Miracle-dz/UniFAR-FTUs huggingface dataset:
Near- and far scrape-off layer transport studies in detached, small-ELM ASDEX Upgrade discharges by means of EMC3-EIRENE

We compare various diagnostics characterizing an ASDEX Upgrade upper single-null discharge to EMC3-EIRENE simulations now including volumetric recombination and main chamber plasma-wall interaction but not yet drifts. The discharge is in a small-ELM regime and is approaching detachment due to a density ramp and nitrogen seeding. Time/ELM averaged upstream density, electron and ion temperature measurements as well as downstream ion saturation current, electron temperature and power flux measurements match the simulation within the error bars before and after reaching detachment, qualifying the code for this regime. Although the Ion Cyclotron Resonance Heating (ICRH) antenna limiters are 35 mm away from the separatrix, i.e. ten times the typical near-SOL power fall-off length λqnear = 3.8 mm, they receive power fluxes of several hundreds of kW exceeding the ones to the outer target in the detached phase and strongly contribute to the particle fueling. This is explained by a substantially larger far-SOL power fall-off length λqfar = 25 mm possibly caused by the small ELMs in the detached phase and the occurrence of a density shoulder.
Physical versus Immunological Purification of Mesenchymal Stem Cells

A prerequisite before dealing with any cell type is to identify it and isolate it from the heterogeneous cell population that it belongs to. Mesenchymal stem cells (MSC) can be found in nearly all tissues and are mostly located in perivascular niches. MSC isolated from Bone marrow, adipose tissue, peripheral blood and different organs had shown promising potential for proliferation and differentiation into different cell types. They exhibit plastic-adherence under standard culture conditions, and this physi- cal method of isolation is widely used as it is the most economic method and yet reveals relatively purified populations of cells after 3 or 4 passages. The complete purification still needs a specific call to different MSCs subsets. This could be achieved by immu nological sorting, which depends on identifying cell marker(s) of such cells. Selecting these cells using antibodies against their specific markers then sorting the cells either by Magnetic or florescence based techniques named Magnetic Activated Cell Sorting (MACS) or Florescence Activated Cell Sorting (FACS) respectively is the principle of such purification techniques. The aim of this chapter is to thoroughly define MSCs and compare between the different available methods for their purification
Application Research of Deep Convolutional Neural Network in Computer Vision

As an important research achievement in the field of brain like computing, deep convolution neural network has been widely used in many fields such as computer vision, natural language processing, information retrieval, speech recognition, semantic understanding and so on. It has set off a wave of neural network research in industry and academia and promoted the development of artificial intelligence. At present, the deep convolution neural network mainly simulates the complex hierarchical cognitive laws of the human brain by increasing the number of layers of the network, using a larger training data set, and improving the network structure or training learning algorithm of the existing neural network, so as to narrow the gap with the visual system of the human brain and enable the machine to acquire the capability of “abstract concepts”. Deep convolution neural network has achieved great success in many computer vision tasks such as image classification, target detection, face recognition, pedestrian recognition, etc. Firstly, this paper reviews the development history of convolutional neural networks. Then, the working principle of the deep convolution neural network is analyzed in detail. Then, this paper mainly introduces the representative achievements of convolution neural network from the following two aspects, and shows the improvement effect of various technical methods on image classification accuracy through examples. From the aspect of adding network layers, the structures of classical convolutional neural networks such as AlexNet, ZF-Net, VGG, GoogLeNet and ResNet are discussed and analyzed. From the aspect of increasing the size of data set, the difficulties of manually adding labeled samples and the effect of using data amplification technology on improving the performance of neural network are introduced. This paper focuses on the latest research progress of convolution neural network in image classification and face recognition. Finally, the problems and challenges to be solved in future brain-like intelligence research based on deep convolution neural network are proposed.
Effect of different typical high speed train pantograph recess configurations on aerodynamic noise

