Miracle-dz/UniFAR-FTUs huggingface dataset:
A review of entamoebahistolytica genome, virulence factors, phylogenetic tree and treatment

The study in this review aims to know and study the parasite Entamoebahistolytica that causes Amoebiasis worldwide. During its life cycle, E. histolytica passes through several phases, trophozoite stage, precyst stage, the cyst stage, the Metacyst stage, and Metacystictrophozoite stage. In this study, the spread of the parasite globally and in the Arab world and methods of treating the disease were also discussed. The Genomic structureof E. histolytica, like other organisms, is characterized by diversity and heterogeneity in its genetic content, which is one of the most important reasons for its survival and its ability to infect. Interestingly, the genome of the E. histolytica contains a large amount of genes presumed to be of bacterial origin. The study of the genetic diversity of E. histolytica gives paths to the developmental change that resulted in the emergence of evolutionary features or traits. Understanding amoebic virulence is important. Several studies have shown that genetic factors influence the virulence of parasitic infections. Studying the virulence of E. histolytica by Serine-rich protein (REHP) gene is among the important issues used in molecular epidemiological studies.
iMASKO: A Genetic Algorithm Based Optimization Framework for Wireless Sensor Networks

In this paper we present the design and implementation of a generic GA-based optimization framework iMASKO (iNL@MATLAB Genetic Algorithm-based Sensor NetworK Optimizer) to optimize the performance metrics of wireless sensor networks. Due to the global search property of genetic algorithms, the framework is able to automatically and quickly fine tune hundreds of possible solutions for the given task to find the best suitable tradeoff. We test and evaluate the framework by using it to explore a SystemC-based simulation process to tune the configuration of the unslotted CSMA/CA algorithm of IEEE 802.15. 4, aiming to discover the most available tradeoff solutions for the required performance metrics. In particular, in the test cases different sensor node platforms are under investigation. A weighted sum based cost function is used to measure the optimization effectiveness and capability of the framework. In the meantime, another experiment is performed to test the framework’s optimization characteristic in multi-scenario and multi-objectives conditions.
Modularizing design patterns with aspects: a quantitative study

Design patterns offer flexible solutions to common problems in software development. Recent studies have shown that several design patterns involve crosscutting concerns. Unfortunately, object-oriented (OO) abstractions are often not able to modularize those crosscutting concerns, which in turn decrease the system reusability and maintainability. Hence, it is important verifying whether aspect-oriented approaches support improved modularization of crosscutting concerns relative to design patterns. Ideally, quantitative studies should be performed to compare OO and aspect-oriented implementations of classical patterns with respect to important software engineering attributes, such as coupling and cohesion. This paper presents a quantitative study that compares aspect-based and OO solutions for the 23 Gang-of-Four patterns. We have used stringent software engineering attributes as the assessment criteria. We have found that most aspect-oriented solutions improve separation of pattern-related concerns, although only 4 aspect-oriented implementations have exhibited significant reuse.
On the sensitivity of TG‐119 and IROC credentialing to TPS commissioning errors

We investigate the sensitivity of IMRT commissioning using the TG‐119 C‐shape phantom and credentialing with the IROC head and neck phantom to treatment planning system commissioning errors. We introduced errors into the various aspects of the commissioning process for a 6X photon energy modeled using the analytical anisotropic algorithm within a commercial treatment planning system. Errors were implemented into the various components of the dose calculation algorithm including primary photons, secondary photons, electron contamination, and MLC parameters. For each error we evaluated the probability that it could be committed unknowingly during the dose algorithm commissioning stage, and the probability of it being identified during the verification stage. The clinical impact of each commissioning error was evaluated using representative IMRT plans including low and intermediate risk prostate, head and neck, mesothelioma, and scalp; the sensitivity of the TG‐119 and IROC phantoms was evaluated by comparing dosimetric changes to the dose planes where film measurements occur and change in point doses where dosimeter measurements occur. No commissioning errors were found to have both a low probability of detection and high clinical severity. When errors do occur, the IROC credentialing and TG 119 commissioning criteria are generally effective at detecting them; however, for the IROC phantom, OAR point‐dose measurements are the most sensitive despite being currently excluded from IROC analysis. Point‐dose measurements with an absolute dose constraint were the most effective at detecting errors, while film analysis using a gamma comparison and the IROC film distance to agreement criteria were less effective at detecting the specific commissioning errors implemented here. PACS number: 87.55. Qr
Nano-Indentation of Anisotropic Material: Numerical Approaches to Extract Elasticities from Nano-Indentation

