Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel R2R3-MYB Transcription Factor BpMYB106 of Birch (Betula platyphylla) Confers Increased Photosynthesis and Growth Rate through Up-regulating Photosynthetic Gene Expression

We isolated a R2R3-MYB transcription factor BpMYB106, which regulates photosynthesis in birch (Betula platyphylla Suk.). BpMYB106 mainly expresses in the leaf and shoot tip of birch, and its protein is localized in the nucleus. We further fused isolated a 1588 bp promoter of BpMYB106 and analyzed it by PLACE, which showed some cis-acting elements related to photosynthesis. BpMYB106 promoter β-glucuronidase (GUS) reporter fusion studies gene, the result, showed the GUS reporter gene in transgenic birch with BpMYB106 promoter showed strong activities in shoot tip, cotyledon margins, and mature leaf trichomes. The overexpression of BpMYB106 in birch resulted in significantly increased trichome density, net photosynthetic rate, and growth rate as compared with the wild-type birch. RNA-Seq profiling revealed the upregulation of several photosynthesis-related genes in the photosynthesis and oxidative phosphorylation pathways in the leaves of transgenic plants. Yeast one-hybrid analysis, coupled with transient assay in tobacco, revealed that BpMYB106 binds a MYB binding site MYB2 in differentially expressed gene promoters. Thus, BpMYB106 may directly activate the expression of a range of photosynthesis related genes through interacting with the MYB2 element in their promoters. Our study demonstrating the overexpression of BpMYB106—a R2R3-MYB transcription factor—upregulates the genes of the photosynthesis and oxidative phosphorylation pathways to improve photosynthesis.
Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape

Perhaps no other topic in contemporary genomics has inspired such diverse viewpoints as the 95+% of the genome, previously known as “junk DNA,” that does not code for proteins. Here, we present a theory in which dark matter RNA plays a role in the generation of a landscape of spatial micro-domains coupled to the information signaling matrix of the nuclear landscape. Within and between these micro-domains, dark matter RNAs additionally function to tether RNA interacting proteins and complexes of many different types, and by doing so, allow for a higher performance of the various processes requiring them at ultra-fast rates. This improves signal to noise characteristics of RNA processing, trafficking, and epigenetic signaling, where competition and differential RNA binding among proteins drives the computational decisions inherent in regulatory events.
Fitting Parametric Curves to Dense and Noisy Points

Abstract : Given a large set of irregularly spaced points in the plane, an algorithm for partitioning the points into subsets and fitting a parametric curve to each subset is described. The points could be measurements from a physical phenomenon, and the objective in this process could be to find patterns among the points and describe the phenomenon analytically. The points could be measurements from a geometric model, and the objective could be to reconstruct the model by a combination of parametric curves. The algorithm proposed here can be used in various applications, especially where given points are dense and noisy.
Journal of Graph Algorithms and Applications Planar Embeddability of the Vertices of a Graph Using a Fixed Point Set Is Np-hard

Let G = (V, E) be a graph with n vertices and let P be a set of n points in the plane. We show that deciding whether there is a planar straight-line embedding of G such that the vertices V are embedded onto the points P is NP-complete, even when G is 2-connected and 2-outerplanar. This settles an open problem posed in [2, 4, 13].
Novel DoS/DDoS Attack Detection and Signature Generation

Denial of Service (DoS) and Distributed DoS (DDoS) attacks are evolving continuously. These attacks make network resources unavailable for legitimate users which results in massive loss of data, resources and money. Combination of Intrusion detection System and Firewall is used by Business Organizations to detect and prevent Organizations‟ network from these attacks. But this combination cannot prevent network from novel attacks as Signatures to detect them are not available. This paper presents a light-Weight mechanism to detect novel DoS/DDoS (Resource Consumption) attacks and automatic Signature generation process to represent them in real time. Experimental results are provided to support the proposed mechanism.
Fast candidate generation for two-phase document ranking: postings list intersection with bloom filters

