Search results for: bootstrap aggregation

Authors: Luminita Marin, Dalila Belei, Carmen Dumea

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Aggregation induced emission (AIE) is an intriguing optical phenomenon recently evidenced by Tang and his co-workers, for which aggregation works constructively in the improving of light emission. The AIE challenging phenomenon is quite opposite to the notorious aggregation caused quenching (ACQ) of light emission in the condensed phase, and comes in line with requirements of photonic and optoelectronic devices which need solid state emissive substrates. This paper reports a series of ten new aggregation induced emission (AIE) low molecular weight compounds based on triazole and pyridine-N-oxide heterocyclic units bonded by short flexible chains, obtained by a „click” chemistry reaction. The compounds present extremely weak luminescence in solution but strong light emission in solid state. To distinguish the influence of the crystallinity degree on the emission efficiency, the photophysical properties were explored by UV-vis and photoluminescence spectroscopy in solution, water suspension, amorphous and crystalline films. On the other hand, the compound morphology of the up mentioned states was monitored by dynamic light scattering, scanning electron microscopy, atomic force microscopy and polarized light microscopy methods. To further understand the structural design – photophysical properties relationship, single crystal X-ray diffraction on some understudy compounds was performed too. The UV-vis absorption spectra of the triazole water suspensions indicated a typical behaviour for nanoparticle formation, while the photoluminescence spectra revealed an emission intensity enhancement up to 921-fold higher of the crystalline films compared to solutions, clearly indicating an AIE behaviour. The compounds have the tendency to aggregate forming nano- and micro- crystals in shape of rose-like and fibres. The crystals integrity is kept due to the strong lateral intermolecular forces, while the absence of face-to-face forces explains the enhanced luminescence in crystalline state, in which the intramolecular rotations are restricted. The studied flexible triazoles draw attention to a new structural design in which small biologically friendly luminophore units are linked together by small flexible chains. This design enlarges the variety of the AIE luminogens to the flexible molecules, guiding further efforts in development of new AIE structures for appropriate applications, the biological ones being especially envisaged.

Keywords: aggregation induced emission, pyridine-N-oxide, triazole

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Authors: Pierluigi Gallo, Francesco Randazzo, Ignazio Gallo

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In recent years, many new and interesting models of successful online business have been developed. Many of these are based on the competition between users, such as online auctions, where the product price is not fixed and tends to rise. Other models, including group-buying, are based on cooperation between users, characterized by a dynamic price of the product that tends to go down. There is not yet a business model in which both sellers and buyers are grouped in order to negotiate on a specific product or service. The present study investigates a new extension of the group-buying model, called fair, which allows aggregation of demand and supply for price optimization, in a cooperative manner. Additionally, our system also aggregates products and destinations for shipping optimization. We introduced the following new relevant input parameters in order to implement a double-side aggregation: (a) price-quantity curves provided by the seller; (b) waiting time, that is, the longer buyers wait, the greater discount they get; (c) payment time, which determines if the buyer pays before, during or after receiving the product; (d) the distance between the place where products are available and the place of shipment, provided in advance by the buyer or dynamically suggested by the system. To analyze the proposed model we implemented a system prototype and a simulator that allows studying effects of changing some input parameters. We analyzed the dynamic price model in fairs having one single seller and a combination of selected sellers. The results are very encouraging and motivate further investigation on this topic.

Keywords: auction, aggregation, fair, group buying, social buying

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Authors: Ezil Sam Leni, Shalen S.

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Transport service monitoring and upkeep are essential components of smart city initiatives. The main risks to the relevant departments and authorities are the ever-increasing vehicular traffic and the conditions of the roads. In India, the economy is greatly impacted by the road transport sector. In 2021, the Ministry of Road Transport and Highways Transport, Government of India, produced a report with statistical data on traffic accidents. The data included the number of fatalities, injuries, and other pertinent criteria. This study proposes a distributed infrastructure for the monitoring, detection, and reporting of potholes to the appropriate authorities. In a distributed environment, the nodes are the edge devices, and local edge servers, and global servers. The edge devices receive the initial model to be employed from the global server. The YOLOv8 model for pothole detection is used in the edge devices. The edge devices run the pothole detection model, gather the pothole images on their path, and send the updates to the nearby edge server. The local edge server selects the clients for its aggregation process, aggregates the model updates and sends the updates to the global server. The global server collects the updates from the local edge servers, performs aggregation and derives the updated model. The updated model has the information about the potholes received from the local edge servers and notifies the updates to the local edge servers and concerned authorities for monitoring and maintenance of road conditions. The entire process is implemented in FedCV distributed environment with the implementation using the client-server model and aggregation entities. After choosing the clients for its aggregation process, the local edge server gathers the model updates and transmits them to the global server. After gathering the updates from the regional edge servers, the global server aggregates them and creates the updated model. Performance indicators and the experimentation environment are assessed, discussed, and presented. Accelerometer data may be taken into consideration for improved performance in the future development of this study, in addition to the images captured from the transportation routes.

