Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of Intimin Subtypes among Escherichia coli Isolates from Ruminant and Human Sources

ABSTRACT The intimin gene eae, located within the locus of enterocyte effacement pathogenicity island, distinguishes enteropathogenic Escherichia coli (EPEC) and some Shiga toxin-producing E. coli (STEC) strains from all other pathotypes of diarrheagenic E. coli. EPEC is a leading cause of infantile diarrhea in developing countries, and intimin-positive STEC isolates are typically associated with life-threatening diseases such as hemolytic-uremic syndrome and hemorrhagic colitis. Here we describe the development of a PCR-restriction fragment length polymorphism (RFLP) assay that reliably differentiates all 11 known intimin types (α1, α2, β, γ, κ, ε, η, ι, λ, θ, and ζ) and three new intimin genes that show less than 95% nucleotide sequence identity with existing intimin types. We designated these new intimin genes Int-μ, Int-ν, and Int-ξ. The PCR-RFLP assay was used to screen 213 eae-positive E. coli isolates derived from ovine, bovine, and human sources comprising 60 serotypes. Of these, 82 were STEC isolates, 89 were stx-negative (stx−) and ehxA-positive (ehxA+) isolates, and 42 were stx− and ehxA-negative isolates. Int-β, the most commonly identified eae subtype (82 of 213 [38.5%] isolates), was associated with 21 serotypes, followed by Int-ζ (39 of 213 [18.3%] isolates; 11 serotypes), Int-θ (25 of 213 [11.7%] isolates; 15 serotypes), Int-γ (19 of 213 [8.9%] isolates; 9 serotypes), and Int-ε (21 of 213 [9.9%] isolates; 5 serotypes). Intimin subtypes α1, α2, κ, λ, ξ, μ, ν, and ι were infrequently identified; and Int-η was not detected. Phylogenetic analyses with the Phylip package of programs clustered the intimin subtypes into nine distinct families (α, β-ξ, γ, κ, ε-η-ν, ι-μ, λ, θ, and ζ). Our data confirm that ruminants are an important source of serologically and genetically diverse intimin-containing E. coli strains.
New Islanding Detection Method for Inverter-Based Distributed Generation Considering Its Switching Frequency

Islanding detection is one of the most important issues for the distributed generation (DG) systems connected to an electric power grid. The conventional passive islanding detection methods inherently have a nondetection zone (NDZ), and active islanding detection methods might cause problems with safety, reliability, stability, and power quality on a power system. This paper proposes a passive islanding detection method with the zero NDZ property by considering the switching frequency from an inverter of the DG system. Moreover, the proposed method does not cause any negative effects in the aforementioned problems because it avoids applying the intended changes such as variations of reactive power and/or harmonics, which are required in the active islanding detection methods. Several case studies are carried out to verify that the proposed method can detect the islanding operation within 20 ms, which is less than 150 ms required in a recloser as the shortest mechanical reclosing (delay) time. Moreover, this value satisfies the requirement of 2 s given in IEEE Std. 1547.
Global Chemical Composition and Antioxidant and Anti-Tuberculosis Activities of Various Extracts of Globularia alypum L. (Globulariaceae) Leaves

In this work, an evaluation of the biological activities of Globularia alypum L. extracts and their global chemical composition was realized. Extracts from G. alypum were obtained by two extraction methods. The composition of polyphenols (8.5–139.95 g gallic acid equivalent/Kg of dry mass), tannins (1.39–18.65 g catechin equivalent/Kg of dry mass), anthocyanins (8.17–70.69 mg cyanidin equivalent/Kg of dry mass) and flavonoids (0.31–19.28 g quercetin equivalent/Kg of dry mass) was evaluated. The samples were subjected to a screening for their antioxidant activities using the DPPH● and ABTS●+ assays. For the first time, the anti-tuberculosis activity (H37Rv) for G. alypum was tested against Mycobacterium tuberculosis. The strongest antioxidant activity was obtained for the methanol extract (IC50 = 15.58 ± 0.168 mg/L) and the best anti-tuberculosis activity was obtained for the petroleum ether extract (IC50 = 77 mg/L). We have found a positive correlation between the total phenolics content and the antioxidant activity R2 = 0.88 (DPPH●) and R2 = 0.97 (ABTS●+). We have found also a positive correlation between the flavonoid content and the antioxidant activity R2 = 0.91 (DPPH●) and R2 = 0.91 (ABTS●+).
Active noise cancellation with a new variable tap length and step size FXLMS algorithm

