Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced drought and heat stress tolerance of tobacco plants with ectopically enhanced cytokinin oxidase/dehydrogenase gene expression

Responses to drought, heat, and combined stress were compared in tobacco (Nicotiana tabacum L.) plants ectopically expressing the cytokinin oxidase/dehydrogenase CKX1 gene of Arabidopsis thaliana L. under the control of either the predominantly root-expressed WRKY6 promoter or the constitutive 35S promoter, and in the wild type. WRKY6:CKX1 plants exhibited high CKX activity in the roots under control conditions. Under stress, the activity of the WRKY6 promoter was down-regulated and the concomitantly reduced cytokinin degradation coincided with raised bioactive cytokinin levels during the early phase of the stress response, which might contribute to enhanced stress tolerance of this genotype. Constitutive expression of CKX1 resulted in an enlarged root system, a stunted, dwarf shoot phenotype, and a low basal level of expression of the dehydration marker gene ERD10B. The high drought tolerance of this genotype was associated with a relatively moderate drop in leaf water potential and a significant decrease in leaf osmotic potential. Basal expression of the proline biosynthetic gene P5CSA was raised. Both wild-type and WRKY6:CKX1 plants responded to heat stress by transient elevation of stomatal conductance, which correlated with an enhanced abscisic acid catabolism. 35S:CKX1 transgenic plants exhibited a small and delayed stomatal response. Nevertheless, they maintained a lower leaf temperature than the other genotypes. Heat shock applied to drought-stressed plants exaggerated the negative stress effects, probably due to the additional water loss caused by a transient stimulation of transpiration. The results indicate that modulation of cytokinin levels may positively affect plant responses to abiotic stress through a variety of physiological mechanisms.
Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands

In prokaryotes, clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (Cas) proteins constitute a defence system against bacteriophages and plasmids. CRISPR/Cas systems acquire short spacer sequences from foreign genetic elements and incorporate these into their CRISPR arrays, generating a memory of past invaders. Defence is provided by short non-coding RNAs that guide Cas proteins to cleave complementary nucleic acids. While most spacers are acquired from phages and plasmids, there are examples of spacers that match genes elsewhere in the host bacterial chromosome. In Pectobacterium atrosepticum the type I-F CRISPR/Cas system has acquired a self-complementary spacer that perfectly matches a protospacer target in a horizontally acquired island (HAI2) involved in plant pathogenicity. Given the paucity of experimental data about CRISPR/Cas–mediated chromosomal targeting, we examined this process by developing a tightly controlled system. Chromosomal targeting was highly toxic via targeting of DNA and resulted in growth inhibition and cellular filamentation. The toxic phenotype was avoided by mutations in the cas operon, the CRISPR repeats, the protospacer target, and protospacer-adjacent motif (PAM) beside the target. Indeed, the natural self-targeting spacer was non-toxic due to a single nucleotide mutation adjacent to the target in the PAM sequence. Furthermore, we show that chromosomal targeting can result in large-scale genomic alterations, including the remodelling or deletion of entire pre-existing pathogenicity islands. These features can be engineered for the targeted deletion of large regions of bacterial chromosomes. In conclusion, in DNA–targeting CRISPR/Cas systems, chromosomal interference is deleterious by causing DNA damage and providing a strong selective pressure for genome alterations, which may have consequences for bacterial evolution and pathogenicity.
Role of AP1 and Gadkin in the traffic of secretory endo-lysosomes

We report that exocytosis of secretory lysosomes in nonspecialized cells does not depend on the mechanisms of late endocytic membrane transport but on Rab27A-like, lysosome-related organelles in specialized cells. We also find that this unconventional secretory process depends on clathrin, the Adaptor Protein complex 1 (AP1) adaptor, and the AP1-binding partner Gadkin.
Hierarchical surface fairing with constraints