Keywords: federated Learning, pothole detection, distributed framework, federated averaging

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Authors: Anna Sikharulidze, Gia Sirbiladze

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For the evaluation of unreliability levels of movement on the closed routes in the vehicle routing problem, the fuzzy operators family is constructed. The interactions between routing factors in extreme conditions on the roads are considered. A multi-criteria decision-making model (MCDM) is constructed. Constructed aggregations are based on the Choquet integral and the associated probability class of a fuzzy measure. Propositions on the correctness of the extension are proved. Connections between the operators and the compositions of dual triangular norms are described. The conjugate connections between the constructed operators are shown. Operators reflect interactions among all the combinations of the factors in the fuzzy MCDM process. Several variants of constructed operators are used in the decision-making problem regarding the assessment of unreliability and possibility levels of movement on closed routes.

Keywords: vehicle routing problem, associated probabilities of a fuzzy measure, choquet integral, fuzzy aggregation operator

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Authors: Yazun Jarrar

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Smoking has effect on platelet aggregation and the activity of anti-platelet drugs. The chemical 20-hydroxyeicosatetraenoic acid (20-HETE) is a cardiotoxic arachidonic acid metabolite which increases platelet aggregation. In this study, we investigated the influence of cigarette smoking on 20-HETE levels and protein expression of 20-HETE producing enzyme CYP4A11 in isolated platelets from smoker and non-smoker volunteers. The protein expression and 20-HETE levels were analyzed using immunoblot and High-Performance Liquid Chromatography with Mass Spectrometry (HPL-MS) assays. The results showed that 20-HETE level was higher significantly among smokers than non-smokers (t-test, p-value<0.05). The protein expression of CYP4A11 was significantly higher (t-test, p-value<0.05) among the platelets of smokers. We concluded that cigarette smoking increased the level of platelet activator 20-HETE through increasing the protein expression of CYP4A11. These findings may increase the understanding of smoking-drug interaction during antiplatelets therapy.

Keywords: smoking, 20-HETE, CYP4A11, platelet

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Authors: Jyun-Guo You, Wei-Lung Tseng

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Herein, this study represents a synthetic route for producing highly luminescent AuNCs based on the integration of two concepts, including thiol-induced luminescence enhancement of ligand-insufficient GSH-AuNCs and Ce3+-induced aggregation of GSH-AuNCs. The synthesis of GSH-AuNCs was conducted by modifying the previously reported procedure. To produce more Au(I)-GSH complexes on the surface of ligand-insufficient GSH-AuNCs, the extra GSH is added to attach onto the AuNC surface. The formed ligand-sufficient GSH-AuNCs (LS-GSH-AuNCs) emit relatively strong luminescence. The luminescence of LS-GSH-AuNCs is further enhanced by the coordination of two carboxylic groups (pKa1 = 2 and pKa2 = 3.5) of GSH and lanthanide ions, which induce the self-assembly of LS-GSH-AuNCs. As a result, the quantum yield of the self-assembled LS-GSH-AuNCs (SA-AuNCs) was improved to be 13%. Interestingly, the SA-AuNCs were dissembled into LS-GSH-AuNCs in the presence of adenosine triphosphate (ATP) because of the formation of the ATP- lanthanide ion complexes. Our assay was employed to detect alkaline phosphatase (ALP) activity over the range of 0.1−10 U/mL with a limit of detection (LOD) of 0.03 U/mL.

Keywords: self-assembly, lanthanide ion, adenosine triphosphate, alkaline phosphatase

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Authors: Ting Ye, Nhan Phan-Thien, Chwee Teck Lim, Lina Peng, Huixin Shi

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In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. In this paper, we aim to apply a particle-based method, Smoothed Dissipative Particle Dynamics (SDPD), to simulate the motion and deformation of RBCs in complex micro-tubes. We first present the theoretical models, including SDPD model, RBC-fluid interaction model, RBC deformation model, RBC aggregation model, and boundary treatment model. After that, we show the verification and validation of these models, by comparing our numerical results with the theoretical, experimental and previously-published numerical results. Finally, we provide some simulation cases, such as the motion and deformation of RBCs in rectangular, cylinder, curved, bifurcated, and constricted micro-tubes, respectively.

Keywords: aggregation, deformation, red blood cell, smoothed dissipative particle dynamics

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Authors: Pooja Mishra, Chris Pollett

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This paper explores efficient ways to implement various media-updating features like news aggregation, video conversion, and bulk email handling. All of these jobs share the property that they are periodic in nature, and they all benefit from being handled in a distributed fashion. The data for these jobs also often comes from a social or collaborative source. We isolate the class of periodic, one round map reduce jobs as a useful setting to describe and handle media updating tasks. As such tasks are simpler than general map reduce jobs, programming them in a general map reduce platform could easily become tedious. This paper presents a MediaUpdater module of the Yioop Open Source Search Engine Web Portal designed to handle such jobs via an extension of a PHP class. We describe how to implement various media-updating tasks in our system as well as experiments carried out using these implementations on an Amazon Web Services cluster.