Division of Biomechanics participates in a project together with Department of Cancer Research and Molecular Medicine, NTNU, on effects of proton pump inhibitor medication on bone quality. This common anti-stomach acid medication seems to result in an increased bone fragility in humans. As a step towards comparing mechanical properties at micro level, between sick and healthy bone tissue, mice femur have been tested at micro level using the increasingly popular tool, nanoindentation. Futher, an analytical finite element model has been created in an effort to increase the understanding of nanoindentation of bone. It is concluded that the experimental protocol is not accurate enough(SD ~ 5GPa for reduced Young's modulus) as a result of multiple factors, mainly indentation locations. The experimental results were compared to the finite element model. It was possible to match the data curves of the experimental tests with the analytical tests by adjusting the model parameters. Unfortunatly, this resulted in divergent results(plastic yield stress of ~ 600MPa and reduced Young's modulus of nearly 60% of the experimental data(32,45 GPa and 20GPa). As an effort to reduce the divergence between the experimental and analytical testing, multiple suggestions were made.
Barriers to Teachers' Use of Environmentally-Based Education in Outdoor Classrooms

Barriers to Teachers’ Use of Environmentally-Based Education in Outdoor Classrooms by Sheri Ruether MA, Walden University, 2004 BS, University of Texas at San Antonio, 1987 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Education Walden University August 2018 Abstract Numerous research studies have shown that when teachers take children outdoors to learn, children show an increase in cognitive, physical, social, and emotional skills. Few researchers have focused, however, on teachers and their decision to use the outdoors as a way of teaching. The purpose of this qualitative study was to explore whether life experiences impact a teacher’s choice to not use the outdoor environment. Ham andNumerous research studies have shown that when teachers take children outdoors to learn, children show an increase in cognitive, physical, social, and emotional skills. Few researchers have focused, however, on teachers and their decision to use the outdoors as a way of teaching. The purpose of this qualitative study was to explore whether life experiences impact a teacher’s choice to not use the outdoor environment. Ham and Shuman’s model of environmental education commitment and Kaplan and Kaplan’s environmental cognition theory served as the conceptual frameworks for this study. The research question was designed to explore the experiences and barriers of teachers and how these experiences and barriers affected a teacher’s decision to use or not use an outdoor classroom when one was available. Data were obtained using individual interviews of a purposeful sample of seven elementary teachers from a large school district in the U.S. state of Georgia who were not using outdoor classrooms at the time of the study. Themes that emerged from data analysis were lack of time in tightly controlled class schedules, lack of administrator support, lack of staff development for teachers, weather, and lack of time to research and prepare lessons. Study findings have the potential to engender positive social change by increasing insight about the barriers teachers perceive to using the natural environment in instruction. With more knowledge about such barriers, administrators may able to encourage teachers to use the natural environment as an extension of the indoor classroom to increase academic achievement and lifelong behaviors in nature among students. Barriers to Teachers’ Use of Environmentally-Based Education in Outdoor Classrooms by Sheri Ruether MA, Walden University, 2004 BS, University of Texas at San Antonio, 1987 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy
Frequency Selective Hybrid Precoding for Limited Feedback Millimeter Wave Systems

Hybrid analog/digital precoding offers a compromise between hardware complexity and system performance in millimeter wave (mmWave) systems. This type of precoding allows mmWave systems to leverage large antenna array gains that are necessary for sufficient link margin, while permitting low cost and power consumption hardware. Most prior work has focused on hybrid precoding for narrow-band mmWave systems, with perfect or estimated channel knowledge at the transmitter. MmWave systems, however, will likely operate on wideband channels with frequency selectivity. Therefore, this paper considers wideband mmWave systems with a limited feedback channel between the transmitter and receiver. First, the optimal hybrid precoding design for a given RF codebook is derived. This provides a benchmark for any other heuristic algorithm and gives useful insights into codebook designs. Second, efficient hybrid analog/digital codebooks are developed for spatial multiplexing in wideband mmWave systems. Finally, a low-complexity yet near-optimal greedy frequency selective hybrid precoding algorithm is proposed based on Gram-Schmidt orthogonalization. Simulation results show that the developed hybrid codebooks and precoder designs achieve very-good performance compared with the unconstrained solutions while requiring much less complexity.
Energy efficiency of downlink packet scheduling in CoMP

