gebhart/patrepeval huggingface dataset:
The in Planta Effective Concentration of Oxytetracycline Against ‘<i>Candidatus</i> Liberibacter asiaticus’ for Suppression of Citrus Huanglongbing (2019)

Huanglongbing (HLB) or greening currently is the most devastating citrus disease worldwide. The fastidious phloem-colonizing bacterium '<i>Candidatus</i> Liberibacter asiaticus' (CLas) is the causal agent of citrus HLB in Florida. Bactericides containing the active ingredient oxytetracycline (OTC) have been used in foliar spray to control citrus HLB in Florida since 2016. However, the minimum concentration of OTC required to suppress CLas in planta remains unknown. We developed a new method for evaluating the effects of OTC treatment on CLas titers in infected plants and determined the relationship between OTC residue levels and control levels achieved for CLas using mathematical modeling in greenhouse and field experiments. In both greenhouse and field, OTC spray did not reduce the titers of CLas, and it produced undetectable or mild levels of OTC residue in leaves within 7 days post-application (DPA). In greenhouse, OTC injection at 0.05 g per tree decreased CLas titers to an undetectable level (cycle threshold value ≥ 36.0) from 7 to 30 DPA and produced a residue level of OTC at 0.68 to 0.73 µg/g of fresh tissue over this period. In the field, OTC injection at 0.50 g per tree resulted in the decline of CLas titers by 1.52 log reduction from 14 to 60 DPA, with residue levels of OTC at 0.27 to 0.33 µg/g of fresh tissue. In both trials, a first-order compart model of OTC residue dynamics in leaves of trunk-injected trees was specified for estimating the retention of effective concentrations. Furthermore, nonlinear modeling revealed significant positive correlations between OTC residue levels in leaves and the control levels for CLas achieved. The results suggested that the minimum concentrations of OTC required to suppress CLas populations in planta to below the detection limit are 0.68 and 0.86 µg/g and that the minimum concentrations of OTC required for initial inhibition of CLas growth in planta are ∼0.17 and ∼0.215 µg/g in leaf tissues under greenhouse and field conditions, respectively. This finding highlights that a minimum concentration of OTC should be guaranteed to be delivered to target CLas in infected plants for effective control of citrus HLB.
Mining the diatom genome for the mechanism of biosilicification (2008)

Ever since the invention of the microscope, scientists and laypeople alike have marveled at the intricate patterning of the silica within the diatom cell wall, termed the frustule (Fig. 1). There are well over 10,000 species of diatoms in marine and freshwaters, and each species has a unique wall morphology (1). Although organisms from multiple kingdoms of life produce siliceous structures (e.g., phytoliths in higher plants, spicules in sponges, frustules in diatom), those produced by diatoms are the most ornate and the most finely detailed. The ability of diatoms to manipulate silicon at the nanoscale exceeds that of human nanotechnology, making the genetic and biochemical underpinnings of biosilicification of great interest in material science. Diatoms are also important ecologically because they are major primary producers supporting the food webs in both marine and fresh waters. Despite the broad scientific interest in the silicification process, the biochemical pathways involved and the underlying genetics are largely a mystery. The sequencing of the first diatom genome (2) has enabled a new suite of approaches in the hunt for pathways involved in biosilicification. In this issue of PNAS, Mock et al. (3) exploit this potential by using whole genome expression profiling to elucidate candidate genes controlling silicification in the marine diatom Thalassiosira pseudonana.
Signed formulas and annotated logics (2002)

The relationship between signed formulas and annotated logics, two approaches that some authors have used to analyze multiple-valued logics (MVLs), is explored. A special case of the signed resolution rule is shown to be equivalent to, and thus to unify, the two inference rules, resolution and reduction, of annotated logic, raising the possibility of an SLD-style resolution rule for annotated logic programs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
LEAF-QA: Locate, Encode & Attend for Figure Question Answering (2020)

