Singularities of bi-Hamiltonian systems

We study the relationship between singularities of bi-Hamiltonian systems and algebraic properties of compatible Poisson brackets. As the main tool, we introduce the notion of linearization of a Poisson pencil. From the algebraic viewpoint, a linearized Poisson pencil can be understood as a Lie algebra with a fixed 2-cocycle. In terms of such linearizations, we give a criterion for non-degeneracy of singular points of bi-Hamiltonian systems and describe their types

Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Critical Assessment of Metagenome Interpretation:A benchmark of metagenomics software

International audienceIn metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets andevaluation metrics complicates proper performance assessment. The CriticalAssessment of Metagenome Interpretation (CAMI) challenge has engaged the globaldeveloper community to benchmark their programs on datasets of unprecedentedcomplexity and realism. Benchmark metagenomes were generated from newlysequenced ~700 microorganisms and ~600 novel viruses and plasmids, includinggenomes with varying degrees of relatedness to each other and to publicly availableones and representing common experimental setups. Across all datasets, assemblyand genome binning programs performed well for species represented by individualgenomes, while performance was substantially affected by the presence of relatedstrains. Taxonomic profiling and binning programs were proficient at high taxonomicranks, with a notable performance decrease below the family level. Parametersettings substantially impacted performances, underscoring the importance ofprogram reproducibility. While highlighting current challenges in computationalmetagenomics, the CAMI results provide a roadmap for software selection to answerspecific research questions

A rapid method for evaluation of partial potato resistance to late blight and of aggressiveness of Phytophthora infestans isolates originating from different regions

The procedure of evaluation is based on mathematical simulation model of the late blight (LB) development in combination with laboratory testing of detached leaflets artificially inoculated with Phytophthora infestans. An incubation period, amount and sizes of lesions and sporulation capacity are estimated. Each couple “tested Phytophthora isolate and tested potato cultivar” is compared with a standard couple “Phytophthora isolate N161 and standard cultivar”. A simulator on the base of these data calculates area under the curve for LB development and yield loss due to LB for a situation when a yield loss of a standard cultivar infected with a standard isolate is equal 35%. Comparison of a new rapid laboratory method and field methods showed satisfactory correlation. Resistance to late blight was evaluated for 47 potato cultivars with the new method. It was also shown that some variations in foliar aggressiveness existed among P. infestans populations from different regions. Supported by ISTC grant #1640

Imaging local dissipation and magnetic field in YBCO films with artificial defects

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Two cases synchronous atypical parathyroid adenomas and papillary thyroid carcinoma

Most clinicians are well aware of the coexistence of medullary thyroid cancer and hyperparathyroidism in hereditary and sporadic multiple endocrine neoplasia syndromes. Тhe reported incidence of nonmedullary thyroid carcinoma in patients with primary hyperparathyroidism (pHPT) is only approximately 3%. Papillary thyroid carcinomas (PTC) is a malignant epithelial tumour. PTC represent up to 87% of all thyroid carcinomas. Atypical parathyroid adenoma (APA) are a subset of parathyroid neoplasms that exhibit some of the features of parathyroid carcinoma but lack unequivocal invasive growth. APA represents about 0.54% of cases of PHPT. As a group, they may be considered tumors of uncertain malignant potential. The clinical importance, and long-term outcomes as well as appropriate operative management and surveillance are not well defined for APA probably due to the overall low prevalence as well as the lack of a standard definition of APA. We report two cases of a 63-year-old woman and 57-year-old man with a synchronous atypical parathyroid adenoma and papillary thyroid carcinoma. One of this patients had a classic symptoms of pHPT, including severe metabolic bone disease and renal disease, but another didnt have. The mean preoperative calcium was 3,48 and 4,1 (range 2.122.6) mmol/l and a mean parathyroid hormone (PTH) of 1300 and 1533 (range 1565) pg/ml, respectively. Thyroid ultrasound didnt show a nodule with features of the thyroid carcinoma in both cases. The thyroid cancer was suspected after intraoperative revision. The patients underwent a total thyroidectomy and surgical excision of the parathyroid adenoma. Surgical pathology showed papillary microcarcinoma in both cases (in the first unilateral, in the second bilateral) and APA. Awareness of this condition will enable clinicians to evaluate for possible thyroid pathology in patients with primary hyperparathyroidism. Both of these endocrine conditions could then be managed with a single surgery involving concomitant resection of the thyroid and parathyroid glands