For high-speed trains, the aerodynamic noise becomes an essential consideration in the train design. The pantograph and pantograph recess are recognised as important sources of aerodynamic noise. This paper studies the flow characteristics and noise contributions of three typical high-speed train roof configurations, namely a cavity, a ramped cavity and a flat roof with side insulation plates. The Improved Delayed Detached-Eddy Simulation approach is used for the flow calculations and the Ffowcs Williams & Hawkings aeroacoustic analogy is used for far-field acoustic predictions. Simulations are presented for a simplified train body at 1/10 scale and 300 km/h with these three roof configurations. In each case, two simplified pantographs (one retracted and one raised) are located on the roof. Analysis of the flow fields obtained from numerical simulations clearly shows the influence of the train roof configuration on the flow behaviour, including flow separations, reattachment and vortex shedding, which are potential noise sources. A highly unsteady flow occurs downstream when the train roof has a cavity or ramped cavity due to flow separation at the cavity trailing edge, while vortical flow is generated by the side insulation plates. For the ramped cavity configuration, moderately large pressure fluctuations appear on the cavity outside walls in the upstream region due to unsteady flow from the upstream edge of the plate. The raised pantograph, roof cavity, and ramped cavity are identified as the dominant noise sources. When the retracted pantograph is located in the ramped roof cavity, its noise contribution is less important. Furthermore, the insulation plates also generate tonal components in the noise spectra. Of the three configurations considered, the roof cavity configuration radiates the least noise at the side receiver in terms of A-weighted level.
Effects of back‐mounted biologgers on condition, diving and flight performance in a breeding seabird

Biologging devices are providing detailed insights into the behaviour and movement of animals in their natural environments. It is usually assumed that this method of gathering data does not impact on the behaviour observed. However, potential negative effects on birds have rarely been investigated before field‐based studies are initiated. Seabirds which both fly and use pursuit diving may be particularly sensitive to increases in drag and load resulting from carrying biologging devices. We studied chick‐rearing adult common guillemots Uria aalge equipped with and without back‐mounted GPS tags over short deployments of a few days. Concurrently guillemots carried small leg‐mounted TDR devices (time‐depth recorders) providing activity data throughout. Changes in body mass and breeding success were followed for device equipped and control guillemots. At the colony level guillemots lost body mass throughout the chick‐rearing period. When‐equipped with the additional GPS tag, the guillemots lost mass at close to twice the rate they did when equipped with only the smaller leg‐mounted TDR device. The elevated mass loss suggests an impact on energy expenditure or foraging performance. When equipped with GPS tags diving performance, time‐activity budgets and daily patterns of activity were unchanged, yet dive depth distributions differed. We review studies of tag‐effects in guillemots Uria sp. finding elevated mass loss and reduced chick‐provisioning to be the most commonly observed effects. Less information is available for behavioural measures, and results vary between studies. In general, small tags deployed over several days appear to have small or no measurable effect on the behavioural variables commonly observed in most guillemot tagging studies. However, there may still be impacts on fitness via physiological effects and/or reduced chick‐provisioning, while more detailed measures of behaviour (e.g. using accelerometery) may reveal effects on diving and flight performance.
Application of Market Innovation Strategies for Banjaran Coffee Products using the Walk Shop

The business development undertaken by this partner group includes several issues. Problems related to the development of marketing activities that have been carried out so far and want to change the marketing concept from online to offline. Although constrained by the limited location of store stock from each coffee partner, they still want to innovate directly through the idea of ​​a tavern. The concept of business planning and product innovation is not yet understood as a tool that effectively recognizes business potential through on-going shop innovation. Marketing problems through other promotional media and cooperation. The method of implementation used to obtain solutions and target outcomes set, through training, technical guidance, and assistance. In the implementation of a team with experts who are experts in their fields, determine the stages and procedures in getting solutions to problems faced by partners, so partners can develop into sustainable businesses, and have competitiveness. The community activity program plan is carried out for 8 months starting from the preparation, implementation, monitoring, and evaluation, presentation, and reporting of activities and writing of publications in International Standard Serial Number (ISSN) journals, national seminar proceedings, and training modules for the implementation of activities.
An account of the plant communities of Tussen die Riviere Game Farm, Orange Free State

As part of the IBP survey of conservation sites, the vegetation of Tussen die Riviere Game Farm,Orange Free State, was surveyed and analysed according to the Braun-Blanquet phytosociological method. A classification of the plant communities occurring there is given. A way by which a hierarchical classification of plant communities in South Africa community is physiognomically classified according of this system are discussed briefly.could be constructed, is suggested. Each plant to Fosberg's (1967) system. Two disadvantages of this system are discussed briefly.
Kajian Hubungan Allometrik dan Biomassa Lamun Thalassia hemprichii sebagai Bioindikator Lingkungan

