A "Mean Quarrelsome Spirit:" Controversy in British Systematics, 1822-1836

British systematics was distinctly marked by a raft of vituperative controversies around the turn of the 1830s. After the local collapse of broad consensus in the Linnaean system by 1820, the emergence of new schemes of classification-most notably, the "quinarian" system of William Sharp Macleay-brought with it an unprecedented register of public debate among zoologists in Britain, one which a young Charles Darwin would bitterly describe to his friend John Stevens Henslow in October 1836 as possessing a "mean quarrelsome spirit," conducted in "a manner anything but like that of gentlemen." This article aims to provide a social and conceptual account of the remarkable tenor of zoological discourse in Britain in the late 1820s and early 1830s, with joint attention to the philosophical and interpersonal commitments at play. In doing so, it analyzes the three of the period's most striking public controversies, each of which counted key advocates of the quinarian system as central participants.

A globally integrated structure of taxonomy to support biodiversity science and conservation

All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.

Medicare and Medicaid Dual-Eligible Special Needs Plan Enrollment and Beneficiary-Reported Experiences With Care

This cross-sectional study analyzes Medicare Advantage surveys to compare Medicare and Medicaid dual-eligible individuals’ experiences with care across 3 established categories of plans.

New heterodont odontocetes from the Oligocene Pysht Formation in Washington State, U.S.A., and a reevaluation of Simocetidae (Cetacea, Odontoceti)

Odontocetes first appeared in the fossil record by the early Oligocene, and their early evolutionary history can provide clues as to how some of their unique adaptations, such as echolocation, evolved. Here, three new specimens from the early to late Oligocene Pysht Formation are described further increasing our understanding of the richness and diversity of early odontocetes, particularly for the North Pacific. Phylogenetic analysis shows that the new specimens are part of a more inclusive, redefined Simocetidae, which now includes Simocetus rayi, Olympicetus sp. 1, Olympicetus avitus, O. thalassodon sp. nov., and a large unnamed taxon (Simocetidae gen. et sp. A), all part of a North Pacific clade that represents one of the earliest diverging groups of odontocetes. Amongst these, Olympicetus thalassodon sp. nov. represents one of the best known simocetids, offering new information on the cranial and dental morphology of early odontocetes. Furthermore, the inclusion of CCNHM 1000, here considered to represent a neonate of Olympicetus sp., as part of the Simocetidae, suggests that members of this group may not have had the capability of ultrasonic hearing, at least during their early ontogenetic stages. Based on the new specimens, the dentition of simocetids is interpreted as being plesiomorphic, with a tooth count more akin to that of basilosaurids and early toothed mysticetes, while other features of the skull and hyoid suggest various forms of prey acquisition, including raptorial or combined feeding in Olympicetus spp., and suction feeding in Simocetus. Finally, body size estimates show that small to moderately large taxa are present in Simocetidae, with the largest taxon represented by Simocetidae gen. et sp. A with an estimated body length of 3 m, which places it as the largest known simocetid, and amongst the largest Oligocene odontocetes. The new specimens described here add to a growing list of Oligocene marine tetrapods from the North Pacific, further promoting faunistic comparisons across other contemporaneous and younger assemblages, that will allow for an improved understanding of the evolution of marine faunas in the region.

Environmental exposure to metals and the development of tauopathies, synucleinopathies, and TDP-43 proteinopathies: A systematic evidence map protocol

BACKGROUND

Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis are incurable and expected to increase in prevalence in the upcoming decades. Environmental exposure to metals has been suggested as a contributing factor to the development of neurodegenerative disease. This systematic evidence map will identify and characterize the epidemiological and experimental data available on the intersection of eighteen metals of environmental concern (i.e., aluminum, antimony, arsenic, barium, beryllium, cadmium, chromium, cobalt, copper, lead, manganese, mercury, nickel, palladium, radium, silver, vanadium, and zinc) and three neurodegenerative disease clusters (i.e., tauopathies, synucleinopathies, and TDP-43 proteinopathies). We aim to describe the type and amount of evidence available (or lack thereof) for each metal and neurodegenerative disease combination and highlight important knowledge gaps and knowledge clusters for future research.

