Miracle-dz/UniFAR-FTUs huggingface dataset:
L ‐ band SAR backscatter sensitivity to forest structure in semi ‐ arid environments : biomass retrieval error analysis at plot level

highlights:  The utility of L‐band synthetic aperture radar (SAR) backscatter data for estimating above ground biomass (ABG) in low biomass conditions (<100 t ha ‐1) and for different species composition was studied.  A water cloud type model was used to assess the relationships between field measured biomass and observed backscatter. Moreover, the retrieval errors were studied by biomass intervals using common empirical and semi‐empirical models.  Strong relationships were found between aboveground biomass and SAR backscatter at all sites. For areas with biomass levels below 30 t ha ‐1 the retrieval errors were as much as 250% of ground measured values due to the significant influence of surface backscatter. The estimation error decreased with biomass, being as low as 30% for the 50‐100 t ha ‐1 intervals.  This study shows that retrieval accuracy of forest biomass from L‐band SAR backscatter is highly variable within the range of forest biomass considered. In particular, larger errors were observed at both ends of the sensitivity interval. Low biomass levels (< 30 t ha ‐1) covered most of the dynamic range of the observed backscatter, indicating retrieval limitations when surface backscatter contributions are not accounted for. Extended Abstract: Many authors have studied the relationships between above ground biomass (AGB) and radar backscatter (Lucas et al. 2010; Luckman 1998; Santoro et al. 2006). However, only few studies provided detailed information on the accuracy of biomass retrieval that can be achieved through inversion of current empirical and/or physical models. Frequently no information on the retrieval accuracy is given, or only an average estimation error is provided for the entire biomass range. Most of the time the retrieved ABG intervals are much larger when compared to the range of ABG where L‐band observations exhibit sufficient sensitivity (0‐100 t/ha). In addition, very limited information on the retrieval accuracy by biomass interval is available. Such information could have significant impacts when modeling carbon storage for regions characterized by different biomass levels. This paper assesses the backscatter relationships for semi‐arid forests characterized by average biomass levels well below the L‐band saturation point (100 t/ha). The main objective was to evaluate the retrieval errors by biomass intervals
Quantitative analysis of circulating cell‐free Epstein–Barr virus (EBV) DNA levels in patients with EBV‐associated lymphoid malignancies

Cell‐free Epstein–Barr virus (EBV) DNA has recently been detected in the plasma and serum of patients with Hodgkin's disease, post‐transplant lymphoproliferative disease (PTLD) and acquired immunodeficiency syndrome‐related lymphoma. However, no data are available on the temporal variation of plasma/serum EBV DNA levels in patients with EBV‐associated lymphoid malignancies during the course of therapy. Using a real‐time quantitative polymerase chain reaction assay, we studied the plasma EBV DNA levels in 13 patients with EBV‐associated lymphoid malignancies (six patients with Hodgkin's disease, four with nasal natural killer/T‐cell lymphoma, two cases of PTLD and one patient with Burkitt's lymphoma) at presentation and during therapy. Plasma EBV DNA was detected in 12 of the 13 patients (median 2266 copies/ml; interquartile range 181–8379 copies/ml), but not in any of 35 healthy control subjects (P < 0·0001). The EBV status in tumour cells was also examined in 12 of these patients using in situ hybridization for EBV‐encoded small RNAs (EBERs). EBER positivity was observed in 11 patients, all of whom had EBV DNA detectable in plasma. The one patient who had no detectable plasma EBV DNA was also negative for EBERs in tumour tissue. Serial measurements of plasma EBV DNA levels were performed in nine of the patients during the course of therapy. All patients who responded to therapy demonstrated a significant reduction of plasma EBV DNA to low or undetectable levels, whereas in two patients with ineffective therapy, disease progression was associated with a rapid increase in plasma EBV DNA levels. We concluded that plasma EBV DNA is detectable in a wide range of EBV‐associated lymphoid malignancies. As plasma EBV DNA levels correlate well with the therapeutic response, such analysis may be a valuable tool for monitoring clinical progress.
The bacteriophage T4 AsiA protein: a molecular switch for sigma 70‐dependent promoters

