Empirical study of long-range connections in a road network offers new ingredient for navigation optimization models

Navigation problem in lattices with long-range connections has been widely studied to understand the design principles for optimal transport networks; however, the travel cost of long-range connections was not considered in previous models. We define long-range connection in a road network as the shortest path between a pair of nodes through highways and empirically analyze the travel cost properties of long-range connections. Based on the maximum speed allowed in each road segment, we observe that the time needed to travel through a long-range connection has a characteristic time Th ~ 29 min, while the time required when using the alternative arterial road path has two different characteristic times Ta ~ 13 and 41 min and follows a power law for times larger than 50 min. Using daily commuting origin–destination matrix data, we additionally find that the use of long-range connections helps people to save about half of the travel time in their daily commute. Based on the empirical results, we assign a more realistic travel cost to long-range connections in two-dimensional square lattices, observing dramatically different minimum average shortest path 〈l〉 but similar optimal navigation conditions.National Natural Science Foundation (China) (number 51208520)National Natural Science Foundation (China) (number 71071165)New England University Transportation Center (Year 23 grant)NEC Corporation of America (Funding award)Massachusetts Institute of Technology (Solomon Buchsbaum AT&T Research Fund)Central South University of Technology (China) (Shenghua Scholar Program

Visible light responsive titania photocatalysts codoped by nitrogen and metal (Fe, Ni, Ag, or Pt) for remediation of aqueous pollutants

Various cation and nitrogen doped and codoped TiO2 photocatalysts, such as N–TiO2, Pt–TiO2, N–Fe–TiO2, N–Ni–TiO2, N–Ag–TiO2 and N–Pt–TiO2, were prepared by an acid-catalysed sol–gel process. The photocatalysts were characterised by X-ray diffraction (XRD), nitrogen adsorption–desorption isotherms, UV–visible diffuse reflectance absorption spectroscopy (UV–vis DRS), and X-ray photoelectron spectroscopy (XPS). The activities of the photocatalysts were evaluated in photodegradation of phenol solutions under simulated sunlight irradiations. A negative effect of some transition metals (iron and nickel) onphotocatalysis was observed on N-metal codoped TiO2, while enhancements in photocatalysis from noble metals (silver and platinum) were obtained. N–Pt codoped TiO2 showed a higher activity under UV–vis irradiations than Degussa P25, with an enhancement of 5.9 times higher. The synergistic effect of N–Pt-codoping was ascribed to the multivalent states of platinum. In addition, photocatalytic activity of N-, Pt-doped and N–Pt-codoped materials were further investigated under visible light irradiations with lambda > 430 nm and lambda > 490 nm. This study therefore demonstrated a promising strategy for design of highly efficient photocatalysts for remediation of aqueous pollutants

Development of an axial flux MEMS BLDC micromotor with increased efficiency and power density

This paper presents a rigorous design and optimization of an axial flux microelectromechanical systems (MEMS) brushless dc (BLDC) micromotor with dual rotor improving both efficiency and power density with an external diameter of only around 10 mm. The stator is made of two layers of windings by MEMS technology. The rotor is developed by film permanent magnets assembled over the rotor yoke. The characteristics of the MEMS micromotor are analyzed and modeled through a 3-D magnetic equivalent circuit (MEC) taking the leakage flux and fringing effect into account. Such a model yields a relatively accurate prediction of the flux in the air gap, back electromotive force (EMF) and electromagnetic torque, whilst being computationally efficient. Based on 3-D MEC model the multi-objective firefly algorithm (MOFA) is developed for the optimal design of this special machine. Both 3-D finite element (FE) simulation and experiments are employed to validate the MEC model and MOFA optimization design

Characterization of viral RNA splicing using whole-transcriptome datasets from host species

RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. However, knowledge on viral AS is limited to a few disease-causing viruses in model species. Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. Two insect transcriptomes (Acheta domesticus and Planococcus citri) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. Two closely related densoviruses (Acheta domesticus densovirus, AdDNV, and Planococcus citri densovirus, PcDNV, Ambidensovirus, Densovirinae, Parvoviridae) were detected and analyzed for AS patterns. The results suggested that although the two viruses shared major AS features, dramatic AS divergences were observed. Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. When applied to large-scale transcriptomics projects with diverse taxonomic sampling, our new method is expected to rapidly expand our knowledge on RNA splicing mechanisms for a wide range of viruses

Efficient COI barcoding using high throughput single-end 400 bp sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

High-throughput monitoring of wild bee diversity and abundance via mitogenomics

1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline. 2. We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan-trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes. 3. The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93�7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species-specific primers suggested that these putative false positives were most likely due to incorrect morphological IDs. Read frequency significantly predicted species biomass frequency (R2 = 24�9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline. 4. Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and istributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high-quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories

Efficient \u3ci\u3eCOI\u3c/i\u3e Barcoding Using High Throughput Single-End 400 bp Sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current highthroughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (for example, a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly, and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

BackgroundPhylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data.ResultsWe generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda.ConclusionsOur best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal

Effect of angiotensin receptor-neprilysin inhibitor on atrial electrical instability in atrial fibrillation

Background and objectiveAround 33.5 million patients suffered from atrial fibrillation (AF), causing complications and increasing mortality and disability rate. Upstream treatment for AF is getting more popular in clinical practice in recent years. The angiotensin receptor-neprilysin inhibitor (ARNI) is one of the potential treatment options. Our study aimed to investigate the effect of ARNI on atrial electrical instability and structural remodeling in AF.MethodsOur research consisted of two parts – a retrospective real-world clinical study and an animal experiment on calmness to verify the retrospective founding. In the retrospective study, we reviewed all patients (n = 110) who had undergone the first AF ablation from 1 August 2018 to 1 March 2022. Patients with ARNI (n = 36) or angiotensin II receptor antagonist (ARB) (n = 35) treatment were enrolled. Their clinical data, ultrasound cardiogram (UCG) and Holter parameters were collected before radiofrequency catheter ablation (RFCA) as baseline and at 24-week follow-up. Univariate and multivariate logistic regression analysis were performed. In the animal experiment, we established an AF model (n = 18) on canines by rapid atrial pacing. After the successful procedure of pacing, all the 15 alive beagles were equally and randomly assigned to three groups (n = 5 each): Control group, ARB group, and ARNI group. UCG was performed before the pacing as baseline. Physiological biopsy, UCG, and electrophysiological study (EPS) were performed at 8-week.ResultsClinical data showed that the atrial arrhythmia rate at 24-week was significantly lower in ARNI group compared to ARB group (P < 0.01), and ARNI was independently associated with a lower atrial arrhythmia rate (P < 0.05) at 24-week in multivariate regression logistic analysis. In the animal experiment, ARNI group had a higher atrial electrical stability score and a shorter AF duration in the EPS compared to Control and ARB group (P < 0.05). In the left atrium voltage mapping, ARNI group showed less low voltage and disordered zone compared to Control and ARB group. Compared to Control group, right atrium diameter (RAD), left ventricle end-diastolic volume index (LVEDVI), E/A, and E/E′ were lower in ARNI group (P < 0.05) at the 8-weeks follow-up, while left atrium ejection fraction (LAEF) and left ventricle ejection fraction (LVEF) were higher (P < 0.01). Compared to ARB group, LVEF was higher in ARNI group at the 8-week follow-up (P < 0.05). ARB and ARNI group had a lower ratio of fibrotic lesions in the left atrium tissues compared to Control group (P < 0.01), but no difference was found between the ARB and the ARNI group.ConclusionARNI could reduce atrial electrical instability in AF in comparison with ARB in both retrospective study and animal experiment