Level-k Phylogenetic Network can be Constructed from a Dense Triplet Set in Polynomial Time

Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks of levels $k=0$ or 1 or 2, these questions were answered with effective polynomial algorithms. For higher levels $k$, partial answers were recently obtained with an $O(|\mathcal{T}|^{k+1})$ time algorithm for simple networks. In this paper we give a complete answer to the general case. The main idea is to use a special property of SN-sets in a level-k network. As a consequence, we can also find the level-k network with the minimum number of reticulations in polynomial time

On the Effectiveness of Adversarial Samples against Ensemble Learning-based Windows PE Malware Detectors

Recently, there has been a growing focus and interest in applying machine learning (ML) to the field of cybersecurity, particularly in malware detection and prevention. Several research works on malware analysis have been proposed, offering promising results for both academic and practical applications. In these works, the use of Generative Adversarial Networks (GANs) or Reinforcement Learning (RL) can aid malware creators in crafting metamorphic malware that evades antivirus software. In this study, we propose a mutation system to counteract ensemble learning-based detectors by combining GANs and an RL model, overcoming the limitations of the MalGAN model. Our proposed FeaGAN model is built based on MalGAN by incorporating an RL model called the Deep Q-network anti-malware Engines Attacking Framework (DQEAF). The RL model addresses three key challenges in performing adversarial attacks on Windows Portable Executable malware, including format preservation, executability preservation, and maliciousness preservation. In the FeaGAN model, ensemble learning is utilized to enhance the malware detector's evasion ability, with the generated adversarial patterns. The experimental results demonstrate that 100\% of the selected mutant samples preserve the format of executable files, while certain successes in both executability preservation and maliciousness preservation are achieved, reaching a stable success rate

Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes

River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding

The Distribution of Microplastics in Beach Sand in Tien Giang Province and Vung Tau City, Vietnam

Microplastics threaten the ecosystem because of undesirable properties such as non-biodegradability, easy-to-absorb persistant organic compounds, etc. They are found worldwide in marine, fresh water and beach sand environments. In this study, microplastics in beach sand samples from two sites in Tien Giang province and two sites in Vung Tau city were investigated. The results showed that the microplastics amount was 0 to 295 pieces/kg dry sand and they mainly distributed near estuarine areas. Microplastics were more prevalent at bathing sites than non-bathing sites. In Tien Giang fragments were the most dominant among the three types of shapes (fragments, fibers, granules) at 60.2%. In Vung Tau granules were most prevalent at 71.7%. The composition of the plastics was confirmed by Fourier-transform infrared spectroscopy. It was revealed that PE, PP and PS were the main types of plastics found in the sampling sites.

Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

Acknowledgements: This work was supported by the Biotechnology and Biological Sciences Research Council grant BBS/E/D/10002070 and the Frimedbio program of the Research Council of Norway (grant number 241016). MKG received studentship funding from a University of Aberdeen Elphinstone scholarship with additional support from the Government of Karnataka. We thank Dr Sebastian Beggel, Dr Bernhard C. Stoeckle, Jens-Eike Täuber and Ms Haiyu Ding at the Aquatic Systems Biology Unit, Technical University of Munich for their support in sampling huchen. We thank Dr Torfinn Nome for supporting bioinformatic analyses. We thank Madhusudhan Gundappa (Twitter: @fish_lines) for providing species illustrations in Figure 1. We also thanks Dr Gareth Gillard (Norwegian University of Life Sciences) for support with the RNA-Seq data. The Earlham Institute performed library preparation and sequencing used in the huchen genome assembly.Peer reviewedPublisher PD

Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites

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CORROSION PROTECTION OF CARBON STEEL USING ZIRCONIUM OXIDE/SILANE PRETREATMENT AND POWDER COATING

Surface pretreatment plays important role in improvement of corrosion resistance and adhesion of organic coatings. A new generation of metal pretreatments based on nanosize zirconium oxide or ogranosilane film has been investigated recently as an alternative method to phosphatation. In this paper, ZrO2/silane composite film on carbon steel was prepared and characterised by field emission scanning electron microscopy, energy dispersive X-ray spectrum and electrochemical measurements. The effect of ZrO2/silane surface treatment on the protection properties of powder coating was studied by salt spray test and adhesion measurement. The results obtained showed that ZrO2 was rapidly precipitated on the steel surface after first 1 minute immersion and ZrO2/silane film formed after 4 minutes immersion give best protective properties. Powder coating on carbon steel with ZrO2/silane pretreatement has equivalent protection performance like powder coating with  phosphate pretreatment

Fast dating using least-squares criteria and algorithms

International audiencePhylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g., human immunodeficiency virus (HIV)). Dating ancestral events is one of the first, essential goals with such data. However, current sophisticated probabilistic approaches struggle to handle data sets of this size. Here, we present very fast dating algorithms, based on a Gaussian model closely related to the Langley–Fitch molecular-clock model. We show that this model is robust to uncorrelated violations of the molecular clock. Our algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g., midpoint). Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra. We distinguish between an unconstrained setting and the case where the temporal precedence constraint (i.e., an ancestral node must be older that its daughter nodes) is accounted for. With rooted trees, the former is solved using linear algebra in linear computing time (i.e., proportional to the number of taxa), while the resolution of the latter, constrained setting, is based on an active-set method that runs in nearly linear time. With unrooted trees the computing time becomes (nearly) quadratic (i.e., proportional to the square of the number of taxa). In all cases, very large input trees (>10,000 taxa) can easily be processed and transformed into time-scaled trees. We compare these algorithms to standard methods (root-to-tip, r8s version of Langley–Fitch method, and BEAST). Using simulated data, we show that their estimation accuracy is similar to that of the most sophisticated methods, while their computing time is much faster. We apply these algorithms on a large data set comprising 1194 strains of Influenza virus from the pdm09 H1N1 Human pandemic. Again the results show that these algorithms provide a very fast alternative with results similar to those of other computer programs. These algorithms are implemented in the LSD software (least-squares dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results. An Online Appendix, providing additional algorithm descriptions, tables, and figures can be found in the Supplementary Material available on Dryad at http://dx.doi.org/10.5061/dryad.968t3

Characterization of wooden breast myopathy: a focus on syndecans and ECM remodeling

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