gebhart/patrepeval huggingface dataset:
The development and deployment of a field-based loop mediated isothermal amplification assay for virulent Dichelobacter nodosus detection on Australian sheep (2018)

Dichelobacter nododus is the causative agent of footrot, a major disease of sheep that creates welfare concerns and large economic loss. The virulence of D. nododus depends on the presence of extracellular proteases, AprV2 and AprB2, which differ by one amino acid. Strains possessing AprV2 can cause clinically virulent disease, while AprB2 may cause clinically benign disease. Current methods for detecting D. nodosus are difficult, laborious and time consuming. New techniques capable of rapidly detecting and typing D. nodosus are needed to aid control programs. Molecular methods, like real-time polymerase chain reaction (rtPCR) can detect aprV2 and aprB2, however, this assay is not field-deployable and cannot support local decision-making during an outbreak. Here we present a field-based molecular assay for detecting aprV2, using loop mediated isothermal amplification (LAMP). The aprV2 LAMP (VDN LAMP) assay was optimised to reliably detect aprV2 from laboratory purified genomic (gDNA) of virulent D. nodosus down to 5x10(-3) ng μL-1, with time to positive (Tp) ≤ 16 minutes, while aprB2 was unreliably detected at 5 ng μL-1 from 16-20 minutes. The use of field collected samples that were rtPCR positive for aprB2 resulted in no amplification, while aprV2 positive field samples by VDN LAMP assay are defined as having Tps' of < 20 minutes and melting temperature between 88.0-88.9°C. When compared to rtPCR, the VDN LAMP was shown to have a diagnostic specificity of 100% and sensitivity of 83.33%. As proof of concept, the VDN LAMP was taken on farm, with all processing occurring in-field. The on farm VDN LAMP successfully detected 91.67% aprV2 positive samples, no aprB2 positive samples (n = 9) or D. nodosus negative (n = 23) samples, with a kappa agreement of 'almost perfect' to rtPCR. This highlights the potential of the assay to inform local treatment decisions for management.
Simple Image Description Generator via a Linear Phrase-based Model (2015)

Generating a novel textual description of an image is an interesting problem that connects computer vision and natural language processing. In this paper, we present a simple model that is able to generate descriptive sentences given a sample image. This model has a strong focus on the syntax of the descriptions. We train a purely bilinear model that learns a metric between an image representation (generated from a previously trained Convolutional Neural Network) and phrases that are used to described them. The system is then able to infer phrases from a given image sample. Based on caption syntax statistics, we propose a simple language model that can produce relevant descriptions for a given test image using the phrases inferred. Our approach, which is considerably simpler than state-of-the- art models, achieves comparable results on the recently release Microsoft COCO dataset.
Interferon‐α/β–mediated innate immune mechanisms in dermatomyositis (2005)

Dermatomyositis has been modeled as an autoimmune disease largely mediated by the adaptive immune system, including a local humorally mediated response with B and T helper cell muscle infiltration, antibody and complement-mediated injury of capillaries, and perifascicular atrophy of muscle fibers caused by ischemia. To further understand the pathophysiology of dermatomyositis, we used microarrays, computational methods, immunohistochemistry and electron microscopy to study muscle specimens from 67 patients, 54 with inflammatory myopathies, 14 with dermatomyositis. In dermatomyositis, genes induced by interferon-alpha/beta were highly overexpressed, and immunohistochemistry for the interferon-alpha/beta inducible protein MxA showed dense staining of perifascicular, and, sometimes all myofibers in 8/14 patients and on capillaries in 13/14 patients. Of 36 patients with other inflammatory myopathies, 1 patient had faint MxA staining of myofibers and 3 of capillaries. Plasmacytoid dendritic cells, potent CD4+ cellular sources of interferon-alpha, are present in substantial numbers in dermatomyositis and may account for most of the cells previously identified as T helper cells. In addition to an adaptive immune response, an innate immune response characterized by plasmacytoid dendritic cell infiltration and interferon-alpha/beta inducible gene and protein expression may be an important part of the pathogenesis of dermatomyositis, as it appears to be in systemic lupus erythematosus.
HPLC Analysis of Reduced and Oxidized Coenzyme Q10 in Human Plasma (2001)

