Miracle-dz/UniFAR-FTUs huggingface dataset:
LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types

Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highly-diversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)-retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotifer-specific and encode a dUTPase domain. However only one lineage contains a canonical env-like fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3′-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements.
Utylizacja odpadÓw laminatÓw poliestrowo-szklanych

Glass fiber-reinforced polyester resin wastes were extracted with methylene chloride (Figs. 1, 2) to yield a comminuted fibrous filler (contg. 70-80 wt. % of glass fibers) and a resin powder. The filler and the powder were re-used as fillers in thermoplastic polymers (PP, Tables 3, 4; polyamide, Table 5), thermosetting phenol molding compounds (Table 6), epoxy resins (Tables 7, 9), and polyester resins (Tables 8, 10). The fibrous filler reclaimed, when used in each polymer examined as a partial or a 100% substitute to replace mineral fillers, glass fibers or wood flour (in phenol molding compounds), was found not to deteriorate, and sometimes even to enhance, the mechanical properties of the polymers. The resin powder was found useful for partially or totally replacing mineral fillers in thermoplastic polymers with their fundamental functional (service) properties remaining unaffected, and also in putties containing polyester or epoxide resins.
Evolving Attackers against Wireless Sensor Networks

Recent technological improvements in wireless communication and electronics have enabled the development of small, low-cost wireless sensor nodes, capable of monitoring everything from human health to the performance of the electricity grid. A natural consequence is a desire to secure systems containing these nodes. Unfortunately, proving that systems are secure is beyond the current state of the art, and testing for security is problematic: test cases often miss attacks that have never previously been seen. In this paper, we use Genetic Programming (GP) to create attacks against Internet of Things devices, to help identify vulnerabilities before systems are attacked for real. To assess the effectiveness of each attacker, we used it against a wireless sensor network (WSN) with publish-subscribe communications, protected by a literature artificial immune intrusion detection system (IDS). The GP attackers succeeded in suppressing significantly more legitimate messages than a hand-coded attacker, whilst decreasing the likelihood of detection. As a consequence, it was possible to tune the IDS, improving its performance. Whilst these results are preliminary, they demonstrate GP holds significant potential for improving the protection of systems with large attack spaces.
Enterprising energy management

Over the last several decades, there has been increasing interest and activity in the filed of energy management. The knowledge gained from the deployment of energy efficient projects is driving a transition from traditional tactical practices to more comprehensive strategic energy management practices. Like many modern management practices, a strategic management approach highlights the need for an information system to set goals, track performance, and communicate results. An enterprise energy management (EEM) information system can support strategic energy management by capturing data about current energy performance, assisting in the creation and tracking of energy performance goals, and communicating results to managers and energy project participants. This paper presents specific EEM system applications that support strategic energy management, which include: modeling and forecasting; benchmarking; energy use and cost analysis; and measurement and verification.
Comparison of selection strategies for marker-assisted backcrossing of a gene

Marker-assisted selection can accelerate recovery of the recurrent parent genome (RPG) in backcross breeding. In this study, computer simulations were used to compare selection strategies with regard to (i) the proportion of the RPG recovered and (ii) the number of marker data points (MDP) required in a backcross programme designed for introgression of one target allele from a donor line into a recipient line. Simulations were performed using a published maize (Zea mays) genetic map consisting of 80 markers. Selection for the target allele was based on phenotypic evaluation. In comparison with a constant population size across all generations, increasing population sizes from generation BC1 to BC3 reduced the number of required MDP by as much as 50% without affecting the proportion of the RPG. A four-stage selection approach, emphasizing in the first generations selection for recombinants on the carrier chromosome of the target allele, reduced the required number of MDP by as much as 75% in comparison to a selection index taking into account all markers across the genome. Adopting the above principles for the design of marker-assisted backcross programmes resulted in substantial savings in the number of MDP required.
On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure

