gebhart/patrepeval huggingface dataset:
Plant Cell Wall Degradation by Saprophytic Bacillus subtilis Strains: Gene Clusters Responsible for Rhamnogalacturonan Depolymerization (2007)

Plant cell wall degradation is a premier event when Bacillus subtilis, a typical saprophytic bacterium, invades plants. Here we show the degradation system of rhamnogalacturonan type I (RG-I), a component of pectin from the plant cell wall, in B. subtilis strain 168. Strain 168 cells showed a significant growth on plant cell wall polysaccharides such as pectin, polygalacturonan, and RG-I as a carbon source. DNA microarray analysis indicated that three gene clusters (yesOPQRSTUVWXYZ, ytePQRST, and ybcMOPST-ybdABDE) are inducibly expressed in strain 168 cells grown on RG-I. Cells of an industrially important bacterium, B. subtilis strain natto, fermenting soybeans also express the gene cluster including the yes series during the assimilation of soybean used as a carbon source. Among proteins encoded in the yes cluster, YesW and YesX were found to be novel types of RG lyases releasing disaccharide from RG-I. Genetic and enzymatic properties of YesW and YesX suggest that strain 168 cells secrete YesW, which catalyzes the initial cleavage of the RG-I main chain, and the resultant oligosaccharides are converted to disaccharides through the extracellular exotype YesX reaction. The disaccharide is finally degraded into its constituent monosaccharides through the reaction of intracellular unsaturated galacturonyl hydrolases YesR and YteR. This enzymatic route for RG-I degradation in strain 168 differs significantly from that in plant-pathogenic fungus Aspergillus aculeatus. This is, to our knowledge, the first report on the bacterial system for complete RG-I main chain degradation.
Film-Cooling Performance of Multiple Arrays of Cylindrical and Fan-Shaped Holes (2015)

Experimental investigations are performed on the suction side of a cooled turbine guide vane. Transient infrared thermography is used to evaluate film-cooling performance of cylindrical and fan-shaped holes in a test facility representing engine conditions. Adiabatic film effectiveness and net heat flux reduction results due to coolant injection through double and multiple rows in the presence and absence of an upstream showerhead are presented. Two double staggered rows at different positions have been cross compared: one at a relatively high convex curvature region and the other close to the maximum throat velocity. A combination of the two double rows is considered to be multiple rows. The tested blowing ratios are in the interval of [0.6–1.2] and [0.3–1.2] for double and multiple rows, respectively. The showerhead cooling is maintained at a nominal blowing ratio. The findings suggest that the choice of best cooling hole shape for film-cooling design can be highly influenced by the number of cooling rows to be used and also the presence (or absence) of showerhead cooling. It is worth noting that the outcome may differ depending on the quantity of interest (i.e., adiabatic film effectiveness or net heat flux reduction).
GRaTIS: Free Bits in the Network (2013)

Recent work has examined techniques to estimate the “best” modulation rate for data networks such as 802.11a/g. While accurate rate estimation yields better rate-selection decisions and increased throughput, those methods must still choose between a handful of modulation rates. Each modulation rate is effective in a range of actual signal-to-noise ratios (SNRs) but the limited number of practical rates means that transmitters are often forced to “step down” to a lower data rate despite having a higher SNR than the minimum required for that lower rate. In this paper we describe, evaluate and implement a practical multiuser communication scheme that exploits these discrete “steps” in modulation rates to transmit two packets in the time normally needed to transmit a single packet, increasing aggregate throughput precisely when it is most needed—when the network is busy and suffers from rate unfairness. Because the method transmits a group of packets simultaneously, we call this scheme Group Rate Transmission with Intertwined Symbols, or GRaTIS. In addition to up to 120% improvement in network throughput achieved by GRaTIS, the technique is backward compatible with 802.11 and doesn’t require complex DSP algorithms as required by competing methods.
ROC with Cost Pareto Frontier Feature Selection Using Search Methods (2020)

