Miracle-dz/UniFAR-FTUs huggingface dataset:
High Step-Up DC–DC Converter With Active Switched-Inductor and Passive Switched-Capacitor Networks

High-gain voltage conversion is a feature required for several applications, especially for power processing of low-voltage renewable sources in grid-connected systems. In this scope, the presented paper proposes a novel transformerless high gain step-up dc–dc converter based on an active switched-inductor and a passive switched-capacitor networks. The main advantages of the proposed converter are the high voltage gain (>10), the reduced voltage stresses across the switches and the reduced number of components when compared to topologies that provide the same voltage gain using similar principles. The detailed analysis of the proposed converter and a comparison considering other topologies previously published in the literature are also presented in this manuscript. In order to verify the proposed converter performance, a prototype has been built for a power of 200 W, input and output voltages of 20 and 260 V, respectively, and switching frequency of 50 kHz. Experimental results validate the effectiveness of the theoretical analysis proving the satisfactory converter performance, which peak efficiency is around 95.5%.
Correlation of Utrophin Levels with the Dystrophin Protein Complex and Muscle Fibre Regeneration in Duchenne and Becker Muscular Dystrophy Muscle Biopsies

Duchenne muscular dystrophy is a severe and currently incurable progressive neuromuscular condition, caused by mutations in the DMD gene that result in the inability to produce dystrophin. Lack of dystrophin leads to loss of muscle fibres and a reduction in muscle mass and function. There is evidence from dystrophin-deficient mouse models that increasing levels of utrophin at the muscle fibre sarcolemma by genetic or pharmacological means significantly reduces the muscular dystrophy pathology. In order to determine the efficacy of utrophin modulators in clinical trials, it is necessary to accurately measure utrophin levels and other biomarkers on a fibre by fibre basis within a biopsy section. Our aim was to develop robust and reproducible staining and imaging protocols to quantify sarcolemmal utrophin levels, sarcolemmal dystrophin complex members and numbers of regenerating fibres within a biopsy section. We quantified sarcolemmal utrophin in mature and regenerating fibres and the percentage of regenerating muscle fibres, in muscle biopsies from Duchenne, the milder Becker muscular dystrophy and controls. Fluorescent immunostaining followed by image analysis was performed to quantify utrophin intensity and β-dystrogylcan and ɣ –sarcoglycan intensity at the sarcolemma. Antibodies to fetal and developmental myosins were used to identify regenerating muscle fibres allowing the accurate calculation of percentage regeneration fibres in the biopsy. Our results indicate that muscle biopsies from Becker muscular dystrophy patients have fewer numbers of regenerating fibres and reduced utrophin intensity compared to muscle biopsies from Duchenne muscular dystrophy patients. Of particular interest, we show for the first time that the percentage of regenerating muscle fibres within the muscle biopsy correlate with the clinical severity of Becker and Duchenne muscular dystrophy patients from whom the biopsy was taken. The ongoing development of these tools to quantify sarcolemmal utrophin and muscle regeneration in muscle biopsies will be invaluable for assessing utrophin modulator activity in future clinical trials.
Analysis of current–voltage characteristics for memristive elements in pattern recognition systems

A topologically simple memristive‐based oscillatory network showing a wide plethora of dynamical behaviors may be a good candidate for the realization of innovative oscillatory associative and dynamic memories for the recognition of spatial–temporal synchronization states. The design of such pattern recognition systems may not leave aside a preliminary thorough investigation of the nonlinear dynamics of the network and its basic components. In a synchronization scenario with almost‐sinusoidal oscillations, each of the memristive elements used in the cells of the network under consideration features an unusual current–voltage behavior. This manuscript models the linear circuitry and the memristive element in each cell so as to capture the observed dynamics and then presents an analytical study explaining the quantitative dependence of memristive current–voltage behavior on excitation amplitude–angular frequency ratio and on initial condition on the system state. This work leads to the first rigorous classification of all possible current–voltage characteristics for a sine‐wave voltage‐driven memristive element. This analytical study shall pave way towards a better understanding of the complex and still unexplored dynamical properties of this nonlinear device, whose distinct features could improve the capabilities of future‐generation pattern recognition systems. Copyright © 2012 John Wiley & Sons, Ltd.
Total Energy Expenditure and Body Composition in Two Free-Living Sympatric Lemurs