Most modern web search engines employ a two-phase ranking strategy: a candidate list of documents is generated using a "cheap" but low-quality scoring function, which is then reranked by an "expensive" but high-quality method (usually machine-learned). This paper focuses on the problem of candidate generation for conjunctive query processing in this context. We describe and evaluate a fast, approximate postings list intersection algorithms based on Bloom filters. Due to the power of modern learning-to-rank techniques and emphasis on early precision, significant speedups can be achieved without loss of end-to-end retrieval effectiveness. Explorations reveal a rich design space where effectiveness and efficiency can be balanced in response to specific hardware configurations and application scenarios.
Substrate integrated waveguide bandpass filter with novel cascaded complementary electric-LC resonators

In this paper, a substrate integrated waveguide (SIW) bandpass filter based on the novel cascaded complementary electric-LC (CCELC) resonator is presented. The unit cell of the SIW with the complementary electric-LC (CELC) resonator is investigated first. It is shown that the SIW with the CELC resonator exhibits a better filtering response and an improved out-of-band performance in comparison to the SIW with the conventional CSRR. By combining two CELC resonators together, a novel cascaded CELC (CCELC) resonator is then proposed to further improve the stopband rejection. A second order SIW bandpass filter with the CCELC resonator is designed and fabricated. Good agreement is achieved between the measurement and the simulation. The proposed SIW bandpass filter with the CCELC resonator shows a very sharp upper transition band and a broad rejection band, and it is low loss, low cost, easy to fabricate and integrate with other microwave circuits.
Batching and Scheduling Jobs on Batch and Discrete Processors

We consider a situation in which the manufacturing system is equipped with batch and discrete processors. Each batch processor can process a batch limited number of jobs simultaneously. Once the process begins, no job can be released from the batch processor until the entire batch is processed. In this paper, we analyze a class of two-machine batching and scheduling problems in which the batch processor plays an important role. Specifically, we consider two performance measures: the makespan and the sum of job completion times. We analyze the complexity of this class of problems, present polynomial procedures for some problems, propose a heuristic, and establish an upper bound on the worst case performance ratio of the heuristic for the NP-complete problem. In addition, we extend our analysis to the case of multiple families and to the case of three-machine batching.
Estimation of oxygen uptake during fast running using accelerometry and heart rate.

UNLABELLED Previous investigations have reported that accelerometer counts plateau during running at increasingly faster speeds. PURPOSE To assess whether biomechanical and/or device limitations cause this phenomenon and the feasibility of generating oxygen uptake (.VO2) prediction equations from the combined use of accelerometry and heart rate during walking and running. METHODS : Sixteen endurance-trained subjects completed two exercise tests on a treadmill. The first was a continuous incremental test to volitional exhaustion to determine ventilatory threshold and peak . VO2. The second was a discontinuous incremental exercise test while walking (3, 5, and 7 km.h(-1)) and running (8, 10, 12, 14, 16, 18, and 20 km.h(-1), or until volitional exhaustion). Subjects completed 3 min of exercise at each speed, followed by 3-5 min of recovery. Activity counts from uni- and triaxial accelerometers, heart rate, and gas exchange were measured throughout exercise. RESULTS All accelerometer outputs rose linearly with speed during walking. During running, uniaxial accelerometer outputs plateaued, whereas triaxial output rose linearly with speed up to and including 20 km.h(-1). Prediction of . VO2 during walking and running using heart rate (R2 = 0.42 and 0.59, respectively), accelerometer counts (R2 = 0.48-0.83 and 0.76, respectively), the combined methodologies (R2 = 0.54-0.85 and 0.80, respectively), and the combined methodologies calibrated with individual data (R2 = 0.99-1.00 and 0.99, respectively) was completed by linear regression. CONCLUSIONS Uni- and triaxial accelerometer outputs have a linear relationship with speed during walking. During running, uniaxial accelerometer outputs plateau because of the biomechanics of running, whereas triaxial accelerometer output has a linear relationship. The combined methodologies predict . VO2 better than either predictor alone; a subject's individually calibrated data further improves . VO2 estimation.
Experimental study of the weld microstructure properties in assembling of natural gas transmission pipelines

