Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of working memory limitations and distributed cognition on solving search problems on complex informational websites

This research has two important sets of purposes. The first set of purposes was to evaluate working memory load and persistent behavior of computer users navigating complex websites, design and test the effectiveness of feedback intended to reduce revisits to previously-visited (dead-end) states, and determine the extent to which reducing revisits improves overall web navigation performance on difficult search tasks. The second purpose was to contribute to the development of the Cognitive Walkthrough for the Web (CWW), verifying and refining the psychological validity of CWW predictions of search difficulty. Participants in the primary experiment completed 36 tasks that varied in difficulty on an experimental website simulating an actual online encyclopedia. The between-subjects independent variables were link color change (no link color change, cumulative link color change, task-specific link color change), heading feedback (heading feedback, no heading feedback), and order (original, revised). The within-subject independent variables were search difficulty (difficult, easy), and task set (first-half, second-half), the latter being a measure of learning effects. Revisits to subordinate links — a clear, direct measure of working memory errors and perseverance — was the main dependent variable. Results showed that task-specific link color change dramatically reduced revisits to subordinate links, and there was a significant interaction of task set with link color change. In the no-link-color condition, individuals varied dramatically in both mean revisits and maximum revisits, and certain individuals, possibly with low working memory capacity or tendency to perseverate, derived the most benefits from task-specific link color change. However, even task-specific feedback reduced clicks on links by only about a half click, and tasks that CWW predicts to be difficult are not significantly reduced in difficulty. The three independent variables that CWW uses to predict search difficulty and usability problems and predicted clicks on links turn out to equally valid for experimental websites with no link color change and for real-world websites that do provide link color change feedback.
Bibliometrics and Social Network Analysis of Doctoral Research: Research Trends In Distance Learning

The study investigated research topics of doctoral dissertations that examined issues in distance learning from 2000-2014. Twelve reviews of research on distance learning, spanning from 1997-2015, were identified. It was found that only one of these reviews of research (Davies, Howell, & Petri, 2010) looked at doctoral dissertations. The authors noted that investigating dissertations was complicated and daunting because 1) only a fraction made full text available and 2) there were a large number of dissertations in the area. To counter for these complications the current study utilized bibliometric and social network analysis to investigate dissertation database listings, including abstracts, keywords, classifications, and other bibliographic data. Bibliographic data for dissertation listings (n=3,954) was exported from the ProQuest Dissertations & Theses A&I (PQDT) database. Software developed for the study formatted the data and imported it into a series of databases. Natural language processing techniques were utilized to pull emergent keywords from dissertation abstracts. Department and University types were analyzed. Dissertation reference sections were investigated utilizing co-citation analysis. Author generated keywords ands. Department and University types were analyzed. Dissertation reference sections were investigated utilizing co-citation analysis. Author generated keywords and
TRPV 4 MEDIATES THE CALCIUM INFLUX REQUIRED FOR FLIGHTLESS-NON-MUSCLE MYOSIN INTERACTION AND COLLAGEN REMODELING

Collagen remodeling by phagocytosis requires cell extension formation, which in turn involves interaction of the actin binding protein Flightless I (FliI) with non-muscle myosin IIA (NMMIIA) at cell-matrix adhesion sites. As Ca 2+ plays a central role in controlling actomyosin-dependent functions, we examined how Ca 2+ controls the generation of cell extensions and collagen remodeling. Ratio fluorimetry demonstrated localized Ca 2+ influx at extensions of fibroblasts. Western Blotting and qPCR showed high expression levels of the Ca 2+ -permeable, Transient Receptor Potential Vanilloid-4 (TRPV4) channel, which coimmunoprecipitated with 1 integrin and localized to adhesions. Blocking antibody to  integrin, the TRPV4-specific antagonist AB159908, or reduction of TRPV4 expression with siRNA, all blocked Ca 2+ influx. These treatments also inhibited interaction of FliI with NMMIIA, reduced the number and length of cell extensions and blocked collagen remodeling. Pull-down assays showed that Ca 2+ depletion inhibited interaction of purified FliI with NMMIIA filaments. Fluorescence resonance energy transfer experiments showed FliINMMIIA interactions require Ca 2+ influx. We conclude that Ca 2+ influx through TRPV4 channels regulates FliI-NMMIIA interactions, which in turn enable generation of the cell extensions essential for collagen remodeling. Jo ur na l o f C el l S ci en ce • A dv an ce a rt ic le
Unleashing Natural Competence in Lactococcus lactis by Induction of the Competence Regulator ComX

