Subaqueous foraging among carnivorous dinosaurs.

Secondary aquatic adaptations evolved independently more than 30 times from terrestrial vertebrate ancestors1,2. For decades, non-avian dinosaurs were believed to be an exception to this pattern. Only a few species have been hypothesized to be partly or predominantly aquatic3-11. However, these hypotheses remain controversial12,13, largely owing to the difficulty of identifying unambiguous anatomical adaptations for aquatic habits in extinct animals. Here we demonstrate that the relationship between bone density and aquatic ecologies across extant amniotes provides a reliable inference of aquatic habits in extinct species. We use this approach to evaluate the distribution of aquatic adaptations among non-avian dinosaurs. We find strong support for aquatic habits in spinosaurids, associated with a marked increase in bone density, which precedes the evolution of more conspicuous anatomical modifications, a pattern also observed in other aquatic reptiles and mammals14-16. Spinosaurids are revealed to be aquatic specialists with surprising ecological disparity, including subaqueous foraging behaviour in Spinosaurus and Baryonyx, and non-diving habits in Suchomimus. Adaptation to aquatic environments appeared in spinosaurids during the Early Cretaceous, following their divergence from other tetanuran theropods during the Early Jurassic17.

Tail-propelled aquatic locomotion in a theropod dinosaur.

In recent decades, intensive research on non-avian dinosaurs has strongly suggested that these animals were restricted to terrestrial environments1. Historical proposals that some groups, such as sauropods and hadrosaurs, lived in aquatic environments2,3 were abandoned decades ago4-6. It has recently been argued that at least some of the spinosaurids-an unusual group of large-bodied theropods of the Cretaceous era-were semi-aquatic7,8, but this idea has been challenged on anatomical, biomechanical and taphonomic grounds, and remains controversial9-11. Here we present unambiguous evidence for an aquatic propulsive structure in a dinosaur, the giant theropod Spinosaurus aegyptiacus7,12. This dinosaur has a tail with an unexpected and unique shape that consists of extremely tall neural spines and elongate chevrons, which forms a large, flexible fin-like organ capable of extensive lateral excursion. Using a robotic flapping apparatus to measure undulatory forces in physical models of different tail shapes, we show that the tail shape of Spinosaurus produces greater thrust and efficiency in water than the tail shapes of terrestrial dinosaurs and that these measures of performance are more comparable to those of extant aquatic vertebrates that use vertically expanded tails to generate forward propulsion while swimming. These results are consistent with the suite of adaptations for an aquatic lifestyle and piscivorous diet that have previously been documented for Spinosaurus7,13,14. Although developed to a lesser degree, aquatic adaptations are also found in other members of the spinosaurid clade15,16, which had a near-global distribution and a stratigraphic range of more than 50 million years14, pointing to a substantial invasion of aquatic environments by dinosaurs.

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Sexual dimorphism in dinosaurs.

Studying fossils from a mass-mortality event reveals evidence for sexual dimorphism and, unusually, equal numbers of males and females in a herd of dinosaurs.

Hepatitis B vaccination status and knowledge, attitude, and practice towards Hepatitis B virus among medical sciences students: A cross-sectional study.

BACKGROUND AND AIMS: Healthcare staff are at high risk of occupational exposure to Hepatitis B and other blood-borne diseases. Lack of education about the knowledge of Hepatitis B virus contributes to an increase in cases. This study aims to determine the knowledge of the Hepatitis B virus among the medical professionals in Duhok province, Kurdistan Region of Iraq, and to determine their knowledge of the importance of vaccination. MATERIALS AND METHODS: This cross-sectional study was conducted in Duhok province, Kurdistan Region of Iraq, among medical science students from November 2022 to February 2023 and a total of 511 students participated in the study. A Self-administered questionnaire comprising 22 items categorized into five sections was distributed to the students either electronically or by paper and pen method. The survey utilized a Five-point Likert scale when assessing respondents' opinions on knowledge, attitude, and practice (KAP). Microsoft Excel and GraphPad Prism 9 were used for statistical analysis. RESULTS: A total of 511 responses were collected from medical, dental, pharmacy, and laboratory students. The average age of the participants was 20.74 ±1.43 years. Among the respondents, only 96 (18.8%) were fully vaccinated against the Hepatitis B virus (received 3 or more doses of the vaccine), while 294 (57.5%) were not vaccinated. Lack of vaccination programs was the major reason for not receiving a vaccination (n = 182, 62%). About 286 (55.96%) of the participants had good knowledge, attitude, and practice on Hepatitis B, manifesting median scores of 26, 18, and 20, respectively. CONCLUSION: In our study, half of the students were found to be unvaccinated, mainly due to the absence of vaccination programs. Vaccinated students exhibited better knowledge, attitude, and practice toward the infection than non-vaccinated students. Therefore, we recommend the implementation of a vaccination program as well as training on infection prevention guidelines to increase awareness and encourage vaccination.

