Window Synchronization Research Articles

Age and Synchronization of Daphnia magna Affect Sensitivity to Teflubenzuron in Acute Standardized Toxicity Tests.

The standard Daphnia sp. acute toxicity test for assessing the adverse effects of chemicals on aquatic invertebrates stipulates the use of neonates that are ≤24 h old (hours post release [hpr]) at the start of the exposure. However, when one is assessing acute effects of chemicals interfering with endocrine relevant-processes such as molting, both age synchronization and absolute age can influence the test outcome, because the occurrence of molting and associated mortality is highly time specific. Hence, a 24-h age synchronization window may mask the real effects of these compounds. To explore the influence of age synchronization and absolute age in standard acute toxicity tests, we exposed D. magna from different synchronization windows and absolute ages (≤4, 4-8, 8-12, ≤12, and ≤24 hpr at the beginning of the exposure) to 0.5-12 µg/L of the chitin synthesis inhibitor (CSI) teflubenzuron (TEF) using the Organisation for Economic Co-operation and Development test guideline 202 (Daphnia sp. 48 h immobilization test). Our results show significant differences in 48-h median lethal concentrations between animals with a synchronization window of ≤4 hpr (2.9 µg/L) and longer synchronization windows such as ≤12 hpr (5.1 µg/L) and ≤24 hpr (16.8 µg/L). A concurrent decreasing trend in molting median effect concentrations was observed for the same synchronization windows: ≤4 hpr (4.0 µg/L), ≤12 hpr (5.9 µg/L), and ≤24 hpr (30.0 µg/L). Together, our results show that both synchronization and absolute age are determinant factors for the sensitivity of D. magna to TEF. A narrow synchronization window (e.g., ≤4 hpr) may provide a more conservative estimate of TEF toxicity and should be considered when one is performing standardized toxicity tests for molting-disrupting compounds such as TEF. Environ Toxicol Chem 2023;42:1806-1815. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2

RNA (ribonucleic acid) structure prediction finds many applications in health science and drug discovery due to its importance in several life regulatory processes. But despite significant advances in the close field of protein prediction, RNA 3D structure still poses a tremendous challenge to predict, especially for large sequences. In this regard, the approach unfolded by Rosetta FARFAR2 (Fragment Assembly of RNA with Full-Atom Refinement, version 2) has shown promising results, but the algorithm is non-deterministic by nature. In this paper, we develop P-FARFAR2: a parallel enhancement of FARFAR2 that increases its ability to assemble low-energy structures via multithreaded exploration of random configurations in a greedy manner. This strategy, appearing in the literature under the term “parallel mechanism”, is made viable through two measures: first, the synchronization window is coarsened to several Monte Carlo cycles; second, all but one of the threads are differentiated as auxiliary and set to perform a weakened version of the problem. Following empirical analysis on a diverse range of RNA structures, we report achieving statistical significance in lowering the energy levels of ensuing samples. And consequently, despite the moderate-to-weak correlation between energy levels and prediction accuracy, this achievement happens to propagate to accuracy measurements.

Noise-induced collective dynamics in the small-world network of photosensitive neurons.

Photosensitive neurons can capture and convert external optical signals, and then realize the encoding signal.It is confirmed thata variety of firing modes could be induced under optical stimuli. As a result, it is interesting to explore the mode transitions of collective dynamics in the photosensitive neuron network under external stimuli. In this work, the collective dynamics of photosensitive neurons in a small-world network with non-synaptic coupling will be discussed with spatial diversity of noise and uniform noise applied on, respectively. The results prove that a variety of different collective electrical activities could be induced under different conditions. Under spatial diversity of noise applied on, a chimera state could be observed in the evolution, and steady cluster synchronization could be detected in the end; even the nodes in each cluster depend on the degree of each node. Under uniform noise applied on, the complete synchronization window could be observed alternately in the transient process, and steady complete synchronization could be detected finally. The potential mechanism is that continuous energy is pumped in the phototubes, and energy exchange and balance between neurons to form the resonance synchronization in the network with different noise applied on. Furthermore, it is confirmed that the evolution of collective dynamical behaviors in the network depends on the external stimuli on each node. Moreover, the bifurcation analysis for the single neuron model is calculated, and the results confirm that the electrical activities of single neuron are sensitive to different kinds of noise.

Linear Frequency Modulation of NbO2-Based Nanoscale Oscillator With Li-Based Electrochemical Random Access Memory for Compact Coupled Oscillatory Neural Network.

