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Abstract Fossilization, or the transition of an organism from the biosphere to the geosphere, is a complex mechanism involving numerous biological and geological variables. Bacteria are one of the most significant biotic players to decompose organic matter in natural environments, early on during fossilization. However, bacterial processes are difficult to characterize as many different abiotic conditions can influence bacterial efficiency in degrading tissues. One potentially important variable is the composition and nature of the sediment on which a carcass is deposited after death. We experimentally examined this by decaying the marine shrimp Palaemon varians underwater on three different clay sediments. Samples were then analyzed using 16S ribosomal RNA sequencing to identify the bacterial communities associated with each clay system. Results show that samples decaying on the surface of kaolinite have a lower bacterial diversity than those decaying on the surface of bentonite and montmorillonite, which could explain the limited decay of carcasses deposited on this clay. However, this is not the only role played by kaolinite, as a greater proportion of gram-negative over gram-positive bacteria is observed in this system. Gram-positive bacteria are generally thought to be more efficient at recycling complex polysaccharides such as those forming the body walls of arthropods. This is the first experimental evidence of sediments shaping an entire bacterial community. Such interaction between sediments and bacteria might have contributed to arthropods’ exquisite preservation and prevalence in kaolinite-rich Lagerstätten of the Cambrian Explosion.

Since the development of Agrivoltaics with panels placed above the plants, a new system is tested with vertical mounted bifacial photovoltaic panels, of which we present the results of the first year of two experimental sites. Such installations bring a lower shading level on the plant compared to fixed tilt or single axis tracking systems and could potentially suit fields with crops having low demands of shading. However, unlike more standard PV systems, few studies have detailed the effects of such devices on field crops. In this first experimental year, bifacial vertically mounted PV system showed interesting results with a stable or even a slight increase in annual crop yields. Also, harvest quality indicators are maintained or present favorable evolution indicating a high potential of vertical PV systems for Agrivoltaics.

Abstract Background The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to separate of vent populations, promoting local adaptation and contributing to bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution. Results We explored genomic patterns of divergence in the early and late stages of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement. Conclusion Our analyses highlight the non-negligible role of natural selection on both the early and late stages of speciation in the iconic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed light on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time.

Sedimentologika is a community-driven Diamond Open Access scientific journal for the publication of work in the broad area of sedimentology and stratigraphy. The journal aims to provide a platform to the academic community and broader society, offering and guaranteeing permanent free publication and free access to peer-reviewed scientific studies focusing on all types of sedimentary processes, deposits, and environments across all spatial and temporal scales, on Earth or any other planetary body. It will publish high-quality research that will advance the field of sedimentary science, and will encourage multidisciplinarity, new teaching practices, tools and methods, and progress in accessibility to science. Sedimentologika is part of an ongoing broader Diamond Open Access movement in geosciences aspiring freedom from the financial barriers and pressures of private publishing houses, to provide direct and equal access to science for all citizens, scientists, and institutions worldwide. The published material will include research, review, methodology and opinion articles, which will be free to share, as the authors will retain the copyright of all the submitted material. Manuscripts will be published in English. Authors can attach a second abstract in a language of their choice, further allowing local communities, students, or decisional bodies to access, at least, a summary of the latest research, thus reducing potential language barriers. Sedimentologika follows Open Science principles to promote ethical dissemination and accessibility of science and knowledge, following high equity, diversity and inclusion standards. Sedimentologika emerged as a solution for the scientific community to sidestep structural inequality of the academic publishing system that is becoming financially unsustainable to its payers (authors, funding agencies), and to commit to bibliodiversity. The objective is to ensure that scientific findings remain accessible to all in order to keep advancing research and informing society on how we understand sedimentology and stratigraphy in the world around us. Sedimentologika is driven by the academic and scientific community for the community and society, promoting self-governance and adapting to the needs expressed by the community.

Abstract Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades.

Introduction: This article reports results from a survey of faculty members with editorial responsibilities. The survey explored what publishing services and platform functionalities respondents found most valuable in their work as editors, how satisfied they were with the services provided by commercial publishers, and to what extent they were aware of alternative publishing practices. Method: The authors used data collected from a survey instrument that was distributed to a sample (n = 515) of faculty members with editorial responsibilities at their institution. Results: Collected data suggest that faculty editors value specific publishing services (e.g., coordination of peer review and copyediting) and platform functionality (e.g., submission and peer-review management) more than others, recognize several challenges facing academic publishing in their disciplines (including the transition to open access publishing models), and are mostly aware of common forms of open access research dissemination such as open access journals and institutional repositories. Discussion: The survey results may be helpful to library publishers in making decisions about what publishing services and platform functionalities to prioritize in the development of their publishing programs. In addition to utilizing the survey data to assess the needs of editors, the authors also identified a number of expanded uses of the survey related to marketing and outreach. Conclusion: Insofar as faculty editors are key stakeholders that library publishers seek to build partnerships with, it is important to understand their needs and preferences as editors. This article provides some insight into these questions that may prove helpful to library publishers.