Abstract Cyber-physical systems (CPS) are finding increasing application in many domains. CPS are composed of sensors, actuators, a central decision-making unit, and a network connecting all of these components. The design of CPS involves the selection of these hardware and software components, and this design process could be limited by a cost constraint. This study assumes that the central decision-making unit is a binary classifier, and casts the design problem as a feature selection problem for the binary classifier where each feature has an associated cost. Receiver operating characteristic (ROC) curves are a useful tool for comparing and selecting binary classifiers; however, ROC curves only consider the misclassification cost of the classifier and ignore other costs such as the cost of the features. The authors previously proposed a method called ROC Convex Hull with Cost (ROCCHC) that is used to select ROC optimal classifiers when cost is a factor. ROCCHC extends the widely used ROC Convex Hull (ROCCH) method by combining it with the Pareto analysis for cost optimization. This paper proposes using the ROCCHC analysis as the evaluation function for feature selection search methods without requiring an exhaustive search over the feature space. This analysis is performed on 6 real-world data sets, including a diagnostic cyber-physical system for hydraulic actuators. The ROCCHC analysis is demonstrated using sequential forward and backward search. The results are compared with the ROCCH selection method and a popular Pareto selection method that uses classification accuracy and feature cost.
DTN trials and router updates (2011)

We describe DTN trials carried out as part of the N4C project over the last year. These trials took place in two locations, Padjelanta national park in northern Sweden between early July and late August 2010 and Galway, on the west coast of Ireland, during early 2011. We also give an overview of the updates made to the hardware and software components used since previous trials and we outline an upcoming DTN trial planned for summer 2011 as part of the SAIL project.
Two-dimensional concurrent HMQC-COSY as an approach for small molecule chemical shift assignment and compound identification (2011)

Chemical shift assignment is the first step toward the structure elucidation of natural products and other chemical compounds. We propose here the use of 2D concurrent HMQC-COSY as an experiment for rapid chemical shift assignment of small molecules. This experiment provides well-dispersed (1)H-(13)C peak patterns that are distinctive for different functional groups plus (1)H-(1)H COSY connectivities that serve to identify adjacent groups. The COSY diagonal peaks, which are phased to be absorptive, resemble (1)H-(13)C HMQC cross peaks. We demonstrate the applicability of this experiment for rapidly and unambiguously establishing correlations between different functional groups through the analysis of the spectrum of a metabolite (jasmonic acid) dissolved in CDCl(3). In addition, we show that the experiment can be used to assign spectra of compounds in a mixture of metabolites in D(2)O.
A multi-factorial approach for middle-of-line design rule validation and optimization in 22FDX® (2018)

In order to allow competitive and low-cost designs in the 22nm FD-SOI technology 22FDX®, novel Middle-of-Line (MOL) constructs have been specifically enabled. Single-Diffusion Break and Gate Tie-Down constructs and their specific design-to-process validation requirements are described. In particular, contact punch-through is investigated and validated using electrical and E-beam inspection methods. As a second step, the Gate Tie-down is optimized thanks to layout Design of Experiments to provide optimal performance and density once implemented in Standard Cells.
Enzymatic Determination of Phosphatidylcholine, Sphingomyelin and Phosphatidylglycerol in Lipid Dispersions, Blood Cell Membranes and Rat Pulmonary Surfactant (1996)

A new micromethod for the determination of sphingomyelin in samples suspended in aqueous solutions, and modified micromethods for determining phosphatidylcholine and phosphatidylglycerol were used to determine phosphatidylcholine and sphingomyelin (detection limits of 1.8 mumol/l), and phosphatidylglycerol (detection limit of 2.3 mumol/l) in lipid dispersions, membranes from sheep erythrocytes and platelets, and pulmonary surfactants from rats of different ages and rats maintained under normobaric hyperoxia for 2 days prior to their sacrifice. The procedures are easy to perform, accurate, require less sample than conventional methods and can also be applied directly to aqueous samples. Phospholipase C and sphingomyelinase were used to release phosphorylcholine from phosphatidylglycerol and sphingomyelin, respectively. The choline released from phosphorylcholine by alkaline phosphatase is reconverted to phosphorylcholine by ATP and choline kinase. In the phophatidylglycerol determination, phospholipase D was used to release glycerol and phosphatidate. The glycerol formed was converted to glycerolphosphate using ATP and glycerol kinase. In all cases, the ADP thus formed was determined by following the enzymatic conversion of NADH to NAD at 340 nm in an coupled pyruvate kinase/lactate dehydrogenase system. Significant variations in the phospholipid composition of rat pulmonary surfactant were found during development; in particular there was an increase in the phosphatidylglycerol content of adult rats as compared with younger rats. Hyperoxia produced changes in the phosphatidylglycerol content of surfactant from adult rats, but not from 2-day old rats.
Machine independent algorithm for concurrent finite-element problems (1996)