METHODS

We will conduct a thorough search using two databases (MEDLINE and Web of Science Core Collection) and grey literature resources. Pre-defined criteria have been developed to identify studies which evaluate at least one of the selected metals and neurodegenerative disease-relevant outcomes (e.g., neuropathology, cognitive function, motor function, disease mortality). At each phase of review, studies will be evaluated by two reviewers. Studies determined to be relevant will be extracted for population, exposure, and outcome information. We will conduct a narrative review of the included studies, and the extracted data will be available in a database hosted on Tableau Public.

CONCLUSION

This protocol documents the decisions made a priori to data collection regarding these objectives.

The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus

BACKGROUND

The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants.

RESULTS

In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum.

CONCLUSION

The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.

Biosystematics studies on Elymus breviaristatus and Elymus sinosubmuticus (Poaceae: Triticeae)

BACKGROUND

Elymus breviaristatus and Elymus sinosubmuticus are perennial herbs, not only morphologically similar but also sympatric distribution. The genome composition of E. sinosubmuticus has not been reported, and the relationship between E. sinosubmuticus and E. breviaristatus is still controversial. We performed artificial hybridization, genomic in situ hybridization, and phylogenetic analyses to clarify whether the two taxa were the same species.

RESULTS

The high frequency bivalent (with an average of 20.62 bivalents per cell) at metaphase I of pollen mother cells of the artificial hybrids of E. breviaristatus (StYH) × E. sinosubmuticus was observed. It illustrated that E. sinosubmuticus was closely related to E. breviaristatus. Based on genomic in situ hybridization results, we confirmed that E. sinosubmuticus was an allohexaploid, and the genomic constitution was StYH. Phylogenetic analysis results also supported that this species contained St, Y, and H genomes. In their F₁ hybrids, pollen activity was 53.90%, and the seed setting rate was 22.46%. Those indicated that the relationship between E. sinosubmuticus and E. breviaristatus is intersubspecific rather than interspecific, and it is reasonable to treated E. sinosubmuticus as the subspecies of E. breviaristatus.

CONCLUSIONS

In all, the genomic constitutions of E. sinosubmuticus and E. breviaristatus were StYH, and they are species in the genus Campeiostachys. Because E. breviaristatus was treated as Campeistachys breviaristata, Elymus sinosubmuticus should be renamed Campeiostachys breviaristata (Keng) Y. H. Zhou, H. Q. Zhang et C. R. Yang subsp. sinosubmuticus (S. L. Chen) Y. H. Zhou, H. Q. Zhang et L. Tan.

Taxonomic Diversity of the Quill Mites of the Family Syringophilidae (Acariformes: Prostigmata) Associated With Old World Parrots (Psittaciformes: Psittaculidae)

The quill mite fauna of the family Syringophilidae Lavoipierre, 1953 (Acariformes: Prostigmata) associated with parrots (Aves: Psittaciformes) are reviewed. Seven new species are described: Pipicobia cyclopsitta Marciniak-Musial, Hromada & Sikora sp. nov. from the Double-Eyed Fig-Parrot Cyclopsitta diophthalma in Papua New Guinea; P. fuscata Marciniak-Musial, Hromada & Sikora sp. nov. from the Dusky Lory Pseudeos fuscata in Papua New Guinea; P. tahitiana Marciniak-Musial, Hromada & Sikora sp. nov. from the Blue Lorikeet Vini peruviana in Tahiti (French Polynesia); P. malherbi Marciniak-Musial, Hromada & Sikora sp. nov. from the Malherbe's Parakeet Cyanoramphus malherbi in New Zealand; Lawrencipicobia eclectus Marciniak-Musial, Hromada & Sikora sp. nov. from the Eclectus Parrot Eclectus roratus in Papua New Guinea; Neoaulobia pseudeos Marciniak-Musial, Hromada & Sikora sp. nov. from the Dusky Lory Pseudeos fuscata in Papua New Guinea; and N. Skorackii Marciniak-Musial, Hromada & Sikora sp. nov. from the Eastern Rosella Platycercus eximius in Australia.