This optimized method for CoQ(10)H(2) analysis provides rapid and precise results with the potential for high throughput. This method is specific and sufficiently sensitive for use in both clinical and research laboratories.
Evaluating uncertainties in net power delivery using dual directional couplers (2006)

Directional couplers are used extensively to monitor power flow in a transmission line. It is essential to evaluate measurement uncertainties of the power delivery systems for many RF applications. For example, in a field probe calibration process, accurate net power measurements are needed to establish the standard fields. This paper employs the complete model equation (using the full four-port S-parameters of the coupler) to evaluate the measurement uncertainties in the net power. Uncertainties can also be estimated with scalar quantities when vector quantities are not available. In such a case, one can use the scalar coupling coefficients, VSWR and/or directivities of a coupler, and assume random phases to derive an uncertainty budget. On the other hand, when both the vector S-parameters of the coupler and the complex reflection coefficients of the load are known, the net power can be determined exactly using the full model equation.
Mechanisms of the lysophosphatidic acid‐induced increase in [Ca2+]iin skeletal muscle cells (2008)

Although lysophosphatidic acid (LPA) is known to increase intracellularfree calcium concentration ([Ca(2+)](i)) in different cell types, the effect of LPA on the skeletal muscle cells is not known. The present study was therefore undertaken to examine the effect of LPA on the [Ca(2+)](i) in C2C12 cells. LPA induced a concentration and time dependent increase in [Ca(2+)](i), which was inhibited by VPC12249, VPC 32183 and dioctanoyl glycerol pyrophosphate, LPA1/3 receptor antagonists. Pertussis toxin, a G(i) protein inhibitor, also inhibited the LPA-induced increase in [Ca(2+)](i). Inhibition of tyrosine kinase activities with tyrphostin A9 and genistein also prevented the increase in [Ca(2+)](i) due to LPA. Likewise, wortmannin and LY 294002, phosphatidylinositol 3-kinase (PI3-K) inhibitors, inhibited [Ca(2+)](i) response to LPA. The LPA effect was also attenuated by ethylene glycolbis(beta-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA), an extracellular Ca(2+) chelator, Ni(2+) and KB-R7943, inhibitors of the Na(+)-Ca(2+) exchanger; the receptor operated Ca(2+) channel (ROC) blockers, 2-aminoethoxydiphenyl borate and SK&F 96365. However, the L-type Ca(2+) channel blockers, verapamil and diltiazem; the store operated Ca(2+) channel blockers, La(3+) and Gd(3+); a sarcoplasmic reticulum calcium pump inhibitor, thapsigargin; an inositol trisphosphate receptor antagonist, xestospongin and a phospholipase C inhibitor, U73122, did not prevent the increase [Ca(2+)](i) due to LPA. Our data suggest that the LPA-induced increase in [Ca(2+)](i) might occur through G(i)-protein coupled LPA(1/3) receptors that may be linked to tyrosine kinase and PI3-K, and may also involve the Na(+)-Ca(2+) exchanger as well as the ROC. In addition, LPA stimulated C2C12 cell proliferation via PI3-K. Thus, LPA may be an important phospholipid in the regulation of [Ca(2+)](i) and growth of skeletal muscle cells.
Quelles stratégies alternatives aux antibiotiques en aquaculture ? (2007)

