Re-telling, Re-cognition, Re-stitution: Sikh Heritagization in Canada

In Canada, the language and techniques of museums and heritage sites have been adopted and adapted by some immigrant communities to make sense of their place within their new country. For some groups, “heritagization” is a new value, mobilized for diverse purposes. New museums and heritage sites serve as a form of ethnic media, becoming community gathering points, taking on pedagogical roles, enacting citizenship, and enabling strategic assertion of identity in the public sphere. This article explores this enactment of heritage and citizen-membership through a case study, the Sikh Heritage Museum, developed in Abbotsford by Indo-Canadians. Established in 2011 in an historic and still-functioning gurdwara, the museum is an example of a community’s desire to balance inward-looking historical consciousness and community belonging, with outward-looking voice, recognition and acceptance by mainstream Canadian society. The museum has also become a site of tension between top-down and bottom-up initiatives, where amateur and local expressions butt up against professionalized government activities such as the Canadian Historical Recognition Program that seek to insert formal recognition and social inclusion policies. The article considers the effects of this resource and power differential on the museum’s development, and on the sensibilities and practices of immigrant “heritage” and “citizenship” in Canada

Testing of worn face mask and saliva for SARS-CoV-2

BackgroundExhaled SARS-CoV-2 can be detected on face masks. We compared tests for SARS-CoV-2 RNA on worn face masks and matched saliva samples.MethodsWe conducted this prospective, observational, case-control study between December 2021 and March 2022. Cases comprised 30 in-center hemodialysis patients with recent COVID-19 diagnosis. Controls comprised 13 hemodialysis patients and 25 clinic staff without COVID-19 during the study period and the past 2 months. Disposable 3-layer masks were collected after being worn for 4 hours together with concurrent saliva samples. ThermoFisher COVID-19 Combo Kit (A47814) was used for RT-PCR testing.ResultsMask and saliva testing specificities were 99% and 100%, respectively. Test sensitivity was 62% for masks, and 81% for saliva (p = 0.16). Median viral RNA shedding duration was 11 days and longer in immunocompromised versus non-immunocompromised patients (22 vs. 11 days, p = 0.06, log-rank test).ConclusionWhile SARS-CoV-2 testing on worn masks appears to be less sensitive compared to saliva, it may be a preferred screening method for individuals who are mandated to wear masks yet averse to more invasive sampling. However, optimized RNA extraction methods and automated procedures are warranted to increase test sensitivity and scalability. We corroborated longer viral RNA shedding in immunocompromised patients

Energy‐efficient colourless photonic technologies for next‐generation DWDM metro and access networks

Within the scope of our EU FP7 C3PO project, we are developing novel, energy-efficient, colourless photonic technologies for low-cost, next-generation dense wavelength-division-multiplexed metro transport and access networks. The colourless transmitters use reflective arrayed photonic integrated circuits, particularly hybrid reflective electroabsorption modulators, and multi-wavelength laser sources, with custom power-efficient driver circuitry. A low-loss piezoelectric beam-steering optical matrix switch allows for dynamic wavelength reconfigurability. Simplifying the required optical and electronic hardware, as well as avoiding the need for expensive, thermally-stabilised tuneable lasers, will yield cost and energy savings for data switching applications in future metro, access, and datacentre interconnection networks. We report on recent advancement towards these low-power optical networks, providing the latest systems results achieved with key enabling hybrid photonic integrated devices and electronic driver/receiver arrays for our targeted applications

Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics. MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de)

Accommodating Ontologies to Biological Reality—Top-Level Categories of Cumulative-Constitutively Organized Material Entities

BACKGROUND: The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. METHODOLOGY/PRINCIPAL FINDINGS: Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. CONCLUSIONS/SIGNIFICANCE: We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle

Entwicklung der Larva, Herkunft des Coeloms und phylogenetische Verwandtshaftsbeziehungen der Phoronida

