Autonomous Partners Research Articles

Evolution of Einkorn wheat centromeres is driven by the mutualistic interplay of two LTR retrotransposons

BackgroundCentromere function is highly conserved across eukaryotes, but the underlying centromeric DNA sequences vary dramatically between species. Centromeres often contain a high proportion of repetitive DNA, such as tandem repeats and/or transposable elements (TEs). Einkorn wheat centromeres lack tandem repeat arrays and are instead composed mostly of the two long terminal repeat (LTR) retrotransposon families RLG_Cereba and RLG_Quinta which specifically insert in centromeres. However, it is poorly understood how these two TE families relate to each other and if and how they contribute to centromere function and evolution.ResultsBased on conservation of diagnostic motifs (LTRs, integrase and primer binding site and polypurine-tract), we propose that RLG_Cereba and RLG_Quinta are a pair of autonomous and non-autonomous partners, in which the autonomous RLG_Cereba contributes all the proteins required for transposition, while the non-autonomous RLG_Quinta contributes GAG protein. Phylogenetic analysis of predicted GAG proteins showed that the RLG_Cereba lineage was present for at least 100 million years in monocotyledon plants. In contrast, RLG_Quinta evolved from RLG_Cereba between 28 and 35 million years ago in the common ancestor of oat and wheat. Interestingly, the integrase of RLG_Cereba is fused to a so-called CR-domain, which is hypothesized to guide the integrase to the functional centromere. Indeed, ChIP-seq data and TE population analysis show only the youngest subfamilies of RLG_Cereba and RLG_Quinta are found in the active centromeres. Importantly, the LTRs of RLG_Quinta and RLG_Cereba are strongly associated with the presence of the centromere-specific CENH3 histone variant. We hypothesize that the LTRs of RLG_Cereba and RLG_Quinta contribute to wheat centromere integrity by phasing and/or placing CENH3 nucleosomes, thus favoring their persistence in the competitive centromere-niche.ConclusionOur data show that RLG_Cereba cross-mobilizes the non-autonomous RLG_Quinta retrotransposons. New copies of both families are specifically integrated into functional centromeres presumably through direct binding of the integrase CR domain to CENH3 histone variants. The LTRs of newly inserted RLG_Cereba and RLG_Quinta elements, in turn, recruit and/or phase new CENH3 deposition. This mutualistic interplay between the two TE families and the plant host dynamically maintains wheat centromeres.

Autonomous partners: asymmetry and masculinity in Amazonian river trade

AbstractTrade on the Iriri River, in the eastern Brazilian Amazonia, is structured around a credit‐barter system between clients and bosses known as aviamento in Portuguese. Nowadays, bosses are river traders born in the riversides who offer goods on credit to riverside dwellers, who later pay these debts with fish and products they collect from the forest. While the system, found in the Amazon basin since colonial times, is perhaps most known for fostering debt‐peonage during the Rubber Boom (1870‐1912), it can also create relations of mutual dependency that promote the autonomy of trade partners within an asymmetrical exchange. When that is the case, this trade is central to how clients and bosses define themselves as hard‐working, reliable, and transparent, personifying qualities they deem essential to masculine honour. In such partnerships (and more dramatically when they break down), the asymmetry of the relation can be challenged through a notion of male equivalence in which men must defend their honour and adhere to a code of conduct that ultimately excludes women and children from trade.

“Do what you say?” The combined effects of framed social intent and autonomous agent behavior on the trust process

Autonomy is becoming increasingly integrated into everyday life. For humans to fully realize the benefits of working alongside autonomy, appropriate trust toward autonomous partners will be necessary. However, research is needed to determine how humans respond to autonomous partners when they behave (un)expectedly. Thus, a series of studies were designed to investigate the effect of framed social intent of an autonomous teammate (Study 1), their unstated behavioral manifestations (Study 2), and the interaction of these variables (Study 3) on participants' trustworthiness perceptions, reliance intentions, and trust behaviors. Participants were to imagine themselves partnering with an autonomous teammate in a team-based, gamified collaboration. Key innovations in this task involved role-based vulnerability (necessitating clear expectations regarding one's stated social intent) and teammate interdependence. Across studies, framed social intent and observable behaviors of an autonomous agent were manipulated. Results demonstrated robust effects of said manipulations, with interactions demonstrating the nuance of (un)met expectations on criteria. We conclude by offering future research and design suggestions aimed at enhancing human-autonomy interactions.