ABSTRACT In biotechnological workhorses like Streptococcus thermophilus and Bacillus subtilis, natural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starter Lactococcus lactis, natural competence has not been established to date. However, in silico analysis of the complete genome sequences of 43 L. lactis strains revealed complete late competence gene sets in 2 L. lactis subsp. cremoris strains (KW2 and KW10) and at least 10 L. lactis subsp. lactis strains, including the model strain IL1403 and the plant-derived strain KF147. The remainder of the strains, including all dairy isolates, displayed genomic decay in one or more of the late competence genes. Nisin-controlled expression of the competence regulator comX in L. lactis subsp. lactis KF147 resulted in the induction of expression of the canonical competence regulon and elicited a state of natural competence in this strain. In contrast, comX expression in L. lactis NZ9000, which was predicted to encode an incomplete competence gene set, failed to induce natural competence. Moreover, mutagenesis of the comEA-EC operon in strain KF147 abolished the comX-driven natural competence, underlining the involvement of the competence machinery. Finally, introduction of nisin-inducible comX expression into nisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence in these strains also, expanding this phenotype to other L. lactis strains of both subspecies. IMPORTANCE Specific bacterial species are able to enter a state of natural competence in which DNA is taken up from the environment, allowing the introduction of novel traits. Strains of the species Lactococcus lactis are very important starter cultures for the fermentation of milk in the cheese production process, where these bacteria contribute to the flavor and texture of the end product. The activation of natural competence in this industrially relevant organism can accelerate research aiming to understand industrially relevant traits of these bacteria and can facilitate engineering strategies to harness the natural biodiversity of the species in optimized starter strains.
Intelligent model predictive/feedback linearization control of half-car vehicle suspension systems.

There exists a level of parametric uncertainty in dynamic systems which if left unaccounted, could impact negatively on performance during implementation. This thesis aims to investigate the effect of acceptably bounded uncertainty, on the performance of Vehicle Suspension Systems (VSS) in the presence of model constraints. The uncertain parameters selected in this work are vehicle sprung mass loading, vehicle forward velocity, suspension spring stiffness coefficients and suspension damper coefficients. A model of a nonlinear, 4 Degree-of-Freedom (DOF) half-car Active Vehicle Suspension Systems (AVSS) with hydraulic actuator dynamics and a similar nonlinear, 4 DOF half-car Passive Vehicle Suspension System (PVSS) model are developed in MATLAB/Simulink ©. A two-loop control configuration is designed for the AVSS. This consists of an inner Proportional plus Integral plus Derivative (PID) force feedback control loop; to stabilize the hydraulic actuator and enables tracking of a desired force and an outer control loop for suspension travel control, with the aim of preventing damage by “topping” or “bottoming” (banging of the suspension components on the top or bottom of the suspension workspace). Three control methods are applied to this outer control loop: PID for performance benchmarking, Model Predictive Control (MPC) and Neural Network-based Feedback Linearization (NNFBL). MPC allows for control of systems in the presence of model constraints. NNFBL utilizes an indirect adaptive Neural Network (NN) based identification to linearize highly nonlinear systems into linear ones, allowing application of other control methods thereafter. The performance of the various AVSS controllers are compared with that of the PVSS in the frequency and time domains. In the frequency domain, a road input disturbance with frequency sweeping from 0− 100Hz is employed to obtain output data for spectral analysis. In the time domain, a sinusoidal bump road input disturbance and a random road input disturbance are utilized to test vehicle performance. The results indicate that the AVSS is less sensitive to uncertainty in model parameters as compared to the PVSS, by performing better under varying conditions.
Use of RetroNectin in studies requiring in vitro HIV-1 infection of human hematopoietic stem/progenitor cells

Human immunodeficiency virus (HIV) causes damage, directly or indirectly, to the whole hematopoietic system including CD34+ hematopoietic stem/progenitor cells (HSPC). CXCR4-tropic strains of HIV-1 may be potent to affect the function of CD34+CXCR4+ progenitor cells either by infecting the cells or by modifying the dynamics of more differentiated hematopoietic cells. However, CD34+ cells are known for the resistance to HIV-1 infection in vitro, restricting the detailed analysis of the impact of HIV upon HSPC. Here the authors report a use of RetroNectin, a recombinant fibronectin fragment used for gene transfer with lentiviral vectors, to overcome the limitation.
A new adaptive routing scheme based on the traffic characteristics in mobile ad hoc networks

We consider an ad hoc network that can form a flat or a hierarchical architecture. Basically all the mobile nodes form a flat network and some mobile nodes are able to be cluster heads, making mobility management easy. We define routing path establishment cost from a source node to a destination node and show the numerical results as the total number of mobile nodes increase in each ad hoc architecture. Through simulation we propose a new adaptive routing scheme based on the traffic characteristics in mobile ad hoc networks.
A Dynamic Weight Congestion Control Algorithm to Achieve Fairness in the MPTCP

