St Petersburg University

While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.

Abstract When surrounded by a transparent emission region, black holes are expected to reveal a dark shadow caused by gravitational light bending and photon capture at the event horizon. To image and study this phenomenon, we have assembled the Event Horizon Telescope, a global very long baseline interferometry array observing at a wavelength of 1.3 mm. This allows us to reconstruct event-horizon-scale images of the supermassive black hole candidate in the center of the giant elliptical galaxy M87. We have resolved the central compact radio source as an asymmetric bright emission ring with a diameter of 42 ± 3 μ as, which is circular and encompasses a central depression in brightness with a flux ratio ≳10:1. The emission ring is recovered using different calibration and imaging schemes, with its diameter and width remaining stable over four different observations carried out in different days. Overall, the observed image is consistent with expectations for the shadow of a Kerr black hole as predicted by general relativity. The asymmetry in brightness in the ring can be explained in terms of relativistic beaming of the emission from a plasma rotating close to the speed of light around a black hole. We compare our images to an extensive library of ray-traced general-relativistic magnetohydrodynamic simulations of black holes and derive a central mass of M = (6.5 ± 0.7) × 10 9 M ⊙ . Our radio-wave observations thus provide powerful evidence for the presence of supermassive black holes in centers of galaxies and as the central engines of active galactic nuclei. They also present a new tool to explore gravity in its most extreme limit and on a mass scale that was so far not accessible.

Abstract The International Mineralogical Association's approved amphibole nomenclature has been revised in order to simplify it, make it more consistent with divisions generally at 50%, define prefixes and modifiers more precisely and include new amphibole species discovered and named since 1978, when the previous scheme was approved. The same reference axes form the basis of the new scheme and most names are little changed but compound species names like tremolitic hornblende (now magnesiohornblende) are abolished and also crossite (now glaucophane or ferroglaucophane or magnesioriebeckite or riebeckite), tirodite (now manganocummingtonite) and dannemorite (now manganogrunerite). The 50% rule has been broken only to retain tremolite and actinolite as in the 1978 scheme so the sodic calcic amphibole range has therefore been expanded. Alkali amphiboles are now sodic amphiboles. The use of hyphens is defined. New amphibole names approved since 1978 include nyböite, leakeite, kornite, ungarettiite, sadanagaite and cannilloite. All abandoned names are listed. The formulae and source of the amphibole end member names are listed and procedures outlined to calculate Fe 3+ and Fe 2+ when not determined by analysis.

Anew model of consumer behavior is developed using a hybrid of cognitive psychology and microeconomics. The development of the model starts with the mental coding of combinations of gains and losses using the prospect theory value function. Then the evaluation of purchases is modeled using the new concept of “transaction utility.” The household budgeting process is also incorporated to complete the characterization of mental accounting. Several implications to marketing, particularly in the area of pricing, are developed. This article was originally published in Marketing Science, Volume 4, Issue 3, pages 199–214, in 1985.

SPAdes-St. Petersburg genome Assembler-was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Assembling isolate bacterial datasets Basic Protocol 2: Assembling metagenomic datasets Basic Protocol 3: Assembling sets of putative plasmids Basic Protocol 4: Assembling transcriptomes Basic Protocol 5: Assembling putative biosynthetic gene clusters Support Protocol 1: Installing SPAdes Support Protocol 2: Providing input via command line Support Protocol 3: Providing input data via YAML format Support Protocol 4: Restarting previous run Support Protocol 5: Determining strand-specificity of RNA-seq data.

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Understanding and predicting new venture initiation requires research using theory-driven models that adequately reflect the complex perception-based processes underlying intentional, planned behaviours such as new venture initiation. We discuss exactly such a model, widely used in social psychology, and demonstrate its applicability to the entrepreneurship domain. Ajzen's intentions-centred ‘theory of planned behaviour’ is parsimonious, well grounded in theory, and robustly predicts a wide variety of planned behaviours. Intentions are the single best predictor of such behaviour, both conceptually and empirically. Intentions formation depends; on attitudes toward the target behaviour which, in turn, reflect beliefs and perceptions. Intentions-based models of entrepreneurial activity are compatible with existing research results and open new approaches to studying venture initiation. Intentions models allow us to better understand the impact of various antecedents of organizational emergence; identifying not only what influences emergence, but also how.

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

Abstract Case and field research studies continue to be rarely published in operations management journals, in spite of increased interest in reporting such types of studies and results. This paper documents the advantages and rigor of case/field research and argues that these methods are preferred to the more traditional rationalist methods of optimization, simulation, and statistical modeling for building new operations management theories. In the process of describing the constructs of inference and generalizability with reference to case research, we find the existing definitions inadequate and thus extend and refine them to better discriminate between alternate research methodologies. We also elaborate on methods for increasing the generalizability of both rationalist and case/field research studies. A major conclusion is that these alternate research methods are not mutually exclusive and, if combined, can offer greater potential for enhancing new theories than either method alone.