The coexistence of high levels of strength and toughness is necessary for the microalloyed steels used in natural gas pipelines. The welding thermal cycle can significantly change the microstructures and therefore the mechanical properties of the girth welded pipelines. Thus, the experimental investigation on the welded material properties is required for assessing the structural integrity of the pipelines. In this article, the metallurgical characteristics of the multi-pass girth welds on API X70 steel pipes with 56 in outside diameter and 0.780 in wall thickness were determined for the first time using chemical analysis and standard metallography. The chemical analysis showed different chemical compositions in different weld passes. The amount of carbon in the weldment increased in comparison with the base metal, although the microalloy elements in the weld gap decreased by increasing the pass number. The metallographic investigation by optical microscope demonstrated the different microstructures in different sub-zones of the welded joint. The images obtained from scanning electron microscope also presented the dendritic and acicular structures in the root and cap passes, respectively. The observed hard phases in the weldment, such as martensite, had direct effects on the mechanical properties of the weldment and heat-affected zone.
Class-Boundary Alignment for Imbalanced Dataset Learning

In this paper, we propose the class-boundaryalignment algorithm to augment SVMs to deal with imbalanced training-data problems posed by many emerging applications (e.g., image retrieval, video surveillance, and gene profiling). Through a simple example, we first show that SVMs can be ineffective in determining the class boundary when the training instances of the target class are heavily outnumbered by the nontarget training instances. To remedy this problem, we propose to adjust the class boundary either by transforming the kernel function when the training data can be represented in a vector space, or by modifying the kernel matrix when the data do not have a vector-space representation (e.g., sequence data). Through theoretical analysis and empirical study, we show that the classboundary-alignment algorithm works effectively with images (data that have a vector-space representation) and video sequences (data that do not have a vector-space representation).
Nonlinear Stabilization Under Sampled and Delayed Measurements, and With Inputs Subject to Delay and Zero-Order Hold

Sampling arises simultaneously with input and output delays in networked control systems. When the delay is left uncompensated, the sampling period is generally required to be sufficiently small, the delay sufficiently short, and, for nonlinear systems, only semiglobal practical stability is generally achieved. For example, global stabilization of strict-feedforward systems under sampled measurements, sampled-data stabilization of the nonholonomic unicycle with arbitrarily sparse sampling, and sampled-data stabilization of LTI systems over networks with long delays, are open problems. In this paper, we present two general results that address these example problems as special cases. First, we present global asymptotic stabilizers for forward complete systems under arbitrarily long input and output delays, with arbitrarily long sampling periods, and with continuous application of the control input. Second, we consider systems with sampled measurements and with control applied through a zero-order hold, under the assumption that the system is stabilizable under sampled-data feedback for some sampling period, and then construct sampled-data feedback laws that achieve global asymptotic stabilization under arbitrarily long input and measurement delays. All the results employ “nominal” feedback laws designed for the continuous-time systems in the absence of delays, combined with “predictor-based” compensation of delays and the effect of sampling.
The Ageing and Rejuvenation of Soft, Glassy 
Complex Fluids