Helically arranged cross struts in azhdarchid pterosaur cervical vertebrae and their biomechanical implications.

Azhdarchid pterosaurs, the largest flying vertebrates, remain poorly understood, with fundamental aspects of their palaeobiology unknown. X-ray computed tomography reveals a complex internal micro-architecture for three-dimensionally preserved, hyper-elongate cervical vertebrae of the Cretaceous azhdarchid pterosaur, Alanqa sp. Incorporation of the neural canal within the body of the vertebra and elongation of the centrum result in a "tube within a tube" supported by helically distributed trabeculae. Linear elastic static analysis and linearized buckling analysis, accompanied with a finite element model, reveal that as few as 50 trabeculae increase the buckling load by up to 90%, implying that a vertebra without the trabeculae is more prone to elastic instability due to axial loads. Subsuming the neural tube into the centrum tube adds considerable stiffness to the cervical series, permitting the uptake of heavy prey items without risking damage to the cervical series, while at the same time allowing considerable skeletal mass reduction.

Geology and paleontology of the Upper Cretaceous Kem Kem Group of eastern Morocco.

The geological and paleoenvironmental setting and the vertebrate taxonomy of the fossiliferous, Cenomanian-age deltaic sediments in eastern Morocco, generally referred to as the "Kem Kem beds", are reviewed. These strata are recognized here as the Kem Kem Group, which is composed of the lower Gara Sbaa and upper Douira formations. Both formations have yielded a similar fossil vertebrate assemblage of predominantly isolated elements pertaining to cartilaginous and bony fishes, turtles, crocodyliforms, pterosaurs, and dinosaurs, as well as invertebrate, plant, and trace fossils. These fossils, now in collections around the world, are reviewed and tabulated. The Kem Kem vertebrate fauna is biased toward large-bodied carnivores including at least four large-bodied non-avian theropods (an abelisaurid, Spinosaurus, Carcharodontosaurus, and Deltadromeus), several large-bodied pterosaurs, and several large crocodyliforms. No comparable modern terrestrial ecosystem exists with similar bias toward large-bodied carnivores. The Kem Kem vertebrate assemblage, currently the best documented association just prior to the onset of the Cenomanian-Turonian marine transgression, captures the taxonomic diversity of a widespread northern African fauna better than any other contemporary assemblage from elsewhere in Africa.

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.

Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make these phenotype descriptions amenable to machine reasoning. Natural language processing tools have been developed to facilitate this task, and the training and evaluation of these tools depend on the availability of high quality, manually annotated gold standard data sets. We describe the development of an expert-curated gold standard data set of annotated phenotypes for evolutionary biology. The gold standard was developed for the curation of complex comparative phenotypes for the Phenoscape project. It was created by consensus among three curators and consists of entity-quality expressions of varying complexity. We use the gold standard to evaluate annotations created by human curators and those generated by the Semantic CharaParser tool. Using four annotation accuracy metrics that can account for any level of relationship between terms from two phenotype annotations, we found that machine-human consistency, or similarity, was significantly lower than inter-curator (human-human) consistency. Surprisingly, allowing curatorsaccess to external information did not significantly increase the similarity of their annotations to the gold standard or have a significant effect on inter-curator consistency. We found that the similarity of machine annotations to the gold standard increased after new relevant ontology terms had been added. Evaluation by the original authors of the character descriptions indicated that the gold standard annotations came closer to representing their intended meaning than did either the curator or machine annotations. These findings point toward ways to better design software to augment human curators and the use of the gold standard corpus will allow training and assessment of new tools to improve phenotype annotation accuracy at scale.

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.

The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by annotating characters with community ontology terms, links between novel species anatomy and the genes that may underlie them can be made. But given the enormity of the legacy literature, how can this largely unexploited wealth of descriptive data be rendered amenable to large-scale computation? To identify the bottlenecks, we quantified the time involved in the major aspects of phenotype curation as we annotated characters from the vertebrate phylogenetic systematics literature. This involves attaching fully computable logical expressions consisting of ontology terms to the descriptions in character-by-taxon matrices. The workflow consists of: (i) data preparation, (ii) phenotype annotation, (iii) ontology development and (iv) curation team discussions and software development feedback. Our results showed that the completion of this work required two person-years by a team of two post-docs, a lead data curator, and students. Manual data preparation required close to 13% of the effort. This part in particular could be reduced substantially with better community data practices, such as depositing fully populated matrices in public repositories. Phenotype annotation required ∼40% of the effort. We are working to make this more efficient with Natural Language Processing tools. Ontology development (40%), however, remains a highly manual task requiring domain (anatomical) expertise and use of specialized software. The large overhead required for data preparation and ontology development contributed to a low annotation rate of approximately two characters per hour, compared with 14 characters per hour when activity was restricted to character annotation. Unlocking the potential of the vast stores of morphological descriptions requires better tools for efficiently processing natural language, and better community practices towards a born-digital morphology. Database URL: http://kb.phenoscape.org

Semiaquatic adaptations in a giant predatory dinosaur.