Background Evolutionary theories that account for the unusual socio-ecological traits and life history features of group-living prosimians, compared with other primates, predict behavioral and physiological mechanisms to conserve energy. Low energy output and possible fattening mechanisms are expected, as either an adaptive response to drastic seasonal fluctuations of food supplies in Madagascar, or persisting traits from previously nocturnal hypometabolic ancestors. Free ranging ring-tailed lemurs (Lemur catta) and brown lemurs (Eulemur sp.) of southern Madagascar have different socio-ecological characteristics which allow a test of these theories: Both gregarious primates have a phytophagous diet but different circadian activity rhythms, degree of arboreality, social systems, and slightly different body size. Methodology and Results Daily total energy expenditure and body composition were measured in the field with the doubly labeled water procedure. High body fat content was observed at the end of the rainy season, which supports the notion that individuals need to attain a sufficient physical condition prior to the long dry season. However, ring-tailed lemurs exhibited lower water flux rates and energy expenditure than brown lemurs after controlling for body mass differences. The difference was interpreted to reflect higher efficiency for coping with seasonally low quality foods and water scarcity. Daily energy expenditure of both species was much less than the field metabolic rates predicted by various scaling relationships found across mammals. Discussion We argue that low energy output in these species is mainly accounted for by low basal metabolic rate and reflects adaptation to harsh, unpredictable environments. The absence of observed sex differences in body weight, fat content, and daily energy expenditure converge with earlier investigations of physical activity levels in ring-tailed lemurs to suggest the absence of a relationship between energy constraints and the evolution of female dominance over males among lemurs. Nevertheless, additional seasonal data are required to provide a definitive conclusion.
Unified MIMO-Multicarrier Designs: A Space–Time Shift Keying Approach

A survey and tutorial is provided on the subject of multiple-input-multiple-output (MIMO) multicarrier (MC) systems relying on the space-time shift keying (STSK) concept. We commence with a brief review of the family of MIMO systems, which is followed by the design of STSK systems in the context of MC modulation-based transmissions over dispersive wireless channels. Specifically, the STSK scheme is amalgamated with orthogonal frequency-division multiplexing, MC code-division multiple access, orthogonal frequency-division multiple access (OFDMA), and single-carrier frequency-division multiple access. We also provide a rudimentary introduction to MC differential STSK employing both conventional differential detection and multiple-symbol differential sphere decoding for the sake of dispensing with channel estimation. We conclude with the design recipes of coherent versus noncoherent MC STSK schemes, complemented by a range of future research ideas.
ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank

Summary As one of the most important tasks in protein sequence analysis, protein remote homology detection is critical for both basic research and practical applications. Here, we present an effective web server for protein remote homology detection called ProtDec-LTR2.0 by combining ProtDec-Learning to Rank (LTR) and pseudo protein representation. Experimental results showed that the detection performance is obviously improved. The web server provides a user-friendly interface to explore the sequence and structure information of candidate proteins and find their conserved domains by launching a multiple sequence alignment tool. Availability and implementation The web server is free and open to all users with no login requirement at http://bioinformatics.hitsz. edu.cn/ProtDec-LTR2.0/. Contact bliu@hit.edu.cn.
Fast and intuitive segmentation of gyri of the human brain

The cortical surface of the human brain consists of a large number of folds forming valleys and ridges, the gyri and sulci. Often, it is desirable to perform a segmentation of a brain image into these underlying structures in order to assess parameters relative to these functional components. Typical examples for this include measurements of cortical thickness for individual functional areas, or the correlation of functional areas derived from fMRI data to corresponding anatomical areas seen in structural imaging. In this paper, we present a novel interactive technique, that allows for fast and intuitive segmentation of these functional areas from T1-weighted MR images of the brain. Our segmentation approach is based exclusively on morphological image processing operations, eliminating the requirement for explicit reconstruction of the brains surface.
Interaction techniques for window management on large high-resolution displays

Large high-resolution displays (LHRDs) present new opportunities for interaction design in areas such as interactive visualization and data analytics. Design processes for graphical interfaces for LHRDs are still challenging. In this paper, we explore the design space of graphical interfaces for LHRDs by engaging in the creation of four prototypes for supporting office work. Specifically, we investigate how users can effectively manage application windows on LHRDs using four window alignment techniques: curved zooming, window grouping, window spinning and side pane navigation. We present the design and implementation of these window alignment techniques in a sample office application. Based on a mixed-methods user study of our prototypes, we contribute insights on designing future graphical interfaces for LHRDs. We show that potential users appreciate techniques, which enhance focus switching without changing the spatial relation between related windows.
Defining the distinct, intrinsic properties of the novel type I interferon, IFNϵ

