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Heuristics for the run-length encoded Burrows–Wheeler transform alphabet ordering problem
Get PDFThe Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the ability to query the compressed data efficiently. However, these methods may not take full advantage of the compressibility of the BWT as they do not modify the alphabet ordering for the sorting step embedded in computing the BWT. Indeed, any such alteration of the alphabet ordering can have a considerable impact on the output of the BWT, in particular on the number of runs. For an alphabet Σ containing σ characters, the space of all alphabet orderings is of size σ!. While for small alphabets an exhaustive investigation is possible, finding the optimal ordering for larger alphabets is not feasible. Therefore, there is a need for a more informed search strategy than brute-force sampling the entire space, which motivates a new heuristic approach. In this paper, we explore the non-trivial cases for the problem of minimizing the size of a run-length encoded BWT (RLBWT) via selecting a new ordering for the alphabet. We show that random sampling of the space of alphabet orderings usually gives sub-optimal orderings for compression and that a local search strategy can provide a large improvement in relatively few steps. We also inspect a selection of initial alphabet orderings, including ASCII, letter appearance, and letter frequency. While this alphabet ordering problem is computationally hard we demonstrate gain in compressibility
BioClocks UK:Driving robust cycles of discovery to impact
Get PDFChronobiology is a multidisciplinary field that extends across the tree of life, transcends all scales of biological organization, and has huge translational potential. For the UK to harness the opportunities presented within applied chronobiology, we need to build our network outwards to reach stakeholders that can directly benefit from our discoveries. In this article, we discuss the importance of biological rhythms to our health, society, economy and environment, with a particular focus on circadian rhythms. We subsequently introduce the vision and objectives of BioClocks UK, a newly formed research network, whose mission is to stimulate researcher interactions and sustain discovery-impact cycles between chronobiologists, wider research communities and multiple industry sectors. This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.</p
Allatostatin-C signaling in the crab Carcinus maenas is implicated in the ecdysis program
Get PDFThe allatostatin (AST) family of neuropeptides are widespread in arthropods. The multitude of structures and pleiotropic actions reflect the tremendous morphological, physiological and behavioral diversity of the phylum. Regarding the AST-C (with C-terminal PISCF motif ) peptides, crustaceans commonly express three (AST-C, AST-CC and AST-CCC) that have likely arisen by gene duplication. However, we know little regarding their physiologically relevant actions. Here, we functionally characterize the cognate receptor for AST-C and AST-CC, determine tissue expression, and comprehensively examine the localization of AST mRNA and peptide. We also measured peptide release, circulating titers and performed bioassays to investigate possible roles. AST-C and AST-CC activate a single receptor (AST-CRd), but this, and other candidate receptors, were not activated by AST-CCC. Whole-mount in situ hybridization and hybridization chain reaction fluorescent in situ hybridization complemented neuropeptide immunolocalization strategies and revealed extensive expression of AST-Cs in the central nervous system. AST-C or AST-CCC expressing neurons were found in the cerebral ganglia, but AST-CC expression was never observed. Of note, we infer that AST-C and AST-CC are co-expressed in every neuron expressing crustacean cardioactive peptide (CCAP) and bursicon (BURS); all four peptides are released from the pericardial organs during a brief period coinciding with completion of emergence. In contrast to other studies, none of the AST-C peptides exhibited any effect on ecdysteroid synthesis or cardiac activity. However, expression of the AST-C receptor on hemocytes suggests a tantalizing glimpse of possible functions in immune modulation following ecdysis, at a time when crustaceans are vulnerable to pathogens.</p
Supernova remnant candidates discovered by the SARAO MeerKAT Galactic Plane Survey
Get PDFContext. Sensitive radio continuum data could bring the number of known supernova remnants (SNRs) in the Galaxy more in line with what is expected. Due to confusion in the Galactic plane, however, faint SNRs can be challenging to distinguish from brighter H II regions and filamentary radio emission. Aims. We exploited new 1.3 GHz SARAO MeerKAT Galactic Plane Survey (SMGPS) radio continuum data, which cover 251° ≤ l ≤ 358° and 2° ≤ l ≤ 61° at | b | ≤ 1.5°, to search for SNR candidates in the Milky Way disk. Methods. We also used mid-infrared data from the Spitzer GLIMPSE, Spitzer MIPSGAL, and WISE surveys to help identify SNR candidates. These candidates are sources of extended radio continuum emission that lack mid-infrared counterparts, are not known as H II regions in the WISE Catalog of Galactic H II Regions, and have not been previously identified as SNRs. Results. We locate 237 new Galactic SNR candidates in the SMGPS data. We also identify and confirm the expected radio morphology for 201 objects classified in the literature as SNRs and 130 previously identified SNR candidates. The known and candidate SNRs have similar spatial distributions and angular sizes. Conclusions. The SMGPS data allowed us to identify a large population of SNR candidates that can be confirmed as true SNRs using radio polarization measurements or by deriving radio spectral indices. If the 237 candidates are confirmed as true SNRs, it would approximately double the number of known Galactic SNRs in the survey area, alleviating much of the discrepancy between the known and expected populations.</p