Suspensions of multiarm star polymers are studied as models for soft colloidal interactionsin colloidal glasses. Establishing a pre-shearing protocol which ensures a reproducible initial state (the "rejuvenation" of the system), we report here the stress evolution from startup for two different concentrations for a range of shear rates using conventional rheological techniques. We show the existence of critical shear rateswhich are functions of the concentration. When the suspensions are sheared at rates below the critical rates, the stress rises to a common value which is also a function of the concentration. The system thus evolves into a yield stress-like fluid. This behavior manifests itself as an evolution from a monotonic, slightly shear-thinning flow curve to a flow curve dominated by a stress plateau. Complementary to the controlled-rate measurements, stress-controlled measurementsshow that for a stress below the critical stress, the rate at which strain is acquired drops several orders of magnitude, providing evidence of a lower branch of the flow curve. In stress-controlled ageing experiments, the material recovers an increasing fraction of the strain acquired under stress with waiting time upon cessation of the (less than critical) stress. The freshly rejuvenated suspension recovers a mere 2%of the acquired strain, while for a waiting time of 104 s the material recovers 97% of the acquired strain. The material thus appears to evolve from a nearly ideal fluid to a nearly ideal solid. We relate this bulk evolution to spatially and temporally resolved Rheo-NMR velocity profiles which clearly show an evolution to a strongly shear-banded state. The velocity of the suspension in the lower shear band is below the uncertainty of the experiment. The growth of the (assumed) zero-shear band is well described by a Gompertz relation. The effects of shear-rate, temperature and waiting time on the Gompertzparameters are investigated. Phenomenological understanding is provided through a scalar model that describes the stress-dependent free-energy landscape. Using a dual-minimum free-energy landscape, the model is able to replicate the behaviour of the stress after startup in shearratecontrolled experiments, the flow curve and the velocity profiles across the gap of a Couette geometry. The Large-Amplitude-Oscillatory-Shear (LAOS) response is reported along with discussions of current LAOS analysis techniques. The stress response to LAOS of the star suspensions is well described in a Cox-Merz manner by a modified Cross model. The modified Cross model highlights an asymmetry in the LAOS response. This constitutes the first ever report of asymmetric LAOS responses. The asymmetry is followed as a function of time using two complementary scalar variables. A speculativeinterpretation is given to account for the evolution of the asymmetry.
Personalizing User Interfaces for improving quality of experience in VoD recommender systems

Recommending content to users involves understanding a) what to present and b) how to present them, so as to increase quality of experience (QoE) and thereby, content consumption. This work attempts to address the question of how to present contents in a way so that the user finds it easy to get to desired content. While the process of User Interface (UI) design is dependent on several human factors, there are basic design components and their combination that have to be common to any recommender system user interface. Personalization of the UI design process involves picking the right components and their combination, and presenting a UI to suit the usage behavior of an individual user, so as to enhance the QoE. This work proposes a system that learns from a user's content consumption patterns and makes some recommendations regarding how to present the content for the user (in the context of Video-On-Demand/Live-TV services on Computer displays), so as to enhance the QoE of the recommender system.
Development and evaluation of control and power hardware for a line side PWM current source inverter

Using PWM current source inverters in drive systems shows some advantages over voltage source inverters such as reduction of losses in the machine due to the lower harmonic content in the machine currents and better EMI behaviour. The paper presents the theoretical and experimental design of a line side PWM current source inverter. The work includes a comparative study of different power semiconductors together with the gate drive circuits as well as the development of the control system maintaining the line side current waveform and the commanded dc-link current.
Regulation of Postsynaptic Function by the Dementia-Related ESCRT-III Subunit CHMP2B

The charged multivesicular body proteins (Chmp1–7) are an evolutionarily conserved family of cytosolic proteins that transiently assembles into helical polymers that change the curvature of cellular membrane domains. Mutations in human CHMP2B cause frontotemporal dementia, suggesting that this protein may normally control some neuron-specific process. Here, we examined the function, localization, and interactions of neuronal Chmp2b. The protein was highly expressed in mouse brain and could be readily detected in neuronal dendrites and spines. Depletion of endogenous Chmp2b reduced dendritic branching of cultured hippocampal neurons, decreased excitatory synapse density in vitro and in vivo, and abolished activity-induced spine enlargement and synaptic potentiation. To understand the synaptic effects of Chmp2b, we determined its ultrastructural distribution by quantitative immuno-electron microscopy and its biochemical interactions by coimmunoprecipitation and mass spectrometry. In the hippocampus in situ, a subset of neuronal Chmp2b was shown to concentrate beneath the perisynaptic membrane of dendritic spines. In synaptoneurosome lysates, Chmp2b was stably bound to a large complex containing other members of the Chmp family, as well as postsynaptic scaffolds. The supramolecular Chmp assembly detected here corresponds to a stable form of the endosomal sorting complex required for transport-III (ESCRT-III), a ubiquitous cytoplasmic protein complex known to play a central role in remodeling of lipid membranes. We conclude that Chmp2b-containing ESCRT-III complexes are also present at dendritic spines, where they regulate synaptic plasticity. We propose that synaptic ESCRT-III filaments may function as a novel element of the submembrane cytoskeleton of spines.
Molecular Pathogenesis and Therapy of Polycythemia Induced in Mice by JAK2 V617F