The foreseen increase in the volume of mobile traffic and the correspondent increase in greenhouse gas emissions is now placing energy efficiency (EE) at the forefront of mobile network design. As a step towards incorporating more energy friendly mobile platforms in future networks, Third Generation Partnership Project Long‐Term Evolution (LTE)‐Advanced has adopted Coordinated Multi‐Point (CoMP) transmission/reception because of its ability to mitigate and/or coordinate inter‐cell interference. However, there is room for reducing energy consumption further by exploiting the inherent flexibility of dynamic resource allocation protocols. To this end packet scheduling schemes play a fundamental role in multi‐user scenarios and provide a potential research playground for optimising energy consumption in future networks. However, there is no effective benchmark in place for experimenting new design approaches. This paper provides a first attempt to analyse the Energy Efficiency of different downlink packet scheduling in CoMP for LTE networks using classical packet scheduling algorithm approaches such as Maximum Carrier to Interference ratio (MCI), Proportional Fairness (PF) and the Round Robin scheduling (RR), and provides some input to future comparison considerations. Copyright © 2013 John Wiley & Sons, Ltd.
ProtoNet 4.0: A hierarchical classification of one million protein sequences

ProtoNet is an automatic hierarchical classification of the protein sequence space. In 2004, the ProtoNet (version 4.0) presents the analysis of over one million proteins merged from SwissProt and TrEMBL databases. In addition to rich visualization and analysis tools to navigate the clustering hierarchy, we incorporated several improvements that allow a simplified view of the scaffold of the proteins. An unsupervised, biologically valid method that was developed resulted in a condensation of the ProtoNet hierarchy to only 12% of the clusters. A large portion of these clusters was automatically assigned high confidence biological names according to their correspondence with functional annotations. ProtoNet is available at: http://www.protonet. cs.huji. ac.il.
Outline Colorization through Tandem Adversarial Networks

When creating digital art, coloring and shading are often time consuming tasks that follow the same general patterns. A solution to automatically colorize raw line art would have many practical applications. We propose a setup utilizing two networks in tandem: a color prediction network based only on outlines, and a shading network conditioned on both outlines and a color scheme. We present processing methods to limit information passed in the color scheme, improving generalization. Finally, we demonstrate natural-looking results when colorizing outlines from scratch, as well as from a messy, user-defined color scheme.
Anesthetic Potency and Influence of Morphine and Sevoflurane on Respiration in &mgr;-Opioid Receptor Knockout Mice

Background The involvement of the &mgr;-opioid receptor (&mgr;OR) system in the control of breathing, anesthetic potency, and morphine- and anesthesia-induced respiratory depression was investigated in mice lacking the &mgr;OR. Methods Experiments were performed in mice lacking exon 2 of the &mgr;OR gene (&mgr;OR−/−) and their wild-type littermates (&mgr;OR+/+). The influence of saline, morphine, naloxone, and sevoflurane on respiration was measured using a whole body plethysmographic method during air breathing and elevations in inspired carbon dioxide concentration. The influence of morphine and naloxone on anesthetic potency of sevoflurane was determined by tail clamp test. Results Relative to wild-type mice, &mgr;OR-deficient mice displayed approximately 15% higher resting breathing frequencies resulting in greater resting ventilation levels. The slope of the ventilation–carbon dioxide response did not differ between genotypes. In &mgr;OR+/+ but not &mgr;OR−/− mice, a reduction in resting ventilation and slope, relative to placebo, was observed after 100 mg/kg morphine. Naloxone increased resting ventilation and slope in both genotypes. Sevoflurane at 1% inspired concentration induced similar reductions in resting ventilation and slope in the two genotypes. Anesthetic potency was 20% lower in mutant relevant to wild-type mice. Naloxone and morphine caused an increase and decrease, respectively, in anesthetic potency in &mgr;OR+/+ mice only. Conclusions The data indicate the importance of the endogenous opioid system in the physiology of the control of breathing with only a minor role for the &mgr;OR. The &mgr;OR gene is the molecular site of action of the respiratory effects of morphine. Anesthetic potency is modulated by the endogenous &mgr;-opioid system but not by the &kgr;- and &dgr;-opioid systems.
A neural control model for bimanual rhythmic movements

Rowing a boat, playing drums, and performing surgery require bimanual coordination. Although bimanual coordination in rhythmic movements has been widely researched, the learning processes of these movements have gone largely unnoticed. A well known fact is that bimanual polyrhythms are difficult to perform. A recent study (Mechsner, F. et al., Nature, vol.414, no.1, p.69-73, 2001) has shown that, presented with altered feedback, subjects are able to perform such otherwise difficult tasks. Following this study, we hypothesize that the brain contains internal representation of the transformation between the perception and execution levels. Our hypothesis predicts gradual improvement in performance and an after effect. We have conducted an experiment in which subjects tapped their index fingers while receiving altered visual feedback and observed the improvement of performance as well as after effects that are fingerprints of the internal representation. We present a neural model which portrays these key phenomena associated with the learning dynamics of bimanual coordination.
Community detection in weighted networks: Algorithms and applications