Keywords: distributed jobs framework, news aggregation, video conversion, email

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Authors: Panos Xenos, Milton Nektarios, John Yfantopoulos

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Background: Policy makers, professional organizations and payers have introduced a variety of initiatives and reforms for the health systems worldwide, aimed at improving hospital efficiency. Their efforts are concentrated in two main categories: to constrain increasing healthcare costs and to enhance quality of services provided. Research Objectives: This study examines the efficiency of 112 Greek public hospitals for the year 2009, evaluates the importance of bootstrapping techniques and investigates the effect of contextual factors on hospital efficiency. Furthermore, the effect of qualitative evidence, on hospital efficiency is explored using data from 28 large hospitals. Methods: We applied Data Envelopment Analysis, augmented by bootstrapping techniques, to estimate efficiency scores. In order to measure the effect of environmental factors on hospital efficiency we used Tobit regression analysis. The significance of our models is evaluated using statistical tests to compare distributions. Results: The Kolmogorov-Smirnov test between the original and the bootstrap-corrected efficiency indicates that their distributions are significantly different (p-value<0.01). The environmental factors, that seem to influence efficiency, are Occupancy Rating and the ratio between Outpatient Visits and Inpatient Days. Results indicate that the inclusion of the quality variable in DEA modelling generates statistically significant variations in efficiency scores (p-value<0.05). Conclusions: The inclusion of quality variables and the use of bootstrap resampling in efficiency analysis impose a statistically significant effect on the distribution of efficiency scores. As a policy conclusion we highlight the importance of these methods on hospital efficiency analysis and, by implication, on healthcare resource allocation.

Keywords: hospitals, efficiency, quality, data envelopment analysis, Greek public hospital sector

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Authors: Sharmin Ferdewsi Rakhi, AHM Mohsinul Reza, Brynley Davies, Jianzhong Wang, Youhong Tang, Jian Qin

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Mass production of microalgae has become a focus of research owing to their promising aspects for sustainable food, biofunctional compounds, and biofuel feedstock. However, low lipid content with optimum algal biomass is still a challenge that must be resolved for commercial use. This research aims to determine the effects of light spectral shift and reactive oxygen species (ROS) on growth and lipid biosynthesis in a green microalga, Chlamydomonas reinhardtii. Aggregation Induced Emission (AIE)-based photosensitisers, CN-TPAQ-PF6 ([C₃₂H₂₃N₄]+) with high ROS productivity, was introduced into the algal culture media separately for effective conversion of the green-yellow-light to the red spectra. The intense photon energy and high-photon flux density in the photosystems and ROS supplementation induced photosynthesis and lipid biogenesis. In comparison to the control, maximum algal growth (0.15 g/l) was achieved at 2 µM CN-TPAQ-PF6 exposure. A significant increase in total lipid accumulation (146.87 mg/g dry biomass) with high proportion of 10-Heptadecanoic acid (C17:1) linolenic acid (C18:2), α-linolenic acid (C18:3) was observed. The elevated level of cellular NADP/NADPH triggered the Acetyl-Co-A production in lipid biogenesis cascade. Furthermore, MTT analysis suggested that this nanomaterial is highly biocompatible on HaCat cell lines with 100% cell viability. This study reveals that the AIE-based approach can strongly impact algal biofactory development for sustainable food, healthy lipids and eco-friendly biofuel.

Keywords: microalgae, photosensitiser, lipid, biomass, aggregation-induced-emission, reactive oxygen species

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Authors: Hamza Javar Magnier, Robin Curtis

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There have been rapid advances in the upstream processing of protein therapeutics, which has shifted the bottleneck to downstream purification and formulation. Finding liquid formulations with shelf lives of up to two years is increasingly difficult for some of the newer therapeutics, which have been engineered for activity, but their formulations are often viscous, can phase separate, and have a high propensity for irreversible aggregation1. We explore means to develop improved predictive ability from a better understanding of how protein-protein interactions on formulation conditions (pH, ionic strength, buffer type, presence of excipients) and how these impact upon the initial steps in protein self-association and aggregation. In this work, we study the initial steps in the aggregation pathways using a minimal protein model based on square-well potentials and discontinuous molecular dynamics. The effect of model parameters, including range of interaction, stiffness, chain length, and chain sequence, implies that protein models fold according to various pathways. By reducing the range of interactions, the folding- and collapse- transition come together, and follow a single-step folding pathway from the denatured to the native state2. After parameterizing the model interaction-parameters, we developed an understanding of low-temperature conformational properties and fluctuations, and the correlation to the folding transition of proteins in isolation. The model fluctuations increase with temperature. We observe a low-temperature point, below which large fluctuations are frozen out. This implies that fluctuations at low-temperature can be correlated to the folding transition at the melting temperature. Because proteins “breath” at low temperatures, defining a native-state as a single structure with conserved contacts and a fixed three-dimensional structure is misleading. Rather, we introduce a new definition of a native-state ensemble based on our understanding of the core conservation, which takes into account the native fluctuations at low temperatures. This approach permits the study of a large range of length and time scales needed to link the molecular interactions to the macroscopically observed behaviour. In addition, these models studied are parameterized by fitting to experimentally observed protein-protein interactions characterized in terms of osmotic second virial coefficients.