We introduce LEAF-QA, a comprehensive dataset of 250 <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">,</sub> 000 densely annotated figures/charts, constructed from real-world open data sources, along with 2 million question-answer (QA) pairs querying the structure and semantics of these charts. LEAF-QA highlights the problem of multimodal QA, which is notably different from conventional visual QA (VQA), and has recently gained interest in the community. Furthermore, LEAF-QA is significantly more complex than previous attempts at chart QA, viz. FigureQA and DVQA, which present only limited variations in chart data. LEAF-QA being constructed from real-world sources, requires a novel architecture to enable question answering. To this end, LEAF-Net, a deep architecture involving chart element localization, question and answer encoding in terms of chart elements, and an attention network is proposed. Different experiments are conducted to demonstrate the challenges of QA on LEAF-QA. The proposed architecture, LEAF-Net also considerably advances the current state-of-the-art on FigureQA and DVQA.
WRAP53 Is Essential for Cajal Body Formation and for Targeting the Survival of Motor Neuron Complex to Cajal Bodies (2010)

The WRAP53 gene gives rise to a p53 antisense transcript that regulates p53. This gene also encodes a protein that directs small Cajal body-specific RNAs to Cajal bodies. Cajal bodies are nuclear organelles involved in diverse functions such as processing ribonucleoproteins important for splicing. Here we identify the WRAP53 protein as an essential factor for Cajal body maintenance and for directing the survival of motor neuron (SMN) complex to Cajal bodies. By RNA interference and immunofluorescence we show that Cajal bodies collapse without WRAP53 and that new Cajal bodies cannot be formed. By immunoprecipitation we find that WRAP53 associates with the Cajal body marker coilin, the splicing regulatory protein SMN, and the nuclear import receptor importinβ, and that WRAP53 is essential for complex formation between SMN-coilin and SMN-importinβ. Furthermore, depletion of WRAP53 leads to accumulation of SMN in the cytoplasm and prevents the SMN complex from reaching Cajal bodies. Thus, WRAP53 mediates the interaction between SMN and associated proteins, which is important for nuclear targeting of SMN and the subsequent localization of the SMN complex to Cajal bodies. Moreover, we detect reduced WRAP53-SMN binding in patients with spinal muscular atrophy, which is the leading genetic cause of infant mortality worldwide, caused by mutations in SMN1. This suggests that loss of WRAP53-mediated SMN trafficking contributes to spinal muscular atrophy.
Comparative simulation study of three control techniques applied to a biped robot (2002)

This paper provides a comparative study, through simulation, of the effectiveness of the local (decoupled) PD control, the computed torque control, and the sliding mode robust control applied to a 5-link biped robot model. The superiority of the sliding mode control in case of existence of large parametric uncertainty is verified. It is argued that sliding mode control appropriately smoothed can be used successfully in actual (experimental or not) bipeds to increase their performance capabilities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Effect of Primary Cancer Cell Culture Models on the Results of Drug Chemosensitivity Assays: The Application of Perfusion Microbioreactor System as Cell Culture Vessel (2015)

To precisely and faithfully perform cell-based drug chemosensitivity assays, a well-defined and biologically relevant culture condition is required. For the former, a perfusion microbioreactor system capable of providing a stable culture condition was adopted. For the latter, however, little is known about the impact of culture models on the physiology and chemosensitivity assay results of primary oral cavity cancer cells. To address the issues, experiments were performed. Results showed that minor environmental pH change could significantly affect the metabolic activity of cells, demonstrating the importance of stable culture condition for such assays. Moreover, the culture models could also significantly influence the metabolic activity and proliferation of cells. Furthermore, the choice of culture models might lead to different outcomes of chemosensitivity assays. Compared with the similar test based on tumor-level assays, the spheroid model could overestimate the drug resistance of cells to cisplatin, whereas the 2D and 3D culture models might overestimate the chemosensitivity of cells to such anticancer drug. In this study, the 3D culture models with same cell density as that in tumor samples showed comparable chemosensitivity assay results as the tumor-level assays. Overall, this study has provided some fundamental information for establishing a precise and faithful drug chemosensitivity assay.
Widespread Occurrence of Ganglioside-Stimulated Protein Kinase in Animal Brains (1997)

