The emergence of insecticide resistant Aedes aegypti mosquitoes has hampered dengue control efforts. WHO susceptibility tests, using several pyrethroid compounds, were conducted on Ae. aegypti larvae ...that were collected and raised to adulthood from Semarang, Surakarta, Kudus and Jepara in Java. The AaNaV gene fragment encompassing kdr polymorphic sites from both susceptible and resistant mosquitoes was amplified, and polymorphisms were associated with the resistant phenotype. The insecticide susceptibility tests demonstrated Ae, aegypti resistance to the pyrethroids, with mortality rates ranging from 1.6%-15.2%. Three non-synonymous polymorphisms (S989P, V1016G and F1534C) and one synonymous polymorphism (codon 982) were detected in the AaNaV gene. Eight AaNaV alleles were observed in specimens from Central Java. Allele 3 (SGF) and allele 7 (PGF) represent the most common alleles found and demonstrated strong associations with resistance to pyrethroids (OR = 2.75, CI: 0.97-7.8 and OR = 7.37, CI: 2.4-22.5, respectively). This is the first report of 8 Ae. aegypti AaNaV alleles, and it indicates the development of resistance in Ae. aegypti in response to pyrethroid insecticide-based selective pressure. These findings strongly suggest the need for an appropriate integrated use of insecticides in the region. The 989P, 1016G and 1534C polymorphisms in the AaNaV gene are potentially valuable molecular markers for pyrethroid insecticide resistance monitoring.
Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ...ligand recognition and subcellular recognition. It is estimated that >50% of the entire human proteome is glycosylated. However, it is still a significant challenge to identify glycosylation sites, which requires expensive/laborious experimental research. Thus, bioinformatics approaches that can predict the glycan occupancy at specific sequons in protein sequences would be useful for understanding and utilizing this important PTM.
In this study, we present a novel bioinformatics tool called GlycoMine, which is a comprehensive tool for the systematic in silico identification of C-linked, N-linked, and O-linked glycosylation sites in the human proteome. GlycoMine was developed using the random forest algorithm and evaluated based on a well-prepared up-to-date benchmark dataset that encompasses all three types of glycosylation sites, which was curated from multiple public resources. Heterogeneous sequences and functional features were derived from various sources, and subjected to further two-step feature selection to characterize a condensed subset of optimal features that contributed most to the type-specific prediction of glycosylation sites. Five-fold cross-validation and independent tests show that this approach significantly improved the prediction performance compared with four existing prediction tools: NetNGlyc, NetOGlyc, EnsembleGly and GPP. We demonstrated that this tool could identify candidate glycosylation sites in case study proteins and applied it to identify many high-confidence glycosylation target proteins by screening the entire human proteome.
The webserver, Java Applet, user instructions, datasets, and predicted glycosylation sites in the human proteome are freely available at http://www.structbioinfor.org/Lab/GlycoMine/.
Jiangning.Song@monash.edu or James.Whisstock@monash.edu or zhangyang@nwsuaf.edu.cn
Supplementary data are available at Bioinformatics online.
Featherweight Java is one of the most popular calculi which specify object-oriented programming features. It has been used as the basis for investigating novel language functionalities, as well as to ...specify and understand the formal properties of existing features for languages in this paradigm. However, when considering mechanized formalization, it is hard to find an implementation for languages with complex structures and binding mechanisms as Featherweight Java. In this paper we formalize Featherweight Java, implementing the static and dynamic semantics in Agda, and proving the main safety properties for this calculus.