The surfaces of complex free-form objects can typically be modeled by a hierarchy of primary surfaces, connecting surfaces and corner patches. Within the context of digital shape reconstruction, these surfaces simultaneously approximate measured data points, satisfy fairness criteria and adhere to continuity constraints according to their dependencies. A new framework algorithm is introduced to perfect existing B-spline surfaces; the algorithm alternates --- in a stepwise manner --- between continuity constraint satisfaction and fairing by the remaining degrees of freedom. Some well-known fairing methods are adapted to this framework. Constrained fairing for n-sided corner patches, composed of quadrilaterals, is also briefly discussed. A few examples illustrate the results.
Optimized methodologies for augmented reality markers based localization

Localization is one of the key research topics in robotics. Although computer vision based methodologies such as Augmented Markers provides a realtime localization approach, the sensing range and localization accuracy are the main limitations for applications. In this paper, we proposed the use of a problem solving tool, TRIZ to overcome these limitations. Among the tools provided by TRIZ, we illustrated the selection of principles for problem solving. To enhance the sensing range, a novel AR marker is presented. To improve the localization accuracy, we presented the use of an AR polyhedron for system localization. With the use of an AR cube for illustration, we further developed a new optimization strategy. It is a weighted sum method which aims to optimize the position of the AR cube by considering the orientation of different AR markers captured by a camera. To evaluate the proposed methods, different experiments have been conducted including static and dynamic localizations. Results show that the proposed solutions and strategy can significantly improve the sensing range and accuracy of the conventional AR localization system.
Securing Wireless Sensor Networks Against Broadcast Service Attacks

Abstract Attacks against broadcast services in wireless sensor networks will have the most catastrophic effects on power and other resource consumptions. As bogus broadcast packets are propagated through sensor nodes without being filtered out, sensor nodes will waste their resources such as power and memory on transmitting and buffering those false packets. In networks where complex Denial-of-Service (DoS) attacks may be launched, each node should be able to limit its effects on resource consumptions. In addition, it is strongly desired to identify compromised sensor node(s) which has injected invalid packets (intrusion detection) and to isolate the nodes (remediation) such that no more DoS attack is possible through the compromised sensor node(s) in the future. A new secure broadcast authentication scheme for sensor networks is proposed in this paper based upon predictive hashing and μTESLA techniques. This new scheme may be used to detect invalid packets as quickly as possible and to isolate links that are from the compromised nodes, which results in enhanced resistance to various security attacks including DoS attacks. We present the details of the scheme along with the simulation results.
M74 X-1 (CXOU J013651.1+154547): An Extremely Variable Ultraluminous X-Ray Source

Ultraluminous X-ray sources (ULXs) have been described variously as the most luminous normal X-ray binaries, hypernovae, and "intermediate-mass" black holes with masses of hundreds to thousands of solar masses. We present results on M74 X-1 (CXOU J013651.1+154547), a ULX in the nearby spiral galaxy M74 (NGC 628), from observations by Chandra and XMM-Newton. M74 X-1 is a persistent source that exhibits extreme variability and changes in spectral state on timescales of several thousand seconds. Its variability timescales and behavior resemble some Galactic microquasars. This suggests that the emission mechanism may be related to relativistically beamed jets and that M74 X-1 could be an extragalactic "microblazar"—a microquasar whose jet axis is aligned with our line of sight. We also note that its spectrum is consistent with the presence of a low-temperature disk blackbody component, which, assuming it is due to radiation from an accretion disk, could indicate that M74 X-1 contains an intermediate-mass black hole.
Receiver diversity with blind fir SIMO channel estimates

Traditionally, the performance of blind SIMO channel estimates has been characterized in a deterministic fashion, by identifying those channel realizations that are not blindly identifiable. In this paper, we focus instead on the performance of Linear Equalizers for fading channels when they are based on blind channel estimates. Our analysis shows that with Zero Forcing Linear Equalizer (ZF-LE) at least one order of the diversity is lost depending on the way by which the scalar ambiguity that results from the blind channel estimation is resolved. However, in some Tx scenarios we are able to recover the diversity with MMSE-LE. Various Tx scenarios are considered in detail.
Ethanol Inhibits Activation of NLRP3 and AIM2 Inflammasomes in Human Macrophages–A Novel Anti-Inflammatory Action of Alcohol