Microservice compositions based on the choreography of BPMN fragments: facing evolution issues

Business Processes (BPs) are commonly used by organizations to describe their goals. However, the existent decentralization found in many organizations forces them to build such BPs by coordinating distributed and fragmented BPs. Within this context, microservices arise as a very interesting and convenient way to address the implementation of such processes due to their low coupling characteristic. In this case, the coordination of such fragmented BPs is usually achieved by means of event-based choreographies. One of the main challenges to be faced by choreographies is their evolution due to the complexity that introduces the need of integrating changes among autonomous and independent partners. We face the challenge of evolving a microservice composition that is globally defined in a BPMN model but executed through a choreography of BPMN fragments. We introduce a protocol to manage the propagation of a change done by one microservice to be integrated into both the BPMN fragments of the rest of the microservices and the global BPMN model. This protocol also supports the negotiation among participants and the automatic suggestion of model adaptations to maintain the functional integrity of the composition. These suggestions are supported by a catalogue of adaptation rules that precisely characterize every possible change and propose actions to be considered by the affected microservices. All the evolution process is done at the modelling level, without managing hard-coded implementations. We have developed specific tools to facilitate the practical adoption of this protocol, and we have validated our work in an experiment with users. We can conclude that the proposed approach is effective to evolve microservice compositions implemented as event-based choreography of BPMN fragments from the local perspective of one partner.

Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons.

Wheat has one of the largest and most repetitive genomes among major crop plants, containing over 85% transposable elements (TEs). TEs populate genomes much in the way that individuals populate ecosystems, diversifying into different lineages, sub-families and sub-populations. The recent availability of high-quality, chromosome-scale genome sequences from ten wheat lines enables a detailed analysis how TEs evolved in allohexaploid wheat, its diploids progenitors, and in various chromosomal haplotype segments. LTR retrotransposon families evolved into distinct sub-populations and sub-families that were active in waves lasting several hundred thousand years. Furthermore, It is shown that different retrotransposon sub-families were active in the three wheat sub-genomes, making them useful markers to study and date polyploidization events and chromosomal rearrangements. Additionally, haplotype-specific TE sub-families are used to characterize chromosomal introgressions in different wheat lines. Additionally, populations of non-autonomous TEs co-evolved over millions of years with their autonomous partners, leading to complex systems with multiple types of autonomous, semi-autonomous and non-autonomous elements. Phylogenetic and TE population analyses revealed the relationships between non-autonomous elements and their mobilizing autonomous partners. TE population analysis provided insights into genome evolution of allohexaploid wheat and genetic diversity of species, and may have implication for future crop breeding.

Contagion: Government Fear of Religion during the COVID-19 Crisis

This paper examines emerging trends in the responses of governments and religious communities to the COVID-19 health crisis. It reviews the initial measures taken by the authorities, along with the early compliance of churches, observing that mutual collaboration represents the "finest hour" in recent church-state relations. However, as questions arose over the potency of the disease, perceived inconsistency of policies, and political acquiescence to racial protest movements, dynamics began to shift. A minority of religious communities appealed to the sovereignty of divine law in order to resist extended prohibitions on communal worship. This paper analyzes the implications of such resistance, urging that governments could better achieve their objectives by treating religious communities as essential, autonomous partners striving towards a shared goal.

LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

BackgroundNon-autonomous VNTR (Variable Number of Tandem Repeats) composite retrotransposons – SVA (SINE-R-VNTR-Alu) and LAVA (L1-Alu-VNTR-Alu) – are specific to hominoid primates. SVA expanded in great apes, LAVA in gibbon. Both SVA and LAVA have been shown to be mobilized by the autonomous LINE-1 (L1)-encoded protein machinery in a cell-based assay in trans. The efficiency of human SVA retrotransposition in vitro has, however, been considerably lower than would be expected based on recent pedigree-based in vivo estimates. The VNTR composite elements across hominoids – gibbon LAVA, orangutan SVA_A descendants and hominine SVA_D descendants – display characteristic structures of the 5′ Alu-like domain and the VNTR. Different partner L1 subfamilies are currently active in each of the lineages. The possibility that the lineage-specific types of VNTR composites evolved in response to evolutionary changes in their autonomous partners, particularly in the nucleic acid binding L1 ORF1-encoded protein, has not been addressed.ResultsHere I report the identification and functional characterization of a highly active human SVA element using an improved mneo retrotransposition reporter cassette. The modified cassette (mneoM) minimizes splicing between the VNTR of human SVAs and the neomycin phosphotransferase stop codon. SVA deletion analysis provides evidence that key elements determining its mobilization efficiency reside in the VNTR and 5′ hexameric repeats. Simultaneous removal of the 5′ hexameric repeats and part of the VNTR has an additive negative effect on mobilization rates. Taking advantage of the modified reporter cassette that facilitates robust cross-species comparison of SVA/LAVA retrotransposition, I show that the ORF1-encoded proteins of the L1 subfamilies currently active in gibbon, orangutan and human do not display substrate preference for gibbon LAVA versus orangutan SVA versus human SVA. Finally, I demonstrate that an orangutan-derived ORF1p supports only limited retrotransposition of SVA/LAVA in trans, despite being fully functional in L1 mobilization in cis.ConclusionsOverall, the analysis confirms SVA as a highly active human retrotransposon and preferred substrate of the L1-encoded protein machinery. Based on the results obtained in human cells coevolution of L1 ORF1p and VNTR composites does not appear very likely. The changes in orangutan L1 ORF1p that markedly reduce its mobilization capacity in trans might explain the different SVA insertion rates in the orangutan and hominine lineages, respectively.