The AsiA protein, encoded by bacteriophage T4, inhibits Eσ70‐dependent transcription at bacterial and early‐phage promoters. We demonstrate that the inhibitory action of AsiA involves interference with the recognition of the −35 consensus promoter sequence by host RNA polymerase. In vitro experiments were performed with a C‐terminally labelled sigma factor that is competent for functional holoenzyme reconstitution. By protease and hydroxyl radical protein footprinting, we show that AsiA binds region 4.2 of σ70, which recognizes the −35 sequence. Direct interference with the recognition of the promoter at this locus is supported by two parallel experiments. The stationary‐phase sigma factor containing holoenzyme, which can initiate transcription at promoters devoid of a −35 region, is insensitive to AsiA inhibition. The recognition of a galP1 promoter by Eσ70 is not affected by the presence of AsiA. Therefore, we conclude that AsiA inhibits transcription from Escherichia coli and T4 early promoters by counteracting the recognition of region 4.2 of σ70 with the −35 hexamer.
Effect of Magnetic Field on the Fiber Orientation during the Filling Process in Injection Molding, Part 1: Simulation and Mold Design

Conductive polymer composite material is increasingly applied in a variety of fields, and its related processing technology has been a focus of research and development. Regarding magnetic fiber, because the orientation and distribution of the fiber affect the electrical and mechanical properties of products, the control of fiber orientation and distribution has been regarded as a key technology. This study used magnetic-assisted injection molding to control the orientation of magnetic fibers during the melt-polymer filling process. A special mold containing a magnetic apparatus was simulated and designed. Its material and thickness of various spacing blocks as well as the optimal layout of magnets in the mold were determined. An actual mold with the same magnet layout was then manufactured accordingly, and the measured magnetic flux density was compared with simulated results. This study also examined the coupled effect of magnetic and flow fields on the orientation of nickel-coated carbon fibers, calculating the magnetic moment produced due to the influence of the magnetic field on the fibers when melt polymer flowed through various positions in the cavity during the filling process. The flow trajectories of the fibers, which were affected by the magnetic field, were also predicted.
Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system

Initiation of DNA replication is tightly controlled during the cell cycle to maintain genome integrity. In order to directly study this control we have previously established a cell-free system from human cells that initiates semi-conservative DNA replication. Template nuclei are isolated from cells synchronized in late G1 phase by mimosine. We have now used DNA combing to investigate initiation and further progression of DNA replication forks in this human in vitro system at single molecule level. We obtained direct evidence for bidirectional initiation of divergently moving replication forks in vitro. We assessed quantitatively replication fork initiation patterns, fork movement rates and overall fork density. Individual replication forks progress at highly heterogeneous rates (304 ± 162 bp/min) and the two forks emanating from a single origin progress independently from each other. Fork progression rates also change at the single fork level, suggesting that replication fork stalling occurs. DNA combing provides a powerful approach to analyse dynamics of human DNA replication in vitro.
An ancestor based extension to Differential Evolution (AncDE) for Single-Objective Computationally Expensive Numerical Optimization

This paper presents the Ancestral Differential Evolution (AncDE) algorithm, which extends the standard Differential Evolution (DE) algorithm by adding an archive of recently discarded ancestors. AncDE adds the ability to occasionally compute difference vectors between current and archived solutions, using these inter-generational difference vectors in place of traditional difference vectors. Results for AncDE are presented for the CEC2015 Bound Constrained Single-Objective Computationally Expensive Numerical Optimization Problems using AncDE/best/1/bin. Summary results are included for standard DE for comparison purposes and these show that AncDE generally outperforms standard DE. These results suggest that the inter-generational difference vectors can help overcome some local optima, leading to faster convergence towards the global optimum. AncDE involves the very small overhead of storing and updating the ancestral cache. This paper introduces two empirically determined stochastic rates; one for updating the ancestral cache and the other for using an ancestral difference vector in place of the normal difference vector.
Molecular and Cellular Changes in the Lumbar Spinal Cord following Thoracic Injury: Regulation by Treadmill Locomotor Training

Traumatic spinal cord injury (SCI) often leads to debilitating loss of locomotor function. Neuroplasticity of spinal circuitry underlies some functional recovery and therefore represents a therapeutic target to improve locomotor function following SCI. However, the cellular and molecular mechanisms mediating neuroplasticity below the lesion level are not fully understood. The present study performed a gene expression profiling in the rat lumbar spinal cord at 1 and 3 weeks after contusive SCI at T9. Another group of rats received treadmill locomotor training (TMT) until 3 weeks, and gene expression profiles were compared between animals with and without TMT. Microarray analysis showed that many inflammation-related genes were robustly upregulated in the lumbar spinal cord at both 1 and 3 weeks after thoracic injury. Notably, several components involved in an early complement activation pathway were concurrently upregulated. In line with the microarray finding, the number of microglia substantially increased not only in the white matter but also in the gray matter. C3 and complement receptor 3 were intensely expressed in the ventral horn after injury. Furthermore, synaptic puncta near ventral motor neurons were frequently colocalized with microglia after injury, implicating complement activation and microglial cells in synaptic remodeling in the lumbar locomotor circuitry after SCI. Interestingly, TMT did not influence the injury-induced upregulation of inflammation-related genes. Instead, TMT restored pre-injury expression patterns of several genes that were downregulated by injury. Notably, TMT increased the expression of genes involved in neuroplasticity (Arc, Nrcam) and angiogenesis (Adam8, Tie1), suggesting that TMT may improve locomotor function in part by promoting neurovascular remodeling in the lumbar motor circuitry.
Review: Emergency Department Use by Older Adults: A Literature Review on Trends, Appropriateness, and Consequences of Unmet Health Care Needs