The major climatic oscillations during the Quaternary Period significantly influenced the evolution and distribution of ancient and modern coastal systems. Here we investigate the morphology and ...sedimentary infilling of submerged Late Quaternary incised valleys along the northern coast of Java Island (Indonesia) using high-resolution geophysical, sedimentological and geochronological data. Our results indicate that the spatial development and morphology of the incised valleys are predominantly controlled by Quaternary glacial–interglacial eustatic fluctuations, within a marked subsiding setting. The valleys were incised during prominent Quaternary lowstands and most of the valley fill was emplaced during the last postglacial sea level rise. The valley fill forms a transgressive succession, consisting mainly of fluvial deposits at the base (possibly amalgamated from older sequences) overlain by shallow marine sediments and capped by hemipelagic deposits. The valley-fill architecture is strongly dependent on the valley morphology (depth of incision, width of the valleys, and extent of the intertidal zone). The shallow marine deposits contained within the narrow and linear valleys are mostly aggrading muds. The vertical incision and valley formation was chiefly controlled by the extent of glacial sea-level fluctuations. The studied sections represent the continental-offshore extension of a paleodeltaic system. The implication of our work is that even in predominantly enclosed shallow marine systems that are located distal to the shelf break, the response of the sedimentary system and ensuing stratigraphic configuration can be effectively impacted by the rapid and abrupt Quaternary global climatic transition and eustatic sea-level fluctuations.
•Java Quaternary incised valley-fill consists of fluvial deposits at the base overlain by estuarine sediments and capped by hemipelagic deposits.•The studied sections represent continental-offshore extension of the paleodeltaic system.•Late Quaternary climatic and eustatic changes impacted sedimentary framework of enclosed shallow marine systems located distal to shelf break.
Interest in automatic crowd behaviour analysis has grown considerably in the last few years. Crowd behaviour analysis has become an integral part all over the world for ensuring peaceful event ...organizations and minimum casualties in the places of public and religious interests. Traditionally, the area of crowd analysis was computed using handcrafted features. However, the real-world images and videos consist of nonlinearity that must be used efficiently for gaining accuracies in the results. As in many other computer vision areas, deep learning-based methods have taken giant strides for obtaining state-of-the-art performance in crowd behaviour analysis. This paper presents a comprehensive survey of current convolution neural network (CNN)-based methods for crowd behaviour analysis. We have also surveyed popular software tools for CNN in the recent years. This survey presents detailed attributes of CNN with special emphasis on optimization methods that have been utilized in CNN-based methods. It also reviews fundamental and innovative methodologies, both conventional and latest methods of CNN, reported in the last few years. We introduce a taxonomy that summarizes important aspects of the CNN for approaching crowd behaviour analysis. Details of the proposed architectures, crowd analysis needs and their respective datasets are reviewed. In addition, we summarize and discuss the main works proposed so far with particular interest on CNNs on how they treat the temporal dimension of data, their highlighting features and opportunities and challenges for future research. To the best of our knowledge, this is a unique survey for crowd behaviour analysis using the CNN. We hope that this survey would become a reference in this ever-evolving field of research.
Animal welfare is life quality aspect of animal that relates to physical and psychological condition, as well as environment where the animals live. Statistically, populations of the dairy cows in ...East Java in 2017 were 273.881. Objective of the research was to study implementation of animal welfare on dairy cows in East Java. Survey was conducted from May to June 2020. Instruments used in this research were standard Office International des Epizooties (OIE) on Terrestrial Health Code 7.11 that comprised of 8 aspects: behavior, morbidity, mortality and culling, the change of weight; body condition; and dairy production, reproductive efficiency, physical appearance, response of handling, and complication post general procedure. Result for the application of animal welfare using standard Office International des Epizooties on Dairy Cow in East Java was categorized adequate/sufficient by percentage 70.73%. Among 29 indicators of measurement, 1 indicator belongs to the least category. The category showed that an area for exercise with average score was 1.38 (27.57%).
Rafflesia zollingeriana Koord. was one of Rafflesia that distributed in Java. Although it has been stated as a different species, R. zollingeriana is sometimes still regarded as a synonym of R. ...patma. In addition, there are several contradictions in description of R. zollingeriana. Therefore, further investigation is needed. This study attempts presents a full the description of the R. zollingeriana female flower. In this study, a full description of female flower of R. zollingeriana and pictures of important characters such as ramenta, annulus, perigone lobes, disc, processes, bractea are presented. This study is also compared the morphology of R. zollingeriana and R. patma, to confirm their differences in size, opening of diaphragm, blotches and warts pattern on perigone lobes and diaphragm, annulus, and ramenta.
PDF