Community detection is an important issue due to its wide use in designing network protocols such as data forwarding in Delay Tolerant Networks (DTN) and worm containment in Online Social Networks (OSN). However, most of the existing community detection algorithms focus on binary networks. Since most networks are weighted such as social networks, DTN or OSN, in this paper, we address the problems of community detection in weighted networks and exploit community for data forwarding in DTN and worm containment in OSN. We propose a novel community detection algorithm, and then introduce two metrics called intra-centrality and inter-centrality, to characterize nodes in communities. Based on these metrics, we propose an efficient data forwarding algorithm for DTN and an efficient worm containment strategy for OSN. Extensive trace-driven simulation results show that the data forwarding algorithm and the worm containment strategy significantly outperform existing works.
Linguistic Methods for Investigating Concepts in Use

In this paper, we present a method for investigating concepts in use. Besides providing an inventory of mental representations as they can be inferred from the speakers’ linguistic behaviour, also their conditions of usage are being analysed. The methodology proposed rests on the assumption that common sense reasoning is observable in the speakers’ displays of their interpretations of the preceding utterances, which in the human-robot communication data investigated here are reformulations of the previous utterance. The linguistic choices speakers make and the order in which they appear allow us to infer the speakers’ underlying hypotheses about language, the communication partner, and the world. 1 Studying Concepts in Use The focus of this paper is on how our mental representations guide our linguistic output. Thus, we are interested in how humans structure their experience and represent information about the world, for instance, about the orientation of objects in a room or an agent’s movement through space, and the linguistic consequences of such representations. For example, we can assume that the way spatial configurations, such as rooms with objects in them, are mentally represented may influence the way speakers talk about them. The most natural source to look at when we want to find out about what goes on in people’s heads may be psychology or, with respect to language, psycholinguistics. Thus, we may want to look at psychological literature to understand speakers’ mental representations of spatial configurations. Experimental psychology provides us with a rich body of data on how humans may store spatial knowledge. For instance, a large body of research shows that one such representation of spatial knowledge may be as a mental model (e.g. JOHNSON-LAIRD 1989). Mental models are analogous to imagined diagrams of states of affairs, they are calculable, finite, economical (such that there may be a few and only a few alternative representations), and their inner structure corresponds to the situation represented (HABEL 1995). However, spatial reasoning does not seem to rely exclusively on mental models; according to ROBERTS & NEWTON (2001), people may also employ strategies that point to very different underlying mental
Approximate Message Passing with Unitary Transformation

Approximate message passing (AMP) and its variants, developed based on loopy belief propagation, are attractive for estimating a vector x from a noisy version of z = Ax, which arises in many applications. For a large A with i. i. d. elements, AMP can be characterized by the state evolution and exhibits fast convergence. However, it has been shown that, AMP mayeasily diverge for a generic A. In this work, we develop a new variant of AMP based on a unitary transformation of the original model (hence the variant is called UT-AMP), where the unitary matrix is available for any matrix A, e.g., the conjugate transpose of the left singular matrix of A, or a normalized DFT (discrete Fourier transform) matrix for any circulant A. We prove that, in the case of Gaussian priors, UT-AMP always converges for any matrix A. It is observed that UT-AMP is much more robust than the original AMP for difficult A and exhibits fast convergence. A special form of UT-AMP with a circulant A was used in our previous work [13] for turbo equalization. This work extends it to a generic A, and provides a theoretical investigation on the convergence.
A Review paper for Detection of Overlapping Communities in Complex Networks

This paper presents a comprehensive study about different methods which were used to detect the communities in networks. Most of the algorithms were failed to perform in all kind of networks i.e. some perform only in weighted networks, some in bi-partite networks and some in directed networks etc. Label propagation algorithm plays the most effective role in community detection as it takes much less time in comparison of many algorithms. But the main disadvantage of this algorithm is that it fails in finding overlapping communities. Despite of its disadvantages it works as a base method for different algorithms like rank based label propagation algorithm and multiple label propagation approach, which are enhancements in label propagation algorithm. So, there must be an algorithm which can be used in most of the networks and able to detect communities both disjoint and overlapping in less running time. We will try to overcome these problems in our research with the help of label sharing approach.
Fast peg-and-hole alignment using visual compliance

This paper presents a visual compliance strategy to deal with the problem of fast peg-and-hole alignment with large position and attitude uncertainty. With the use of visual compliance and adoption of a light-weight 3-DOF active peg, decoupled alignment for position and attitude is realized. The active peg is capable of high-speed motion and with less dynamic defects than a traditional robot arm. Two high-speed cameras, one configured as eye-in-hand and the other as eye-to-hand are adopted to provide with the task-space feedback. Visual constraints for effecting the visual compliant motion are analyzed. Alignment experiments show that peg-and-hole alignment with the proposed approach could be successfully realized with robust convergence, and on average, the alignment could be realized within 0.7 s in our experimental setting.