Diversity of Culicoides (Diptera: Ceratopogonidae) in Rural Settlements and Degraded Seasonal Deciduous Forests

Biting midges are widespread in Brazilian natural ecosystems. However, deforestation and other activities that impact the environment are reducing natural habitats where biting midges proliferate. The objective of this study was to verify whether there is variation in the composition, richness, abundance, and seasonality of biting midges between wild and rural environments, in a forest area with intense deforestation. Biting midges were captured using 6 traps installed at an average height of 1.5 m in the peridomicile, intradomicile, and deciduous seasonal forests, once a month from May 2012 to April 2013. In total, 2,182 specimens of 13 species of the genus Culicoides were captured. Species richness was similar in the intradomicile (13 species), forest (12), and peridomicile (11), but species diversity was greater in the peridomicile (H' = 0.803) compared with the intradomicile (H' = 0.717) and forest (H' = 0.687). The order of species dominance varied between the forest (Culicoides paucienfuscatus Barbosa > Culicoides leopodoi Ortiz > Culicoides foxi Ortiz > Culicoides ignacioi Forattini) and peridomicile + intradomicile habitats (C. paucienfuscatus > C. foxi > C. filariferus Hoffman > C. ignacioi). The activity of these dipterans was strongly influenced by meteorological variables, as biting midges are predominant in the rainy season (80.7% of specimens), when higher rainfall, relative humidity, and lower temperatures prevail. The abundance of biting midges was higher in the peridomicile + intradomicile (83.7% of specimens) compared with the degraded forest (16.3%), a result that reflects the loss of forest habitat due to intense and progressive deforestation.

Landscape Anthropization Affects Mosquito Diversity in a Deciduous Forest in Southeastern Mexico

Mosquitoes (Diptera: Culicidae) are considered the group of insects that most impacts human health. Land use change, conversion of conserved sites into agricultural environments, urbanization, defaunation, and introduction of domestic animals can affect mosquito diversity positively or negatively, increasing the risk of transmission of zoonotic diseases. Here, we describe the diversity of adult mosquitoes in two environments (deciduous forest and anthropized zone) over 2 yr (2014-2016), using eight CDC traps at each site in three climatic seasons (rainy, cold, and dry). We captured 795 individuals belonging to 22 species. We constructed rank-abundance curves to determine spatial and temporal changes in the mosquito communities. We measured alpha diversity using the Shannon index (H'), Shannon exponential (eH) and Simpson dominance (Ds), and beta diversity using Jaccard's coefficient of similarity (Ij). The most abundant species were Culex quinquefasciatus (40.5%), Culex coronator (18.3%), and Anopheles pseudopunctipennis (12.4%). The highest mosquito diversity was in the deciduous forest during the rainy season. Beta diversity analysis showed that species overlap varied among climatic seasons, with the sites sharing 65% species during the rainy season, but only 33% of species during the dry season. We found differences in the diversity of mosquitoes at the two sites, and the mosquito assemblage of the anthropized zone was significantly different from that of the deciduous forest.

The Natural Products Atlas 2.0: a database of microbially-derived natural products

Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.

BacDive in 2022: the knowledge base for standardized bacterial and archaeal data

The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms.

A supergene underlies linked variation in color and morphology in a Holarctic songbird

The genetic architecture of a phenotype can have considerable effects on the evolution of a trait or species. Characterizing genetic architecture provides insight into the complexity of a given phenotype and, potentially, the role of the phenotype in evolutionary processes like speciation. We use genome sequences to investigate the genetic basis of phenotypic variation in redpoll finches (Acanthis spp.). We demonstrate that variation in redpoll phenotype is broadly controlled by a ~55-Mb chromosomal inversion. Within this inversion, we find multiple candidate genes related to melanogenesis, carotenoid coloration, and bill shape, suggesting the inversion acts as a supergene controlling multiple linked traits. A latitudinal gradient in ecotype distribution suggests supergene driven variation in color and bill morphology are likely under environmental selection, maintaining supergene haplotypes as a balanced polymorphism. Our results provide a mechanism for the maintenance of ecotype variation in redpolls despite a genome largely homogenized by gene flow.