Keywords: protein folding, native-ensemble, conformational fluctuation, aggregation

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Authors: Parvaneh Eskandari, Rachel O'Reilly

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In the last years, controlling the self-assembly behavior of stimuli-responsive nano-objects, including micelles, vesicles, worm-like, etc., at different conditions is considered a pertinent challenge in the polymer community. The aim of the project was to synthesize aggregation-induced emission (AIE)-active stimuli-responsive polymeric nano-objects to control the self-assemblies morphologies of the prepared nano-objects. Two types of nanoobjects, micelle and vesicles, including PDMAEMA-b-P(BzMA-TPEMA) [PDMAEMA: poly(N,Ndimethylaminoethyl methacrylate); P(BzMA-TPEMA): poly[benzyl methacrylate-co- tetraphenylethene methacrylate]] were synthesized by using reversible addition−fragmentation chain-transfer (RAFT)- mediated polymerization-induced self-assembly (PISA), which combines polymerization and self-assembly in a single step. Transmission electron microscope and dynamic light scattering (DLS) analysis were used to confirm the formed self-assemblies morphologies. The controlled self-assemblies were applied as nitrophenolic compounds (NPCs) adsorbents from wastewater, thanks to their CO2-responsive part, PDMAEMA. Moreover, the fluorescence-active part of the prepared nano-objects, P(BzMA-TPEMA), played a key role in the detection of the NPCs at the aqueous solution. The optical properties of the prepared nano-objects were studied by UV/Vis and fluorescence spectroscopies. For responsivity investigations, the hydrodynamic diameter and Zeta-potential (ζ-potential) of the sample's aqueous solution were measured by DLS. In the end, the prepared nano-objects were used for the detection and adsorption of different NPCs.

Keywords: aggregation-induced emission polymers, stimuli-responsive polymers, reversible addition−fragmentation chain-transfer polymerization, polymerization-induced self-assembly, wastewater treatment

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Authors: Muhammad Tufail, Jawad Hussain, Hammad Hussain, Imran Hafeez, Naveed Ahmad

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Road safety performance index is a composite index which combines various indicators of road safety into single number. Development of a road safety performance index using appropriate safety performance indicators is essential to enhance road safety. However, a road safety performance index in developing countries has not been given as much priority as needed. The primary objective of this research is to develop a general Road Safety Performance Index (RSPI) for developing countries based on the facility as well as behavior of road user. The secondary objectives include finding the critical inputs in the RSPI and finding the better method of making the index. In this study, the RSPI is developed by selecting four main safety performance indicators i.e., protective system (seat belt, helmet etc.), road (road width, signalized intersections, number of lanes, speed limit), number of pedestrians, and number of vehicles. Data on these four safety performance indicators were collected using observation survey on a 20 km road section of the National Highway N-125 road Taxila, Pakistan. For the development of this composite index, two methods are used: a) Principal Component Analysis (PCA) and b) Equal Weighting (EW) method. PCA is used for extraction, weighting, and linear aggregation of indicators to obtain a single value. An individual index score was calculated for each road section by multiplication of weights and standardized values of each safety performance indicator. However, Simple Average technique was used for weighting and linear aggregation of indicators to develop a RSPI. The road sections are ranked according to RSPI scores using both methods. The two weighting methods are compared, and the PCA method is found to be much more reliable than the Simple Average Technique.

Keywords: indicators, aggregation, principle component analysis, weighting, index score

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Authors: Chung Danbi, Linton Oliver, Whang Yoon-Jae

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Supermodularity, or complementarity, is a popular concept in economics which can characterize many objective functions such as utility, social welfare, and production functions. Further, supermodular dominance captures a preference for greater interdependence among inputs of those functions, and it can be applied to examine which input set would produce higher expected utility, social welfare, or production. Therefore, we propose and justify a consistent testing for a useful implication of supermodular dominance. We also conduct Monte Carlo simulations to explore the finite sample performance of our test, with critical values obtained from the recentered bootstrap method, with and without the selective recentering, and the subsampling method. Under various parameter settings, we confirmed that our test has reasonably good size and power performance. Finally, we apply our test to compare the geographic and distant knowledge spillover in terms of their effects on social welfare using the National Bureau of Economic Research (NBER) patent data. We expect localized citing to supermodularly dominate distant citing if the geographic knowledge spillover engenders greater social welfare than distant knowledge spillover. Taking subgroups based on firm and patent characteristics, we found that there is industry-wise and patent subclass-wise difference in the pattern of supermodular dominance between localized and distant citing. We also compare the results from analyzing different time periods to see if the development of Internet and communication technology has changed the pattern of the dominance. In addition, to appropriately deal with the sparse nature of the data, we apply high-dimensional methods to efficiently select relevant data.