Особливості позиціонування зовнішньополітичних пріоритетів Європейського Союзу

У статті здійснено комплексне дослідження особливостей позиціонування зовнішньополітичних пріоритетів Європейського Союзу. Встановлено, що хоча модель стратегічного суверенітету офіційно не була визначена як підґрунтя для формування пулу зовнішньополітичних пріоритетів ЄС, об’єднання опирається на її базові принципи, що потребує опанування Європейським Союзом мислення геополітичної сили. Доведено, що коло зовнішньополітичних пріоритетів ЄЄ на 2019–224 рр. визначається «геополітичним» статусом Європейської Комісії, яка сфокусувала свою діяльність на розробці всеосяжної стратегії щодо Африки; підтвердженні європейських перспектив Західних Балкан; стратегічному партнерстві зі Сполученим Королівством; орієнтації на світове лідерство (геополітичну суб’єктність); збереження трансатлантичної безпекової платформи в умовах створення системи європейської оборони. Обґрунтовано, що для ЄС важливо зберігати і реформувати трансатлантичне партнерство як центр європейської безпеки і найважливіший компонент міжнародного порядку та водночас інвестувати в безпеку Європи, щоб стати більш автономним партнером в рамках НАТО і джерелом безпеки для сусідніх країн Європи. Досягнення такого балансу потребує від ЄС і його держав-членів зміцнити європейські центри НАТО, та конкурувати з ним в Косово та Африці. В умовах зростаючої невизначеності та перманентних геополітичних ризиків ЄС повинен слідувати стратегічному курсу дій, який має громадську підтримку, та забезпечити свою здатність діяти автономно, основою якої є консенсус між державами-членами об’єднання щодо формату зовнішньої політики та її пріоритетів.

Hagfish genome reveals parallel evolution of 7SL RNA-derived SINEs

BackgroundShort interspersed elements (SINEs) are ubiquitous components of eukaryotic genomes. SINEs are composite transposable elements that are mobilized by non-long terminal repeat (non-LTR) retrotransposons, also called long interspersed elements (LINEs). The 3′ part of SINEs usually originated from that of counterpart non-LTR retrotransposons. The 5′ part of SINEs mostly originated from small RNA genes. SINE1 is a group of SINEs whose 5′ part originated from 7SL RNA, and is represented by primate Alu and murine B1. Well-defined SINE1 has been found only from Euarchontoglires, a group of mammals, in contrast to the wide distribution of SINE2, which has a tRNA-derived sequence, from animals to plants to protists. Both Alu and B1 are mobilized by L1-type non-LTR retrotransposons, which are the only lineage of autonomous non-LTR retrotransposons active in these mammalian lineages.ResultsHere a new lineage of SINE1 is characterized from the seashore hagfish Eptatretus burgeri genome. This SINE1 family, designated SINE1-1_EBu, is young, and is transposed by RTE-type non-LTR retrotransposon, not L1-type. Comparison with other SINE families from hagfish indicated the birth of SINE1-1_EBu through chimera formation of a 7SL RNA-derived sequence and an older tRNA-derived SINE family. It reveals parallel evolution of SINE1 in two vertebrate lineages with different autonomous non-LTR retrotransposon partners. The comparison between two SINE1 lineages supports that the RNA secondary structure of the Alu domain of 7SL RNA is required for the efficient retrotransposition.ConclusionsThe hagfish SINE1 is the first evident SINE1 family found outside of Euarchontoglires. Independent evolution of SINE1 with similar RNA secondary structure originated in 7SL RNA indicates the functional importance of 7SL RNA-derived sequence in the proliferation of SINEs.