We present a new haplotype-based statistic (nSL) for detecting both soft and hard sweeps in population genomic data from a single population. We compare our new method with classic single-population haplotype and site frequency spectrum (SFS)-based methods and show that it is more robust, particularly to recombination rate variation. However, all statistics show some sensitivity to the assumptions of the demographic model. Additionally, we show that nSL has at least as much power as other methods under a number of different selection scenarios, most notably in the cases of sweeps from standing variation and incomplete sweeps. This conclusion holds up under a variety of demographic models. In many aspects, our new method is similar to the iHS statistic; however, it is generally more robust and does not require a genetic map. To illustrate the utility of our new method, we apply it to HapMap3 data and show that in the Yoruban population, there is strong evidence of selection on genes relating to lipid metabolism. This observation could be related to the known differences in cholesterol levels, and lipid metabolism more generally, between African Americans and other populations. We propose that the underlying causes for the selection on these genes are pleiotropic effects relating to blood parasites rather than their role in lipid metabolism.
Frontiers in Aging Neuroscience Aging Neuroscience Review Article Aβ and Oxidative Stress Oxidative Stress in Ad and Aging Oxidative Stress in Ad and Hypoxia Oxidative Stress in Ad and Hyperglycemia

The cause of modifi ed APP processing and Aβ 42 accumulation in sporadic cases of AD is unclear, but is likely to include oxidative stress (OS). OS and Aβ are linked each other because Aβ induces OS in vivo OS increases is believed to be an early event in AD pathology (Nunomura et al., 2001; Cutler et al., 2004) as it contributes to membrane damage, cytoskeleton alterations and cell death (Perry et al., 2000). Thus, the identifi cation of a large number of oxidatively modi-fi ed proteins in common AD and AD animal models (Sultana et al., 2009) suggests that OS plays an important role in AD pathogenesis. Moreover, extensive oxidative damage observed in " mild cog-nitive impairment " (MCI) brain regions (Lovell and Markesbery, 2001) suggest that OS may be an early event in progression from normal aging to AD pathology. Based on these notions, it seems likely that increased production of oxygen free radicals (reactive oxygen species, ROS) may act as important mediators of synap-tic loss and eventually promote neurofi brillary tangles and senile plaques formation (Kern and Behl, 2009). Our studies, as described below, strengthen the hypothesis that OS may be a basic common pathway of Aβ accumulation and toxicity, which is in turn common to most AD risk factors (Zhu et al., 2004). INTRODUCTION Alzheimer's disease (AD) is one of the most common age-related disorders (Bachman et al., 1993). AD is classifi ed into two forms: sporadic AD, which is correlated to aging, and a rare familial early-onset AD (FAD), caused by gene mutations. The pathological hallmarks of the disease are intraneuronal neu-rofi brillary tangles (NFTs) composed of hyperphosphorylated tau protein and deposition of amyloid-β (Aβ) fi brils in the extracellular space. Central to the disease is the altered proteolytic processing of the Aβ precursor protein (APP), resulting in overproduction and aggregation of neurotoxic forms of Aβ. APP is an integral membrane protein with a single, membrane spanning domain, a large, extracellular, N-terminus, and a shorter, cytoplasmic C-terminus. The amyloidogenic processing of APP involves two sequential cleavages operated by the β-and γ-secretases at the N-and C-termini of Aβ respectively. The β-secretase (BACE1) cleaves APP at the beginning of the sequence of Aβ, generating an extracellular soluble fragment, called sβAPP, and an intracellular C-terminal end, termed C99. C99 is further cleaved, within the membrane, by the γ-secretase. The γ-cleavage produces Aβ fragments of different length, these being …
Development of an exoskeleton robot for human wrist and forearm motion assist

Exoskeleton is an external structural mechanism with joints and links corresponding to those of the human body. It transmits torques from actuators through rigid exoskeletal links to the human joints when it is worn. We have been developing exoskeleton robots for assisting the motion of physically weak individuals such as elderly or slightly disabled in daily life. In this paper we propose a three degree of freedom (3DOF) exoskeleton robot for the forearm pronation/supination motion, wrist flexion/ extension motion and ulnar/radial deviation. The paper describes wrist anatomy toward the development of the robot, the hardware design of the exoskeleton (mechanical structure and mechanism, sensors and actuators, power transmission and safety aspects) and potential control methods. Force control using force/torque sensors located at wrist and forearm and electromyographic (EMG) signals based control using skin surface EMG signals of forearm and wrist muscles are the potential control methods for the robot. Experiments have been performed to evaluate the proposed exoskeleton.
Physiological Basis of Clinically Used Coronary Hemodynamic Indices