Keywords: supermodularity, supermodular dominance, stochastic dominance, Monte Carlo simulation, bootstrap, subsampling

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Authors: John Pomerat, Aviv Segev

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Recently, deep learning has had many theoretical breakthroughs. For deep learning to be successful in the industry, however, there need to be practical algorithms capable of handling many real-world hiccups preventing the immediate application of a learning algorithm. Although AI promises to revolutionize the healthcare industry, getting access to patient data in order to train learning algorithms has not been easy. One proposed solution to this is data- sharing. In this paper, we propose an alternative protocol, based on multi-party computation, to train deep learning models while maintaining both the privacy and security of training data. We examine three methods of training neural networks in this way: Transfer learning, average ensemble learning, and series network learning. We compare these methods to the equivalent model obtained through data-sharing across two different experiments. Additionally, we address the security concerns of this protocol. While the motivating example is healthcare, our findings regarding multi-party computation of neural network training are purely theoretical and have use-cases outside the domain of healthcare.

Keywords: neural network aggregation, multi-party computation, transfer learning, average ensemble learning

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to re-investigate the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high internode certainty, relative gene support, and high gene concordance factor. The evidence stems from five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup, such as slow-evolving species, while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: novel measures of phylogenetic support for phylogenomic data, gene concordance factor confidence, relative gene support, internode certainty, origin of tetrapods

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Authors: Krishan Kumar, Mohit Mittal, Pramod Kumar

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Wireless sensor network is one of the most promising communication networks for monitoring remote environmental areas. In this network, all the sensor nodes are communicated with each other via radio signals. The sensor nodes have capability of sensing, data storage and processing. The sensor nodes collect the information through neighboring nodes to particular node. The data collection and processing is done by data aggregation techniques. For the data aggregation in sensor network, clustering technique is implemented in the sensor network by implementing self-organizing feature map (SOFM) neural network. Some of the sensor nodes are selected as cluster head nodes. The information aggregated to cluster head nodes from non-cluster head nodes and then this information is transferred to base station (or sink nodes). The aim of this paper is to manage the huge amount of data with the help of SOM neural network. Clustered data is selected to transfer to base station instead of whole information aggregated at cluster head nodes. This reduces the battery consumption over the huge data management. The network lifetime is enhanced at a greater extent.

Keywords: artificial neural network, data clustering, self organization feature map, wireless sensor network

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to reassess the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high gene support confidence with confidence intervals exceeding 95%, high internode certainty, and high gene concordance factor. The evidence stems from two datasets containing recently deciphered whole genomes of two lungfish species, as well as five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa diminishes the number of orthologues and leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction (LBA) and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: gene support confidence (GSC), origin of land vertebrates, coelacanth, two whole genomes of lungfishes, confidence intervals

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Authors: Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu

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The role of glycyl residues in the protein structure has lingered within the research community for the last several decades. Glycyl residue is the only amino acid that is achiral due to the lack of a side chain and can, therefore, exhibit Ramachandran conformations that are disallowed for L-amino acids. The structural and functional significance of glycyl residues with L-disallowed conformation, however, remains obscure. Through statistical analysis of various datasets, we found that the glycyls with L-disallowed conformations are over-represented at disease-associated sites and tend to be evolutionarily conserved. The mutations of L-disallowed glycyls tend to destabilize the native conformation, reduce protein solubility, and promote inter-molecular aggregations. We uncovered a structural motif referred to as “β-crescent” formed around the L-disallowed glycyl, which prevents β-sheet aggregation by disrupting the alternating pattern of β-pleats. The L-disallowed conformation of glycyls also holds predictive power to infer the pathogenic missense variants. Altogether, our observations highlight that the L-disallowed conformation of glycyls is selected to facilitate native folding and prevent inter-molecular aggregations. The findings may also have implications for designing more stable proteins and prioritizing the genetic lesions implicated in diseases.

Keywords: Ramachandran plot, β-sheet, protein stability, protein aggregation

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Authors: M.F. Elkady, Sahar Zaki, Desouky Abd-El-Haleem

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Silver nanoparticles (AgNPs) are already widely prepared using different technologies. However, there are limited data on the effects of hydrogen ion concentration on nano-silver production. In this investigation, the impact of the pH reaction medium toward the particle size, agglomeration and the yield of the produced bio-synthesized silver were established. Quasi-spherical silver nanoparticles were synthesized through the biosynthesis green production process using the Egyptian E. coli bacterial strain 23N at different pH values. The formation of AgNPs has been confirmed with ultraviolet–visible spectra through identification of their characteristic peak at 410 nm. The quantitative production yield and the orientation planes of the produced nano-silver were examined using X-ray spectroscopy (EDS) and X-ray diffraction (XRD). Quantitative analyses indicated that the silver production yield was promoted at elevated pH regarded to increase the reduction rate of silver precursor through both chemical and biological processes. As a result, number of the nucleus and thus the size of the silver nanoparticles were tunable through changing pH of the reaction system. Accordingly, the morphological structure and size of the produced silver and its aggregates were determined using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images. It was considered that the increment in pH value of the reaction media progress the aggregation of silver clusters. However, the presence of stain 23N biomass decreases the possibility of silver aggregation at the pH 7.