Team Structure and Team Building Improve Human–Machine Teaming With Autonomous Agents

Research suggests that humans and autonomous agents can be more effective when working together as a combined unit rather than as individual entities. However, most research has focused on autonomous agent design characteristics while ignoring the importance of social interactions and team dynamics. Two experiments examined how the perception of teamwork among human–human and human–autonomous agents and the application of team building interventions could enhance teamwork outcomes. Participants collaborated with either a human or an autonomous agent. In the first experiment, it was revealed that manipulating team structure by considering your human and autonomous partner as a teammate rather than a tool can increase affect and behavior, but does not benefit performance. In the second experiment, participants completed goal setting and role clarification (team building) with their teammate prior to task performance. Team building interventions led to significant improvements for all teamwork outcomes, including performance. Across both studies, participants communicated more substantially with human partners than they did with autonomous partners. Taken together, these findings suggest that social interactions between humans and autonomous teammates should be an important design consideration and that particular attention should be given to team building interventions to improve affect, behavior, and performance.

Characterization of a novel Helitron family in insect genomes: insights into classification, evolution and horizontal transfer

BackgroundHelitrons play an important role in shaping eukaryotic genomes due to their ability to transfer horizontally between distantly related species and capture gene fragments during the transposition. However, the mechanisms of horizontal transfer (HT) and the process of gene fragment capturing of Helitrons still remain to be further clarified.ResultsHere, we characterized a novel Helitron family discontinuously distributed in 27 out of 256 insect genomes. The most prominent characteristic of Hel1 family is its high sequence similarity among species of different insect orders. Related elements were also identified in two spiders, representing the first report of spider Helitrons. All these elements were classified into 2 families, 9 subfamilies and 35 exemplars based on our new classification criteria. Autonomous partners of Helitron were reconstructed in the genomes of three insects and one spider. Integration pattern analysis showed that majority of Hel1A elements in Papilio xuthus and Pieris rapae inserted into introns. Consistent with filler DNA model, stepwise sequence acquisition was observed in Sfru_Hel1Aa, Sfru_Hel1Ab and Sfru_Hel1Ac in Spodoptera frugiperda. Remarkably, the evidence that Prap_Hel1Aa in a Lepdidoptera insect, Pieris rapae, was derived from Cves_Hel1Aa in a parasitoid wasp, Cotesia vestalis, suggested the role of nonregular host-parasite interactions in HT of Helitrons.ConclusionsWe proposed a modified classification criteria of Helitrons based on the important role of the 5′-end of Helitrons in transposition, and provided evidence for stepwise sequence acquisition and recurrent HT of a novel Helitron family. Our findings of the nonregular host-parasite interactions may be more conducive to the HT of transposons.

Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

BackgroundTransposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2.5-Mb emphasizes the need for biologists to rethink the fundamental nature of the relationship between viruses and cellular life.ResultsHerein, we performed the first comprehensive analysis of miniature inverted-repeat transposable elements (MITEs) in the 5170 viral genomes for which sequences are currently available. Four hundred and fifty one copies of ten miniature inverted-repeat transposable elements (MITEs) were found and each MITE had reached relatively large copy numbers (some up to 90) in viruses. Eight MITEs belonging to two DNA superfamilies (hobo/Activator/Tam3 and Chapaev–Mirage–CACTA) were for the first time identified in viruses, further expanding the organismal range of these two superfamilies. TEs may play important roles in shaping the evolution of pandoravirus genomes, which were here found to be very rich in MITEs. We also show that putative autonomous partners of seven MITEs are present in the genomes of viral hosts, suggesting that viruses may borrow the transpositional machinery of their cellular hosts’ autonomous elements to spread MITEs and colonize their own genomes. The presence of seven similar MITEs in viral hosts, suggesting horizontal transfers (HTs) as the major mechanism for MITEs propagation.ConclusionsOur discovery highlights that TEs contribute to shape genome evolution of pandoraviruses. We concluded that as for cellular organisms, TEs are part of the pandoraviruses’ diverse mobilome.