The type I interferons (IFNs) are a family of cytokines with diverse biological activities, including antiviral, antiproliferative, and immunoregulatory functions. The discovery of the hormonally regulated, constitutively expressed IFNϵ has suggested a function for IFNs in reproductive tract homeostasis and protection from infections, but its intrinsic activities are untested. We report here the expression, purification, and functional characterization of murine IFNϵ (mIFNϵ). Recombinant mIFNϵ (rmIFNϵ) exhibited an α-helical fold characteristic of type I IFNs and bound to IFNα/β receptor 1 (IFNAR1) and IFNAR2, but, unusually, it had a preference for IFNAR1. Nevertheless, rmIFNϵ induced typical type I IFN signaling activity, including STAT1 phosphorylation and activation of canonical type I IFN signaling reporters, demonstrating that it uses the JAK–STAT signaling pathway. We also found that rmIFNϵ induces the activation of T, B, and NK cells and exhibits antiviral, antiproliferative, and antibacterial activities typical of type I IFNs, albeit with 100–1000-fold reduced potency compared with rmIFNα1 and rmIFNβ. Surprisingly, although the type I IFNs generally do not display cross-species activities, rmIFNϵ exhibited high antiviral activity on human cells, suppressing HIV replication and inducing the expression of known HIV restriction factors in human lymphocytes. Our findings define the intrinsic properties of murine IFNϵ, indicating that it distinctly interacts with IFNAR and elicits pathogen-suppressing activity with a potency enabling host defense but with limited toxicity, appropriate for a protein expressed constitutively in a sensitive mucosal site, such as the reproductive tract.
BIOMASS PYROLYSIS PROCESSES: PERFORMANCE PARAMETERS AND THEIR INFLUENCE ON BIOCHAR SYSTEM BENEFITS

This study focuses on performance of biomass pyrolysis processes for use in biochar systems. Objectives are to understand the range of control of such processes and how this affects potential benefits of pyrolysis biochar systems, in particular for climate change mitigation. Slow, intermediate and fast pyrolysis processes are reviewed. Product yield distributions change depending on feedstock composition and preparation, control of temperature and material flows. These allow some control over distribution of main products – char, liquids and gases. Typical yield ranges for pyrolysis processes are defined. Variability associated with char yield is estimated at ±5% (relative). Char yield should be considered an underlying, but minor source of variability in pyrolysis biochar systems. A model study is used to compare effects on greenhouse gas balance and electricity generating capability of slow, intermediate and fast pyrolysis processes with direct combustion; there is a trade-off between these benefits following from the different product yield distributions. High char yields allow greater net CO2 benefits but lower electrical output from slow or intermediate pyrolysis. Higher liquid and/or gas yields allow greater electrical output from fast pyrolysis but less than from direct combustion. Fast pyrolysis and direct combustion have similar net CO2 effects when retained char is low. If the objectives of pyrolysis biochar systems are for climate change mitigation then processes with higher char yields should be preferred. The model is sensitive to the reference case chosen for fossil fuel substitution and to the stability of biochar-carbon in soils – a major uncertainty in the analysis of pyrolysis biochar systems. Financial analysis shows the trend in income value for pyrolysis and combustion processes is opposite to the trend in climate change mitigation benefits. Lifecycle CO2 analysis suggests dominant factors in pyrolysis biochar systems relate to carbon sequestration in biochar and fossil fuels substitution by renewable electricity.
The IDO inhibitor 1-methyl tryptophan activates the aryl hydrocarbon receptor response in mesenchymal stromal cells

The catabolism of tryptophan (Trp) by indoleamine 2,3-dioxygenase (IDO) is a key step in tolerance effected by a variety of cell types, including mesenchymal stromal cells (MSCs). Trp catabolism generates molecules known as kynurenines, whose tolerance mechanisms involve activation of the Aryl Hydrocarbon Receptor (AHR). A synthetic analog of Trp, 1-methyl tryptophan (1MT), is a selective inhibitor of IDO enzymatic activity being utilized in cancer immunotherapy trials. We hypothesized 1MT might activate AHR independently of its effects on IDO. We demonstrate MSCs express AHR protein, and that in vitro treatment with 1MT causes AHR nucleotranslocation. Upon analyzing mRNA, we observed transcriptional upregulation of cytochrome p450 1a1 and 1b1 by 1MT racemic mixture (R-MT), consistent with AHR-activation. RNA-sequencing identified Nrf2, MAPK12 and IL-1a as downstream targets of 1MT. We demonstrate 1a1 and 1b1 activation by 1MT in IDO+ MSC following interferon-γ (IFN-γ) activation, suggesting AHR signaling is uncoupled from IDO catalytic function. Such a mechanism of action for 1MT may extend its usage to a wider range of patients, irrespective of tumor IDO expression. These observations support a novel paradigm by which AHR-activating compounds like 1MT can be used in cancer immunotherapy to stimulate a pro-inflammatory response.
Human artificial chromosome (HAC) vector with a conditional centromere for correction of genetic deficiencies in human cells