Agromorphological Characterization of Biofortified Cassava Genotypes (Manihot esculenta)
No full textCassava is an important food security crop and millions of people rely on it as a major source of food around the world. Cassava is a main staple in Ghana and an ideal candidate for biofortification to improve its nutritional content to mitigate malnutrition and increase food security. The objective of the study was to assess the genetic diversity of 21 biofortified cassava accessions using agromorphological descriptors to determine significant variations among the genotypes for breeding programs. The trial was carried out in a complete randomized block design with two replications at the University of Ghana, Legon. Data were collected at 3, 6, 9, and 12 months after planting. Significant differences were observed for all quantitative traits that were measured. There was a positive correlation between fresh root weight and the number of storage roots and also the number of leaf lobes and the length of the petiole. The first two principal component analyses (PCAs) explained 53.023% of the total variance. The key traits that influenced PC1 and PC2 included the total weight of commercial storage roots, leaf retention, average weight, number of storage roots, height at first branching, petiole length, and percentage of dry matter, further emphasizing the diverse traits among these genotypes and their breeding potential. Genotypes WC 2 and WC 14 made substantial contributions, while WC 15 signifies exceptional trait diversity and are promising candidates for enhancing genetic diversity in breeding programs. The dendrogram revealed phylogenetic relationships among the cassava germplasms, forming two main groups and subgroups. This study revealed substantial phenotypic diversity, providing a foundation for future breeding programs to improve food and nutrition security.</p
Evaluation of Nutritional Value of Four High-Sugar Ryegrass Varieties on the Loess Plateau under Different Cutting Methods
No full textTo explore the effects of cutting methods on the nutritional value of different high-sugar ryegrass, four high-sugar ryegrass varieties, namely ‘AberStar’ ‘AberMagic’ ‘AberAvon’ and ‘Premium’ were planted in the Loess Plateau. Dynamic sampling was conducted to investigate the effects of multiple cutting and once cutting on the yield, nutritional quality dynamics, yield stability and complete a comprehensive evaluation. The results showed that the yield of four varieties under multiple cutting was significantly higher than that of under once cutting during the growth period, but the yield stability was 5.38%~23.91% lower than that under once cutting. The stability of crude protein content under multiple cutting was significantly higher than that of under once cutting (P<0. 05), the lowest stability of soluble carbohydrates was 31. 77%~45. 20%. The regeneration rate and intensity of the four varieties increased and then decreased, they under multiple cutting were 18.12%~105.21% and 18.41%~92.63% higher than that under once cutting，and the peak reached at 108 days. The food equivalent unit of multiple cutting was significantly higher than that of once cutting (P<0. 05). Among all treatments, the ‘AberStar’ showed the best yield and quality performance under multiple cutting. In this study, we identified high-yield and high-quality varieties of high-sugar ryegrass and their cutting methods, which will provide scientific basis for the cultivation and management measures of high-sugar ryegrass in the Loess Plateau region
Optimizing Maize Yield With Hybrids Tolerant of High Plant Density in West and Central Africa
Get PDFThe use of high plant density tolerant maize hybrids was one of the most successful interventions that boosted maize yield in the developed world. However, very little research has been conducted in the improvement of maize for high plant density tolerance in West and Central Africa (WCA). This study aimed to identify high plant density-tolerant maize hybrids adapted to multiple environments. Forty-eight maize hybrids were evaluated under three plant densities (low = 53,333, medium = 66,666, and high = 88, 888 plants ha−1). The experiment was conducted in four different environments in Ghana using 8 × 6 alpha lattice design with split plot arrangement. Plant density was the main plot and hybrids arranged in incomplete blocks within each plant density. The results revealed that the relative grain yield performance of the genotypes was dependent on plant density. Optimum plant density for the hybrids varied with growing environments. The highest grain yield of 9.5, 9.2, and 8.6 t ha−1 were obtained from the high plant density in Legon (minor season), Fumesua, and Legon (off-season), respectively, and it was 26.7%, 22.7%, and 30% increase in comparison to the respective yield under the low density. F1 hybrids M131 × CML16, CML16 × TZEI1, CML16 × 87,036, TZEI387 × CML16, and ENT11 × 87,036 are good candidates for high-density planting in high-yielding environments. Grain yield performance of the maize hybrids was highest under high plant density for most of the growing environments. Thus, implementing high-density planting for maize hybrids could be one of the options for increasing maize yield in West and Central Africa.</p
The Effectiveness of a Simplified Model Structure for Crowd Counting
