gebhart/patrepeval huggingface dataset:
The AP2/EREBP Gene PUCHI Co-Acts with LBD16/ASL18 and LBD18/ASL20 Downstream of ARF7 and ARF19 to Regulate Lateral Root Development in Arabidopsis (2013)

The developmental process of lateral root formation consists of priming, initiation, primordium development and the emergence of lateral roots from the primary root. Molecular genetic studies with Arabidopsis have revealed several key transcriptional regulators involved in lateral root development. However, their functional interaction has not been fully characterized yet. Here we utilized a genetic approach to understand some of these interactions, revealing that PUCHI functioning in morphogenesis of early lateral root primordium is regulated downstream of ARF7/ARF19 and acts with LBD16(ASL18)/LBD18(ASL20) to regulate lateral root development. We showed that auxin-responsive expression of PUCHI was significantly reduced in arf7 or arf19 single mutants and completely abolished in arf7 arf19 double mutants. Consistent with this, β-glucuronidase (GUS) expression under the PUCHI promoter in arf7 arf19 was greatly reduced in the lateral root primordium compared with that in the wild type and did not respond to exogenous auxin. Results of GUS expression analyses under the PUCHI, LBD16 or LBD18 promoter in lbd16, lbd18 single and double mutants or puchi demonstrated that PUCHI and LBD16 or LBD18 do not regulate each other's expression. Lateral root phenotypes of double and triple mutants of lbd16, lbd18 and puchi showed that the puchi mutation in lbd16 and lbd18 mutants synergistically decreased the number of emerged lateral roots. These analyses also showed that puchi affected lateral root primordium development of lbd16 or lbd18 additively but differentially. Taken together, these results suggest that PUCHI co-acts with LBD16 and LBD18 to control lateral root primordium development and lateral root emergence.
Increase in electromigration resistance by enhancing backflow effect (1992)

The backflow effect on electromigration has been studied in terms of experiment and theory. The difference of electromigration resistance between the two materials Al-2%Cu/Ti and the stress gradient caused by a discontinuous SiO/sub 2/ overcoating layer were used to enhance the backflow intentionally to restrain the electromigration and improve the lifetime of metallization. A theoretical model is proposed to explain the formation of backflow.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Geochemistry of Sulfur in Petroleum Systems (1990)

A renaissance in the 1980s concerning geochemistry of sulfur in fossil fuels makes an update of the subject timely. Papers developed from the 1989 ACS Symposium in Dallas provide a cross-section of recent research and progress in our understanding of the abundance and nature of organically bound sulfur in fossil fuels. This chapter furnishes an overview of our understanding of sulfur introduction into the geologic systems and biogenic materials that produce petroleum and natural gas. Many of the geochemical considerations also apply to coal and lignite deposits. A brief historical account leads to a summary of the most recent advances, an appraisal of current understanding, and some remaining challenges and opportunities for further research.
A prioritized reservation protocol for fiber optic ring local area computer networks (2003)

The authors describe the design and analysis of a fiber-optic ring local computer network using a priority-oriented reservation method as the medium access control (MAC) protocol. Using the proposed approach, any station of any priority can be placed anywhere on the ring without degrading performance considerably. A performance model is presented as well as a comparison with well-known MAC protocols. Performance results show that this protocol is efficient in applications where high volumes of data must be transmitted as quickly as possible. This is the case for applications such as video, high-resolution graphics, and computer room networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Polymer Sol–Gel Composite Inverse Opal Structures (2015)

We report on the formation of composite inverse opal structures where the matrix used to form the inverse opal contains both silica, formed using sol-gel chemistry, and poly(ethylene glycol), PEG. We find that the morphology of the inverse opal structure depends on both the amount of PEG incorporated into the matrix and its molecular weight. The extent of organization in the inverse opal structure, which is characterized by scanning electron microscopy and optical reflectance data, is mediated by the chemical bonding interactions between the silica and PEG constituents in the hybrid matrix. Both polymer chain terminus Si-O-C bonding and hydrogen bonding between the polymer backbone oxygens and silanol functionalities can contribute, with the polymer mediating the extent to which Si-O-Si bonds can form within the silica regions of the matrix due to hydrogen-bonding interactions.
Overlap junctions for high coherence superconducting qubits (2017)