Oscillatory neural network (ONN)-based classification of clustered data relies on frequency synchronization to injected signals representing input data, showing a more efficient structure than a conventional deep neural network. A frequency tunable oscillator is a core component of the network, requiring energy-efficient, and area-scalable characteristics for large-scale hardware implementation. From a hardware viewpoint, insulator-metal transition (IMT) device-based oscillators are attractive owing to their simple structure and low power consumption. Furthermore, by introducing non-volatile analog memory, non-volatile frequency programmability can be obtained. However, the required device characteristics of the oscillator for high performance of coupled oscillator have not been identified. In this article, we investigated the effect of device parameters of IMT oscillator with non-volatile analog memory on coupled oscillators network for classification of clustered data. We confirmed that linear conductance response with identical pulses is crucial to accurate training. In addition, considering dispersed clustered inputs, a wide synchronization window achieved by controlling the hold voltage of the IMT shows resilient classification. As an oscillator that satisfies the requirements, we evaluated the NbO2-based IMT oscillator with non-volatile Li-based electrochemical random access memory (Li-ECRAM). Finally, we demonstrated a coupled oscillator network for classifying spoken vowels, achieving an accuracy of 85%, higher than that of a ring oscillator-based system. Our results show that an NbO2-based oscillator with Li-ECRAM has the potential for an area-scalable and energy-efficient network with high performance.

Synchronization of a genetic oscillator with the cell division cycle

Genetic circuits that control specific cellular functions are never fully insulated against influences of other parts of the cell. For example, they are subject to periodic modulation by the cell cycle through volume growth and gene doubling. To investigate possible effects of the cell cycle on oscillatory gene circuits dynamics, we modelled a simple synthetic genetic oscillator, the repressilator, and studied hallmarks of the resulting nonlinear dynamics. We found that the repressilator coupled to the cell cycle shows typical quasiperiodic motion with discrete Fourier spectra and windows in parameter space with synchronization of the two oscillators, with a devil’s stair case indicating the Arnold tongues of synchronization. In the case of identical parameters for the three genes of the repressilator and simultaneous gene duplication, we identify two classes of synchronization windows, symmetric and asymmetric, depending on whether the trajectories satisfy a discrete three-fold rotation symmetry, corresponding to cyclic permutation of the three genes. Unexpectedly changing the gene doubling time revealed that the width of the Arnold tongues is connected to that three-fold symmetry of the synchronization trajectories: non-simultaneous gene duplication increases the width of asymmetric synchronization regions, for some of them by an order of magnitude. By contrast, there is only a small or even a negative effect on the window size for symmetric synchronization. This observation points to a control mechanism of synchronization via the location of the genes on the chromosome.

Attentive and Appreciative: Designers Connecting with More-Than-Human Beings

This essay considers a design student project that practised methods and languages for connecting designers with the more-than-human. The term refers to ecologist David Abram’s phrase “the more-than-human world” as a way of considering our entanglement with earthly nature. Alongside ecological thinking, we drew upon New Zealand Māori and Canadian First Nation scholars and worked with local cultural advisors. This project was offered across two design classes, beginning with one in Vancouver, Canada, and the other in Dunedin, New Zealand, with a six-week synchronous window. These schools connected through DESIS, a network of labs that research social innovation and sustainability. Teachers and students were able to share their approaches and progress online, culminating in an online exhibition and conversation. Key ideas explored included Karl Wixon’s “whakapapa-centred design” and Robin Wall-Kimmerer’s “grammar of animacy,” indigenous values that centre the natural world as sentient and present with the world of humans. Students were tasked with becoming advocates for a more-than-human being. They drew upon multiple frames to learn about this being and conceive of possible different relationships. After conducting a series of immersive research activities including meditative, phenomenological and academic approaches, students drew upon their design skills to translate and share their learning. The outcomes are a variety of prototypes, designed to share this advocacy as experiences for others. Through a combination of online and embodied learning, many explorations brought to light understandings about the fundamental interconnectedness of humans with the earth, with all species and with each other.

Optimal operation mode selection for energy-efficient light-weight multi-hop time synchronization in linear wireless sensor networks

We explored the joint effect of synchronization window and offset/drift mode selection on the time synchronization of linear wireless sensor networks (LWSNs). Recent advances in the field along with the availability of capable hardware led to adoption of LWSNs in diverse areas like monitoring of roads, pipelines, and tunnels. The linear topology applications are susceptible to single point of failure; therefore, energy efficient operation of LWSNs is even more important than the traditional WSNs. To address the challenge, we investigate the time synchronization mode selection for the optimum operation of a multi-hop and low-overhead LWSN. We investigate two modes of synchronization: synchronization by using only offset and synchronization by using offset in addition to the clock drift. Furthermore, we investigate the effects of synchronization window size. Our experimental results reveal that computation of offset alone for smaller window sizes and resynchronization periods is sufficient in achieving acceptable degree of synchronization.