Malgré des réglementations contraignantes, l’usage des antibiotiques en préventif est encore répandu en aquaculture, particulièrement pendant les phases critiques (stades précoces, métamorphose, transferts d’animaux), mais aussi chez des animaux en croissance. En plus des améliorations que l’on peut encore apporter en matière de zootechnie et de prophylaxie traditionnelle, des méthodes alternatives sont maintenant disponibles ou en développement. Les préparations microbiennes commercialisées pour les élevages terrestres sont de plus en plus utilisées pour les élevages de crevettes et de poissons, mais chaque espèce ou élevage demanderait des expérimentations particulières pour déterminer les produits et les doses les plus efficaces. En effet, les réponses des animaux à l’ajout des probiotiques peuvent être variables et l’absence de données fiables freine leur application en routine. Les probiotiques d’origine terrestre contenant des Lactobacillus, des Bacillus ou d’autres bactéries de genres connexes, ou bien encore des levures, ne conviennent pas pour les mollusques bivalves comme les huîtres, les coquilles St Jacques, les palourdes. Seules quelques bactéries marines sélectionnées protègent les larves de bivalves contre les infections bactériennes. Cependant, l’utilisation pratique de ces bactéries gram (-) pose de nombreux problèmes d’autorisation légale, de production, de conservation et de distribution. L’intérêt des probiotiques réside dans leurs effets multiples, qui associent à des activités antibactériennes, des effets sur l’hôte telles que la stimulation de la réponse immunitaire ou celle de la croissance, bien que les mécanismes d’action ne soient pas clairement identifiés. Par contre ils n’ont pas la même efficacité que les antibiotiques pour stopper une infection. Les prébiotiques comme les fructo-oligosaccharides constituent une autre possibilité d’améliorer la santé des animaux, et des essais ont montré leur efficacité chez les alevins de turbot par exemple. Une troisième alternative est représentée par les peptides antimicrobiens. Ces molécules ont un large spectre d’activité antimicrobienne. Ils peuvent tuer des bactéries gram (-) et gram (+), des champignons ou des virus enveloppés. Plusieurs de ces peptides viennent d’être découverts chez les invertébrés marins (crevettes et huîtres), où ils sont un élément essentiel de la défense de ces animaux sans immunité acquise. Ils pourraient remplacer avantageusement les antibiotiques à terme. Ils devraient générer moins de résistances chez les microorganismes cibles, car ils agissent sur les membranes cellulaires et ils devraient être plus vite dégradés sans produire de résidus.
Cooling the Foot to Prevent Diabetic Foot Wounds (2005)

The etiology of neuropathic diabetic foot wounds can be summarized by the following formula: pressure x cycles of repetitive stress = ulceration. The final pathway to ulceration consists of an inflammatory response, leading to tissue breakdown. Mitigation of this response might reduce the risk of ulceration. This proof-of-concept trial evaluates whether simple cooling of the foot can safely reduce the time to thermal equilibrium after activity. After a 15-min brisk walk, the six nondiabetic volunteers enrolled were randomly assigned to receive either air cooling or a 10-min 55 degrees F cool water bath followed by air cooling. The process was then repeated with the intervention reversed, allowing subjects to serve as their own controls. There was a rise in mean +/- SD skin temperature after 15 min of activity versus preactivity levels (87.8 degrees +/- 3.9 degrees versus 79 degrees +/- 2.2 degrees F; P = .0001). Water cooling immediately brought the foot to a point cooler than preactivity levels for all subjects, whereas air cooling required an average of nearly 17 min to do so. Ten minutes of cooling required a mean +/- SD of 26.2 +/- 5.9 min to warm to preactivity levels. No adverse effects resulted from the intervention. We conclude that cooling the foot may be a safe and effective method of reducing inflammation and may serve as a prophylactic or interventional tool to reduce skin breakdown risk.
Performance of erbium-doped fibre amplifiers (1990)

The field of rare-earth-doped fibre lasers and amplifiers has expanded rapidly in recent years and there are now numerous groups working actively in the area. A variety of glass hosts, dopants and pump sources have been used, with the goal of achieving low-threshold, diode-laser-pumped operation of fibre lasers and amplifiers, particularly those operating in either the second or third telecommunication windows.
Causal connectivity of evolved neural networks during behavior (2005)