Seagrass has long been known to be very sensitive to environmental changes, especially caused by human activities (anthropogenic disturbance) and has been used as a bioindicator for environmental condition. This research aimed to study interaction of Thalassia hemprichii measured and derived variables (metrics), at two locations i.e., inhabited island (high anthropogenic location) and uninhabited island (low anthropogenic location). Confirmative approach was conducted using a developed conceptual model based on preliminary studies, the conceptual model was analyzed in multivariate context using data from field observation. The result showed that Thalassia hemprichii dominated and have higher above ground biomass value in inhabited area which indicated high nutrient input, meanwhile uninhabited area showed a higher below ground biomass value. Above ground of Thalassia hemprichii that have direct effect on its biomass and below ground metrics was leaf width, meanwhile leaf length of Thalassia hemprichii have indirect effect on its biomass and below ground metrics. The result also indicated some different metric covariations which were influenced by the degree of Thalassia hemprichii density. Leaf length, leaf width, density, and percent cover of Thalassia hemprichii potentially could be used as components in multimetric index and bioindicator for environmental quality. Keywords: anthropogenic disturbance, path analysis, structural equation modeling, Thalassia hemprichii
UV‐aided graphene oxide reduction by TiO2 towards TiO2/reduced graphene oxide composites for dye‐sensitized solar cells

Electron transport layer is one of the important layer in the dye‐sensitized solar cells (DSSCs) which is responsible for the transport of photo‐generated electrons by the dye to the outer circuit. TiO2 has been widely used as electron transport material in DSSCs. However, improving the electrical conductivity of TiO2 without sacrificing the surface area is one of the important strategies to improve the efficiency of the DSSCs. Here graphene oxide (GO) is added as an additive into the TiO2 network towards the preparation of TiO2/reduced graphene oxide (RGO) composites by UV assisted photocatalytic reduction method. The RGO/TiO2 composites with different compositions of RGO were characterized and the performance of DSSCs using the prepared material as photoanode was studied. Furthermore, through the D and G band Raman peaks, the reduction of GO to RGO was confirmed. The optical properties of the prepared material were analyzed using UV‐visible spectroscopy and photoluminescence analysis, respectively. The carrier lifetime of the TiO2 and TiO2/RGO composites was studied using time resolved photoluminescence studies. The high‐resolution transmission electron microscope images of prepared TiO2/RGO composites were found to have sheet‐like structure surrounding the near spherical nanoparticles, which could be attributed to that of RGO and TiO2, respectively. The binding energy states of the prepared material were studied using X‐ray photoelectron spectroscopy (XPS) spectra. The incorporation of RGO in TiO2 was found to improve the Brunauer–Emmett–Teller (BET) surface area of TiO2 and distribution of pores in TiO2 and TiO2/RGO composites was found to be uniform. The DSSCs were fabricated using the prepared TiO2 and TiO2/RGO composites as photoanodes and their power conversion efficiencies were analyzed.
Giant taxon‐character matrices II: a response to Laing et al. (2017)

The trend towards big data analyses in evolutionary biology has been observed in phylogenetics via the assembly of giant datasets composed of genomic and phenotypic data. We recently (Simões et al., 2017. Giant taxon‐character matrices: Quality of character constructions remains critical regardless of size. Cladistics 33, 198–219) presented a critique of the phylogenetic character concepts used in current morphological datasets, with the caution that giant datasets did not obviate the empirical requirement of rigor in character construction. Laing et al. (2017. Giant taxon‐character matrices: The future of morphological systematics. Cladistics, https://doi.org/10.1111/cla.12197) have since argued that we had ‘suggested’ that large datasets inherently contain flawed characters, and that we had presented a substandard methodology of phylogenetic analysis. Laing et al. concluded by discussing their approach to phylogenetic signal, total evidence and the inevitability of large datasets. We here reply to Laing et al. by reviewing what we actually wrote regarding dataset size, characters and methodology. We show that Laing et al.'s. central premise is unsupported, thus characterizing a Straw Man argument, and deeply misrepresents our original study. In part two, we discuss total evidence and phylogenetic signal issues raised by Laing et al. that are of major consequence to the appropriate construction of large morphological datasets.
pycoalescence and rcoalescence: Packages for simulating spatially explicit neutral models of biodiversity