Method for rapid synchronization of different growth cycles of Plasmodium falciparum in vitro and application in differential gene expression profile of 3D7 after dihydroartemisinin treatment

Plasmodium culture in vitro is often used as an antimalarial drug evaluation model, but the lifecycle of P. falciparum culture in vitro tends to be disordered, which affects the research and evaluation of antimalarial drug mechanism in vitro. By combining magnetic bead separation method with sorbitol synchronization method, a synchronization method was constructed to quickly acquire different lifecycles of P. falciparum and obtain large amounts of parasite with a narrow synchronization window in a short period. Furthermore, the dihydroartemisinin(DHA) was used to treat the early trophozoite phase of P. falciparum 3 D7 for 4 h. Then mRNA was extracted and RNA-seq was conducted to analyze the differential expression of mRNA after drug treatment and obtain the differential gene expression profile. Differential expression of up-regulated genes and down-regulated genes was analyzed according to the screening criteria of |log_2FC|>1 and P<0.05. There, 262 genes were up-regulated and 77 genes were down-regulated. GO functional enrichment analysis of all the differentially expressed genes showed that the enrichment items mainly included cell membrane components, transporter activity, serine/threonine kinase activity, Maurer's clefts(MCs), rhoptry, antigen variation and immune evasion. The enrichment of KEGG pathway included malaria, fatty acid metabolism and peroxisome. Protein-protein interaction(PPI) analysis showed that the down-regulated genes in the modules with high degree of association included rhoptry, myosin complex, transporter and other genes related to the important life activities of malaria invasion and immune escape; the up-regulated genes were mainly related to various toxic exportins of malaria, such as PfSBP1 of MCs. qRT-PCR was used to verify the expression level of some genes, and most of the results were the same as the sequencing results. SBP1 was significantly up-regulated, while some antigenic protein expression levels were down-regulated. Above all, key molecules of DHA therapy were mainly involved in the parasites' rhoptry, transporter, antigenic variation, plasmodium exportin. These results offer us many hints to guide the further studies on mechanism of artemisinin and provide a new way for development of new antimalarial drugs.

On the Low Complexity Implementation of the DFT-Based BFSK Demodulator for Ultra-Narrowband Communications

The DFT-based demodulator for BFSK has been introduced for applications where the received signal experiences a carrier frequency offset (CFO) much larger than the symbol rate. The Ultra-Narrowband (UNB) communication techniques have been introduced for implementing the emerging Low Power Wide Area Networks (LPWAN). Since UNB communication is prone to CFO, a DFT-based BFSK demodulator is an interesting option for this type of communication. However, for proper operation in a large frequency offset, the DFT-based demodulator requires a complex window synchronization which is not desirable for low power nodes. The main source of complexity, is calculating the DFT of a window which slides over the preamble. In this work, the complexity is alleviated by considering the window synchronization algorithm and its implementation together. First, a new window synchronization algorithm is proposed which is designed such that an efficient class of implementations of the sliding DFT (SDFT), called Single Bin SDFT (SB-SDFT) in this work, can be used. Moreover, a new stable implementation of SB-SDFT is designed to enable zero-padding which is required by the demodulator. The complexity of the proposed algorithm implemented using the SB-SDFT, scales more efficiently compared to the conventional algorithm when the range of tolerable CFO increases. Using the proposed method, for a CFO tolerance in the order of 14.5 times the symbol rate (±14.5 kHz for a symbol rate equal to 100 Hz), the number of complex operations is reduced by more than 85% (and memory by 90%) compared to the conventional method.

Information Dynamics of the Brain, Cardiovascular and Respiratory Network during Different Levels of Mental Stress.