In recent years resulting investigations in living microbialites have provided significant data that have been critical to disentangle the role of the various biotic and abiotic processes contributing to their development. Despite these efforts separating the impact and magnitude of these processes remain a difficult task. At present the Maquinchao Basin in northeastern Patagonia, Argentina, contains both fossil and living microbialites. Thus, the region provides a unique opportunity to investigate the impact of intrinsic and extrinsic parameters in carbonate precipitation. Early investigations (Austral summer 2011) in living microbialites concluded that organomineralization was related to both photosynthetic activity in the more surficial layer (green), and sulfate-reduction in the lower part (beige). Field investigations in the same area four years later showed that the pounds previously containing abundant active mats had dried out, and in general revealed the absence of globular structured clusters of minerals in the microbial mats. Here we present microscale investigations using optical microscopy and SEM along with the 16SrRNA gene sequence diversity, and the physico-chemical parameters of the hosting waters. They were carried out in successive seasonal samplings in November 2015, April-May 2016, August 2016, February 2017, and March 2018. All microbialite samples show regular occurrences of sulfate reducing bacteria (SRB) along with filaments of unknown origin. Carbonates are observed associated with erect filaments in shallow and active running water locations whereas the mineral phase is located below organic matter film in comparatively deeper and calmer water areas. Additionally, seasonal changes in the physico-chemical properties of the hosting waters indicate that extrinsic parameters, especially evaporation, might play a more substantial role in the precipitation of these carbonates than previously proposed. The environmental differences between 2011 and 2015 in meteorological conditions, regional volcanic activity and associated deposits in the basin are analyzed. We concluded that they are likely responsible of the decrease of the mineralization processes, and particularly those associated with photosynthetic activity. These results call for caution when interpreting the degree of biological impact on the formation of microbialites in the geological record. Local extrinsic factors might have a changeable impact over time switching mineral precipitation from biotic to abiotic and vice-versa, which can be undistinguishable in fossilized microbialites.

Abstract Background This paper examines perinatal death reporting and reviews in Bungoma county, Kenya, where substantial progress has been made, providing important insights for wider scale up to other contexts. Methods Quantitative methods were used to analyse trends in perinatal death reporting and reviews between 2014 and 2017 throughout Kenya based on data from the District Health Information System. Qualitative methods helped further understand the success of perinatal death reporting and review in Bungoma county through focus group discussions and individual interviews at 5 hospitals and 1 health centre. Thematic analysis was used to draw out codes for the analysis. Results Only 13 of the 47 counties in Kenya conduct perinatal death reviews. In 2017, the year after the perinatal death review system was introduced, only 3.6% of perinatal deaths were reviewed in Kenya. Bungoma county has made the greatest strides in Kenya, reviewing 59% of the perinatal deaths that occurred within the county in 2017. Bungoma accounted for 51% of all the perinatal deaths reviewed in Kenya. Factors contributing to the success in Bungoma include harmonisation of facility based perinatal reporting tools with the national level; prioritising the need to document and report mortalities; tailoring continual medical education and supportive supervision visits to needs identified from the review; and better documentation and referral processes. Supportive management and administrative staff have also helped drive forward implementation of actions and increased health staff motivation to reduce perinatal deaths and improve quality of care. Conclusions Successful implementation of perinatal death reviews requires clear delineation of roles and responsibilities for action, which are routinely monitored to track implementation progress. As in other low-income settings, Bungoma county has demonstrated that in Kenya, perinatal death reviews can be effectively implemented and sustained, through a focus on learning, solution-oriented responses, influencing those in a power to act, accountability for results, and observable quality of care improvements.

This is a book review of Poet-Librarians in the Library of Babel: Innovative Meditations on Librarianship and its application to the Scholarly Communication field.