Older adults use emergency departments (EDs) more than any other age group and are more prone to subsequent adverse events. This article reviews the literature on ED use by older adults within the context of evaluating their need for emergency care and the extent to which access to primary and supportive care services affect use. While a substantial research literature describes general patterns of ED use, there is much less research on ED use as a function of other health service use. Gaps in the research literature result in a limited understanding of the full scope of the issue and opportunities for practice and policy intervention.
Neuroadaptation of GABAergic transmission in the central amygdala during chronic morphine treatment

We investigated possible alterations of pharmacologically‐isolated, evoked GABAA inhibitory postsynaptic potentials (eIPSPs) and miniature GABAA inhibitory postsynaptic currents (mIPSCs) in the rat central amygdala (CeA) elicited by acute application of µ‐opioid receptor (MOR) agonists (DAMGO and morphine; 1 µM) and by chronic morphine treatment with morphine pellets. The acute activation of MORs decreased the amplitudes of eIPSPs, increased paired‐pulse facilitation (PPF) of eIPSPs and decreased the frequency (but not the amplitude) of mIPSCs in a majority of CeA neurons, suggesting that acute MOR‐dependent modulation of this GABAergic transmission is mediated predominantly via presynaptic inhibition of GABA release. We observed no significant changes in the membrane properties, eIPSPs, PPF or mIPSCs of CeA neurons during chronic morphine treatment compared to CeA of naïve or sham rats. Superfusion of the MOR antagonist CTOP (1 µM) increased the mean amplitude of eIPSPs in a majority of CeA neurons to the same degree in both naïve/sham and morphine‐treated rats, suggesting a tonic activation of MORs in both conditions. Superfusion of DAMGO decreased eIPSP amplitudes and the frequency of mIPSCs equally in both naïve/sham and morphine‐treated rats but decreased the amplitude of mIPSCs only in morphine treated rats, an apparent postsynaptic action. Our combined findings suggest the development of tolerance of the CeA GABAergic system to inhibitory effects of acute activation of MORs on presynaptic GABA release and possible alteration of MOR‐dependent postsynaptic mechanisms that may represent important neuroadaptations of the GABAergic and MOR systems during chronic morphine treatment.
Improved Booth Encoding for Reduced Area Multiplier

In designing high density circuit, size is a major concern in design. This paper presents a simple modification to the Booth Multiplier that can effectively reduce the area with an accepted scarified in speed. A conventional Booth Multiplier consists of Booth Encoder, Partial Product and Summation Tree. Rizalafande[1] introduced new design technique in generating the partial product's row. Meanwhile Hsin-Lei[2] introduced a novel circuit for Booth Encoder/Decoder which claims his design a smaller design. In this propose design, we are still using Rizalafande's architecture but replace the booth encoder with Hsin-Lei encoder. The design was implemented using the FLEX10K EPF10K70RC240-4 device and Altera MaxPlus+II software.
Representing and classifying arguments on the Semantic Web

Abstract Until recently, little work has been dedicated to the representation and interchange of informal, semi-structured arguments of the type found in natural language prose and dialogue. To redress this, the research community recently initiated work towards an Argument Interchange Format (AIF). The AIF aims to facilitate the exchange of semi-structured arguments among different argument analysis and argumentation-support tools. In this paper, we present a Description Logic ontology for annotating arguments, based on a new reification of the AIF and founded in Walton's theory of argumentation schemes. We demonstrate how this ontology enables a new kind of automated reasoning over argument structures, which complements classical reasoning about argument acceptability. In particular, Web Ontology Language reasoning enables significantly enhanced querying of arguments through automatic scheme classifications, instance classification, inference of indirect support in chained argument structures, and inference of critical questions. We present the implementation of a pilot Web-based system for authoring and querying argument structures using the proposed ontology.
Molecular Techniques for Determining Microbial Diversity and Community Structure in Natural Environments