The finite-element method, initially developed for mechanical and civil engineering applications, is now applied to electromagnetics. This paper describes how parallel processing applies to finite-element simulations. The methods discussed are the parallel Gaussian elimination and the parallel active column solver. Both methods reduce the time taken to determine the global coefficient matrix. The paper discusses the suitability of row- and column-based approaches when applying the parallel Gaussian method to parallel processing. The parallel active column solver uses a skyline storage technique.
Involvement of post-digestion "hydrophobic" peptides in plasma cholesterol-lowering effect of dietary plant proteins. (1986)

Peptides remaining or appearing during protein digestion were examined for a possibility of their involvement in the regulation of cholesterol levels in plasma. Plant proteins were somewhat inferior in digestibility to casein and their digestive products were abundant in 'hydrophobic' peptides relative to casein. The 'hydrophobic' peptides bound well to bile acid. There was a correlation between the plasma cholesterol level in rats given various food proteins and the hydrophobicity of their digestive products (peptic-pancreatic digests). The preponderance of hydrophobicity seems to favor an explanation for the cholesterol-lowering effects of plant proteins such as soy protein isolate and wheat gluten.
Some Good and Some Bad: Sand Fly Salivary Proteins in the Control of Leishmaniasis and in Autoimmunity (2022)

Sand flies are hematophagous insects responsible for the transmission of vector-borne diseases to humans. Prominent among these diseases is Leishmaniasis that affects the skin and mucous surfaces and organs such as liver and spleen. Importantly, the function of blood-sucking arthropods goes beyond merely transporting pathogens. The saliva of vectors of disease contains pharmacologically active components that facilitate blood feeding and often pathogen establishment. Transcriptomic and proteomic studies have enumerated the repertoire of sand fly salivary proteins and their potential use for the control of Leishmaniasis, either as biomarkers of vector exposure or as anti-<i>Leishmania</i> vaccines. However, a group of specific sand fly salivary proteins triggers formation of cross-reactive antibodies that bind the ectodomain of human desmoglein 1, a member of the epidermal desmosomal cadherins. These cross-reactive antibodies are associated with skin autoimmune blistering diseases, such as pemphigus, in certain immunogenetically predisposed individuals. In this review, we focus on two different aspects of sand fly salivary proteins in the context of human disease: The good, which refers to salivary proteins functioning as biomarkers of exposure or as anti-<i>Leishmania</i> vaccines, and the bad, which refers to salivary proteins as environmental triggers of autoimmune skin diseases.
Dictionary Learning for Image Coding Based on Multisample Sparse Representation (2014)

In this brief we propose a multisample sparse representation (MSR)-based online dictionary-learning approach to encode images more efficiently. To minimize the reconstructed error while handling a variety of image samples, we develop a multisample sparse representation method capable of obtaining sparser coefficients combined with learning dictionaries on-the-fly. With a well-learned dictionary, we further derive an MSR-based image coding approach to encode the quantized sparse coefficients with reduced reconstructed errors. Experimental results demonstrate rapid convergence of the proposed dictionary-learning algorithm and improved rate-distortion performance over other competitive image compression schemes both subjectively and quantitatively, validating the effectiveness of the proposed approach.
Horizontal Stabilisation of Sheathed Timber Frame Structures Using Plastic Design Methods – Introducing a Handbook Part 3: Basics of the Plastic Design Method (2016)