Abstract Background The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested that Copia LTR-retrotransposons display specific dynamic compared to the more abundant and diverse Gypsy elements. Indeed, Copia elements show a relative scarcity and the prevalence of only a few clades in specific hosts. Thus, BEL/Pao seems to be the second most abundant superfamily. However, the generality of these assumptions remains to be assessed. Therefore, we carried out the first large-scale comparative genomic analysis of LTR-retrotransposons in molluscs. The aim of this study was to analyse the diversity, copy numbers, genomic proportions and distribution of LTR-retrotransposons in a large host phylum. Results We compare nine genomes of molluscs and further added LTR-retrotransposons sequences detected in databases for 47 additional species. We identified 1709 families, which enabled us to define 31 clades. We show that clade richness was highly dependent on the considered superfamily. We found only three Copia clades, including GalEa and Hydra which appear to be widely distributed and highly dominant as they account for 96% of the characterised Copia elements. Among the seven BEL/Pao clades identified, Sparrow and Surcouf are characterised for the first time. We find no BEL or Pao elements, but the rare clades Dan and Flow are present in molluscs. Finally, we characterised 21 Gypsy clades, only five of which had been previously described, the C-clade being the most abundant one. Even if they are found in the same number of host species, Copia elements are clearly less abundant than BEL/Pao elements in copy number or genomic proportions, while Gypsy elements are always the most abundant ones whatever the parameter considered. Conclusions Our analysis confirms the contrasting dynamics of Copia and Gypsy elements in metazoans and indicates that BEL/Pao represents the second most abundant superfamily, probably reflecting an intermediate dynamic. Altogether, the data obtained in several taxa highly suggest that these patterns can be generalised for most metazoans. Finally, we highlight the importance of using database information in complement of genome analyses when analyzing transposable element diversity.

In Brief This article explores the opportunities and challenges that early career librarians face when advancing their careers, desired qualities for leaders or managers of all career stages, and how early career librarians can develop those qualities. Our survey asked librarians at all career stages to share their sentiments, experiences, and perceptions of leadership and management. Through our feminist critique, we explore the relationships to power that support imbalances in the profession and discuss best practices such as mentoring, individualized support, and self-advocacy. These practices will be of use to early career librarians, as well as supervisors and mentors looking to support other librarians.

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. We found significant environmental parameters influencing the overall microbial community distribution, but no strong relationship with given phylotypes and paleoclimatic signals or sediment age. Our results support a weak recording of early diagenetic processes and their actors by bulk prokaryotic sedimentary DNA in Lake Ohrid, replaced by specialized low-energy clades of the deep biosphere and a marked imprint of erosional processes on the subsurface DNA pool of Lake Ohrid.

The growth of makerspaces and 3D services in libraries means new opportunities to utilize library expertise, partnerships, and exemptions to inform patrons about copyright in creative environments. Wide access to 3D printing, trademarks, and patents are relevant topics, but this paper only focuses on copyright. Little to no literature has been produced about how to educate makers about copyright for 3D objects. This paper will present a framework to encourage creators of 3D objects to analyze and interpret copyright information for their own purposes. It also discusses the process of designing and embedding learning tools into the database for SHAPES, a project for inter-library loans of 3D renderings. NOTE: New information about the methods and progress of this project has been added since the Kraemer Copyright Conference.

This qualitative study examines perceptions of open access from focus groups including thirty-eight faculty who identify as Black, Indigenous, and People of Color (BIPOC). In responses, BIPOC faculty reflect on the culture and support of open access within their departments, institutions, and professional associations. It was at a time of increased discussion about knowledge equity, the impact of access to research during the 2020 pandemic, and a precursor to the 2022 U.S. Office of Science and Technology Policy Memo to expand access to data and publications sponsored by all federal funding agencies. In general, BIPOC faculty face compounded risks with open access and inequities in scholarly publishing. However, participants believe open publishing processes allow more flexibility and connection to communities. The investigators use the grounded theory method for analysis, provide themes as well as direct quotes from the data, and discuss practical applications for supporting BIPOC scholars with engagement in open access.

Introduction Chronic diseases such as cancer, cardiovascular disease, stroke, and diabetes are responsible for most deaths in the United States. Lifestyle factors — poor nutrition, sedentary living, and tobacco use — appear to play a prominent role in the development of many chronic diseases. This study determined the behavioral and clinical impact of a therapeutic lifestyle-modification intervention on a group of community volunteers. Methods Participants included 348 volunteers aged 24 to 81 years from the Rockford, Ill, metropolitan area who participated in a randomized clinical trial. The intervention group attended a 40-hour educational course delivered as lectures during a 4-week period. Participants learned the importance of making better lifestyle choices and how to make improvements in nutrition and physical activity. Changes in nutrition, physical activity behavior, and several chronic disease risk factors were assessed at baseline and 6 months. Results Intervention participants showed significant 6-month improvement in all nutrition and physical activity measures except calories from protein and whole-grain servings and all clinical measures except blood glucose, total cholesterol, triglycerides, and high-sensitivity C-reactive protein. Total cholesterol and low-density lipoprotein cholesterol were worse after 6 months in both groups but only significantly worse in the control group. The control group experienced small but significant improvements in systolic and diastolic blood pressure and high-density lipoproteins. Change-score comparisons between the intervention and control groups were significant for all nutrition and physical activity variables except total steps per week and daily sodium intake and were also significant for the clinical measures of weight, body fat, and body mass index. Conclusion This therapeutic lifestyle-modification program can significantly improve nutrition and physical activity behavior and can reduce many of the risk factors associated with common chronic diseases.