In this study, an analysis of brain, cardiovascular and respiratory dynamics was conducted combining information-theoretic measures with the Network Physiology paradigm during different levels of mental stress. Starting from low invasive recordings of electroencephalographic, electrocardiographic, respiratory, and blood volume pulse signals, the dynamical activity of seven physiological systems was probed with one-second time resolution measuring the time series of the , , and brain wave amplitudes, the cardiac period (RR interval), the respiratory amplitude, and the duration of blood pressure wave propagation (pulse arrival time, PAT). Synchronous 5-min windows of these time series, obtained from 18 subjects during resting wakefulness (REST), mental stress induced by mental arithmetic (MA) and sustained attention induced by serious game (SG), were taken to describe the dynamics of the nodes composing the observed physiological network. Network activity and connectivity were then assessed in the framework of information dynamics computing the new information generated by each node, the information dynamically stored in it, and the information transferred to it from the other network nodes. Moreover, the network topology was investigated using directed measures of conditional information transfer and assessing their statistical significance. We found that all network nodes dynamically produce and store significant amounts of information, with the new information being prevalent in the brain systems and the information storage being prevalent in the peripheral systems. The transition from REST to MA was associated with an increase of the new information produced by the respiratory signal time series (RESP), and that from MA to SG with a decrease of the new information produced by PAT. Each network node received a significant amount of information from the other nodes, with the highest amount transferred to RR and the lowest transferred to , , and . The topology of the physiological network underlying such information transfer was node- and state-dependent, with the peripheral subnetwork showing interactions from RR to PAT and between RESP and RR, PAT consistently across states, the brain subnetwork resulting more connected during MA, and the subnetwork of brain–peripheral interactions involving different brain rhythms in the three states and resulting primarily activated during MA. These results have both physiological relevance as regards the interpretation of central and autonomic effects on cardiovascular and respiratory variability, and practical relevance as regards the identification of features useful for the automatic distinction of different mental states.

Achieving Robust Mobile Web Content Delivery Performance Based on Multiple Coordinated QUIC Connections

In order to minimize the downloading time of short-lived applications like Web browsing, Web application, and short video clips, the recently standardized HTTP/2 adopts stream multiplexing on one single TCP connection. However, aggregating all content objects within one single connection suffers from the head-of-line blocking issue. Quick UDP Internet connection (QUIC), by eliminating such an issue on the basis of UDP, is expected to further reduce the content downloading time. However, in mobile network environments, the single connection strategy still leads to a degraded and high-variant completion time due to the unexpected hindrance of congestion window growth caused by the common but uncertain fluctuations in round trip time and also random loss event at the air interface. To retain resilient congestion window against such network fluctuations, we propose an intelligent connection management scheme based on QUIC which not only employs adaptively multiple connections but also conducts a tailored state and congestion window synchronization between these parallel connections upon the detection of network fluctuation events. According to the performance evaluation results obtained from an LTE-A/Wi-Fi testing network, the proposed multiple QUIC scheme can effectively overcome the limitations of different congestion control algorithms (e.g., the loss-based new reno/CUBIC and the rate-based BBR), achieving substantial performance improvement in both median (up to 59.1%) and 95th completion time (up to 72.3%). The significance of this piece of work is to achieve highly robust short-lived content downloading performance against various uncertainties of network conditions as well as with different congestion control schemes.

NbO2-Based Frequency Storable Coupled Oscillators for Associative Memory Application

Oscillatory neural networks with nano-oscillators and synapse devices are a promising alternative to implement neuromorphic systems owing to its fast recognition speed and low power consumption. In this paper, we demonstrate a compact frequency storable oscillator using nanoscale two-terminal NbO2 insulator-metal-transition devices along with TaOx-based resistive switching memory (RRAM) devices. By controlling RRAM resistance, we realized a wide range of analog oscillation frequencies. The synchronization window of two coupled oscillators, which is a key parameter for determining pattern recognition, increases with the increasing coupling capacitance and decreasing RRAM resistance of the reference oscillator. The simple device structure (metal-NbO2-metal-TaOx-metal), small device area (4F2), and frequency storability of NbO2-based coupled oscillator device show a strong potential for future integrated neuromorphic device application.

Evaluating the spatial range of the effect of synchronized antiparasitic treatments on the abundance of sea lice Caligus rogercresseyi (Boxshall & Bravo, 2000) in Chile

Sea lice are the most important ectoparasites affecting farmed salmonids in marine water worldwide and pharmacological treatments are widely used to control their abundance. Synchronization of antiparasitic treatments among closely located salmon farms has been recently evaluated as a promising strategy for improving treatment performance. However, the optimum distance at which farms should synchronize their treatments is not clear. We used a repeated measures linear mixed effects model to evaluate the impact of two nationwide treatment synchronization procedures conducted in Chile in 2014 and 2015 on subsequent adult lice counts up to 13 weeks after the procedure. Each treatment synchronization procedure consisted of two 2-week synchronization windows, in which farms were required to treat their fish. A period of 3 weeks elapsed between the two windows. Treatment synchronization was measured as the number of neighbouring farms that treated their fish within a certain geographical threshold, each of them weighted by its distance from the farm of interest. We tested four different thresholds: 5, 10, 20 and 30 km. The results indicate that the abundance of adult lice on farms that synchronized treatments with their neighbours within a distance of 5 km was lower than the abundance on non-synchronized farms from weeks 4 to 11 after the procedure. Our findings suggest the treatment synchronization effect was distance dependent and greater when neighbouring farms up to 5 km joined the procedure.