Title and Content 1 General Introduction 5 Coelomogenesis in young larvae of Phoronis ovalis and P. muelleri 13 Introduction 13 Material and Methods 15 Terminology 16 Results 17 Coelomogenesis in P. ovalis 17 Overview 17 Gastrulation 20 Young larva 22 Late larva 27 Nephridia in the larva of P. ovalis 30 Origin of the coelom in P. muelleri 33 Overview 33 Gastrula stage 34 Young larva after gastrulation 36 Two lobed larva 37 Discussion 38 Origin of the coelom in Phoronida 38 Homology of P. ovalis larva with the actinotroch larva 39 The condition in the ground pattern of Phoronida 40 Literature 42 Morphological and molecular affinities of Phoronida and Brachiopoda 45 Introduction 45 Material and Methods 46 Examined taxa 46 Molecular data 47 Morphological data 48 Phylogenetic analysis 49 Results 52 Morphological data 52 Combined data 53 Sequence data 55 Phoroniformea 57 Character congruence 57 Character descriptions 58 Discussion 72 Groundpattern of the Phoronida 72 Evolution of characters within Phoronida 75 The Phoroniformea hypothesis 76 Literature 77 Summary 85 Zusammenfassung 87 Appendix 89Although Phoronis ovalis Wright, 1856 was the first phoronid described, it is one of the least well studied. Its external features are very different from that of other phoronid larva. The lecithotrophic, slug-like larva possesses a distinct rim around the mouth opening on the ventral side. A blunt outgrowth grows on the ventral side of the larva and posterior to the mouth opening, which contains the opening of the anus. Tentacles are not developed during the whole larval life. In this study, the internal development of the early larva of P. ovalis is described for the first time. The late blastula of P. ovalis short before gastrulation is spherical in shape. With the invagination on the vegetal pole the embryo is transformed into a gastrula. The two sheets of ecto- and endoderm reduces the blastocoelic space to a narrow slit. In the dorsal roof of the archenteron the opening of anus occurs. From here a short hollow tube, the future intestine, leads into the mass of endodermal cells in the posterior area of the larva. Going further dorsad, this in cross section round tube becomes a slit in the center of the larval body, in the same manner like the developing pharynx. During further development both slits meet and fuse in the centre of the larva in order to form the digestive tract. The intestinal anlage is not functional; but all cells of the larva contain a large amount of yolk vesicles, which nurish the larva. The coelom of P. ovalis arises out of one compact mesodermal anlage, which originates from a compact mass of cells, which migrate into the blastocoelic space short before gastrulation. After gastrulation, a compact mesodermal band surrounds the archenteron. From here, a cell sheet grows apicad between the cell sheets of ecto- and endoderm. Lateral, the mesoderm becomes double layered, and coelom formation is accomplished by fluid ingression and diverging of the cell layers. Later in development, this coelomic anlage becomes separated into one anterior coelomic compartment, encompassing the pharynx from anterior, and a second posterior, still compact mesoderm, which encircles the intestine. A subepidermal neuropil is formed on the apical end of the larva, sending two processes lateral and caudad alongside the anterior and posterior coelom and coelomic anlage. A third neuropil process courses dorsal alongside of the anterior coelom up till the dorsal center of the larva. Lateral to the posterior mesoderm two protonephridia are formed, which consists of an unbranched terminal complex, and an angled duct. The development of Phoronis muelleri de Selys-Longchamps, 1903 starting from the time