Fabrication of sub-micron Josephson junctions is demonstrated using standard processing techniques for high-coherence, superconducting qubits. These junctions are made in two separate lithography steps with normal-angle evaporation. Most significantly, this work demonstrates that it is possible to achieve high coherence with junctions formed on aluminum surfaces cleaned in situ with Ar milling before the junction oxidation. This method eliminates the angle-dependent shadow masks typically used for small junctions. Therefore, this is conducive to the implementation of typical methods for improving margins and yield using conventional CMOS processing. The current method uses electron-beam lithography and an additive process to define the top and bottom electrodes. Extension of this work to optical lithography and subtractive processes is discussed.
Dissimilarity-Based Detection of Schizophrenia (2010)

We propose to approach the detection of patients affected by schizophrenia by means of dissimilarity-based classification techniques applied to brain magnetic resonance images. Instead of working with features directly, pairwise distances between expert delineated regions of interest (ROIs) are considered as representations based on which learning and classification can be performed. Experiments were carried out on a set of 64 patients and 60 controls and several pairwise dissimilarity measurements have been analyzed. We demonstrate that good results are possible and especially significant improvements can be obtained when combining over different ROIs and different distance measures. The lowest error rate obtained is 0.210.
Genetic and morphological characteristics of two ecotypes of Eustigmatos calaminaris sp. nov. (Eustigmatophyceae) inhabiting Zn- and Pb-loaded calamine mine spoils. (2014)

Knowledge on species diversity and distribution of eustigmatophycean algae (Stramenopiles) in the environment is currently very limited. Some of them are considered promising organisms for industrial application. Phylogenetic analysis of two strains (E120, E5) of a coccoid microalga isolated from highly Zn- and Pb-polluted calamine mine spoils revealed that they belong to the genus Eustigmatos. Cells of both strains were morphologically identical. Some features of their vegetative cells and zoospores differed from other described nominal Eustigmatos species. 18S rDNA sequences of E120 and E5 were identical but also differed in two or three nucleotide substitutions from the other Eustigmatos species (E. vischeri, E. magnus, E. polyphem). Only 1 - 3 nucleotide substitutions in 18S rDNA sequence were found among all the examined Eustigmatos species. ITS1-5.8S rDNA-ITS2 region was more variable (15 - 22 differences) than 18S rDNA, except for E120 and E5 strains which differed in only one nucleotide substitution (in 5.8S rDNA). Genetic differences found between the isolated strains (E120, E5) and the other Eustigmatos species were comparable to those observed among all nominal Eustigmatos species studied. This suggests that the isolates represent a new species. The name Eustigmatos calaminaris sp. nov. (referred to the locality) has been proposed. The E120 strain from the mine spoil with higher heavy metal contents was more Zn- and Pb-resistant than E5 from the less polluted ground. Their high, though varied resistance to Zn/Pb stress, together with the very slight genetic divergence between them, indicate that they represent two ecotypes of the same new species.
Identification of the Retinoic Acid-Inducible Gprc5a As a New Lung Tumor Suppressor Gene (2007)

Gprc5a functions as a tumor suppressor in mouse lung, and human GPRC5A may share this property. The Gprc5a-deficient mouse is a novel model to study lung carcinogenesis and chemoprevention.
Using automatic persistent memoization to facilitate data analysis scripting (2011)

Programmers across a wide range of disciplines (e.g., bioinformatics, neuroscience, econometrics, finance, data mining, information retrieval, machine learning) write scripts to parse, transform, process, and extract insights from data. To speed up iteration times, they split their analyses into stages and write extra code to save the intermediate results of each stage to files so that those results do not have to be re-computed in every subsequent run. As they explore and refine hypotheses, their scripts often create and process lots of intermediate data files. They need to properly manage the myriad of dependencies between their code and data files, or else their analyses will produce incorrect results.
Polysaccharides from Larch Biomass (2012)