We describe adaptations for a semiaquatic lifestyle in the dinosaur Spinosaurus aegyptiacus. These adaptations include retraction of the fleshy nostrils to a position near the mid-region of the skull and an elongate neck and trunk that shift the center of body mass anterior to the knee joint. Unlike terrestrial theropods, the pelvic girdle is downsized, the hindlimbs are short, and all of the limb bones are solid without an open medullary cavity, for buoyancy control in water. The short, robust femur with hypertrophied flexor attachment and the low, flat-bottomed pedal claws are consistent with aquatic foot-propelled locomotion. Surface striations and bone microstructure suggest that the dorsal "sail" may have been enveloped in skin that functioned primarily for display on land and in water.

Dinosaur footprints and other ichnofauna from the cretaceous Kem Kem beds of Morocco.

We describe an extensive ichnofossil assemblage from the likely Cenomanian-age 'lower' and 'upper' units of the 'Kem Kem beds' in southeastern Morocco. In the lower unit, trace fossils include narrow vertical burrows in cross-bedded sandstones and borings in dinosaur bone, with the latter identified as the insect ichnotaxon Cubiculum ornatus. In the upper unit, several horizons preserve abundant footprints from theropod dinosaurs. Sauropod and ornithischian footprints are much rarer, similar to the record for fossil bone and teeth in the Kem Kem assemblage. The upper unit also preserves a variety of invertebrate traces including Conichnus (the resting trace of a sea-anemone), Scolicia (a gastropod trace), Beaconites (a probable annelid burrow), and subvertical burrows likely created by crabs for residence and detrital feeding on a tidal flat. The ichnofossil assemblage from the Upper Cretaceous Kem Kem beds contributes evidence for a transition from predominantly terrestrial to marine deposition. Body fossil and ichnofossil records together provide a detailed view of faunal diversity and local conditions within a fluvial and deltaic depositional setting on the northwestern coast of Africa toward the end of the Cretaceous.

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

BACKGROUND: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. RESULTS: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. CONCLUSIONS: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/

The ornithologist Alfred Russel Wallace and the controversy surrounding the dinosaurian origin of birds.

Over many years of his life, the British naturalist Alfred Russel Wallace (1823-1913) explored the tropical forests of Malaysia, collecting numerous specimens, including hundreds of birds, many of them new to science. Subsequently, Wallace published a series of papers on systematic ornithology, and discovered a new species on top of a volcano on Ternate, where he wrote, in 1858, his famous essay on natural selection. Based on this hands-on experience, and an analysis of an Archaeopteryx fossil, Wallace suggested that birds may have descended from dinosaurian ancestors. Here, we describe the "dinosaur-bird hypothesis" that originated with the work of Thomas H. Huxley (1825-1895). We present the strong evidence linking theropod dinosaurs to birds, and briefly outline the long and ongoing controversy around this concept. Dinosaurs preserving plumage, nesting sites and trace fossils provide overwhelming evidence for the dinosaurian origin of birds. Based on these recent findings of paleontological research, we conclude that extant birds indeed descended, with some modifications, from small, Mesozoic theropod dinosaurs. In the light of Wallace's view of bird origins, we critically evaluate recent opposing views to this idea, including Ernst Mayr's (1904-2005) arguments against the "dinosaur-bird hypothesis", and document that this famous ornithologist was not correct in his assessment of this important aspect of vertebrate evolution.

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

BACKGROUND: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. DESCRIPTION: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. CONCLUSIONS: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.

A new pterosaur (Pterodactyloidea: Azhdarchidae) from the Upper Cretaceous of Morocco.

The Kem Kem beds in South Eastern Morocco contain a rich early Upper (or possibly late Lower) Cretaceous vertebrate assemblage. Fragmentary remains, predominantly teeth and jaw tips, represent several kinds of pterosaur although only one species, the ornithocheirid Coloborhynchus moroccensis, has been named. Here, we describe a new azhdarchid pterosaur, Alanqa saharica nov. gen. nov. sp., based on an almost complete well preserved mandibular symphysis from Aferdou N'Chaft. We assign additional fragmentary jaw remains, some of which have been tentatively identified as azhdarchid and pteranodontid, to this new taxon which is distinguished from other azhdarchids by a remarkably straight, elongate, lance-shaped mandibular symphysis that bears a pronounced dorsal eminence near the posterior end of its dorsal (occlusal) surface. Most remains, including the holotype, represent individuals of approximately three to four meters in wingspan, but a fragment of a large cervical vertebra, that probably also belongs to A. saharica, suggests that wingspans of six meters were achieved in this species. The Kem Kem beds have yielded the most diverse pterosaur assemblage yet reported from Africa and provide the first clear evidence for the presence of azhdarchids in Gondwana at the start of the Late Cretaceous. This, the relatively large size achieved by Alanqa, and the additional evidence of variable jaw morphology in azhdarchids provided by this taxon, indicates a longer and more complex history for this clade than previously suspected.