“I Choose... YOU!” Membership preferences in human–robot teams

Although groups of robots are expected to interact with groups of humans in the near future, research related to teams of humans and robots is still scarce. This paper contributes to the study of human–robot teams by describing the development of two autonomous robotic partners and by investigating how humans choose robots to partner with in a multi-party game context. Our work concerns the successful development of two autonomous robots that are able to interact with a group of two humans in the execution of a task for social and entertainment purposes. The creation of these two characters was motivated by psychological research on learning goal theory, according to which we interpret and approach a given task differently depending on our learning goal. Thus, we developed two robotic characters implemented in two robots: Emys (a competitive robot, based on characteristics related to performance-orientation goals) and Glin (a relationship-driven robot, based on characteristics related to learning-orientation goals). In our study, a group of four (two humans and two autonomous robots) engaged in a card game for social and entertainment purposes. Our study yields several important conclusions regarding groups of humans and robots. (1) When a partner is chosen without previous partnering experience, people tend to prefer robots with relationship-driven characteristics as their partners compared with competitive robots. (2) After some partnering experience has been gained, the choice becomes less clear, and additional driving factors emerge as follows: (2a) participants with higher levels of competitiveness (personal characteristics) tend to prefer Emys, whereas those with lower levels prefer Glin, and (2b) the choice of which robot to partner with also depends on team performance, with the winning team being the preferred choice.

The rise of professional unions in Germany. Challenge and threat for established industrial relations?

AbstractThe author analyses the rise of professional unions, one of the most remarkable developments in German labour movement since the early 2000s. By means of strikes, they managed to get officially accepted as autonomous partners for collective bargaining. The author asks whether their emergence challenges or even threats the established systems of industrial relations.

SOCIAL ROBOT: DEFINING THE CONCEPT

Социальная робототехника является одним из актуальных междисциплинарных направлений. Разработка социальных робототехнических платформ требует совместных усилий специалистов различных областей, в том числе гуманитарной для решения социокультурных задач. Для эффективного междисциплинарного сотрудничества необходимо разработать единый терминологический аппарат, поскольку содержание термина «социальный робот» нуждается в теоретическом осмыслении и более четкой дефиниции. Цель. Представить обзор основных подходов к содержанию понятия «социальный робот», выявить определяющие характеристики социального робота в современном контексте социальной робототехники. Метод проведения работы. В работе применялись лексикографический метод и классификация. Результаты. В статье проанализированы различные подходы к определению понятия «социальный робот» и история становления термина. Предпринята попытка выявить специфические особенности социальных роботов. Основной характеристикой социального робота названа способность к построению взаимодействия с человеком с использованием сложившихся семиотических систем и учетом социального и ситуативного контекста. Социальный робот встраивается в сложившуюся классификацию типов взаимодействия с человеком в качестве автономного социального партнера. Область применения результатов. Полученные результаты составляют теоретическую базу междисциплинарного направления «социальная робототехника» и могут быть использованы для проведения фундаментальных и прикладных исследований в данной области и в учебных курсах по направлениям «Социология», «Робототехника», «Этика технологий», «Искусственный интеллект» и др.

A decision support system for the collaborative selection of strategies in enterprise networks

Collaborative networks (CN) consist of autonomous and heterogeneous partners, and each defines its own objectives and formulates its own strategies, which are selected and activated to achieve these objectives. The heterogeneity that characterises network partners could lead to contradictions appearing among the strategies formulated in each CN enterprise. Consequently, the strategies formulated in one enterprise could negatively influence the achievement of the objectives defined in other enterprises of the same network. These contradictions lead to strategies misalignments, which worsens the network performance. In order to deal with these misalignments, a DSS is proposed to support the process of selecting the strategies among all those formulated, with the aim of achieving higher alignment levels. The proposed DSS considers the impacts that each strategy formulated in each enterprise has on the performance of the objectives defined by each network partner. This allows enterprises to select a set of aligned strategies. The selection of proper strategies to be activated in each enterprise strongly influences the CN's performance level, and higher levels of network adaptability, agility and competitiveness are achieved. The proposed DSS is validated under real conditions in a food industry network. The DSS is evaluated by emulating real collaborative conditions and is compared with the equivalent non-collaborative decision making perspective used for selecting strategies. The results demonstrate that the collaborative approach outperforms the performance level of the non-collaborative one and is more effective for handling the robustness and the long-term operation of the CN.