The filtered-X least mean square (FxLMS) algorithm is widely used for active noise cancellation (ANC). Some variants of FxLMS algorithms have been studied to reduce computational complexity or to improve convergence rate. In general applications, a long tap length is usually required for the conventional FxLMS method which convergence rate is very slow though its structure is possibly very easy to implement. In this paper, a new ANC system is proposed with a variable tap length and step size FxLMS algorithm. Taking into account the effect of the lowpass filter in the secondary path of an ANC system, the impulse response of the control filter is modeled with a two-sided exponential decay envelope to develop our algorithm. Simulation results show that the proposed algorithm does provide a significant performance improvement on convergence rate and noise reduction ratio compared to the fixed tap FxLMS and previously proposed variable step size FxLMS algorithms.
Effect of organics, biofertilizers and crop residue application on soil microbial activity in rice – wheat and rice-wheat mungbean cropping systems in the Indo-Gangetic plains

Abstract The aim of this study was to investigate the response of soil microbial parameters to nutrient management practices involving organic amendments, farmyard manure (FYM), vermicompost (VC), crop residues (CR) and biofertilizers (BF) in rice–wheat and rice–wheat–mung bean cropping system of the Indo-Gangetic Plains, India. Soil microbial biomass C (Cmic), basal respiration, ergosterol, glomalin, soil enzymes (glucosidases, phosphatases and dehydrogenases), FDA activity, organic carbon (Corg), Cmic-to-Corg ratio and metabolic quotient (qCO2) were estimated in soil samples collected at 0–15 cm depth. The highest Corg (0.64%) and Cmic (103.8 μg g−1) soil levels occurred in the treatment receiving a combination of VC, CR and BF. Soil respiration, Corg and Cmic-to-Corg ratio were significantly enhanced by the input of CR to plots receiving FYM and VC. The qCO2 was the highest in plots receiving a combination of FYM, CR and BF followed by control (no nutrient input) and least in plots receiving a combination of VC, crop residue and biofertilizer. These results indicate that the organic practices involving VC, CR and BF improved soil microbial characteristics and Corg in rice–wheat systems.
Factors influencing women's decisions for choice of surgery for Stage I and Stage II breast cancer in Western Australia.

BACKGROUND Internal and external factors have been reported to influence decision-making by women for breast cancer surgery. AIM OF THE STUDY The aim of the study was to describe the factors those women with Stage I or Stage II breast cancer, perceived to be important when selecting either modified radical mastectomy or breast conserving treatment. DESIGN/METHOD A descriptive correlational study was conducted. A consecutive sample of women with a diagnosis of breast cancer during a 6-month period was selected from the Health Department of Western Australia Cancer Registry. RESULTS Women who had breast conserving treatment rated the surgeon's preference as a more important factor in decision-making than women who had modified radical mastectomy. The lack of difference in long-term survival between the types of surgery was also a more important influence on decision-making for the breast conserving treatment group compared with women who had received modified radical mastectomy. Women in rural areas tended to choose modified radical mastectomy rather than breast conserving treatment. The surgeon, family and general practitioner were important sources of information. A significant association was found between women's involvement in decision-making and their use of a general practitioner as an information source. Many women wanted the decision about surgery to be entirely their own; the breast conserving treatment group preferred a more active role in decision-making compared with those who chose modified radical mastectomy. Most women had participated in the decision-making process as much as they wished, had enough time in which to make their decisions and had received sufficient information. A correlation between adequacy of information and sufficient time for decision-making was found. CONCLUSION Findings may be useful to nurses and other health professionals who endeavour to provide adequate information and support to women during their initial treatment decision-making experience.
Bio-economic Impact of Strategic Changes in Murrah River Buffalo Management

The aim of this paper was to evaluate the effects of changes in the strategy to manage the bio-economic efficiency of a Murrah Buffalo production system in the province of Camagüey, Cuba, located 21o north and 77o west, 217 meters above sea level. The climate is tropical humid (Aw) of plains. The mean annual precipitations were 1 180 mm (71% between May and October), the temperatures were between 24 and 29 °C. The soil is brown, without carbonates, and brown-red fersiallitic. The system comprises 5 100 ha and has 536 workers/year. A strategy to introduce management changes in agro-technical, food, reproductive, replacement, health, salary policy, and training was implemented as part of an innovation package with a systemic and participatory approach. The evaluation lasted eight years, and it was critical to increase dairy production in more than 200 000 kg/year in 2012, in comparison to 2004, with improvements in natality and reduction of operational expenses of the system. It was concluded that the strategy had a determining effect on the system's indicators.
Heterostyly accelerates diversification via reduced extinction in primroses

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower–pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification.
Two amino acid substitutions in the tomato mosaic virus 30-kilodalton movement protein confer the ability to overcome the Tm-2(2) resistance gene in the tomato