There are two species of the genus Larix Mill, Larix sibirica Ledeb. (Figure 1) and Larix gmelinii (Rupr.) Rupr., considered to be the most abundant trees in the Russian Federation: the total stock of their wood exceeds 26 billion m3. Traditionally, the main economic value of larch wood consists of the manufacture of roundwood (timber), the value of which is connected with the high quality of lumber from this breed of tree. Larch wood can sometimes be used in insignificant quantities in pulp-and-paper manufacture to obtain pulp. About 40% of this valuable breed (as bark, sawdust) enters waste through existing lumber manufacturing processes. Such an irrational approach to the development of larch wood does not allow exploitation of the richest potential of the given renewed source. Meanwhile, biologically active compounds contained in larch biomass can be used for the manufacture of products for medical, food and agricultural purposes with maximal benefit. The development of complex technology for chemical processing of larch biomass and waste timber will considerably raise the economic value of this biological resource.
Determination of rare earth elements in geological samples by inductively coupled plasma source mass spectrometry (1987)

The prototype inductively coupled plasma source mass spectrometer (ICP-MS) operated by the British Geological Survey is described. Preliminary work on its application to the determination of the rare earth elements in geological materials is discussed.
Transcription termination in vitro by bacteriophage T7 RNA polymerase. The role of sequence elements within and surrounding a rho-independent transcription terminator. (1992)

rho-Independent transcription terminators in Escherichia coli contain a dG+dC-rich dyad-symmetrical structure that encodes an RNA hairpin structure and an adjacent, downstream dA+dT-rich region which encodes uridines at the 3'-end of the transcript. In the threonine (thr) attenuator, there are at least six sequence segments in the DNA that might affect termination: the sequence upstream of the attenuator, the deoxythymidine-rich stretch immediately preceding the G+C-rich region, the G+C-rich region itself and its hairpin loop-encoding region, the deoxyadenosine tract following the G+C-rich region, and the following downstream sequence. Our previous studies (Jeng, S.-T., Gardner, J.F., and Gumport, R.I. (1990) J. Biol. Chem. 265, 3823-3830) indicate that both the stability and sequence of the RNA hairpin formed by the G+C-rich region and the length of the uridine tract encoded by the deoxyadenosine stretch influence the termination of T7 RNA polymerase in vitro. In this report, we demonstrate that the template deoxythymidine run upstream of the G+C-rich region, the loop-encoding segment, and the sequences upstream and downstream of the thr attenuator also affect termination. These results indicate that: 1) a deoxythymidine tract is not absolutely required for termination, but increasing the number of deoxythymidines from one to nine base pairs causes T7 RNA polymerase to terminate more efficiently; 2) a template with the natural loop sequence reversed results in a higher termination efficiency than one encoded by the the wild-type attenuator; 3) the termination of T7 RNA polymerase is affected by sequences both proximal and distal to the thr attenuator.
Automatic generation of software interfaces for supporting decision-making processes. An application of domain engineering and machine learning (2019)

Information dashboards are sophisticated tools. Although they enable users to reach useful insights and support their decision-making challenges, a good design process is essential to obtain powerful tools. Users need to be part of these design processes, as they will be the consumers of the information displayed. But users are very diverse and can have different goals, beliefs, preferences, etc., and creating a new dashboard for each potential user is not viable. There exist several tools that allow users to configure their displays without requiring programming skills. However, users might not exactly know what they want to visualize or explore, also becoming the configuration process a tedious task. This research project aims to explore the automatic generation of user interfaces for supporting these decision-making processes. To tackle these challenges, a domain engineering, and machine learning approach is taken. The main goal is to automatize the design process of dashboards by learning from the context, including the end-users and the target data to be displayed.
Comments on “Researcher Bias: The Use of Machine Learning in Software Defect Prediction” (2016)

