from ideal Al sites, in the context of the current debate, on Mg doped nitride semiconductors.
Binge Eating Disorder and Food Addiction (2011)

Binge eating disorder (BED) shares many characteristics with addictive behaviors (e.g., diminished control, continued use despite negative consequences), and a body of scientific literature is building to support addiction conceptualizations of problematic eating. Despite similarities, BED and "food addiction" may represent unique yet overlapping conditions. Although the exploration of food addiction is relatively new, understanding the relationship between food addiction and BED may be informative in understanding the mechanisms underlying the development and maintenance of problematic eating. In the following paper, we 1) examine the theoretical similarities and differences between BED and addiction, 2) review recent empirical evidence that speak to the relationship between BED and food addiction and 3) discuss the implications of associations between BED and food addiction with respect to clinical interventions.