Get PDFCrowd counting, a method for measuring crowd sizes, has seen significant advancements with deep learning techniques, which have proven highly effective in accurate estimation. However, the improvement in these methods' accuracy is frequently achieved at the cost of more intricate model architectures. This article discusses how to construct high-performance crowd counting models using only simple structures. We propose the fuss-free structure, a simple and efficient architecture with a backbone network and multiscale feature fusion. It exhibits notable adaptability, ensuring that slight replacing its components do not lead to a substantial decline in performance. The multiscale feature fusion structure is an uncomplicated design that consists of three distinct pathways, each featuring only a focus transition module (FTM). It combines the features from these pathways by directly employing the concatenation operation. By selecting appropriate components, our proposed structure has been trained and evaluated across four public datasets, demonstrating an accuracy that rivals that of existing complex models. Furthermore, a comprehensive evaluation is conducted by replacing the backbones of various models such as CCTrans and the proposed structure with different networks, including MobileNet-v3, ConvNeXt-Tiny, and Swin-Transformer-Small. The experimental results further indicate that excellent crowd counting performance can be achieved with the simple structure proposed by us. Code is available at https://github.com/erdongsanshi/Fuss-Free-structure.</p
Seasonal stem growth analysis shows early stem growth of Miscanthus from high latitudes yields more biomass but stem traits negatively interact to limit seasonal growth
Get PDFHigh yielding perennial grasses are utilised as biomass for the bioeconomy and to displace fossil fuels. Miscanthus is a perennial grass used as a source of biomass but most of the cultivated crop is limited to a naturally occurring hybrid M. × giganteus. Miscanthus species originate from an extensive latitudinal and longitudinal range across Asia and thus have considerable potential to diversify the crop and improve yield. In previous studies stem morphological traits correlated strongly with yield in Miscanthus but little is known about how the development of stem growth may be optimised across the growth season. The aims of this study are to identify strategies to optimise seasonal growth duration and improve yield. To do this yield and seasonal stem elongation were measured from large numbers of diverse genotypes and functional data analysis used to characterise and compare the diverse perennial stem growth strategies. A diversity trial of over 900 genotypes was established in three replicates in the field at Aberystwyth, UK. Stem elongation was measured across the entire season for 3 consecutive years and the Richards growth function was fitted to model growth. Differentials, double differentials and integrals of the parameterised functions produced six growth characteristics, describing the growth rate, the timing and duration of the logarithmic growth phase and the integral of stem growth. Plants were also assessed for yield and moisture content. Growth traits from all plants in the diversity trial were moderately correlated, were correlated with biomass moisture content but less so to accumulated dry weight of biomass. Plants that grew for longer tended to have lower growth rates, but individual exceptions were identified. Plants with a similar duration of logarithmic growth achieved greater growth rates and harvestable yield if growth began earlier in the season and early season growth was mostly explained by latitude and altitude from which the accessions were collected. Stem growth traits were highly heritable and there was a significant effect of species on all growth characteristics. We discuss the possible interactions between growth and developmental control in perennials that may be exploited to improve yield in these crops.</p
The ‘roots/routes to fruit’ model:Developing a ‘fruitful’ collaborative network across universities
Get PDFThis study explores the development and dynamics of the Wales Collaborative for Learning Design (WCLD), a multidisciplinary network across eight Welsh universities. Funded by Welsh Government, the WCLD aimed to foster collaboration in digital learning design while supporting individual and collective academic growth. The study aimed to investigate what factors impact on the development and sustainability of a personal and professional, multidisciplinary Higher Education collaborative network. Using a collective autoethnographic approach, the research explored the network’s evolution, highlighting the interplay of person attributes, facilitating conditions, and professional relationships. Findings revealed key factors including trust, open-mindedness, and consistent communication as essential to the network’s sustainability and success. Further findings illustrate how positive constraints, diverse career stages, and interdisciplinary opportunities underpin growth and productivity. ‘Outcomes’ included enhanced institutional impact, significant personal and professional conversations, and the cross-pollination of ideas within and beyond the network. When considered as a process, the findings underscore the value of cultivating intentional, yet adaptable, collaborative networks to support higher education innovation and personal academic development. This culminates in the ‘Roots/routes to Fruit’ model. This original contribution builds on existing theory surrounding significant, collaborative networks and provides a process for future interdisciplinary, multi-institutional, collaborative networks to build upon