Abstract We present measurements of the properties of the central radio source in M87 using Event Horizon Telescope data obtained during the 2017 campaign. We develop and fit geometric crescent models (asymmetric rings with interior brightness depressions) using two independent sampling algorithms that consider distinct representations of the visibility data. We show that the crescent family of models is statistically preferred over other comparably complex geometric models that we explore. We calibrate the geometric model parameters using general relativistic magnetohydrodynamic (GRMHD) models of the emission region and estimate physical properties of the source. We further fit images generated from GRMHD models directly to the data. We compare the derived emission region and black hole parameters from these analyses with those recovered from reconstructed images. There is a remarkable consistency among all methods and data sets. We find that >50% of the total flux at arcsecond scales comes from near the horizon, and that the emission is dramatically suppressed interior to this region by a factor >10, providing direct evidence of the predicted shadow of a black hole. Across all methods, we measure a crescent diameter of 42 ± 3 μ as and constrain its fractional width to be <0.5. Associating the crescent feature with the emission surrounding the black hole shadow, we infer an angular gravitational radius of GM / Dc 2 = 3.8 ± 0.4 μ as. Folding in a distance measurement of gives a black hole mass of . This measurement from lensed emission near the event horizon is consistent with the presence of a central Kerr black hole, as predicted by the general theory of relativity.

Motivation: The emergence of high-throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long-read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian-size genomes. Results: In this manuscript, we demonstrate performance of the state-of-the-art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST-LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference. Availability and implementation: http://cab.spbu.ru/software/quast-lg. Supplementary information: Supplementary data are available at Bioinformatics online.

Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.

Purpose To provide important empirical evidence to support the role of knowledge management within firms. Design/methodology/approach Data were collected using a mail survey sent to CEOs representing firms with 50 or more employees from a cross‐section of industries. A total of 1,743 surveys were mailed out and 443 were returned and usable (27.8 percent response rate). The sample was checked for response and non‐response bias. Hypotheses were tested using structural equation modelling. Findings This paper presents knowledge management as a coordinating mechanism. Empirical evidence supports the view that a firm with a knowledge management capability will use resources more efficiently and so will be more innovative and perform better. Research limitations/implications The sample slightly over‐represented larger firms. Data were also collected in New Zealand. As with most studies, it is important to replicate this study in different contexts. Practical implications Knowledge management is embraced in many organizations and requires a business case to justify expenditure on programs to implement knowledge management behaviours and practices or hardware and software solutions. This paper provides support for the importance of knowledge management to enhance innovation and performance. Originality/value This paper is one of the first to find empirical support for the role of knowledge management within firms. Further, the positioning of knowledge management as a coordinating mechanism is also an important contribution to our thinking on this topic.

Abstract We present the first Event Horizon Telescope (EHT) images of M87, using observations from April 2017 at 1.3 mm wavelength. These images show a prominent ring with a diameter of ∼40 μ as, consistent with the size and shape of the lensed photon orbit encircling the “shadow” of a supermassive black hole. The ring is persistent across four observing nights and shows enhanced brightness in the south. To assess the reliability of these results, we implemented a two-stage imaging procedure. In the first stage, four teams, each blind to the others’ work, produced images of M87 using both an established method (CLEAN) and a newer technique (regularized maximum likelihood). This stage allowed us to avoid shared human bias and to assess common features among independent reconstructions. In the second stage, we reconstructed synthetic data from a large survey of imaging parameters and then compared the results with the corresponding ground truth images. This stage allowed us to select parameters objectively to use when reconstructing images of M87. Across all tests in both stages, the ring diameter and asymmetry remained stable, insensitive to the choice of imaging technique. We describe the EHT imaging procedures, the primary image features in M87, and the dependence of these features on imaging assumptions.

The paper examines the acquisition, depreciation and transfer of knowledge acquired through learning by doing in service organizations. The analysis is based on weekly data collected over a one and a half year period from 36 pizza stores located in Southwestern Pennsylvania. The 36 stores, which are franchised from the same corporation, are owned by 10 different franchisees. We find evidence of learning in these service organizations: as the organizations gain experience in production, the unit cost of production declines significantly. Knowledge acquired through learning by doing is found to depreciate rapidly in these organizations. Knowledge acquired through learning by doing is found to depreciate rapidly in these organizations. Knowledge is found to transfer across stores owned by the same franchisee but not across stores owned by different franchisees. Theoretical and practical implications of the work are discussed.

Purpose To introduce and provide an overview of the various issues related to environmental (green) supply chain management performance measurement. Design/methodology/approach The work relies on experiences, case studies and other literature related to performance measurement in environmental supply chains. It seeks to integrate works in supply chain management, environmental management, and performance management into one framework. A systems framework forms the discussion outline with a focus on controls/pressures, inputs, tools, and outputs as major categories for evaluation and review. Findings Provides an integrative framework for study, design and evaluation of green supply chain management performance tools. The findings also identify a number of issues that need to still be addressed. Research limitations/implications We have only one design of the issues in which numerous categorizations could be provided. There is limited research in this area and new and current models/developments can provide additional insight. Implications of the work is that these gaps exist and that significantly more work needs to be completed in this field. Practical implications A very useful source of information for practitioners that seek to implement these systems within and between organizations. Also, the paper provides numerous areas which researchers could complete additional research and develop research agendas. Originality/value This paper provides some of the very first insights into development of a green supply chain management performance measurement system. Typically performance measurement systems are internally and business focused, we expand on these issues by considering inter-organizational and environmental issues within a business context.

Graph-theoretic ideas are used to analyze cooperation structures in games. Allocation rules, selecting a payoff for every possible cooperation structure, are studied for games in characteristic function form. Fair allocation rules are defined, and these are proven to be unique, closely related to the Shapley value, and stable for a wide class of games.