The Tm-2(2) resistance gene is used in most commercial tomato cultivars for protection against infection with tobacco mosaic virus and its close relative tomato mosaic virus (ToMV). To study the mechanism of this resistance gene, cDNA clones encompassing the complete genome of a ToMV strain (ToMV-2(2)) that was able to break the Tm-2(2) resistance were generated. Chimeric full-length viral cDNA clones were constructed under the control of the cauliflower mosaic virus 35S RNA promoter, combining parts of the wild-type virus and ToMV-2(2). Using these clones in cDNA infection experiments, we showed that the 30-kDa movement protein of ToMV-2(2) is responsible for overcoming the Tm-2(2) resistance gene in the tomato. DNA sequence analysis revealed four amino acid exchanges between the 30-kDa proteins from wild-type ToMV and ToMV-2(2), Lys-130 to Glu, Gly-184 to Glu, Ser-238 to Arg, and Lys-244 to Glu. To clarify the involvement of the altered amino acid residues in the resistance-breaking properties of the ToMV-2(2) movement protein, different combinations of these amino acid exchanges were introduced in the genome of wild-type ToMV. Only one mutant strain which contained two amino acid substitutions, Arg-238 and Glu-244, was able to multiply in Tm-2(2) tomato plants. Both amino acid exchanges are found within the carboxy-terminal region of the movement protein, which displays a high variability among different tobamoviruses and has been shown to be dispensable for virus transport in tobacco plants. These observations suggest that the resistance conferred by the Tm-2(2) gene against ToMV depends on specific recognition events in this host-pathogen interaction rather than interfering with fundamental functions of the 30-kDa protein.
Pattern-Based Topic Models for Information Filtering

Topic modelling, such as Latent Dirichlet Allocation (LDA), was proposed to generate statistical models to represent multiple topics in a collection of documents, which has been widely utilized in the fields of machine learning and information retrieval, etc. But its effectiveness in information filtering is rarely known. Patterns are always thought to be more representative than single terms for representing documents. In this paper, a novel information filtering model, Pattern-based Topic Model (PBTM), is proposed to represent the text documents not only using the topic distributions at general level but also using semantic pattern representations at detailed specific level, both of which contribute to the accurate document representation and document relevance ranking. Extensive experiments are conducted to evaluate the effectiveness of PBTM by using the TREC data collection Reuters Corpus Volume 1. The results show that the proposed model achieves outstanding performance.
Obstacles to Scholarly Publishing in the Social Sciences and Humanities: A Case Study of Vietnamese Scholars

Publishing scientific research is very important in contributing to the knowledge of a discipline and in sharing research findings among scientists. Based on the quantity and quality of publications, one can evaluate the research capacity of a researcher or the research performance of a university or a country. However, the number of quality publications in Vietnam is very low in comparison with those in the other countries in the region or in the world, especially in the fields of social sciences and humanities. Employing both quantitative and qualitative approaches, the current study investigates university lecturers’ attitudes towards research and publication and the obstacles to local and international publication at one of the main universities in social sciences and humanities in Vietnam. The study found the main barriers to publication are funding and time for research and publication, among many other obstacles. From the analysis of the data, the study would also argue that lecturers’ obstacles to publication may vary across faculties (or disciplines), ages, qualifications, education, research and publication experience. The findings in this study may be applied to other institutions in Vietnam or in other countries where English is used as a foreign language.
Role of PDK 1 in insulin-signaling pathway for glucose metabolism in 3 T 3L 1 adipocytes

TETSUYA YAMADA,1,2 HIDEKI KATAGIRI,1 TOMOICHIRO ASANO,3 MASATOSHI TSURU,2 KOUICHI INUKAI,4 HIRAKU ONO,5 TATSUHIKO KODAMA,6 MASATOSHI KIKUCHI,5 AND YOSHITOMO OKA1,2 1Division of Molecular Metabolism and Diabetes, Department of Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, 980-8574; 2Third Department of Internal Medicine, Yamaguchi University School of Medicine, Yamaguchi 755-8505; 3Department of Internal Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-8566; 4Fourth Department of Medicine, Saitama Medical School, Saitama 350-0495; 5Institute for Adult Disease, Asahi Life Foundation, Tokyo 160; 6Department of Molecular Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
Fluorescence in situ Hybridization for the Detection of Malignant Bile Duct Strictures: Has FISH Found a New Pond?