Background A somatic activating mutation (V617F) in the JAK2 tyrosine kinase was recently discovered in the majority of patients with polycythemia vera (PV), and some with essential thrombocythemia (ET) and chronic idiopathic myelofibrosis. However, the role of mutant JAK2 in disease pathogenesis is unclear. Methods and Findings We expressed murine JAK2 WT or V617F via retroviral bone marrow transduction/transplantation in the hematopoietic system of two different inbred mouse strains, Balb/c and C57Bl/6 (B6). In both strains, JAK2 V617F, but not JAK2 WT, induced non-fatal polycythemia characterized by increased hematocrit and hemoglobin, reticulocytosis, splenomegaly, low plasma erythropoietin (Epo), and Epo-independent erythroid colonies. JAK2 V617F also induced leukocytosis and neutrophilia that was much more prominent in Balb/c mice than in B6. Platelet counts were not affected in either strain despite expression of JAK2 V617F in megakaryocytes and markedly prolonged tail bleeding times. The polycythemia tended to resolve after several months, coincident with increased spleen and marrow fibrosis, but was resurrected by transplantation to secondary recipients. Using donor mice with mutations in Lyn, Hck, and Fgr, we demonstrated that the polycythemia was independent of Src kinases. Polycythemia and reticulocytosis responded to treatment with imatinib or a JAK2 inhibitor, but were unresponsive to the Src inhibitor dasatinib. Conclusions These findings demonstrate that JAK2 V617F induces Epo-independent expansion of the erythroid lineage in vivo. The fact that the central erythroid features of PV are recapitulated by expression of JAK2 V617F argues that it is the primary and direct cause of human PV. The lack of thrombocytosis suggests that additional events may be required for JAK2 V617F to cause ET, but qualitative platelet abnormalities induced by JAK2 V617F may contribute to the hemostatic complications of PV. Despite the role of Src kinases in Epo signaling, our studies predict that Src inhibitors will be ineffective for therapy of PV. However, we provide proof-of-principle that a JAK2 inhibitor should have therapeutic effects on the polycythemia, and perhaps myelofibrosis and hemostatic abnormalities, suffered by MPD patients carrying the JAK2 V617F mutation.
Sequential Monte Carlo Radio-Frequency tomographic tracking

Radio Frequency (RF) tomographic tracking is the process of tracking moving targets by analyzing changes of attenuation in wireless transmissions. This paper presents a novel sequential Monte Carlo (SMC) method for RF tomographic tracking of a single target using a wireless sensor network. The algorithm incorporates on-line Expectation Maximization (EM) to estimate model parameters. Based on experimental measurements, we introduce a new measurement model for the attenuation caused by a target. We assess performance through numerical simulation and demonstrate that it significantly outperforms previous RF tomographic tracking procedures.
Interaction of Age and Intersignal Interval on Acoustic Reflex Amplitude

We studied the effect of intersignal interval (ISI) on the averaged acoustic reflex in nine young and nine elderly subjects. Over the range of ISIs from 1.5 to 9 sec, there was an interaction between ISI and age group, but the effect was unique to reflex mode. Results emphasize the importance of measuring both crossed and uncrossed reflex waveforms, in the study of aging, and of controlling the ISI in order to avoid overestimation of aging effects.