Nowadays, a growing number of mobile equipments have more than one single network interface. For instance, smart phones have 3G/4G and Wi-Fi interfaces at the same time. Regular TCP restricts communications to a single path per transport connection. MPTCP (Multipath TCP) is a set of extensions to traditional TCP to improve the robustness and performance of end-to-end transport layer connections using more than one interface simultaneously. A key issue in the design of MPTCP is the fairness to traditional TCP flows. In this paper, we do a research on the congestion control mechanism of MPTCP and propose a dynamic weighted congestion control algorithm, which can improve the fault of the congestion control algorithm in the RFC 6356 when the subflows have share bottleneck. When the subflow increases the window size, dynamic weight algorithm will increase weight of the congestion window by the size of the congestion window. A MPTCP flow with the dynamic weighted congestion algorithm can allocate their traffic by the throughput of the subflow and get more fairness to traditional TCP flows than the MPTCP in RFC 6356.
The hidden spatial dimension of alpha: 10 Hz perceptual echoes propagate as periodic travelling waves in the human brain

Alpha oscillations play a special role in vision. During sensory processing, reverse-correlation techniques revealed that white-noise luminance sequences elicit a robust occipital ~10 Hz response that periodically reverberates the input sequence for up to 1 s. These perceptual echoes constitute the impulse response function of the visual system. However, the spatial dimension of perceptual echoes remains unknown: do they reverberate across the cortex simultaneously? Does stimulation over multiple visual coordinates evoke multiple synchronized echoes, or do they show consistent phase differences? Here, we tested the spatial dimension of perceptual echoes in two electroencephalogram (EEG) experiments manipulating the location of the visual stimulation. When a single disc flickered a white-noise luminance sequence in the upper visual field, we observed a single “echo wave” originating in posterior sensors and spatially propagating towards frontal ones (i.e. periodic travelling wave). The presentation of two independent flickering discs in separate visual hemifields produced two simultaneous and superimposed echo waves propagating in opposite directions, one in response to each stimulus. Strikingly, at many electrode sites, the phase of the two echoes differed, with a phase advance for the contralateral stimulus location. EEG source reconstruction tentatively located the waves within contralateral parieto-occipital cortex. In conclusion, the alpha rhythm processes stimulus information as a travelling wave that propagates across the cortical representation of retinotopic space in the human brain. In line with the “cortical scanning” hypothesis (Pitts & McCulloch, 1947), these results suggest the existence of an additional spatial dimension embedded in the phase of the alpha rhythm. Significance statement How does the spatial dimension of sensory processing relate to the temporal dimension of brain rhythms? Using correlation techniques, we characterized perceptual echoes, the average electroencephalogram response induced by visual stimuli that change luminance randomly. We found that perceptual echoes are actually periodic waves that travel through human visual cortex. Strikingly these periodic waves show consistent phase differences across the visual field, processing screen locations sequentially across distinct phases of the cycle following basic retinotopy. These results suggest the existence of an additional “hidden” spatial dimension in sensory cortex, encoded in the phase of the alpha oscillatory cycle. This could mean that perceptual echoes behave like sweeps of a sonar, processing the visual field in cycles of ~100 ms duration.
A heterochromatin domain forms gradually at a new telomere and is highly dynamic at stable telomeres

Heterochromatin domains play important roles in chromosome biology, organismal development and aging. In the fission yeast Schizosaccharomyces pombe and metazoans, heterochromatin is marked by histone H3 lysine 9 dimethylation. While factors required for heterochromatin have been identified, the dynamics of heterochromatin formation are poorly understood. Telomeres convert adjacent chromatin into heterochromatin. To form a new heterochromatic region in S. pombe, an inducible DNA double-strand break (DSB) was engineered next to 48 bp of telomere repeats in euchromatin, which caused formation of new telomere and gradual spreading of heterochromatin. However, spreading was highly dynamic even after the telomere had reached its stable length. The system also revealed the presence of repeats located at the boundaries of euchromatin and heterochromatin that are oriented to allow the efficient healing of a euchromatic DSB to cap the chromosome end with a new telomere. Telomere formation in S. pombe therefore reveals novel aspects of heterochromatin dynamics and the presence of failsafe mechanisms to repair subtelomeric breaks, with implications for similar processes in metazoan genomes.
Advanced whole genome sequencing and analysis of fetal genomes from amniotic fluid