Objective In the pathogenesis of coronary atherosclerosis, local macrophage-driven inflammation and secretion of proinflammatory cytokines, interleukin-1β (IL-1β) in particular, are recognized as key factors. Moderate alcohol consumption is associated with a reduced risk of coronary artery disease mortality. Here we examined in cultured human macrophages whether ethanol modulates the intracellular processes involved in the secretion of IL-1β. Results Ethanol decreased dose-dependently the production of mature IL-1β induced by activators of the NLRP3 inflammasome, i.e. ATP, cholesterol crystals, serum amyloid A and nigericin. Ethanol had no significant effect on the expression of NLRP3 or IL1B mRNA in LPS-primed macrophages. Moreover, secretion of IL-1β was decreased in parallel with reduction of caspase-1 activation, demonstrating that ethanol inhibits inflammasome activation instead of synthesis of pro-IL-1β. Acetaldehyde, a highly reactive metabolite of ethanol, had no effect on the ATP-induced IL-1β secretion. Ethanol also attenuated the secretion of IL-1β triggered by synthetic double-stranded DNA, an activator of the AIM2 inflammasome. Ethanol conferred the inhibitory functions by attenuating the disruption of lysosomal integrity and ensuing leakage of the lysosomal protease cathepsin B and by reducing oligomerization of ASC. Conclusion Ethanol-induced inhibition of the NLRP3 inflammasome activation in macrophages may represent a biological pathway underlying the protective effect of moderate alcohol consumption on coronary heart disease.
Design of an Early Response System using EGT-based overlay network

The main objective of this paper is to design Evolutionary Game Theory (EGT) based overlay network structure with the combination of network reciprocity and group selection mechanisms to achieve evolutionary cooperation among individual nodes. Each node in the proposed network structure has ability to detect the DDoS attacks using Non-parametric sliding window based change point detection algorithm. It analyzes every incoming traffic behavior changes and generates the attack patterns based on the traffic profile. The proposed network structure is considered as a tree like structure in the experimental analysis, which monitors the network traffic and provides faster detection during the distributed flooding attack. As a result, our network detects the DDoS attacks at the intermediate stage itself with the sharing nature of attack patterns, without any interruption to legitimate users. Moreover, it provides excellent detection accuracy (98%) and high degree of efficiency during high probability of network traffic.
Perception of Utility in Autonomic VoIP Systems

The transmission of voice-over-Internet protocol (VoIP) network traffic is used in an increasing variety of applications and settings. Many of these applications involve communications where VoIP systems are deployed under unpredictable conditions with poor network support. These conditions make it difficult for users to configure and optimize VoIP systems and this creates a need for self configuring and self optimizing systems. To build an autonomic system for VoIP communications, it is valuable to be able to measure the user perceived utility of a system. In this paper we identify factors important to the estimation of user perceived utility in task dependent VoIP communications.
Acoustic Features for Classification Based Speech Separation

Speech separation can be effectively formulated as a binary classiﬁcation problem. A classiﬁcation based system produces a binary mask using acoustic features in each time-frequency unit. So far, only pitch and am-plitude modulation spectrogram have been used as unit level features. In this paper, we study other acoustic features and show that they can signiﬁcantly improve both voiced and unvoiced speech separation performance. To further explore complementarity in terms of discriminative power, we propose a group Lasso approach for feature combination. The ﬁnal combined feature set yields promising results in both matched and unmatched test conditions.
Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs

DYX1C1, DCDC2, and KIAA0319 are three of the most replicated dyslexia candidate genes (DCGs). Recently, these DCGs were implicated in functions at the cilium. Here, we investigate the regulation of these DCGs by Regulatory Factor X transcription factors (RFX TFs), a gene family known for transcriptionally regulating ciliary genes. We identify conserved X‐box motifs in the promoter regions of DYX1C1, DCDC2, and KIAA0319 and demonstrate their functionality, as well as the ability to recruit RFX TFs using reporter gene and electrophoretic mobility shift assays. Furthermore, we uncover a complex regulation pattern between RFX1, RFX2, and RFX3 and their significant effect on modifying the endogenous expression of DYX1C1 and DCDC2 in a human retinal pigmented epithelial cell line immortalized with hTERT (hTERT‐RPE1). In addition, induction of ciliogenesis increases the expression of RFX TFs and DCGs. At the protein level, we show that endogenous DYX1C1 localizes to the base of the cilium, whereas DCDC2 localizes along the entire axoneme of the cilium, thereby validating earlier localization studies using overexpression models. Our results corroborate the emerging role of DCGs in ciliary function and characterize functional noncoding elements, X‐box promoter motifs, in DCG promoter regions, which thus can be targeted for mutation screening in dyslexia and ciliopathies associated with these genes. —Tammimies, K. , Bieder, A. , Lauter, G. , Sugiaman‐Trapman, D. , Torchet, R. , Hokkanen, M. ‐E. , Burghoorn, J., Castrén, E. , Kere, J., Tapia‐Páez, I. , Swoboda, P. Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor (RF) X transcription factors through X‐box promoter motifs. FASEB J. 30, 3578–3587 (2016). www.fasebj. org
A Linear Stochastic Dynamical Model of ENSO. Part I: Model Development

Singular vector analysis and Floquet analysis are carried out on a linearized variant of the Zebiak-Cane atmosphere-ocean model of El Nino-Southern Oscillation (ENSO), hereinafter called the nominal model. The Floquet analysis shows that the system has a single unstable mode. This mode has a shape and frequency similar to ENSO and is well described by delayed oscillator physics. Singular vector analysis shows two interesting features. (i) For any starting month and time period of optimization the singular vector is shaped like one of two nearly orthogonal patterns. These two patterns correspond approximately to the real and imaginary parts of the adjoint of the ENSO mode for the time-invariant basic-state version of the system that was calculated in previous work. (ii) Contour plots of the singular values as a function of starting month and period of optimization show a ridge along end times around December. This result along with a study of the time evolution of the associated singular vectors shows that the growth of the singular vectors has a strong tendency to peak in the boreal winter. For the case of a stochastically perturbed ENSO model, this result indicates that the annual cycle in the basic state of the ocean is sufficient to produce strong phase locking of ENSO to the annual cycle; it is not necessary to invoke either nonlinearity or an annual cycle in the structure of the noise. The structures of the ENSO mode, of the optimal vectors, and of the phase locking to the annual cycle are robust to a wide range of values for the following parameters: the coupling strength, the ocean mechanical damping, and the reflection efficiency of Rossby waves that are incident on the western boundary. Four variant models were formed from the nominal coupled model by changing the aforementioned parameters in such a way as to (i) make the model linearly stable and (ii) affect the ratio of optimal transient growth to the amplitude of the first Floquet multiplier (i.e., the decay rate of the ENSO mode). Each of these four models is linearly stable to perturbations but is shown to support realistic ENSO variability via transient growth for plausible values of stochastic forcing. For values of these parameters that are supported by observations and theory, these results show the coupled system to be linearly stable and that ENSO is the result of transient growth. Supporting evidence is found in a companion paper.
What Are Robots?

However, there are significant research challenges in developing and testing rehabilitation robots so that they meet the requirements of end users. The technology must be capable of improving a person’s impaired or allayed function. To do this, robots have to be able to recognise and respond to the complexity of individual human physiology and behaviour so they can mirror established rehabilitative interventions. In other words, robots have to understand how humans work.
Variability of throughput in pointing device tests: button-up or button-down?