Design of shear walls has been a topic of major discussions to develop a common European code for design of timber structures. The main problem has been that shear walls are fastened to the substrate in different ways in different countries and that this fact must be reflected in the code. In this part the requirements are given that must be met for the ductile characteristics of the sheathing-to-framing joints in order for the plastic design method to be applicable. The method is based on the plastic lower bound theory. The fundamental prerequisites for the method are that the static equilibrium for the structure is fulfilled and that the sheathing-to-framing joints are ductile. What requirements that should be made on the mechanical properties of the joints for the plastic design methods to be applicable and the precaution measures to take to avoid brittle behaviour are discussed. The two main principles for anchoring of sheathed timber frame shear walls, fully and partially anchored, are illustrated showing the static behaviour of the walls and the force distribution in the framing members and the sheathings. In addition, a general description of the design in the serviceability limit state is given. For medium-rise and taller buildings the serviceability limit state needs to be taken into account. There are no specified criteria for deformations in the present code.
Group-Oriented Fingerprinting for Multimedia Forensics (2004)

Digital fingerprinting of multimedia data involves embedding information in the content signal and offers protection to the digital rights of the content by allowing illegitimate usage of the content to be identified by authorized parties. One potential threat to fingerprinting is collusion, whereby a group of adversaries combine their individual copies in an attempt to remove the underlying fingerprints. Former studies indicate that collusion attacks based on a few dozen independent copies can confound a fingerprinting system that employs orthogonal modulation. However, in practice an adversary is more likely to collude with some users than with other users due to geographic or social circumstances. To take advantage of prior knowledge of the collusion pattern, we propose a two-tier group-oriented fingerprinting scheme where users likely to collude with each other are assigned correlated fingerprints. Additionally, we extend our construction to represent the natural social and geographic hierarchical relationships between users by developing a more flexible tree-structure-based fingerprinting system. We also propose a multistage colluder identification scheme by taking advantage of the hierarchial nature of the fingerprints. We evaluate the performance of the proposed fingerprinting scheme by studying the collusion resistance of a fingerprinting system employing Gaussian-distributed fingerprints. Our results show that the group-oriented fingerprinting system provides the superior collusion resistance over a system employing orthogonal modulation when knowledge of the potential collusion pattern is available.
Synthesis of a One-Bead One-Compound Combinatorial Peptide Library (2003)

The four general methods to generate and screen a huge combinatorial peptide library (>107 peptides) are: biological libraries such as filamentous phage (), plasmid (), or polysome () libraries; the “one-bead one-compound” synthetic combinatonal library method or the “Selectlde process” (, , ); synthetic peptide library methods that require deconvolution, such as an iterative approach (,), positional scanning (); orthogonal partition approach (), or recurse deconvolution (); and synthetic library using affinity column selection method (,).
Supplemental Figure Legends from Tumor-Specific Inhibition of <i>In Situ</i> Vaccination by Distant Untreated Tumor Sites (2023)

&lt;p&gt;Supplemental Figure Legends&lt;/p&gt;
A Deep Learning Approach to Network Intrusion Detection (2018)

Network intrusion detection systems (NIDSs) play a crucial role in defending computer networks. However, there are concerns regarding the feasibility and sustainability of current approaches when faced with the demands of modern networks. More specifically, these concerns relate to the increasing levels of required human interaction and the decreasing levels of detection accuracy. This paper presents a novel deep learning technique for intrusion detection, which addresses these concerns. We detail our proposed nonsymmetric deep autoencoder (NDAE) for unsupervised feature learning. Furthermore, we also propose our novel deep learning classification model constructed using stacked NDAEs. Our proposed classifier has been implemented in graphics processing unit (GPU)-enabled TensorFlow and evaluated using the benchmark KDD Cup '99 and NSL-KDD datasets. Promising results have been obtained from our model thus far, demonstrating improvements over existing approaches and the strong potential for use in modern NIDSs.
Research on Applied Dynamic Equivalence Model for Wind Farm Based on Double-fed Wind Power Generating Units (2012)