In deriving clinically used hemodynamic indices such as fractional flow reserve and coronary flow velocity reserve, simplified models of the coronary circulation are used. In particular, myocardial resistance is assumed to be independent of factors such as heart contraction and driving pressure. These simplifying assumptions are not always justified. In this review we focus on distensibility of resistance vessels, the shape of coronary pressure-flow lines, and the influence of collateral flow on these lines. We show that (1) the coronary system is intrinsically nonlinear because resistance vessels at maximal vasodilation change diameter with pressure and cardiac function; (2) the assumption of collateral flow is not needed to explain the difference between pressure-derived and flow-derived fractional flow reserve; and (3) collateral flow plays a role only at low distal pressures. We conclude that traditional hemodynamic indices are valuable for clinical decision making but that clinical studies of coronary physiology will benefit greatly from combined measurements of coronary flow or velocity and pressure.
Candidate Gene–Environment Interaction Research

Studying how genetic predispositions come together with environmental factors to contribute to complex behavioral outcomes has great potential for advancing the understanding of the development of psychopathology. It represents a clear theoretical advance over studying these factors in isolation. However, research at the intersection of multiple fields creates many challenges. We review several reasons why the rapidly expanding candidate gene–environment interaction (cG×E) literature should be considered with a degree of caution. We discuss lessons learned about candidate gene main effects from the evolving genetics literature and how these inform the study of cG×E. We review the importance of the measurement of the gene and environment of interest in cG×E studies. We discuss statistical concerns with modeling cG×E that are frequently overlooked. Furthermore, we review other challenges that have likely contributed to the cG×E literature being difficult to interpret, including low power and publication bias. Many of these issues are similar to other concerns about research integrity (e.g., high false-positive rates) that have received increasing attention in the social sciences. We provide recommendations for rigorous research practices for cG×E studies that we believe will advance its potential to contribute more robustly to the understanding of complex behavioral phenotypes.
Calibrating a neural network‐based urban change model for two metropolitan areas of the Upper Midwest of the United States

We parameterized neural net‐based models for the Detroit and Twin Cities metropolitan areas in the US and attempted to test whether they were transferable across both metropolitan areas. Three different types of models were developed. First, we trained and tested the neural nets within each region and compared them against observed change. Second, we used the training weights from one area and applied them to the other. Third, we selected a small subset (∼1%) of the Twin Cities area where a lot of urban change occurred. Four model performance metrics are reported: (1) Kappa; (2) the scale which correct and paired omission/commission errors exceed 50%; (3) landscape pattern metrics; and (4) percentage of cells in agreement between model simulations. We found that the neural net model in most cases performed well on pattern but not location using Kappa. The model performed well only in one case where the neural net weights from one area were used to simulate the other. We suggest that landscape metrics are good to judge model performance of land use change models but that Kappa might not be reliable for situations where a small percentage of urban areas change.
Accuracy Control and Performance Enhancement of Linear Solvers for the Integrated Water Flow Model

In this paper, we describe the accuracy control and performance enhancement of linear solvers for the Integrated Water Flow Model (IWFM). This model is used by the State of California Department of Water Resources to assess the impact of climate change on water resources and the analysis of different conjunctive use scenarios across California. IWFM simulates groundwater, surface water and surface-groundwater interaction using an implicitly formulated Galerkin finite element approximation of the groundwater head in a multi-layer aquifer system. The computational efficiency of the simulation is governed by the efficiency of linear solvers for sequences of large-scale sparse linearized systems of equations. We firstly understand how multi-layer aquifer flow and stream-groundwater interaction affects the scaling, conditioning and sparsity structure of the linear systems. These properties guide the choice of scaling which, together with preconditioning, not only offset the ill-conditioning effects of multi-scale flow, but significanly improve the control of the linear solver forward error. Improved error control ensures that the accuracy of the solver is consistent with the accuracy of the initial data. We implemented a preconditioned Krylov subspace linear solver based on the Generalized Minimum RESidual (GMRES) algorithm and incomplete LU preconditioners and demonstrate how scaling improves forward error control in IWFM. We also performance benchmarked the new linear solver against the SOR method, a classical stationary iterative linear solver used in IWFM, and find an overall 7.7x speedup for the largest tested dataset. Further performance profiling shows that the new linear solver removes a major performance bottleneck in IWFM for the other datasets. Department of Computer Science, Kemper Hall, UC Davis, CA 95616 Corresponding author email: mfdixon@ucdavis.edu Bay-Delta Office, Department of Water Resources, 1416 9th Street, Sacramento, CA 95814
Obstacle avoidance for mobile robot navigation in unknown environment using geometrical information of mobile camera images