of gastrulationis is depicted in this study, in order to obtain comparable data for the origin of the mesoderm in the Phoronida. In P. muelleri, precursors of mesoderm cells occur on the edges of the invaginating archenteron in the blastocoelic space. By the same time the stomodeum is formed, these cells taper the inner wall of the blastocoelic space. These cells acquire polarity and differentiate into myoepithelial cells around the mouth opening and underneath the apical plate. They do not form a complete epithelial lining. According to other authors, they form a complete lining of the coelom in the episphere later in development. In comparison to P. ovalis, the coelom is therefore formed from single cells, which transform the blastocoelic space into a coelomic cavity. The position of the protonephridia in larva of P. ovalis and P. muelleri, as well as the location of the apical neuropil is used to homologize both larval types. The anterior coelom of the P. ovalis larva corresponds to the tentacle coelom formed late in the life of the actinotroch larva. There is no episphere formed in the larva of P. ovalis. The actinotroch trunk coelom is in accordance with the position of the posterior coelomic anlage in P. ovalis. The ventral extension from the larval body of P. ovalis has no correspondence in the actinotroch larva. The systematic of the Phoronida and their position in the metazoan tree is unresolved. In this study an elaborate morphological matrix is compiled, containing characters from Phoronida and Brachiopoda. An analysis using the parsimony criterion is conducted using this matrix and a matrix from 18s rRNA sequences. The Phoronida appear monophyletic in this analysis, with P. ovalis as sistertaxon to the rest of the Phoronida. The results further indicate the monophyly of the genus Phoronopsis Gilchrist, 1907, as well as a monophyletic grouping of P. hippocrepia Wright, 1856, P. australis Haswell, 1883 and P. ijimai Oka, 1897. The Brachiopods form the sistergroup to the phoronids. The results of this analysis, as well as the examination on the origin of the coelom and the structure and position of the protonephridia of the phoronid larvae allows advanced statements about the type of larva in the stemlineage of the Phoronida. The results are further used to reconstruct a hypothetical representative in the stemlineage of the Phoronida.Obwohl Phoronis ovalis Wright, 1856 der erste beschriebene Phoronida war, ist er einer der am wenigsten untersuchten. Seine äußeren Merkmale unterscheiden sich stark von dem Aussehen anderer Phoronidenlarven. Die lecithotrophe, schneckenförmige Larve hat einen ausgeprägten Rand um die Mundöffnung auf der Ventralseite. Hinter der Mundöffnung wächst ein stumpfer Auswuchs auf der Ventralseite der Larve, auf dem sich die Afteröffnung befindet. Während der gesamten Larvalphase werden keine Tentakel entwickelt. In dieser Arbeit wird die innere Entwicklung der frühen Larve von P. ovalis zum ersten Mal beschrieben. Die späte Blastula von P. ovalis, kurz vor der Gastrulation ist kugelförmig. Mit der Invagination am vegetalen Pol wird der Embryo in eine Gastrula überführt. Die beiden Blätter des Ekto- und Endoderms verkleinern den Blastocoel-Raum zu einem schmalen Schlitz. In der dorsalen Wand des Archenterons erscheint die Afteröffnung, von der eine kurze, hohle Röhre in die posteriore endodermale Zellmasse führt. Diese im Querschnitt runde Röhre verengt sich dorsad zu einem Schlitz im Zentrum der Larve, genauso wie der Pharynx. In der weiteren Entwicklung der Larve treffen und vereinigen sich beide Schlitze und bilden einen durchgehenden Darmtrakt. Die Darmanlage ist nicht funktionsfähig, aber alle Zellen der Larve enthalten eine große Menge an