Shepperd et al. find that the reported performance of a defect prediction model shares a strong relationship with the group of researchers who construct the models. In this paper, we perform an alternative investigation of Shepperd et al.'s data. We observe that (a) research group shares a strong association with other explanatory variables (i.e., the dataset and metric families that are used to build a model); (b) the strong association among these explanatory variables makes it difficult to discern the impact of the research group on model performance; and (c) after mitigating the impact of this strong association, we find that the research group has a smaller impact than the metric family. These observations lead us to conclude that the relationship between the research group and the performance of a defect prediction model are more likely due to the tendency of researchers to reuse experimental components (e.g., datasets and metrics). We recommend that researchers experiment with a broader selection of datasets and metrics to combat any potential bias in their results.
Multi-media software for teaching discrete event simulation (1993)

ABSTRACI' Multi-media software is being developed for an undergraduate introductory course to discrete event and visual interactive simulation. It is part of a larger project, funded by the U.K. Government, to provide computer based learning courses in various different subjects. The simulation course uses WINDOWS based software, called Learn-OR, which provides video, hypertext links and links to simulation software. The simulation module, covers: model structure, activity cycle diagrams, distribution sampling, model validation and experimentation.
Short-term load forecasting via ARMA model identification including non-gaussian process considerations (2003)

In this paper, the short-term load forecast by use of autoregressive moving average (ARMA) model including non-Gaussian process considerations is proposed. In the proposed method, the concept of cumulant and bispectrum are embedded into the ARMA model in order to facilitate Gaussian and non-Gaussian process. With embodiment of a Gaussianity verification procedure, the forecasted model is identified more appropriately. Therefore, the performance of ARMA model is better ensured, improving the load forecast accuracy significantly. The proposed method has been applied on a practical system and the results are compared with other published techniques.
Novel PCR-Based Methods Enhance Characterization of Vaginal Microbiota in a Bacterial Vaginosis Patient before and after Treatment (2013)

Deep characterization, even by next-generation sequencing, of the vaginal microbiota in healthy women or posttreatment bacterial vaginosis patients is limited by the dominance of lactobacilli. To improve detection, we offer two approaches: quantitative PCR (qPCR) using phylogenetic branch-inclusive primers and sequencing of broad-spectrum amplicons generated with oligomers that block amplification of lactobacilli.
Generation of Three-Dimensional Hepatocyte/Gelatin Structures with Rapid Prototyping System (2006)

Using rapid prototyping technology, three-dimensional (3D) structures composed of hepatocytes and gelatin hydrogel have been formed. This technique employs a highly accurate 3D micropositioning system with a pressure-controlled syringe to deposit cell/biomaterial structures with a lateral resolution of 10 microm. The pressure-activated micro-syringe is equipped with a fine-bore exit needle for which a wide variety of 3D patterns with different arrays of channels (through-holes) were created. More than 30 layers of a hepatocyte/gelatin mixture were laminated into a high spacial structure using this method. The laminated hepatocytes remained viable and performed biological functions in the construct for more than 2 months. The rapid prototyping technology offers potential for eventual high-throughout production of artificial human tissues or organs.
SARS update: Additional cases being investigated in Beijing, China (2004)

Since 22 April, the World Health Organization has reported two people who have been classified as probable cases of severe acute respiratory syndrome (SARS), and seven people who remain under investigation for possible SARS infection
N-acetylcysteine enhances receptor-mediated phagocytosis by human neutrophils. (1992)