Dealing with change in process choreographies: Design and implementation of propagation algorithms

Enabling process changes constitutes a major challenge for any process-aware information system. This not only holds for processes running within a single enterprise, but also for collaborative scenarios involving distributed and autonomous partners. In particular, if one partner adapts its private process, the change might affect the processes of the other partners as well. Accordingly, it might have to be propagated to concerned partners in a transitive way. A fundamental challenge in this context is to find ways of propagating the changes in a decentralized manner. Existing approaches are limited with respect to the change operations considered as well as their dependency on a particular process specification language. This paper presents a generic change propagation approach that is based on the Refined Process Structure Tree, i.e., the approach is independent of a specific process specification language. Further, it considers a comprehensive set of change patterns. For all these change patterns, it is shown that the provided change propagation algorithms preserve consistency and compatibility of the process choreography. Finally, a proof-of-concept prototype of a change propagation framework for process choreographies is presented. Overall, comprehensive change support in process choreographies will foster the implementation and operational support of agile collaborative process scenarios.

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons).

BackgroundThe Drosophila INterspersed Elements-1 (DINE-1/INE1) transposable elements (TEs) are the most abundant component of the Drosophila melanogaster genome and have been associated with functional gene duplications. DINE-1 TEs do not encode any proteins (non-autonomous) thus are moved by autonomous partners. The identity of the autonomous partners has been a mystery. They have been allied to Helitrons (rolling-circle transposons), MITEs (DNA transposons), and non-LTR retrotransposons by different authors.ResultsWe report multiple lines of bioinformatic evidence that illustrate the relationship of DINE-1 like TEs to endonuclease-encoding rolling-circle TEs (Helentrons). The structural features of Helentrons are described, which resemble the organization of the non-autonomous partners, but differ significantly from canonical Helitrons. In addition to the presence of an endonuclease domain fused to the Rep/Helicase protein, Helentrons have distinct structural features. Evidence is presented that illustrates that Helentrons are widely distributed in invertebrate, fish, and fungal genomes. We describe an intermediate family from the Phytophthora infestans genome that phylogenetically groups with Helentrons but that displays Helitron structure. In addition, evidence is presented that Helentrons can capture gene fragments in a pattern reminiscent of canonical Helitrons.ConclusionsWe illustrate the relationship of DINE-1 and related TE families to autonomous partners, the Helentrons. These findings will allow their proper classification and enable a more accurate understanding of the contribution of rolling-circle transposition to the birth of new genes, gene networks, and genome composition.

Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods

BackgroundInsertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structural properties of the elements (de novo methods) or using an additional library-based method using profile HMM searches.ResultsIn this study, we have developed three different work flows dedicated to ISs and MITEs detection: the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats; the third one use 28 in-house transposase alignment profiles with HMM search methods. We have compared the respective performances of each method using a reference dataset of 30 archaeal and 30 bacterial genomes in addition to simulated and real metagenomes. Compared to a BLAST-based method using ISFinder as library, de novo methods significantly improve ISs and MITEs detection. For example, in the 30 archaeal genomes, we discovered 30 new elements (+20%) in addition to the 141 multi-copies elements already detected by the BLAST approach. Many of the new elements correspond to ISs belonging to unknown or highly divergent families. The total number of MITEs has even doubled with the discovery of elements displaying very limited sequence similarities with their respective autonomous partners (mainly in the Inverted Repeats of the elements). Concerning metagenomes, with the exception of short reads data (<300 bp) for which both techniques seem equally limited, profile HMM searches considerably ameliorate the detection of transposase encoding genes (up to +50%) generating low level of false positives compare to BLAST-based methods.ConclusionCompared to classical BLAST-based methods, the sensitivity of de novo and profile HMM methods developed in this study allow a better and more reliable detection of transposons in prokaryotic genomes and metagenomes. We believed that future studies implying ISs and MITEs identification in genomic data should combine at least one de novo and one library-based method, with optimal results obtained by running the two de novo methods in addition to a library-based search. For metagenomic data, profile HMM search should be favored, a BLAST-based step is only useful to the final annotation into groups and families.

English

Objective: The sharing of personally identifiable information across organizational boundaries to facilitate patient identification in Utah presents significant policy challenges. Our objective was to create a focus area maturity model to describe and evaluate our progress in developing a policy framework to support a statewide master person index (sMPI) for healthcare and public health operations and research in Utah.Materials and Methods: We used various artifacts, including minutes from policy guidance committee meetings over a span of 18 months, a report from Utah’s Digital Health Services Commission, and a draft technical requirements document to retrospectively analyze our work and create a focus area maturity model describing the domain of policy needed to support the sMPI. We then used our model to assess our progress and future goals.Conclusions: The focus area maturity model provides an orderly path that can guide the complex process of developing a functional statewide master person index among diverse, autonomous partners. While this paper focuses on our experience in Utah, we believe that the arguments for using a focus area maturity model to guide the development of state or regional MPIs is of general interest.