Human artificial chromosome (HAC)-based vectors offer a promising system for delivery and expression of full-length human genes of any size. HACs avoid the limited cloning capacity, lack of copy number control, and insertional mutagenesis caused by integration into host chromosomes that plague viral vectors. We previously described a synthetic HAC that can be easily eliminated from cell populations by inactivation of its conditional kinetochore. Here, we demonstrate the utility of this HAC, which has a unique gene acceptor site, for delivery of full-length genes and correction of genetic deficiencies in human cells. A battery of functional tests was performed to demonstrate expression of NBS1 and VHL genes from the HAC at physiological levels. We also show that phenotypes arising from stable gene expression can be reversed when cells are “cured” of the HAC by inactivating its kinetochore in proliferating cell populations, a feature that provides a control for phenotypic changes attributed to expression of HAC-encoded genes. This generation of human artificial chromosomes should be suitable for studies of gene function and therapeutic applications.
AMERICIUM - FROM DISCOVERY TO THE SMOKE DETECTOR AND BEYOND*

Since its isolation by Seaborg and his colleagues in 1944, americium has proven to be an element that is quite useful. Discussion of the discovery, announcement of and naming of this element, its characteristics, isotopes, applications [including in smoke detectors], use as a portable gamma ray source, and as a fuel for spacecraft will be described. The chemistry of americium and also work being done to reduce the radio-toxicity of the waste from the reprocessing of used nuclear fuel will also be noted.
QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors.
Flexural behaviour of glass fibre-reinforced polymer and ultra-high-strength fibre-reinforced concrete composite beams subjected to elevated temperature

Composite beams consisting of pultruded glass fibre-reinforced polymer (GFRP) I-beams and ultra-high-strength fibre-reinforced concrete (UFC) slabs have been developed for use in short-span bridges. Fibre-reinforced polymer bolts (fibre-reinforced polymer threaded rods) and epoxy adhesive were used to connect the UFC slab to the GFRP I-beam. The authors conducted material tests and large-scale static bending tests at room and elevated temperatures (less than 90°C) to investigate the flexural behaviour of GFRP-UFC composite beams subjected to elevated temperature. The test results demonstrated that the mechanical properties of the GFRP I-beams, fibre-reinforced polymer bolts and epoxy adhesive were significantly deteriorated at elevated temperatures due to the glass transition of their polymer resin matrices. As a result, the stiffness and ultimate flexural capacity of the GFRP-UFC composite beams under elevated temperatures were significantly reduced. More than 85% of the flexural capacity of the GFRP-UFC composite beams was retained up to 60°C but that was decreased to 50% at 90°C. Fibre model analysis results confirmed that the stiffness of the GFRP-UFC composite beams is not significantly affected by actual hot environments, where there is a moderate temperature gradient across the beam cross-section.
ASElux: an ultra‐fast and accurate allelic reads counter

Motivation Mapping bias causes preferential alignment to the reference allele, forming a major obstacle in allele‐specific expression (ASE) analysis. The existing methods, such as simulation and SNP‐aware alignment, are either inaccurate or relatively slow. To fast and accurately count allelic reads for ASE analysis, we developed a novel approach, ASElux, which utilizes the personal SNP information and counts allelic reads directly from unmapped RNA‐sequence (RNA‐seq) data. ASElux significantly reduces runtime by disregarding reads outside single nucleotide polymorphisms (SNPs) during the alignment. Results When compared to other tools on simulated and experimental data, ASElux achieves a higher accuracy on ASE estimation than non‐SNP‐aware aligners and requires a much shorter time than the benchmark SNP‐aware aligner, GSNAP with just a slight loss in performance. ASElux can process 40 million read‐pairs from an RNA‐sequence (RNA‐seq) sample and count allelic reads within 10 min, which is comparable to directly counting the allelic reads from alignments based on other tools. Furthermore, processing an RNA‐seq sample using ASElux in conjunction with a general aligner, such as STAR, is more accurate and still ˜4× faster than STAR + WASP, and ˜33× faster than the lead SNP‐aware aligner, GSNAP, making ASElux ideal for ASE analysis of large‐scale transcriptomic studies. We applied ASElux to 273 lung RNA‐seq samples from GTEx and identified a splice‐QTL rs11078928 in lung which explains the mechanism underlying an asthma GWAS SNP rs11078927. Thus, our analysis demonstrated ASE as a highly powerful complementary tool to cis‐expression quantitative trait locus (eQTL) analysis. Availability and implementation The software can be downloaded from https://github.com/abl0719/ASElux. Supplementary information Supplementary data are available at Bioinformatics online.