Ganglioside-stimulated protein kinase, designated PKJ, had been found in several animal brains. These include guinea pig, rabbit, rat, and duck brains. All of the four brain PKJ could be extracted from the particulate fractions using nonionic detergent nonidet P-40 and purified by using identical DEAE-cellulose and phenyl-Sepharose chromatographic methods. These results suggest that PKJ from different animal brains has similar ionic and hydrophobic characteristics. All four of the partially purified PKJ preparations could undergo autophosphorylations in the presence of trisialoganglioside GT1b and 32P-ATP. Analyses of the autophosphorylated proteins by using SDS-polyacrylamide gel electrophoresis and subsequent autoradiography revealed one major radioactive band with apparent M(r) = 68,000. The range of ganglioside-stimulated autophosphorylation was between 6- and 10-fold. The structural similarities of the different animal brain PKJ were further determined by using one-dimensional peptide mapping techniques. Limited proteolytic cleavages of the 32P-labeled 68-kD bands with staphylococcal aureus V-8 protease resulted in four major radioactive fragments with apparent M(r) corresponding to 22, 20, 18 and 15 kD, respectively. By contrast, digestion with chymotrypsin revealed only two major radioactive bands with apparent M(r) of 43 and 26 kD, respectively. These findings indicate that PKJ from guinea pig, rabbit, rat, and duck brains may have similar primary structures.
Massive model visualization: An investigation into spatial partitioning (2009)

The current generation of visualization software is incapable of handling the interactive rendering of arbitrarily large models. While many solutions have been proposed for Massive Model Visualization, very few are able to achieve the full capabilities needed for a computer visualization solution. In most cases this is due to overly complex approaches that, while achieving impressive frame rates, make it virtually impossible to implement features like part manipulation. What is needed is a simple approach with rendering performance bounded by screen complexity not model size, with primitive traceability to the original model to facilitate part manipulation, and capability to be modified in near-real-time. This thesis introduces MMDr, a simple system to achieve interactive frame rates on extremely large data sets, while retaining support for most if not all the features required for a computer visualization solution.
O sistema de visita e a preservação da arte rupestre em dois sítios de ar livre do Nordeste português: o Vale do Côa e Mazouco (2003)

Since the opening of the Parque Arqueológico Vale do Côa (Côa Valley Archaeological Park - PAVC) the visitation scheme implemented in the Côa has come under intensescrutiny and criticism, done mostly by Portuguese archaeologists and by the local community. Considering these criticisms and some examples of different results of management strategies implemented in other Rock Art sites in the Northeastern area of Portugal and also in the World, the aim of this paper will be to discuss visitor access systems in a preservation versus public access socio-economic perspective. Since visitors are one of the main stakeholders in Cultural Heritage resources (CHR) management their feelings and opinions on public access schemes will also be assessed by means of a survey that aims to determine visitor satisfaction visitor satisfaction levels in the Côa Valley. Likewise, stakeholders and local community views on development and visitor management will be considered, resorting to interviews and to articles published in the local and national press. The intent of this paper will be to demonstrate that Rock Art sites, due to their specific nature, and specially the ones situated in this area of the Iberian Peninsula, require particular approaches, namely in the implementation of visitor access systems.
<title>Extract zero-crossings in a single-pass filtering</title> (1997)

Zero-crossings extracted from LoG filtering are widely used for pattern recognition and computer vision. Recursive filtering techniques have been applied to reduce the computational complexity of LoG filtering. However, extracting zero-crossings remains a time-consuming task and usually requires a second scanning process after filtering. This paper presents an algorithm using a line buffer to extract zero-crossings along with LoG filtering hence avoiding the need for an additional convolution and extra memory units. Because we know where the sign of two pixels crosses zero, the exact location of each zero-crossing can be calculated down to sub-pixel level by linear interpolation. The line buffer can be implemented easily in hardware, and real-time processing can be achieved.
Aroylation of Fused Pyrimidines; Synthesis of 4-Aroylfuro[2,3-d]-, 4-Aroylthieno[2,3-d]-, and 4-Aroylisoxazolo[5,4-d]pyrimidines (1997)