Neutral theory proposes that some macroscopic biodiversity patterns can be explained in terms of drift, speciation and immigration, without invoking niches. There are many different varieties of neutral model, all assuming that the fitness of an individual is unrelated to its species identity. Variants that are spatially explicit provide a means for making quantitative predictions about spatial biodiversity patterns. We present software packages that make spatially explicit neutral simulations straightforward and efficient. The packages allow the user to customize both dispersal and landscape structure in a wide variety of ways. We provide a Python package pycoalescence and a functionally equivalent R package rcoalescence. In both packages, the core routines are written in C++ and make use of coalescence methods to optimize performance. We explain the technical details of the packages and give examples for their application, with a particular focus on two scenarios of ecological and evolutionary interest—a landscape with habitat fragmentation, and an archipelago of islands. Spatially explicit neutral models represent an important tool in ecology for understanding the processes of biodiversity generation and predicting outcomes at large scales. The effort required to implement these complex spatially explicit simulations efficiently has thus far been a barrier to entry. Our packages increase the accessibility of these models and encourage further investigation of the primary mechanisms underpinning biodiversity.
MetaCompass: Reference-guided Assembly of Metagenomes

Metagenomic studies have primarily relied on de novo approaches for reconstructing genes and genomes from microbial mixtures. While database driven approaches have been employed in certain analyses, they have not been used in the assembly of metagenomes. Here we describe the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods. When combined with de novo assembly approaches, we show that MetaCompass can generate more complete assemblies than can be obtained by de novo assembly alone, and improve on assemblies from the Human Microbiome Project (over 2,000 samples).
Skeletal muscle fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH-dependent regulation of adipogenesis

Fibro adipogenic progenitors (FAPs) promote satellite cell differentiation in adult skeletal muscle regeneration. However, in pathological conditions, FAPs are responsible for fibrosis and fat infiltrations. Here we show that the NOTCH pathway negatively modulates FAP differentiation both in vitro and in vivo. However, FAPs isolated from young dystrophin-deficient mdx mice are insensitive to this control mechanism. Nonetheless, factors released by hematopoietic cells restore the sensitivity to NOTCH adipogenic inhibition. An unbiased mass spectrometry-based proteomic analysis of FAPs from muscles of wild type and mdx mice, revealed that the synergistic cooperation between NOTCH and inflammatory signals controls FAP differentiation. These results offer a basis for rationalizing the pathological outcomes of fat infiltrations in skeletal muscle and may suggest new therapeutic strategies to mitigate the detrimental effects of fatty depositions in muscles of dystrophic patients. Highlights Single-cell mass cytometry reveals that wt and mdx FAPs are in different cell states. Activation of the NOTCH signaling pathway negatively regulates adipogenesis of wt but not mdx FAPs. Deep proteomics suggests a mechanism explaining the different sensitivity of mdx- FAPs to NOTCH. TNF-a stimulation restores the anti-adipogenic effect of NOTCH in mdx FAPs.
Systematic Review of Beef Protein Effects on Gut Microbiota: Implications for Health

ABSTRACT The influence of diet on the gut microbiota is an emerging research area with significant impact on human health and disease. However, the effects of beef, the most consumed red meat in the United States, on gut microbial profile are not well studied. Following Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols, the objective of this systematic review was to conduct a rigorous and thorough review of the current scientific literature regarding the effects of beef protein and the resulting bioactivity of beef protein and amino acids on the gut microbiota, with the goal of identifying gaps in the literature and guiding future research priorities. Utilizing MEDLINE Complete, PubMed, ScienceDirect, Scopus, and Google Scholar databases, we conducted searches including terms and combinations of the following: animal protein, amino acid, beef, bioactive compounds, diet, health, microbiome, peptide, processed beef, and protein. We identified 131 articles, from which 15 were included in our review. The effects of beef on mouse and rat models were mostly consistent for the bacterial phylum level. Short-term (1–4-wk) beef intakes had little to no effect on microbial profiles in humans. Most studies utilized high beef feeding (240–380 g/d), and no study examined recommended amounts of protein [∼3.71 oz/d (105 g/d) meats, poultry, and eggs, or ∼26 oz/week (737 g/wk) from these food sources] according to US dietary guidelines. Additionally, the majority of animal and human studies with adverse findings examined the impact of beef in the context of a diet high in fat or sugar. In conclusion, an extensive gap exists in the literature regarding beef and the microbiota. More studies are necessary to elucidate the role of the microbiota following the consumption of beef, especially in interaction with other dietary compounds, and how beef preparation, processing, and cooking methods differentially influence the biological effects of beef on human health.