Routine cytology for the diagnosis of biliary and pancreatic malignancies has exceptionally poor sensitivity and has spurred a search for new technology in the evaluation of these diseases. The recent study by Kipp et al. in this issue of the Journal, compares one of these novel techniques (fluorescence in situ hybridization to standard cytology) for the detection of malignant biliary strictures. Although larger studies are indicated, the modality shows considerable promise for future clinical use.
A New Sense for Depth of Field

This paper examines a novel source of depth information: focal gradients resulting from the limited depth of field inherent in most optical systems. Previously, autofocus schemes have used depth of field to measured depth by searching for the lens setting that gives the best focus, repeating this search separately for each image point. This search is unnecessary, for there is a smooth gradient of focus as a function of depth. By measuring the amount of defocus, therefore, we can estimate depth simultaneously at all points, using only one or two images. It is proved that this source of information can be used to make reliable depth maps of useful accuracy with relatively minimal computation. Experiments with realistic imagery show that measurement of these optical gradients can provide depth information roughly comparable to stereo disparity or motion parallax, while avoiding image-to-image matching problems.
Global Change Could Amplify Fire Effects on Soil Greenhouse Gas Emissions

Background Little is known about the combined impacts of global environmental changes and ecological disturbances on ecosystem functioning, even though such combined impacts might play critical roles in shaping ecosystem processes that can in turn feed back to climate change, such as soil emissions of greenhouse gases. Methodology/Principal Findings We took advantage of an accidental, low-severity wildfire that burned part of a long-term global change experiment to investigate the interactive effects of a fire disturbance and increases in CO2 concentration, precipitation and nitrogen supply on soil nitrous oxide (N2O) emissions in a grassland ecosystem. We examined the responses of soil N2O emissions, as well as the responses of the two main microbial processes contributing to soil N2O production – nitrification and denitrification – and of their main drivers. We show that the fire disturbance greatly increased soil N2O emissions over a three-year period, and that elevated CO2 and enhanced nitrogen supply amplified fire effects on soil N2O emissions: emissions increased by a factor of two with fire alone and by a factor of six under the combined influence of fire, elevated CO2 and nitrogen. We also provide evidence that this response was caused by increased microbial denitrification, resulting from increased soil moisture and soil carbon and nitrogen availability in the burned and fertilized plots. Conclusions/Significance Our results indicate that the combined effects of fire and global environmental changes can exceed their effects in isolation, thereby creating unexpected feedbacks to soil greenhouse gas emissions. These findings highlight the need to further explore the impacts of ecological disturbances on ecosystem functioning in the context of global change if we wish to be able to model future soil greenhouse gas emissions with greater confidence.
Dietary saccharides and sweet tastants have differential effects on colonization of Drosophila oocytes by Wolbachia endosymbionts

ABSTRACT Wolbachia bacteria are widespread, maternally transmitted endosymbionts of insects. Maintenance of sufficient Wolbachia titer in maternal germline cells is required for transmission efficacy. The mechanisms that regulate Wolbachia titer are not well understood; however, dietary sucrose was reported to elevate oocyte Wolbachia titer in Drosophila melanogaster whereas dietary yeast decreased oocyte titer. To further investigate how oocyte Wolbachia titer is controlled, this study analyzed the response of wMel Wolbachia to diets enriched in an array of natural sugars and other sweet tastants. Confocal imaging of D. melanogaster oocytes showed that food enriched in dietary galactose, lactose, maltose and trehalose elevated Wolbachia titer. However, oocyte Wolbachia titers were unaffected by exposure to the sweet tastants lactulose, erythritol, xylitol, aspartame and saccharin as compared to the control. Oocyte size was generally non-responsive to the nutrient-altered diets. Ovary size, however, was consistently smaller in response to all sugar- and sweetener-enriched diets. Furthermore, most dietary sugars administered in tandem with dietary yeast conferred complete rescue of oocyte titer suppression by yeast. All diets dually enriched in yeast and sugar also rescued yeast-associated ovary volume changes. This indicates oocyte colonization by Wolbachia to be a nutritionally sensitive process regulated by multiple mechanistic inputs. Summary: The density of Wolbachia infection in Drosophila oocytes is significantly increased by dietary sugars, but not sugar alcohols or artificial sweeteners.
Fiber Nonlinearity Equalizer Based on Support Vector Classification for Coherent Optical OFDM

A support vector machine (SVM)-based classification nonlinear equalizer (NLE) is demonstrated, for the first time, in coherent optical orthogonal frequency-division multiplexing (CO-OFDM). For a 40-Gb/s 16 quadrature amplitude modulated (16QAM) CO-OFDM system at 400 km of transmission, SVM-NLE reduces the fiber-induced nonlinearity penalty by about 1 dB in comparison to the benchmark artificial-neural-network (ANN)-based and inverse-Volterra-series-transfer-function-based NLEs.