Keywords: silver nanoparticles, biosynthesis, reaction media pH, nano-silver characterization

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Authors: Auxeeliya Jesudoss, Ashraph Sulaiman, Ratnakar Kotnana

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V2V communication brings up several questions of scalability issues although message sharing in vehicular ad-hoc networks comprises of both Vehicle-to-Vehicle communications (V2V) and Vehicle to Infrastructure communication (V2I). It is not an easy task for a vehicle to verify all signatures of the messages sent by its neighboring vehicles in a timely manner, without resulting in message loss. Moreover, the communication overhead of a vehicle to authenticate another vehicle would increase together with the security of the system. Another issue to be addressed is the continuous mobility of vehicles which requires at least some information on the node’s own position to be revealed to the neighboring vehicles. This may facilitate the attacker to congregate information on a node’s position or its mobility patterns. In order to tackle these issues, this paper introduces a RSU aggregated message deliverance scheme called RAMeD. With RAMeD, roadside units (RSUs) are responsible for verifying the identity of the vehicles entering in its range, collect messages from genuine vehicles and to aggregate similar messages into groups before sending them to all the vehicles in its communication range. This aggregation will tremendously improve the rate of message delivery and reduce the message lose ratio by avoiding similar messages being sent to the vehicles redundantly. The proposed protocol is analyzed extensively to evaluate its merits and efficiency for vehicular communication.

Keywords: vehicular ad-hoc networks, V2V, V2I, VANET communication, scalability, message aggregation

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Authors: Ajibade T., Omotesho O. A., Ayinde O. E, Ajibade E. T., Muhammad-Lawal A.

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This study was carried out to examine the extent and magnitude of food security amongst farming rural households in Nigeria. Data used for this study was collected from a total of two hundred and forty rural farming households using a two-stage random sampling technique. The main tools of analysis for this study include descriptive statistics and a constructed food security index using the identification and aggregation procedure. The headcount ratio in this study reveals that 71% of individuals in the study area were food secure with an average per capita calorie and protein availability of 4,213.92kcal and 99.98g respectively. The aggregated household daily calorie availability and daily protein availability per capita were 3,634.57kcal and 84.08g respectively which happens to be above the food security line of 2,470kcal and 65g used in this study. The food insecure households fell short of the minimum daily per capita calorie and protein requirement by 2.1% and 24.9%. The study revealed that the area is food insecure due to unequal distribution of the available food amongst the sampled population. The study recommends that the households should empower themselves financially in order to enhance their ability to afford the food during both on and off seasons. Also, processing and storage of farm produce should be enhanced in order to improve on availability throughout the year.

Keywords: farming household, food security, identification and aggregation, food security index

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Authors: Selma Sbit, Mohamed Bechir Dadi, Belgacem Chibani Rhaimi

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Incorporating Home eNodeB (HeNB) in cellular networks, e.g. Long Term Evolution Advanced (LTE-A), is beneficial for extending coverage and enhancing capacity at low price especially within the non-line-of sight (NLOS) environments such as homes. HeNB or femtocell is a small low powered base station which provides radio coverage to the mobile users in an indoor environment. This deployment results in a heterogeneous network where the available spectrum becomes shared between two layers. Therefore, a problem of Inter Cell Interference (ICI) appears. This issue is the main challenge in LTE-A. To deal with this challenge, various techniques based on frequency, time and power control are proposed. This paper deals with the impact of carrier aggregation and higher order MIMO (Multiple Input Multiple Output) schemes on the LTE-Advanced performance. Simulation results show the advantages of these schemes on the system capacity (4.10⁹ b/s/Hz when bandwidth B=100 MHz and when applying MIMO 8x8 for SINR=30 dB), maximum theoretical peak data rate (more than 4 Gbps for B=100 MHz and when MIMO 8x8 is used) and spectral efficiency (15 b/s/Hz and 30b/s/Hz when MIMO 4x4 and MIMO 8x8 are applying respectively for SINR=30 dB).

Keywords: capacity, carrier aggregation, LTE-Advanced, MIMO (Multiple Input Multiple Output), peak data rate, spectral efficiency

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Authors: Abdel Ghany F. Shoair, Mai M. A. H. Shanab

Abstract:

The basic aqueous systems NiSO4.6H₂O / K₂S₂O₈ (PH= 14) or NiSO₄.6H₂O / KBrO₃ (PH = 11.5) were ‎investigated ‎for the ‎catalytic conversion benzyl alcohol and ‎some para-substituted benzyl ‎alcohols to their ‎corresponding ‎acids in 75-97 % yield at room ‎temperature. The active species ‎was isolated and characterized by scanning ‎electron ‎microscopy (SEM), ‎‎transmission electron microscopy (TEM), X-ray ‎powder diffraction, EDX and ‎‎FT-IR ‎techniques and identified as NiO₂ nanoparticles (NPNPs). The SEM and ‎TEM images of nickel peroxide samples show a fine spherical-like ‎aggregation of ‎NiO₂ molecules with a nearly homogeneous partial size and confirm the ‎aggregation's size ‎to ‎be in the range of 2-3 nm. The yields, turnover (TO) and turn ‎over frequencies (TOF) were calculated. ‎It was noticed ‎that the aromatic alcohols ‎containing para-substituted electron donation groups gave better ‎‎yields than ‎those having electron-withdrawing groups. The optimum conditions for this ‎‎catalytic reaction ‎were studied using benzyl alcohol as a model. The mechanism ‎of the ‎catalytic conversion reaction was ‎suggested, in which the produced ‎(NPNPs) convert alcohols ‎to acids in two steps through the formation of the ‎‎corresponding aldehyde. The produced ‎NiO, because of this conversion, is ‎converted again to (NPNPs) by ‎an excess of K₂S₂O₈ or KBrO₃. This ‎catalytic cycle continues ‎until all the substrate is oxidized.