The ability to quantify the number and kinds of microorganisms within a community is fundamental to the understanding of the structure and function of an ecosystem. The simple morphology of most microbes provides few clues for their identification and physiological traits are often ambiguous. In addition, many organisms resist cultivation, which is essential to their characterization. Recombinant DNA techniques have provided a means whereby many of the obstacles associated with cultivation and description can be overcome and subsequently has allowed many new insights into the complexity of natural microbial communities. Molecular approaches based on 16S ribosomal RNA (rRNA) sequence analysis allow direct investigation of the community structure, diversity, and phylogeny of microorganisms in almost any environment, while quantification of the individual types of microorganisms or entire microbial communities may be addressed by nucleic acid hybridization techniques. Furthermore, the use of fluorescently labeled population-specific rRNA probes allows microscopic examination of individual cells in complex microbial assemblages as well as their interactions in situ. In this review, we discuss strategies for characterizing microbial communities without the need for cultivation.
Max-Plus Algebra for Complex Variables and Its Application to Discrete Fourier Transformation

A generalization of the max-plus transformation, which is known as a method to derive cellular automata from integrable equations, is proposed for complex numbers. Operation rules for this transformation is also studied for general number of complex variables. As an application, the max-plus transformation is applied to the discrete Fourier transformation. Stretched coordinates are introduced to obtain the max-plus transformation whose imaginary part coinsides with a phase of the discrete Fourier transformation.
Neofunctionalization of Duplicated Tic40 Genes Caused a Gain-of-Function Variation Related to Male Fertility in Brassica oleracea Lineages1[W][OPEN]

Divergent duplicated genes in the Brassica oleracea gain a novel function that could restore the fertility of a Brassica napus male-sterile mutant. Gene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes.
Leisure-Time Physical Activity and All-Cause Mortality

Background Physical inactivity is a major public health problem associated with increased mortality risk. It is, however, poorly understood whether vigorous physical activity is more beneficial for reducing mortality risk than activities of lower intensity. The aim of this study was to examine associations of the intensity and volume of leisure-time physical activity with all-cause mortality among middle-aged women and men while considering sociodemographic and health related factors as covariates. Methods Questionnaire survey data collected in 2000-02 among 40–60-year-old employees of the City of Helsinki (N = 8960) were linked with register data on mortality (74% gave permission to the linkage) providing a mean follow-up time of 12-years. The analysis included 6429 respondents (79% women). The participants were classified into three groups according to intensity of physical activity: low moderate, high moderate and vigorous. The volume of physical activity was classified into three groups according to tertiles. Cox regression analysis was used to calculate hazard ratios (HR) and 95% confidence intervals (CIs) for all-cause mortality. Results During the follow up 205 participants died. Leisure-time physical activity was associated with reduced risk of mortality. After adjusting for covariates the vigorous group (HR = 0.54, 95% CI 0.34–0.86) showed a reduced risk of mortality compared with the low moderate group whereas for the high moderate group the reductions in mortality risk (HR = 0.72, 95% CI 0.48–1.08) were less clear. Adjusting for the volume of physical activity did not affect the point estimates. Higher volume of leisure-time physical activity was also associated with reduced mortality risk; however, adjusting for the covariates and the intensity of physical activity explained the differences. Conclusions For healthy middle-aged women and men who engage in some physical activity vigorous exercise may provide further health benefits preventing premature deaths.
Detecting and Removing Web Application Vulnerabilities with Static Analysis and Data Mining

Although a large research effort on web application security has been going on for more than a decade, the security of web applications continues to be a challenging problem. An important part of that problem derives from vulnerable source code, often written in unsafe languages like PHP. Source code static analysis tools are a solution to find vulnerabilities, but they tend to generate false positives, and require considerable effort for programmers to manually fix the code. We explore the use of a combination of methods to discover vulnerabilities in source code with fewer false positives. We combine taint analysis, which finds candidate vulnerabilities, with data mining, to predict the existence of false positives. This approach brings together two approaches that are apparently orthogonal: humans coding the knowledge about vulnerabilities (for taint analysis), joined with the seemingly orthogonal approach of automatically obtaining that knowledge (with machine learning, for data mining). Given this enhanced form of detection, we propose doing automatic code correction by inserting fixes in the source code. Our approach was implemented in the WAP tool, and an experimental evaluation was performed with a large set of PHP applications. Our tool found 388 vulnerabilities in 1.4 million lines of code. Its accuracy and precision were approximately 5% better than PhpMinerII's and 45% better than Pixy's.