Design of mechanical metamaterials using a level-set based topology optimization method

Metamaterials are a family of artificially engineered materials consisting of an array of periodically arranged microstructures, offering unusual material properties that may not be easily found in nature. This paper will propose a new topological shape optimization method for the design of mechanical metamaterials with negative Poisson’s ratios, by integrating the numerical homogenization method with a powerful level set method. The homogenization method is used to calculate the effective properties of the microstructure, and the level set method is utilized to implement shape and topology optimization of the microstructure until the desired material properties are obtained. The proposed method can retain the unique features of the level set methods, while avoid unfavourable numerical issues occurred in the conventional level set methods. Several typical numerical examples are used to showcase the effectiveness of the proposed design method

SCHISTOSOMIASIS: GEOSPATIAL SURVEILLANCE AND RESPONSE SYSTEMS IN SOUTHEAST ASIA

Geographic information system (GIS) and remote sensing (RS) from Earth-observing satellites offer opportunities for rapid assessment of areas endemic for vector-borne diseases including estimates of populations at risk and guidance to intervention strategies. This presentation deals with GIS and RS applications for the control of schistosomiasis in China and the Philippines. It includes large-scale risk mapping including identification of suitable habitats for Oncomelania hupensis, the intermediate host snail of Schistosoma japonicum. Predictions of infection risk are discussed with reference to ecological transformations and the potential impact of climate change and the potential for long-term temperature increases in the North as well as the impact on rivers, lakes and water resource developments. Potential integration of geospatial mapping and modeling in schistosomiasis surveillance and response systems in Asia within Global Earth Observation System of Systems (GEOSS) guidelines in the health societal benefit area is discussed

Oh my aching gut: irritable bowel syndrome, Blastocystis, and asymptomatic infection

Blastocystis is a prevalent enteric protozoan that infects a variety of vertebrates. Infection with Blastocystis in humans has been associated with abdominal pain, diarrhea, constipation, fatigue, skin rash, and other symptoms. Researchers using different methods and examining different patient groups have reported asymptomatic infection, acute symptomatic infection, and chronic symptomatic infection. The variation in accounts has lead to disagreements concerning the role of Blastocystis in human disease, and the importance of treating it. A better understanding of the number of species of Blastocystis that can infect humans, along with realization of the limitations of the existing clinical laboratory diagnostic techniques may account for much of the disagreement. The possibility that disagreement was caused by the emergence of particular pathogenic variants of Blastocystis is discussed, along with the potential role of Blastocystis infection in irritable bowel syndrome (IBS). Findings are discussed concerning the role of protease-activated receptor-2 in enteric disease which may account for the presence of abdominal pain and diffuse symptoms in Blastocystis infection, even in the absence of fever and endoscopic findings. The availability of better diagnostic techniques and treatments for Blastocystis infection may be of value in understanding chronic gastrointestinal illness of unknown etiology

Millipede genomes reveal unique adaptations during myriapod evolution

This is the final version. Available from Public Library of Science via the DOI in this record.The final genome assemblies have been deposited to NCBI database with accession numbers JAAFCF000000000 and JAAFCE000000000. The mRNA and sRNA transcriptomic data generated in this study have been deposited to the NCBI database under the following BioProject accessions: PRJNA564202 (Helicorthomorpha holstii) and PRJNA564195 (Trigoniulus corallinus).The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs-including species-specific microRNA arm switching-providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes-and in particular the reconstruction of the myriapod ancestral situation-for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely.Hong Kong Research Grants Council (RGC) General Research FundHong Kong Research Grants Council (RGC) General Research FundThe Chinese University of Hong Kong (CUHK

Electroacupuncture for poststroke spasticity (EAPSS): protocol for a randomised controlled trial

Introduction Spasticity is a common complication of stroke. Current therapies for poststroke spasticity (PSS) have been reported to be associated with high costs, lack of long-term benefit and unwanted adverse events (AEs). Electroacupuncture (EA) has been used for PSS, however, its efficacy and safety is yet to be confirmed by high-quality clinical studies. This study is designed to evaluate the add-on effects and safety profile of EA when used in combination with usual care (UC). Methods and analysis This study is a parallel group randomised controlled trial. A total of 136 participants will be included and randomly assigned to either the treatment group (EA plus UC) or the control group (UC alone). Prior to the main trial, a pilot study involving 30 participants will be conducted to assess the feasibility of the trial protocol. EA will be administered by registered acupuncturists for 20min to 30 min, three times per week for 4 weeks. The primary outcome measure (Modified Ashworth Scale) and secondary outcome measures (Fugl-Meyer Assessment and Barthel Index) will be evaluated at baseline, the end of treatment (week 4) and the end of follow-up (week 8). AEs will be monitored, recorded and reported, and their causality will be explored. Ethics and dissemination Ethics approval was obtained from the ethics committees of Guangdong Provincial Hospital of Chinese Medicine and RMIT University in December 2016. The results will be disseminated in a peer-reviewed journal, and PhD theses and might be presented at international conferences

Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees

This is the final version. Available on open access from Elsevier via the DOI in this recordAvailability of data and materials: The final chromosome assembly was submitted to NCBI Assembly under accession number JACJUM000000000 in NCBI. The raw reads generated in this study have been deposited to the NCBI database under the BioProject accessions: PRJNA654728, the genome annotation files were deposited in the Figshare (https://doi.org/10.6084/m9.figshare.19633668). The microRNA sequences of known species were obtained from both miRbase [42] and MirGeneDB [21].The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.Hong Kong Research Grant Council Collaborative Research FundGeneral Research FundChinese University of Hong Kon

Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability; The final assemblies were submitted to NCBI Assembly under accession numbers WWPM00000000 (Glomeris maerens), JAAFCF000000000 (Helicorthomorpha holstii), WWPL00000000 (Anaulaciulus tonginus), JAAIVG000000000 (Niponia nodulosa), JAAFCE000000000 (Trigoniulus corallinus), JAHWFP000000000 (Lithobius niger), JAHWFO000000000 (Rhysida immarginata) and JAFIDM000000000 (Thereuonema tuberculata) in NCBI. The raw reads generated in this study were deposited to the NCBI database under the BioProject accessions PRJNA598061 (Glomeris maerens), PRJNA564202 (Helicorthomorpha holstii), PRJNA598060 (Anaulaciulus tonginus), PRJNA606398 (Niponia nodulosa), PRJNA564195 (Trigoniulus corallinus), PRJNA738717 (Lithobius niger), PRJNA701115 (Rhysida immarginata) and PRJNA699399 (Thereuonema tuberculata). The genome annotation files were deposited in the Figshare (https://doi.org/10.6084/m9.figshare.15088722). The databases are available for download from the following websites: eggNOG http://eggnog5.embl.de/download/eggnog_5.0/, GO http://geneontology.org/, KEGG https://www.genome.jp/kegg/pathway.html, and KOG https://www.hsls.pitt.edu/obrc/index.php?page=URL1144075392. Source data are provided with this paper.Code availability: The scripts for carrying out analyses of this study were deposited in Zenodo: https://doi.org/10.5281/zenodo.571873479 and https://doi.org/10.5281/zenodo.648262594.Animals display a fascinating diversity of body plans. Correspondingly, genomic analyses have revealed dynamic evolution of gene gains and losses among animal lineages. Here we sequence six new myriapod genomes (three millipedes, three centipedes) at key phylogenetic positions within this major but understudied arthropod lineage. We combine these with existing genomic resources to conduct a comparative analysis across all available myriapod genomes. We find that millipedes generally have considerably smaller genomes than centipedes, with the repeatome being a major contributor to genome size, driven by independent large gains of transposons in three centipede species. In contrast to millipedes, centipedes gained a large number of gene families after the subphyla diverged, with gains contributing to sensory and locomotory adaptations that facilitated their ecological shift to predation. We identify distinct horizontal gene transfer (HGT) events from bacteria to millipedes and centipedes, with no identifiable HGTs shared among all myriapods. Loss of juvenile hormone O-methyltransferase, a key enzyme in catalysing sesquiterpenoid hormone production in arthropods, was also revealed in all millipede lineages. Our findings suggest that the rapid evolution of distinct genomic pathways in centipede and millipede lineages following their divergence from the myriapod ancestor, was shaped by differing ecological pressures

Genome of the ramshorn snail Biomphalaria straminea-an obligate intermediate host of schistosomiasi

This is the final version. Available on open access from Oxford University Press via the DOI in this recordData Availability: The raw genome and RNA sequencing data have been deposited in the SRA under Bioproject No. PRJNA673593. The final chromosome assembly was submitted to NCBI Assembly under accession No. JADKLZ000000000. All data can also be found in the GigaScience Database [75].BACKGROUND: Schistosomiasis, or bilharzia, is a parasitic disease caused by trematode flatworms of the genus Schistosoma. Infection by Schistosoma mansoni in humans results when cercariae emerge into water from freshwater snails in the genus Biomphalaria and seek out and penetrate human skin. The snail Biomphalaria straminea is native to South America and is now also present in Central America and China, and represents a potential vector host for spreading schistosomiasis. To date, genomic information for the genus is restricted to the neotropical species Biomphalaria glabrata. This limits understanding of the biology and management of other schistosomiasis vectors, such as B. straminea. FINDINGS: Using a combination of Illumina short-read, 10X Genomics linked-read, and Hi-C sequencing data, our 1.005 Gb B. straminea genome assembly is of high contiguity, with a scaffold N50 of 25.3 Mb. Transcriptomes from adults were also obtained. Developmental homeobox genes, hormonal genes, and stress-response genes were identified, and repeat content was annotated (40.68% of genomic content). Comparisons with other mollusc genomes (including Gastropoda, Bivalvia, and Cephalopoda) revealed syntenic conservation, patterns of homeobox gene linkage indicative of evolutionary changes to gene clusters, expansion of heat shock protein genes, and the presence of sesquiterpenoid and cholesterol metabolic pathway genes in Gastropoda. In addition, hormone treatment together with RT-qPCR assay reveal a sesquiterpenoid hormone responsive system in B. straminea, illustrating that this renowned insect hormonal system is also present in the lophotrochozoan lineage. CONCLUSION: This study provides the first genome assembly for the snail B. straminea and offers an unprecedented opportunity to address a variety of phenomena related to snail vectors of schistosomiasis, as well as evolutionary and genomics questions related to molluscs more widely