Dotter, von denen die Larve sich ernährt. Das Coelom von P. ovalis entsteht aus einer kompakten Mesodermanlage, die aus einer kompakten Zellmasse entsteht, welche kurz vor der Gastrulation in den Blastocoelraum wandern. Nach der Gastrulation umgibt ein kompaktes Band von Mesodermzellen das Archenteron. Von diesem wächst eine Zellschicht apicad, zwischen die Schichten des Ecto- und Endoderms. Lateral wird das Mesoderm doppelschichtig und Coelom bildet sich durch den Einstrom von Flüssigkeit und das Auseinanderweichen der Zellschichten. Später in der Entwicklung teilt sich die Coelomanlage in einen vorderen Coleomteil, der den Pharynx von anterior umgreift, und ein zweites, noch kompaktes hinteres Mesoderm, welches den Darm umschließt. Ein subepidemales Neuropil bildet sich am anterioren Ende der Larve, von dem aus zwei Fortsätze lateral und caudad entlang des Coeloms verlaufen. Ein Dritter neuropiler Fortsatz verläuft dorsad entlang des vorderen Coeloms bis zum dorsalen Zentrum der Larve. Lateral zum posterioren Mesoderm sind zwei Protonephridien ausgebildet, die aus einem unverzweigten Terminalkomplex und einem gewinkelten Kanal bestehen. Die Entwicklung von Phoronis muelleri de Selys-Longchamps, 1903 vom Beginn der Gastrulation wird in dieser Arbeit dargestellt. Dies ist notwendig, um vergleichbare Daten für die Herkunft des Mesoderms innerhalb der Phoroniden zu bekommen. In P. muelleri, erscheinen Vorläufer von Mesodermzellen an dern Rändern des sich einstülpenden Archenterons im Blastocoelraum. Zu selben Zeit, wenn das Stomodeum gebildet wird, kleiden diese Zellen die innere Wand des Blastocoels aus. Diese Zellen werden polar und differenzieren sich in Myoepithelzellen um die Mundöffnung und unterhalb der Apikalplatte. Sie formen keine durchgehende epithelial Auskleidung. Nach anderen Autoren wird eine vollständige Auskleidung des Coeloms der Episphäre erst später in der Entwicklung gebildet. Im Vergleich zu P. ovalis wird das Coelom hier aus einzelnen Zellen gebildet, welche den Balstocoelraum in einen Coelomraum überführen. Die Position der Protonephridien in den Larven von P. ovalis und P. muelleri und die Lage des apikalen Neuropils wird genutzt, um eine Homologie der beiden Larventypen zu erstellen. Das vordere Coelom der Larve von P. ovalis entspricht dem Tentakelcoelom der Actinotrocha-Larve, welches erst spät in der Larvalentwicklung gebildet wird. Es gibt eine Episphäre in der Larve von P. ovalis. Der Rumpf der Actinotrocha entspricht in der Lage der Position der hinteren Coelomanlage von P. ovalis. Die ventrale Ausstülpung aus dem larvalen Körper von P. ovalis hat keine Entsprechung in der Actinotrocha. Die Systematik der Phoroniden und ihre Stellung im Baum der Metazoen sind ungelöst. In dieser Arbeit wird eine ausführliche Datenmatrix zusammengestellt, welche Merkmale der Phoroniden und Brachiopoden beinhaltet. Eine Analyse mit dieser Matrix und einer Matrix aus 18S rRNA Sequenzen wird mit dem Sparsamkeitsprinzip wird durchgeführt. In dieser Analyse erscheinen die Phoroniden monophyletisch, mit P. ovalis als Schwestergruppe zu den übrigen Phoroniden. Die Ergebnisse deuten auf eine Monophylie der Gattung Phoronopsis Gilchrist, 1907 hin, und auf eine monophyletische Gruppierung von P. hippocrepia Wright, 1856, P. australis Haswell, 1883 und P. ijimai Oka, 1897. Die Brachiopoden bilden die Schwestergruppe der Phoroniden. Die Ergebnisse dieser Analyse und die Untersuchung der Herkunft der Coelomräume und der Struktur und Position der Protonephridien in den Phoronidenlarven erlauben weiterführende Aussagen über den Larventyp in der Stammlinie der Phoronida. Die Ergebnisse werden weiter genutzt, um den Hypothetischen Vertreter in der Stammlinie der Phoronida zu rekonstruieren