4-Aroylfuro[2,3-dl-(4), 4-aroylthieno[2.3-dl-(7and S), and 4aroylisoxazolo[5.4-d]pyrimidines(13) were synthesized by aroylation of the fused chloro-(3a and 12) or bromopyrimidines (3b, 5, and 6) with arenecarbaldehydes (2) catalyzed by an imidazolium salt (la).The fused aroylpyrimidines (4 and 7) were also synthesized by oxidative decyanation of a-phenylheteroareneacetonitriles (10 and 11).
The Lipid Organisation in the Skin Barrier (2000)

The main function of the skin is to protect the body against exogenous substances. The skin barrier is located in the outermost layer of the skin, the stratum corneum. This layer consists of keratin enriched cells embedded in lipid lamellae. These lamellae form the main barrier for diffusion of substances through the skin. In diseased skin the barrier function is often impaired. For a full understanding of the properties of the human skin barrier, insight in the stratum corneum lipid organisation is of great importance. In this paper a short description of the lipid organisation in normal human stratum corneum will be given, after which the role the main lipid classes play in the stratum corneum lipid organisation will be described. In addition the effect of cholesterol sulfate and calcium on the lipid organisation will be discussed. Finally a new model, the "sandwich model", will be proposed that describe the localisation of the fluid phases in the stratum corneum.
Detection of respiratory motion in fluoroscopic images for adaptive radiotherapy (2008)

Respiratory motion limits the potential of modern high-precision radiotherapy techniques such as IMRT and particle therapy. Due to the uncertainty of tumour localization, the ability of achieving dose conformation often cannot be exploited sufficiently, especially in the case of lung tumours. Various methods have been proposed to track the position of tumours using external signals, e.g. with the help of a respiratory belt or by observing external markers. Retrospectively gated time-resolved x-ray computed tomography (4D CT) studies prior to therapy can be used to register the external signals with the tumour motion. However, during treatment the actual motion of internal structures may be different. Direct control of tissue motion by online imaging during treatment promises more precise information. On the other hand, it is more complex, since a larger amount of data must be processed in order to determine the motion. Three major questions arise from this issue. Firstly, can the motion that has occurred be precisely determined in the images? Secondly, how large must, respectively how small can, the observed region be chosen to get a reliable signal? Finally, is it possible to predict the proximate tumour location within sufficiently short acquisition times to make this information available for gating irradiation? Based on multiple studies on a porcine lung phantom, we have tried to examine these questions carefully. We found a basic characteristic of the breathing cycle in images using the image similarity method normalized mutual information. Moreover, we examined the performance of the calculations and proposed an image-based gating technique. In this paper, we present the results and validation performed with a real patient data set. This allows for the conclusion that it is possible to build up a gating system based on image data, solely, or (at least in avoidance of an exceeding exposure dose) to verify gates proposed by the various external systems.
New CFOA-Based Single-Element-Controlled Sinusoidal Oscillators (2006)

New single-element-controlled sinusoidal oscillator (SECO) circuits using only two current-feedback operational amplifiers (CFOAs) and only five passive elements [two/three grounded capacitors (GC) and three/two resistors] are presented, which not only enlarge the previously known class of two-CFOA-GC SECOs but also provide new configurations that possess properties not available in the previously known circuits. The new oscillators are useful from the viewpoint of applications in several instrumentation and measurement situations such as oscillator-based capacitance measurement schemes, realization of very low frequency oscillators, and the design of voltage-controlled oscillators. Experimental results based upon commercially available AD844-type CFOAs are included, which confirm the practical workability of the new oscillator configurations
Designing sparse graphs via structure tensor for block transform coding of images (2015)