Keywords: Nickel, oxidation, catalysts, benzyl alcohol

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Authors: Wahizatul Afzan Azmi, Nur Ain Farhah Ros Saidon Khudri, Mohamad Haris Hussain, Tse Seng Chuah

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Malaysia houses a broad range of palm trees species and some of these palm trees are very crucial for the country’s social and economic development, especially the oil palm trees. However, the destructive pest of the various palms species, Rhynchophorus ferrugineus (Coleoptera: Curculionidae) or known as Red Palm Weevil (RPW) was first detected in Terengganu in 2007. Recently, the pattern of infestation has move from coastal lines toward inland areas. After the coconut plantations, it is presumed that the RPW will be a serious threat to the oil palm plantations in Malaysia. Thus, this study was carried out to detect the presence and distribution of Red Palm Weevil (RPW) in selected oil palm plantations of Terengganu. A total of 42 traps were installed in the three oil palm plantations in Terengganu and were inspected every week for two months. Oil palm plantation A collected significantly higher adults RPW compared to the other locations. Generally, females of RPW were significantly higher than male individuals. Females were collected more as the synthetic aggregation pheromone used, ferrugineol was synthesized from the male aggregation pheromone of adult RPW. Oil palm plantation A collected the highest number of RPW might be due to the abundance of soft part in the host plant as the oil palm trees age ranged between 6 to 10 years old. As a conclusion, RPW presence was detected in some oil palm plantations of Terengganu and immediate action is crucially needed before it is too late.

Keywords: red palm weevil, pest, oil palm, pheromone

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Authors: Jessica Chorostecki, Aashka Shah, Fen Bao, Ginny Bao, Edwin George, Navid Seraji-Bozorgzad, Veronica Gorden, Christina Caon, Elliot Frohman

Abstract:

Background: Parkinson’s Disease (PD) is a neuro degenerative disorder associated with the loss of dopaminergic cells and the presence α-synuclein (AS) aggregation in of Lewy bodies. Both dopaminergic cells and AS are found in the retina. Optical coherence tomography (OCT) allows high-resolution in-vivo examination of retinal structure injury in neuro degenerative disorders including PD. Methods: We performed a cross-section OCT study in patients with definite PD and healthy controls (HC) using Spectral Domain SD-OCT platform to measure the peripapillary retinal nerve fiber layer (pRNFL) thickness and total macular volume (TMV). We performed intra-retinal segmentation with fully automated segmentation software to measure the volume of the RNFL, ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL), and the outer nuclear layer (ONL). Segmentation was performed blinded to the clinical status of the study participants. Results: 101 eyes from 52 PD patients (mean age 65.8 years) and 46 eyes from 24 HC subjects (mean age 64.1 years) were included in the study. The mean pRNFL thickness was not significantly different (96.95 μm vs 94.42 μm, p=0.07) but the TMV was significantly lower in PD compared to HC (8.33 mm3 vs 8.58 mm3 p=0.0002). Intra-retinal segmentation showed no significant difference in the RNFL volume between the PD and HC groups (0.95 mm3 vs 0.92 mm3 p=0.454). However, GCL, IPL, INL, and ONL volumes were significantly reduced in PD compared to HC. In contrast, the volume of OPL was significantly increased in PD compared to HC. Conclusions: Our finding of the enlarged OPL corresponds with mRNA expression studies showing localization of AS in the OPL across vertebrate species and autopsy studies demonstrating AS aggregation in the deeper layers of retina in PD. We propose that the enlargement of the OPL may represent a potential biomarker of AS aggregation in PD. Longitudinal studies in larger cohorts are warranted to confirm our observations that may have significant implications in disease monitoring and therapeutic development.