Bridging a Gap in Metabarcoding Research: The ASV Table Registry

Metabarcoding is a tool to routinely identify species in environmental mass-samples and thereby analyze their species composition. Using metabarcoding techniques outperforms the traditional species identification by human experts in amount, speed and quality when well curated reference data are available.Therefore, metabarcoding can be seen as the future standard method for all biological research areas where species occurrence and distribution is in question, e.g., ecological research or monitoring projects (Porter and Hajibabaei 2018).A common outcome of metabarcoding research are Amplicon Sequence Variant tables (ASV, Callahan et al. 2017). These tables combine the extracted sequences of all sampling plots with the occurrences of each sequence within a single plot. To identify the species, each sequence is searched in one or more reference databases that hold sequences and their known taxon identifications (e.g., Barcode Of Life Data system (BOLD) or the German Barcode of Life library (GBOL)). The sequence searches utilise tools like BLAST, BOLD identification engine, or vsearch. Found taxa and their taxonomy are added to the ASV tables as taxon assignments.The number and precision of taxon assignments will increase with the growth of available sequences and quality of identifications in reference databases over time (Weigand et al. 2019). The introduction of new marker sequences and improvements in search tools will further enhance the taxon assignments. Thus, the taxon assignments in ASV tables are subject to change. Projects with the aim of building up species inventories on a large scale (GBOL) or monitoring programs, like the Automated Multisensor Stations for Monitoring of BioDiversity (Wägele et al. 2022), quickly produce data sets with thousands of sequences at numerous locations.Currently, most ASV tables are stored as supplements to publications or in private repositories. This makes analysis across multiple research projects difficult and error prone as sequences and their taxon assignments are often not accessible. Efforts, like the European Bioinformatics Institute metagenomics with Mgnify serve the needs for uploading and annotating environmental DNA samples (Mitchell et al. 2017), but a registry for ASV tables with complete data life cycles is lacking.To fill this gap, we develop an ASV Table Registry as part of the German Barcode of Life III - Dark Taxa project. This allows users to:register ASV tables and sequencesupload and manage ASV tables with versioningpublish ASV tables with DOIssearch by sequences, taxa, and occurrence dataretrieve API-based dataassign taxonomic names with various tools and reference databaseskeep track of the applied search methods and parametersThe data life cycle of the uploaded ASV tables consists of several draft versions (each re-annotation with the identification pipeline creates a new draft version) and eventually a published version with a DOI. New draft versions can be created from the published version, then re-annotated and published again. The tracking of former taxon assignments allows researchers to re-evaluate data of former studies, compare them, and add new results. The ASV Table Registry developed here aims to make ASV tables FAIR (Findable, Accessible, Interoperable, and Reusable) and to foster the shared use in research projects.Future development focuses on the incorporation of the MIxS standard (Yilmaz et al. 2011) and on submission of the published data to International Nucleotide Sequence Database Collaboration (INSDC) using established dataflows from the German Federation for Biological Data (GFBio) and NFDI4biodiversity.The ASV data portal is accessible at: https://bolgermany.de/metabarcoding; the source code at: https://gitlab.leibniz-lib.de/GBOL/asv-table-registry

Fiat or Bona Fide Boundary—A Matter of Granular Perspective

BACKGROUND: Distinguishing bona fide (i.e. natural) and fiat (i.e. artificial) physical boundaries plays a key role for distinguishing natural from artificial material entities and is thus relevant to any scientific formal foundational top-level ontology, as for instance the Basic Formal Ontology (BFO). In BFO, the distinction is essential for demarcating two foundational categories of material entity: object and fiat object part. The commonly used basis for demarcating bona fide from fiat boundary refers to two criteria: (i) intrinsic qualities of the boundary bearers (i.e. spatial/physical discontinuity, qualitative heterogeneity) and (ii) mind-independent existence of the boundary. The resulting distinction of bona fide and fiat boundaries is considered to be categorial and exhaustive. METHODOLOGY/PRICIPAL FINDINGS: By referring to various examples from biology, we demonstrate that the hitherto used distinction of boundaries is not categorial: (i) spatial/physical discontinuity is a matter of scale and the differentiation of bona fide and fiat boundaries is thus granularity-dependent, and (ii) this differentiation is not absolute, but comes in degrees. By reducing the demarcation criteria to mind-independence and by also considering dispositions and historical relations of the bearers of boundaries, instead of only considering their spatio-structural properties, we demonstrate with various examples that spatio-structurally fiat boundaries can nevertheless be mind-independent and in this sense bona fide. CONCLUSIONS/SIGNIFICANCE: We argue that the ontological status of a given boundary is perspective-dependent and that the strictly spatio-structural demarcation criteria follow a static perspective that is ignorant of causality and the dynamics of reality. Based on a distinction of several ontologically independent perspectives, we suggest different types of boundaries and corresponding material entities, including boundaries based on function (locomotion, physiology, ecology, development, reproduction) and common history (development, heredity, evolution). We argue that for each perspective one can differentiate respective bona fide from fiat boundaries