The graph Fourier transform (GFT) - adaptive to the signal structures of local pixel blocks - has recently been shown to be a good alternative to fixed transforms, e.g., the Discrete Cosine Transform (DCT), for image coding. However, the majority of proposed GFTs assume an underlying 4-connected graph structure with vertical and horizontal edges only. In this paper, we propose a design methodology to select more general sparse graph structures and edge weights, on which GFTs are defined for block-based coding. Specifically, we first cluster blocks via the Lloyd-Max algorithm based on their principal gradients, which are eigenvectors of the computed structure tensors. For each cluster a graph template with edges orthogonal to the principal gradient is designed. Finally, optimal edge weights are computed assuming each template is a graph describing the inter-pixel correlation in a Gaussian Markov Random Field (GMRF). Experimental results show that GFTs derived from our graph templates lead to sparser signal representations and fewer encoding bits than DCT for a set of natural test images.
Antigen-Reactive T Cell Enrichment for Direct, High-Resolution Analysis of the Human Naive and Memory Th Cell Repertoire (2013)

Ag-specific CD4(+) T cells orchestrating adaptive immune responses are crucial for the development of protective immunity, but also mediate immunopathologies. To date, technical limitations often prevented their direct analysis. In this study, we report a sensitive flow cytometric assay based on magnetic pre-enrichment of CD154(+) T cells to visualize rare Ag-reactive naive and memory Th cells directly from human peripheral blood. The detection limit of ≈ 1 cell within 10(5)-10(6) permitted the direct enumeration and characterization of auto-, tumor-, or neo-Ag-reactive T cells within the naive and even memory CD4(+) T cell repertoire of healthy donors. Furthermore, the analysis of high target cell numbers after pre-enrichment of rare Ag-specific T cells from large blood samples dramatically improved the identification of small subpopulations. As exemplified in this work, the dissection of the Ag-specific memory responses into small cytokine-producing subsets revealed great heterogeneity between pathogens, but also pathogen-related microsignatures refining Th cell subset classification. The possibility to directly analyze CD4(+) T cells reactive against basically any Ag of interest at high resolution within the naive and memory repertoire will open up new avenues to investigate CD4(+) T cell-mediated immune reactions and their use for clinical diagnostics.
Carrier transport through boron-doped amorphous diamond-like carbon <i>p</i> layer of amorphous silicon based <i>p–i–n</i> solar cells (1999)

The current transport mechanisms in boron-doped amorphous diamond-like carbon (p-a-DLC:H) used as part of the p layer of hydrogenated amorphous silicon (a-Si:H) solar cells are investigated by studying the temperature dependence of the dark current–voltage characteristics of the solar cell. The cell structure is glass/SnO2/p-a-DLC:H/p-a-SiC:H/i-a-Si:H/n-μc-Si:H/Al. The temperature dependence of the reverse saturation current and the ideality factor shows that carriers transport dominantly over the p-a-DLC:H by thermionic emission at higher temperatures above about 300 K and through the tunneling process by a hopping mechanism in the p-a-DLC:H at lower temperatures. Using the Schottky barrier model, it is shown that the lowering of the Schottky barrier height by inserting the interfacial p-a-DLC:H between the SnO2 and p-a-SiC:H causes the open circuit voltage and the short wavelength response of the cells to be enhanced.
Steric effects in di- and tri-arylmethane dyes. Part X. Electronic absorption spectra of bridged derivatives of malachite green and crystal violet (1971)

The isopropylidene group has been introduced singly and doubly into ortho-positions of Malachite Green and Crystal Violet in order to determine molecular conformation. The electronic absorption spectra of these dyes are discussed with particular reference to their bearing on intensity variations of the first band of ortho-derivatives of Malachite Green. The introduction of two isopropylidene bridges into Malachite Green and Crystal Violet produces considerable bathochromic shifts that can only be attributed to distortion of the aryl nuclei.Molecular planarity enforced by introduction of a 4,2′-isopropylidene bridge into 2,7-bisdimethylamino-10-(4′-dimethylaminophenyl)anthracene stabilises the cation formed by C9-protonation of the anthracene nucleus so that in 98% acetic acid about 60% of the amine is so protonated.