Keywords: Optical Coherence Tomography, biomarker, Parkinson's disease, alpha-synuclein, retina

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Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

Abstract:

Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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Authors: Trapti Pathak

Abstract:

Fishes can change their body colour according to their surroundings by. They do so by either aggregation or dispersion of melanosomes within the skin. These movements can regulate by means of sympathetic nerves with the help of cytoskeleton. Employing the melanophores on isolated scales of the fingerling of teleost fish, it is attempted to characterise the concerned nerves and the receptors located on melenocytes along with implication of microtubules a part of cytoskeleton in the pigmentary translocation in the fish. The scales from dorso-lateral trunk of the fish represented the sympathetic– neuromelanophore preparations which were stimulated by chemical means, such as adrenergic agonist, antagonist and the microtubule-disrupting drugs such as yuhombine, dopamine, colchicine etc. Adrenaline is an adrenergic agonist which is strongly induced the dorse-dependent concentration of pigment in innervated melanophores while Yohimbine is an adrenergic antagonist which is known to block effectively the α2-adrenoceptors inhibited the action of adrenaline. Colchicine effectively interferes with melanosome aggregating action of adrenaline. From these results it is concluded that the chromatic fibres of adrenergic nature innervate the melanophores and these cells do possess α2-adrenoceptors which mediate the melanosome aggregation and the movements of pigment granules through microtubules means of transport within the cell. These movements of pigment are linked to paling or darkening achieved of teleost fish respectively when they approach to their background.

Keywords: melenophores, agonists, antagonist, colour change

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Authors: Selina Lin, Justin M Fan, Vincent Zhang, Cindy Chen, Daniel Lam, Jason Yan, Ning Zhang

Abstract:

Depression is one of the most common mental disorders in the United States, and past studies have shown a concerning increase in the rates of depression in youth populations over time. Furthermore, depression is an especially important issue for Asian Americans because of the anti-Asian violence taking place during the COVID-19 pandemic. While Asian American adolescents are reluctant to seek help for mental health issues, past research has found a prevalence of depressive symptoms in them that have yet to be fully investigated. There have been studies conducted to understand and observe the impacts of multifarious factors influencing the mental well-being of Asian American adolescents; however, they have been generally limited to qualitative investigation, and very few have attempted to quantitatively evaluate the relationship between depression levels and a comprehensive list of factors for those levels at the same time. To better quantify these relationships, this project investigated the prevalence of depression in Asian American teenagers mainly from the Greater Philadelphia Region, aged 12 to 19, and, with an anonymous survey, asked participants 48 multiple-choice questions pertaining to demographic information, daily behaviors, school life, family life, depression levels (quantified by the PHQ-9 assessment), school and family support against depression. Each multiple-choice question was assigned as a factor and variable for statistical and dominance analysis to determine the most influential factors on depression levels of Asian American adolescents. The results were validated via Bootstrap analysis and t-tests. While certain influential factors identified in this survey are consistent with the literature, such as parent-child relationship and peer pressure, several dominant factors were relatively overlooked in the past. These factors include the parents’ relationship with each other, the satisfaction with body image, sex identity, support from the family and support from the school. More than 25% of participants desired more support from their families and schools in handling depression issues. This study implied that it is beneficial for Asian American parents and adolescents to take programs on parents’ relationships with each other, parent-child communication, mental health, and sexual identity. A culturally inclusive school environment and more accessible mental health services would be helpful for Asian American adolescents to combat depression. This survey-based study paved the way for further investigation of effective approaches for helping Asian American adolescents against depression.

Keywords: Asian American adolescents, depression, dominance analysis, t-test, bootstrap analysis

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Authors: Jianuo Sun, Jinghan Wang, Sirui Zhang, Chenhan Xu, Hongxia Hao, Hong Zhou

Abstract:

In recent years, the diversification and industrialization of drug-related crimes have posed significant threats to public health and safety globally. The widespread and increasingly younger demographics of drug users and the persistence of drug-impaired driving incidents underscore the urgency of this issue. Drug detection, a specialized forensic activity, is pivotal in identifying and analyzing substances involved in drug crimes. It relies on pharmacological and chemical knowledge and employs analytical chemistry and modern detection techniques. However, current drug detection methods are limited by their inability to perform semi-quantitative, real-time field analyses. They require extensive, complex laboratory-based preprocessing, expensive equipment, and specialized personnel and are hindered by long processing times. This study introduces an alternative approach using nucleic acid aptamers and Aggregation-Induced Emission (AIE) technology. Nucleic acid aptamers, selected artificially for their specific binding to target molecules and stable spatial structures, represent a new generation of biosensors following antibodies. Rapid advancements in AIE technology, particularly in tetraphenyl ethene-based luminous, offer simplicity in synthesis and versatility in modifications, making them ideal for fluorescence analysis. This work successfully synthesized, isolated, and purified an AIE molecule and constructed a probe comprising the AIE molecule, nucleic acid aptamers, and exonuclease for cocaine detection. The probe demonstrated significant relative fluorescence intensity changes and selectivity towards cocaine over other drugs. Using 4-Butoxytriethylammonium Bromide Tetraphenylethene (TPE-TTA) as the fluorescent probe, the aptamer as the recognition unit, and Exo I as an auxiliary, the system achieved rapid detection of cocaine within 5 mins in aqueous and urine, with detection limits of 1.0 and 5.0 µmol/L respectively. The probe-maintained stability and interference resistance in urine, enabling quantitative cocaine detection within a certain concentration range. This fluorescent sensor significantly reduces sample preprocessing time, offers a basis for rapid onsite cocaine detection, and promises potential for miniaturized testing setups.

Keywords: drug detection, aggregation-induced emission (AIE), nucleic acid aptamer, exonuclease, cocaine

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