Object selection and activation in graphical user interfaces is usually connected to the changes in the state of the buttons on the mouse. In input device testing the position of the mouse cursor at the time of button-down or button-up events is used. We measured the effect the choice of event has on throughput in a standard Fitts' paradigm pointing device test. 12 participants used two mice with button-down and button-up events as the target selection trigger. Button-down events produced 0.2 bps higher throughput than button-up events. Because of this, it is important to choose the relevant event to be used in pointing device tests and to report the choice along with the results. Otherwise results may be misleading and inter-study comparisons of throughput values may be inaccurate.
CS 229 Project report : Extracting vital signs from video

In both developing and developed countries, reducing the cost of medical care is a primary goal of science and government. In this project we seek to find and extract information from a video of a human that tells us the pulse rate and the oxygen level of the blood, with the eventual aim to create a virtual pulse oximeter. Features to be extracted were chosen to be related to the three color channel intensity values, with the idea that changing color of the video would relate to blood flow around the body. Extensive pre-processing was required on both the video data and the pulse oximeter data to enable training. Early results showed that feature selection was vital in reducing the mean-squared error of the output. At the end of this report, we outline further work to be done.
Correlations between slant wet delays measured by microwave radiometry

We present an analysis of the correlation between the atmospheric slant wet delays in different directions using data from a microwave radiometer. The correlations between wet delays observed in different directions using different temporal constraints are compared to a model derived from theories of turbulence. The agreement between the model and the radiometer data was good, and the average squared difference between zenith mapped slant wet delays could be predicted with an accuracy of 0.01-0.04 cm/sup 2/. Our analysis shows a large short-term variability which variance has a seasonal dependence of about /spl plusmn/26%, largely depending on the refractivity structure constant C/sub n/. We also demonstrate how the model can be used to characterize the stability of a microwave radiometer.
Submitted in partial requirement for the MPhil in Computer Speech and Language Processing Speaker Tracking

This project investigates the problem of labelling segments in a speaker-tracking system. A mathematical representation of each segment is sought which encaptures the speakerdependent information available. It is shown that both the covariance matrix and the Maximum Likelihood Linear Regression (MLLR) matrix provide such a representation with over 90% success rate in a speaker identification task. Several alternative distance metrics to measure the “closeness” of the segments are investigated and it is found the covariance data performs best on those based on the mathematical means of the eigenvalues of one matrix relative to another. The MLLR matrix is by contrast found to work best with elementwisemetrics confirming the hypothesis that the individual elements of the matrix are more significant in this case. Several hierarchical clustering schemes are then investigated and shown to produce speakerspecific groups on two and three speaker problems. A full-scale implementation is then described and tested on data from the 1996 Broadcast News database. A new criterion for evaluating the clusters is defined and shown to be a good indication of speaker split. Six clustering schemes are evaluated using this new criterion and the discriminative LanceWilliams scheme is found to perform the best. Furthest neighbour clustering is also shown to perform well in some cases. Tree diagrams for the best cases of three and four clusters are presented and explained in terms of the clustering strategywhich produced them. They illustrate the feasibility of such a system, with only a few segments being obviously mis-classified. Possible improvements for the system are then discussed and finally recommendations for further work are given. Declaration This thesis is substantiallymy own work. Where reference has been made to other research this is acknowledged in the text and bibliography. It has not been submitted in whole or part for a degree at any other university. The length of this thesis including footnotes, appendices and bibliography is 14943 words.
Verifying Business Process Compatibility

We describe a process-algebraic approach to verifying process interactions for business collaboration described in Business Process Modelling Notation. We first overview our process semantics for BPMN in the language of Communicating Sequential Processes; we then use a simple example of business collaboration to demonstrate how our semantic model may be used to verify compatibility between business participants in a collaboration.