Amniocentesis is typically performed to identify large chromosomal abnormalities within the fetus. Here we demonstrate that it is feasible to generate an accurate whole genome sequence (WGS) of a fetus from an amniotic sample. DNA from cells and the amniotic fluid were isolated and sequenced from 31 amniocenteses. Concordance of variant calls between the two DNA sources and with parental libraries was high. Two fetal genomes were found to harbor potentially detrimental variants in CHD8 and LRP1, variations in these genes have been associated with Autism Spectrum Disorder (ASD) and Keratosis pilaris atrophicans, respectively. We also discovered drug sensitivities and carrier information of fetuses for a variety of diseases. In this study, we demonstrate for the first time the sequencing of the whole genome of fetuses from amniotic fluid and show that much more information than large chromosomal abnormalities can be gained from an amniocentesis.
Cross -validation for unsupervised learning

Cross-validation (CV) is a popular method for model-selection. Unfortunately, it is not immediately obvious how to apply CV to unsupervised or exploratory contexts. This thesis discusses some extensions of cross-validation to unsupervised learning, specifically focusing on the problem of choosing how many principal components to keep. We introduce the latent factor model, define an objective criterion, and show how CV can be used to estimate the intrinsic dimensionality of a data set. Through both simulation and theory, we demonstrate that cross-validation is a valuable tool for unsupervised learning.
Design of direct controllers of PID type by receptive field neural networks

A direct controller of PID type using receptive field neural networks is suggested. This method does not put too much restriction on the type of the plant to be controlled and it has a stable performance for the type of inputs it has been trained for. Unlike backpropagation or other supervised methods of training, this approach does not require the knowledge of the appropriate form of controller output for each given input and neither does it require identification of the plant or its inverse model. The parameters of the PID controller in this method are determined by weight perturbation. Simulation results show a satisfactory performance.
Analysis And Overview Of Routing Protocols And Security Attacks In Wireless Sensor Networks

The collections of large number of sensor nodes are called wireless sensor networks. It is one of the domineering technologies in near future and also poses the unique challenges for the researchers to related field. Sensor networks are tiny nodes with sensing, computation capability. The fault tolerance, high sensing fidelity, flexibility and rapid deployment are some of the characteristic of sensor network which make it exiting in the field of remote sensing. Though there is another side too. In a very large scale sensor network individual sensors are subject to security compromise. Attacker can overhear the messages sent by another sensor node due to broadcast nature of communication. With increasing requirement of WSN in the areas of military and other areas, the security threats also increases. However the open nature of the wireless communication channels, the lack of infrastructure, the fast deployment practices, and the hostile environments where they may be deployed, make them vulnerable to a wide range of security attacks. The key issues in WSN are security, energy consumption and proper communication . In this paper we surveyed all the possible security attacks and all the geographical routing protocols in WSN . Some possible security attacks in wireless sensor network are Sink hole attack, Sybil attack, selective forwarding attack, wormhole attack and hello flood attack. This paper presents a thorough review of all the routing protocols as well as all these attacks which are given above in WSN. Keyword-WSN,QOS,C4ISRT,SGPSR,GPSR,Sybilattck, Sinkhole attack, Black hole attack, Wormhole attack, Hello flood.
Fitness effects of cis-regulatory variants in the Saccharomyces cerevisiae TDH3 promoter

Variation in gene expression is widespread within and between species, but fitness consequences of this variation are generally unknown. Here we use mutations in the Saccharomyces cerevisiae TDH3 promoter to assess how changes in TDH3 expression affect cell growth. From these data, we predict the fitness consequences of de novo mutations and natural polymorphisms in the TDH3 promoter. Nearly all mutations and polymorphisms in the TDH3 promoter were found to have no significant effect on fitness in the environment assayed, suggesting that the wild type allele of this promoter is robust to the effects of most new cis-regulatory mutations.
A SIMPLE pipeline for mapping point mutations

A forward genetic screen is one of the best methods for revealing the regulatory functions of genes. In plants, this technique is highly efficient since it is relatively easy to grow and screen the phenotypes of hundreds or thousands of individuals. The cost-efficiency and ease of data production afforded by next-generation sequencing techniques have created new opportunities for mapping induced mutations. The principles of genetic mapping remain the same. However, the details have changed, which allows for rapid mapping of causal mutations. Current mapping tools are often not user-friendly and complicated or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA change(s). The pipeline has been validated in Arabidopsis and can be readily applied to other species.
Application of feedforward and recurrent neural networks to chemical plant predictive modeling

The authors explore the use of backpropagation and recurrent backpropagation neural networks for the indentification of the dynamics of a chemical process. The authors build predictive models for plant variables and compare the performance of the feedforward and recurrent neural networks on this prediction problem. The authors also consider the training efficiency of two recurrent backpropagation learning laws-namely, R.J. Williams, and D. Zipser's teacher forced learning law (1989) and F.S. Tsung's law (1991). In this study, the Tsung law performed significantly better (faster learning speed and lower ultimate error level) than the teacher forced learning law. <<ETX>>