To show how causal interactions in neural dynamics are modulated by behavior, it is valuable to analyze these interactions without perturbing or lesioning the neural mechanism. This paper proposes a method, based on a graph-theoretic extension of vector autoregressive modeling and 'Granger causality,' for characterizing causal interactions generated within intact neural mechanisms. This method, called 'causal connectivity analysis' is illustrated via model neural networks optimized for controlling target fixation in a simulated head-eye system, in which the structure of the environment can be experimentally varied. Causal connectivity analysis of this model yields novel insights into neural mechanisms underlying sensorimotor coordination. In contrast to networks supporting comparatively simple behavior, networks supporting rich adaptive behavior show a higher density of causal interactions, as well as a stronger causal flow from sensory inputs to motor outputs. They also show different arrangements of 'causal sources' and 'causal sinks': nodes that differentially affect, or are affected by, the remainder of the network. Finally, analysis of causal connectivity can predict the functional consequences of network lesions. These results suggest that causal connectivity analysis may have useful applications in the analysis of neural dynamics.
Data in support of Gallium (Ga3+) antibacterial activities to counteract E. coli and S. epidermidis biofilm formation onto pro-osteointegrative titanium surfaces (2016)

This paper contains original data supporting the antibacterial activities of Gallium (Ga(3+))-doped pro-osteointegrative titanium alloys, obtained via Anodic Spark Deposition (ASD), as described in "The effect of silver or gallium doped titanium against the multidrug resistant Acinetobacter baumannii" (Cochis et al. 2016) [1]. In this article we included an indirect cytocompatibility evaluation towards Saos2 human osteoblasts and extended the microbial evaluation of the Ga(3+) enriched titanium surfaces against the biofilm former Escherichia coli and Staphylococcus epidermidis strains. Cell viability was assayed by the Alamar Blue test, while bacterial viability was evaluated by the metabolic colorimetric 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay. Finally biofilm morphology was analyzed by Scanning Electron Microscopy (SEM). Data regarding Ga(3+) activity were compared to Silver.
An evaluation of permanent deformation properties of crumb rubber modified (CRM) asphalt concrete mixtures (1995)

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Versatile Particle-Based Route to Engineer Vertically Aligned Silicon Nanowire Arrays and Nanoscale Pores (2015)

Control over particle self-assembly is a prerequisite for the colloidal templating of lithographical etching masks to define nanostructures. This work integrates and combines for the first time bottom-up and top-down approaches, namely, particle self-assembly at liquid-liquid interfaces and metal-assisted chemical etching, to generate vertically aligned silicon nanowire (VA-SiNW) arrays and, alternatively, arrays of nanoscale pores in a silicon wafer. Of particular importance, and in contrast to current techniques, including conventional colloidal lithography, this approach provides excellent control over the nanowire or pore etching site locations and decouples nanowire or pore diameter and spacing. The spacing between pores or nanowires is tuned by adjusting the specific area of the particles at the liquid-liquid interface before deposition. Hence, the process enables fast and low-cost fabrication of ordered nanostructures in silicon and can be easily scaled up. We demonstrate that the fabricated VA-SiNW arrays can be used as in vitro transfection platforms for transfecting human primary cells.
Resurrection of vitamin D deficiency and rickets (2006)

The epidemic scourge of rickets in the 19th century was caused by vitamin D deficiency due to inadequate sun exposure and resulted in growth retardation, muscle weakness, skeletal deformities, hypocalcemia, tetany, and seizures. The encouragement of sensible sun exposure and the fortification of milk with vitamin D resulted in almost complete eradication of the disease. Vitamin D (where D represents D2 or D3) is biologically inert and metabolized in the liver to 25-hydroxyvitamin D [25(OH)D], the major circulating form of vitamin D that is used to determine vitamin D status. 25(OH)D is activated in the kidneys to 1,25-dihydroxyvitamin D [1,25(OH)2D], which regulates calcium, phosphorus, and bone metabolism. Vitamin D deficiency has again become an epidemic in children, and rickets has become a global health issue. In addition to vitamin D deficiency, calcium deficiency and acquired and inherited disorders of vitamin D, calcium, and phosphorus metabolism cause rickets. This review summarizes the role of vitamin D in the prevention of rickets and its importance in the overall health and welfare of infants and children.
State of Transcatheter Aortic Valve Implantation in Spain Versus Europe and Non-European Countries. (2018)