The effect of the sulphur compound N-acetylcysteine (NAC) on certain receptor-mediated cellular functions [chemiluminescence (CL), phagocytosis and degranulation] in human neutrophils was studied, to evaluate how a scavenger of certain toxic oxygen product can protect the phagocyte and the bystander tissue cells from oxidative damage. When using IgG-opsonized yeast particles as stimulating agent, preincubating the neutrophils with NAC (0.25 mg/ml = 1.5 mM) increased both the CL response and phagocytosis. Higher concentrations of NAC (0.50-1.00 mg/ml = 3-6 mM) decreased the CL response, whereas the phagocytic capacity was still enhanced. This effect was more pronounced with adherent neutrophils than with neutrophils in suspension. No increased CL or phagocytic activity was, however, induced by NAC when C3bi-opsonized particles were used as a prey. From the fact that NAC (i) inhibited extracellularly localized myeloperoxidase dependent activities, and (ii) had no effect on neutrophils from patients with chronic granulomatous disease (CGD), we conclude that the scavenger effect of NAC not only reduces the accumulation of oxidative metabolites per se, but also enhances receptor-mediated phagocytosis by protecting Fc(IgG)-receptors from oxidative damage mediated by myeloperoxidase (MPO) and hydrogen peroxide (H2O2). Since NAC can increase phagocytosis and reduce the extracellularly produced oxidative metabolites, we furthermore conclude that NAC possesses some ideal properties as an anti-inflammatory agent.
Biologically Inspired Information Processing Technologies: Reaction-Diffusion Paradigm (2005)

Chemical reaction-diffusion media represent information processing means capable to efficiently solve problems of high computational complexity. Distributed character and complex nonlinear dynamics of chemical reactions inherent in the medium is the basis of large-scale parallelism and complex logical operations performed by the medium as primitives and equivalent to hundreds of binary fixed-point operations. Photo-sensitive catalysts controlling the dynamics (modes of functioning) of the medium enable to easily perform input of initial data and output of computational results. It was found during the last decades that chemical reaction-diffusion media can be effectively used for image processing, finding the shortest paths in a labyrinth and solving some other problems of high computational complexity. Spatially non uniform control of the medium by physical stimuli and fabrication multi level reaction-diffusion systems seem to be promising way enabling low cost and effective information processing devices that meet the commercial needs.
Synthesis and Configuration of Some Hydroxymilbemycin Derivatives Including 22,23‐Dihydroavermectin B<sub>1b</sub> Aglycone (1990)

Abstract The synthesis of several configurationally defined hydroxymilbemycin derivatives is described. One of these allylic alcohols is the known 5‐ O ‐[( tert ‐butyl)dimethylsilyl]‐13α‐hydroxymilbemycin D (= 5‐ O ‐[( tert ‐butyl)‐dimethylsilyl]‐22,23‐dihydroavermectin B 1b , aglycone; 15D ), the synthesis of which represents LI conversion of the milbemycin to the avermectin series of natural products. The configurations at C(13), C(14), and C(15) of the new milbemycin derivatives were determined by NMR experiments and force‐field calculations.
Antibiotic resistance in Staphylococcus aureus: concerns, causes and cures (2003)

Methicillin-resistant Staphylococcus aureus (MRSA) is currently a predominant and dangerous nosocomial pathogen. Unfortunately, infections caused by this organism are becoming more difficult to treat as further evolution of drug resistance occurs within the pathogen. Vancomycin has become the drug of choice for treating MRSA infections. However, treatment failures, adverse side effects and the emergence of vancomycin-resistant MRSA are leading to urgent requirements for alternative antiMRSA therapies. Linezolid is a new agent recently developed for Gram-positive infections, including MRSA. However, resistance to this drug is already developing. The need for superior antiMRSA drugs is therefore highly evident. This article explores some of the opportunities for the development of new treatments for MRSA. These arise principally from extensions of existing drug classes and the discovery of novel agents by genome-driven technologies. Other possibilities concern the re-evaluation of earlier pharmacophores that have not so far been developed as antiMRSA agents.
Highly Enantioselective Thiourea‐Catalyzed Nitro‐Mannich Reactions (2004)

Approaching “privileged” status? A new and highly effective enantioselective catalyst for the nitro-Mannich reaction was identified by modification of thiourea-based Strecker catalysts (see scheme). Products are obtained in high enantiomeric purity and up to 16:1 diastereoselectivity. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z461814_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.