Aiming at complicated simulation calculation due to adoption of detailed model for wind farm,the dynamic equivalence of wind farm is studied.The wind farms which share the same unit type and parameter are chosen and wind speed equivalence based multiple units parallel method is proposed;wind farms which own the same unit type but different parameters are taken as an example of the adoption of homology equivalence based capacity weighting method.On the base of DIgSILENT/PowerFactory and by comparison of the simulation method of multiple units parallel method,capacity weighted model and the detailed model under circumstance of wind speed change and transient faults,precision and acceptability of different models are verified,the result of which shows that the method is practical and effective.
AVALIAÇÃO DA QUALIDADE NUTRICIONAL DA LEUCENA EM BANCO FORRAGEIRO DE CORTE NO SUDESTE DO PARÁ (2013)

RESUMO: A utilização de bancos forrageiros de espécies lenhosas tem sido utilizada como uma alternativa sustentável para alimentação animal. O estudo foi realizado no assentamento Belo Horizonte I, no município de São Domingos do Araguaia - PA. Objetivou-se avaliar a qualidade nutricional da leucena (Leucaena leucocephala) em banco forrageiro de corte. O plantio das mudas foi realizado em fileiras espaçadas 1 m, com 3 m entre plantas. Para a avaliação foi realizado o corte das plantas a 70 cm do solo em março de 2010. As amostras foram separadas em fração não utilizável (caule ? 1 cm) e utilizável (folhas, vagem e galhos ? 1 cm) para a determinação do teor de proteína bruta (PB), fósforo (P), cálcio (Ca), magnésio (Mg), cobre (Cu), Ferro (Fe), manganês (Mn) e zinco (Zn). A avaliação da leucena durante o período chuvoso do ano demonstrou que a fração utilizável dessa forrageira atendeu aos requerimentos mínimos de PB, P, K, Ca, Mn e Fe para bovinos de corte em fase de lactação. PALAVRAS-CHAVE: leguminosa forrageira, Leucaena leucocephala, sistema silvipastoril.
Selective parity RARE imaging (2007)

Abstract This work describes a novel method for rapid acquisition with relaxation enhancement (RARE)/fast spin‐echo (FSE) imaging that removes the constraint of compliance with the Carr‐Purcell‐Meiboom‐Gill (CPMG) condition. In a multiecho sequence, echoes with either odd or even parities are acquired. The refocusing angles are chosen using a recursive algorithm, so that the signal amplitude satisfies a predetermined modulation function. In the examples given in this article an exponential decay to a plateau is used. At each echo the echo parity that gives the desired signal amplitude for the minimum refocusing angle is selected. It is further shown that in the presence of an initial magnetization having an arbitrary phase distribution, the complex conjugate of the signal of one echo parity has to be taken and its k ‐space coordinates reversed. T ‐weighted images are presented and initial applications to diffusion‐weighted imaging (DWI) and functional imaging shown. Magn Reson Med 58:643–649, 2007. © 2007 Wiley‐Liss, Inc.
Transcriptional regulation in the yeast GAL gene family: a complex genetic network (1995)

Regulation of the GAL structural genes in the yeast Saccharomyces cerevisiae is implemented by the products of GAL-specific (GAL4, GAL80, GAL3) and general (GAL11, SWI1, 2, 3, SNF5, 6, numerous glucose repression) genes. Recent work has 1) yielded significant new insights on the DNA binding and transcription activation/Gal80 protein binding functions of the Gal4 activator protein, 2) described the characterization of purified Gal4 protein-Gal80 protein complexes, 3) deconvoluted the multiple and complex glucose repression pathways acting on GAL genes, 4) suggested a new mechanism for the Gal3 protein-mediated induction of GAL structural gene expression, 5) introduced Gal1 protein, a structural gene product, into the regulation scheme, and 6) extended our already substantial understanding of GAL regulatory gene control. The mechanisms which control structural and regulatory gene expression in the GAL family are compared and GAL structural/regulatory gene chromatin structure is discussed.
Supplementary text from Exosomal Annexin II Promotes Angiogenesis and Breast Cancer Metastasis (2023)

&lt;p&gt;Supplementary text&lt;/p&gt;