General variable neighborhood search for home healthcare routing and scheduling problem with time windows and synchronized visits

Home healthcare centers are facing increasing demands and researchers are attracted by the related routing and scheduling issue that is presented in literature as a VRP with synchronization and time windows constraints. The goal is to optimize the assignment of visits to home caregivers and the sequence of visits execution. In this paper, a General Variable Neighborhood Search is provided. Experiments conducted on benchmark instances from the literature clearly show that our method is fast and outperforms the existing approaches on half of the instances.

Local Search Analysis for a Vehicle Routing Problem with Synchronization and Time Windows Constraints in Home Health Care Services

This paper presents the vehicle routing problem with time windows and synchronization constraints (VRPTWSyn) in the context of home health care services. We propose a new approach for solving the considered problem. To build an initial solution, we develop a constructive heuristic based on the best insertion heuristic, taking in consideration the synchronization constraints. In order to improve the initial solution, we propose an Iterated Local Search (ILS) metaheuristic coupled with a variant of the Random Variable Neighborhood Descent method (RVND) which uses a random ordering of neighborhoods in local search phase (RVND-ILS algorithm). Computational experiments have been conducted on 15 benchmark instances from the literature. The proposed algorithm, obtains solutions as good as any reported results. In this paper, we propose many neighborhood structures for the problem, and a study of these operators has been conducted as well.

Clock auto-synchronization method for BESIII ETOF upgrade**Supported by National Natural Science Foundation of China (10979003, 11005107), CAS Center for Excellence in Particle Physics (CCEPP)

An automatic clock synchronization method implemented in a field programmable gate array (FPGA) is proposed in this paper. It is developed for the clock system which will be applied in the end-cap time of flight (ETOF) upgrade of the Beijing Spectrometer (BESIII). In this design, an FPGA is used to automatically monitor the synchronization circuit and deal with signals coming from the external clock synchronization circuit. By testing different delay time of the detection signal and analyzing the signal state returned, the synchronization windows can be found automatically by the FPGA. The new clock system not only retains low clock jitter which is less than 20ps root mean square (RMS), but also demonstrates automatic synchronization to the beam bunches. So far, the clock auto-synchronizing function has been working successfully under a series of tests. It will greatly simplify the system initialization and maintenance in the future.

A Frame-Parallel 2 Gpixel/s Video Decoder Chip for UHDTV and 3-DTV/FTV Applications

The first single-chip design that supports real-time H.264/Advanced Video Coding decoding of 8k ( $7680\times 4320$ ) 60 frames/s is realized. It also supports multiview decoding for up to 32720p views or 161080p views. To significantly improve the throughput and reduce the memory bandwidth requirement, frame-level parallelism is exploited for the proposed design. First, a frame dependency protection scheme enables frame-parallel decoding, by reusing multiple replicas of an existing design. This results in a system throughput of 2 Gpixels/s, at least 3.75 times better than previous chips. Moreover, a reference window synchronization scheme and a 2-level hybrid caching structure are proposed to achieve 44% memory bandwidth reduction of motion compensation, by utilizing frame-level data reuse. The bandwidth reduction results in 22% Dynamic Random-Access Memory power saving of the whole decoder.

MiRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.

Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multipanel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. The project manager handles multiple samples of multiple groups. The read alignment is imported in BAM file format. Implemented features comprise sorting, zooming, highlighting, editing, filtering, saving, exporting, etc. Currently, miRseqViewer supports 84 organisms whose annotation is available at miRBase. miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr. sanghyuk@ewha.ac.kr.

Minimum Spanning Tree Dynamic Demonstration System Implementation

The graph vertices design into classes, for each vertex in the design of the abscissa, ordinate and in-degree members, realizes the dynamic demonstration minimum spanning tree. Dynamic visualize Prime algorithm and kruskal algorithm implementation process. Around two window synchronization of animation, " in order to find the minimum edge " list box list the minimum edge of a minimum spanning tree ,with thick line in the left window drawing the found minimum edge and On the edge of the vertex, in the right box demo the process of algorithm dynamic execution.

Graph Traversal Dynamic Demonstration System Design and Implementation

The graph vertices design into classes, for each vertex in the design of the abscissa, ordinate and in-degree members, realizes the dynamic demonstration graph traversal algorithm. Around two window synchronization of animation, " traversal sequence " list box list dfs (bfs ) traversal sequence ,with thick line in the left window drawing traversed through the vertices and edges, and in "traversed stack (queue) changes in" real-time text box displays the current traversed through vertices, in the right box demo the process of algorithm dynamic execution.