Routine TAVI practice in Spain differed in some key aspects of preprocedural, intraprocedural, and postprocedural management. Future studies will help to unify strategies and assess their impact on clinical results.
Biohydrogels for medical applications: A short review (2018)

Hydrogels have been widely used as drug delivery systems for scaffold production (in different soft and hard tissue engineering, including bones), thanks to their biocompatibility and biodegradability. In addition to the possibility of synthesizing a wide range of hydrogels from various natural and synthetic polymers, they are suitable for scaffold production. Moreover, they can have antimicrobial, antitumor and analgesic functions due to their intrinsic properties or through addition of proper biologically active agents. In this article, different types of hydrogels are reviewed alongside their application areas. Different methods are applied for the preparation of hydrogels and their compositions, and are strongly correlated with the morphological and mechanical properties of the synthesized hydrogels, which had a great influence on the performances of the respective scaffolds. The most effective ways to produce the desired scaffolds are mold casting, especially, 3D printing and electrospinning due to the ability to manipulate and control the shape and size of the desired scaffold as well as their microstructure.
Exponential suppression of bit or phase errors with cyclic error correction (2021)

Realizing the potential of quantum computing requires sufficiently low logical error rates<sup>1</sup>. Many applications call for error rates as low as 10<sup>-15</sup> (refs. <sup>2-9</sup>), but state-of-the-art quantum platforms typically have physical error rates near 10<sup>-3</sup> (refs. <sup>10-14</sup>). Quantum error correction<sup>15-17</sup> promises to bridge this divide by distributing quantum logical information across many physical qubits in such a way that errors can be detected and corrected. Errors on the encoded logical qubit state can be exponentially suppressed as the number of physical qubits grows, provided that the physical error rates are below a certain threshold and stable over the course of a computation. Here we implement one-dimensional repetition codes embedded in a two-dimensional grid of superconducting qubits that demonstrate exponential suppression of bit-flip or phase-flip errors, reducing logical error per round more than 100-fold when increasing the number of qubits from 5 to 21. Crucially, this error suppression is stable over 50 rounds of error correction. We also introduce a method for analysing error correlations with high precision, allowing us to characterize error locality while performing quantum error correction. Finally, we perform error detection with a small logical qubit using the 2D surface code on the same device<sup>18,19</sup> and show that the results from both one- and two-dimensional codes agree with numerical simulations that use a simple depolarizing error model. These experimental demonstrations provide a foundation for building a scalable fault-tolerant quantum computer with superconducting qubits.
Photocatalysts: Energy States of a Core‐Shell Metal Oxide Photocatalyst Enabling Visible Light Absorption and Utilization in Solar‐to‐Fuel Conversion of Carbon Dioxide (Adv. Energy Mater. 14/2016) (2016)

In article number 1600583, Yong-Hoon Kim, Jeung Ku Kang, and co-workers describe core-shell metal oxides with energy states enabling fast photo-catalytic electron-hole separation, where their shells are constructed to create the valence band maximum extending the photoactive spectrum for visible light absorption. These visible light sensitizing core-shell photocatalysts allow efficient solar-to-fuel conversion of carbon dioxide into value-added fuels such as methanol.
Short-term electric load forecasting via fuzzy-neural collaboration (1999)

An important element of effective power system operation is the well-planned short term scheduling of power generating units. The power system operator uses historical load data to schedule the available generating units to meet the hourly system loads in an economical and reliable manner. A Fuzzy Logic (FL) expert system is integrated with Artificial Neural Networks (ANN) for a more reliable operation of short-term load forecasting. 
The 24 hours ahead forecasted load is obtained through two steps. First, the FL module carries the job of mapping the highly non-linear relationship between the weather parameters and it's impact on the daily electric load peak. Second, the 12 ANN modules are trained using historical hourly load and weather data, combined with the FL output data, to perform the final forecast. A comparison made between this model, an ANN model, and an Autoregressive Moving Average (ARMA) model shows the efficiency and accuracy of this new approach.