In this paper, a novel and robust algorithm for avoiding obstacles in an unknown environment is proposed that utilises the geometrical analysis of the distances present in the images. A mobile camera with pan feature is used for increasing the field of view of the robot. Low level image properties red green blue colour; hue saturation value colour and brightness gradient are used for obstacle detection. Once the positions of the obstacles are determined in the image these are transformed into actual distances by the geometrical analysis and a safe passage is determined. The algorithm has been successfully implemented to avoid obstacles during navigation of a mobile robot. It has been observed that the proposed algorithm increases the robustness of obstacle avoidance and helps in the effective path planning of an autonomous mobile robot.
Modelling of Silicon Solar Panel by MATLAB/Simulink and Evaluating the Importance of Its Parameters in a Space Application

This paper starts by describing a silicon solar panel model based on a comprehensive solar cell equivalent circuit. Then, as a case study, four similar modelled panels are considered in lateral sides of a satellite as its power source. Considering the panel model with different combinations of its equivalent circuit essential elements, the model operation is evaluated in a orbit attitude with some eclipse times. The variations in output characteristics of the panels due to changes in received solar irradiance and panels' temperature are calculated for each equivalent configuration. The values of maximum generated power and total generated energy during a satellite typical period are compared for different spin rates. Finally, the best topology for panel equivalent circuit is stated based on the compared results.
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

MOTIVATION Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs. RESULTS We introduce the IDBA-UD algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. Several non-trivial techniques have been employed to tackle the problems. Instead of using a simple threshold, we use multiple depthrelative thresholds to remove erroneous k-mers in both low-depth and high-depth regions. The technique of local assembly with paired-end information is used to solve the branch problem of low-depth short repeat regions. To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs. Comparison of the performances of IDBA-UD and existing assemblers (Velvet, Velvet-SC, SOAPdenovo and Meta-IDBA) for different datasets, shows that IDBA-UD can reconstruct longer contigs with higher accuracy. AVAILABILITY The IDBA-UD toolkit is available at our website http://www.cs. hku.hk/~alse/idba_ud
Perception based heterogeneous subsurface scattering for film

Many real world materials exhibit complex subsurface scattering of light. This internal light interaction creates the perception of translucency for the human visual system. Translucent materials and simulation of the subsurface scattering of light has become an expected necessity for generating warmth and realism in computer generated imagery. The light transport within heterogenous materials, such as marble, has proved challenging to model and render. The current material models available to digital artists have been limited to homogeneous subsurface scattering despite a few publications documenting success at simulating heterogeneous light transport. While the publications successfully simulate this complex phenomenon, the material descriptions have been highly specialized and far from intuitive. By combining the measurable properties of heterogeneous translucent materials with the defining properties of translucency, as perceived by the human visual system, a description of heterogeneous translucent materials that is suitable for artist use in a film production pipeline can be achieved. Development of the material description focuses on integration with the film pipeline, ease of use, and reasonable approximation of heterogeneous translucency based on perception. Methods of material manipulation are explored to determine which properties should be modifiable by artists while maintaining the perception of heterogenous translucency.
Arteriolar Genesis and Angiogenesis Induced by Endothelial Nitric Oxide Synthase Overexpression Results in a Mature Vasculature

Background—Generation of physiologically active vascular beds by delivery of combinations of growth factors offers promise for vascular gene therapy. Methods and Results—In a mesenteric model of physiological angiogenesis, combining endothelial nitric oxide synthase (eNOS) (and hence NO production) with VEGF and angiopoietin-1 overexpression resulted in a more functional vascular phenotype than growth factor administration alone. eNOS gene delivery upregulated eNOS, VEGF, and Ang-1 to similar levels as gene transfer with VEGF or Ang-1. eNOS overexpression resulted in neovascularization to a similar extent as VEGF and Ang-1 combined, but not by sprouting angiogenesis. Whereas combining Ang-1 and VEGF increased both exchange vessels and conduit vessels, neither growth factor nor eNOS alone resulted in vessels with smooth muscle cell (SMC) coverage. In contrast, combining all three generated microvessels with SMCs (arteriolar genesis) and further increased functional vessels. Use of a vasodilator, prazosin, in combination with Ang1 and VEGF, but not alone, also generated SMC-positive vessels. Conclusion—Coexpression of eNOS, VEGF, and Ang-1 results in a more mature vascularization of connective tissue, and generates new arterioles as well as new capillaries, and provides a more physiological therapeutic approach than single growth factor administration, by combining hemodynamic forces with growth factors.