Fine-Tuning Word Embeddings for Hierarchical Representation of Data Using a Corpus and a Knowledge Base for Various Machine Learning Applications

Word embedding models have recently shown some capability to encode hierarchical information that exists in textual data. However, such models do not explicitly encode the hierarchical structure that exists among words. In this work, we propose a method to learn hierarchical word embeddings (HWEs) in a specific order to encode the hierarchical information of a knowledge base (KB) in a vector space. To learn the word embeddings, our proposed method considers not only the hypernym relations that exist between words in a KB but also contextual information in a text corpus. The experimental results on various applications, such as supervised and unsupervised hypernymy detection, graded lexical entailment prediction, hierarchical path prediction, and word reconstruction tasks, show the ability of the proposed method to encode the hierarchy. Moreover, the proposed method outperforms previously proposed methods for learning nonspecialised, hypernym-specific, and hierarchical word embeddings on multiple benchmarks.

Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?

OBJECTIVE

Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD).

METHODS

21 healthy controls and 41 patients with OLD completed two bronchoscopies. In addition to negative controls (NCS) and oral wash (OW) samples, we gathered protected bronchoalveolar lavage in two fractions (PBAL1 and PBAL2) and protected specimen brushes (PSB). After DNA extraction, we amplified the V3V4 region of the 16S rRNA gene, and performed paired-end sequencing (Illumina MiSeq). Initial bioinformatic processing was carried out in the QIIME-2 pipeline, identifying amplicon sequence variants (ASVs) with the DADA2 algorithm. Potentially contaminating ASVs were identified and removed using the decontam package in R and the sequenced NCS.

RESULTS

A final table of 551 ASVs consisted of 19 × 106 sequences. Alpha diversity was lower in the second exam for OW samples, and borderline lower for PBAL1, with larger differences in subjects not having received intercurrent antibiotics. Permutational tests of beta diversity indicated that within-individual changes were significantly lower than between-individual changes. A non-parametric trend test showed that differences in composition between the two exams (beta diversity) were largest in the PSBs, and that these differences followed a pattern of PSB > PBAL2 > PBAL1 > OW. Time between procedures was not associated with increased diversity.

CONCLUSION

The airways microbiota varied between examinations. However, there is compositional microbiota stability within a person, beyond that of chance, supporting the notion of a transient airways microbiota with a possibly more stable individual core microbiome.

Phenotypic variation of floral organs in flowering crabapples and its taxonomic significance

BACKGROUND

In angiosperms, phenotypic variation of floral organs is often considered as the traditional basis for the evolutionary relationship of different taxonomic groups above the species level. However, little is known about that at or below the species level. Here, we experimentally tested the phenotypic variation of Malus floral organs using combined methods of intraspecific uniformity test, interspecific distinctness analysis, principal component analysis, Pearson correlation analysis, and Q-type cluster analysis. The ancestor-inclined distribution characteristic analysis of Malus species and cultivars floral attributes was also carried out, so as to explore its taxonomic significance.

RESULTS

15/44 phenotypic traits (e.g., flower shape, flower type, flower diameter, ...) were highly consistent, distinguishable, and independent and could be used as the basis for Malus germplasm taxonomy. The studied 142 taxa were divided into two groups (A, B) and five sub-groups (A₁, A₂, B₁, B₂, B₃), with significantly variable floral phenotypic attributes between groups and within sub-groups. Malus natural species were relatively clustered in the same section (series) while homologous cultivars showed evidence of ancestor-inclined distribution characteristics. However, no significant correlation between the evolutionary order of sections (Sect. Docyniopsis → Sect. Chloromeles → Sect. Sorbomalus → Sect. Eumalus) and group/sub-groups (B₃ → B₂ → B₁ → A).

CONCLUSIONS

Phenotypic variation of floral organs could better explore the genetic relationship between Malus taxa. The findings improved our cognition of floral phenotypic variation taxonomic significance under the species level.

Predicting Long-Term Outcomes in First-Admission Psychosis: Does the Hierarchical Taxonomy of Psychopathology Aid DSM in Prognostication?

The Hierarchical Taxonomy of Psychopathology (HiTOP) is an empirical, dimensional model of psychological symptoms and functioning. Its goals are to augment the use and address the limitations of traditional diagnoses, such as arbitrary thresholds of severity, within-disorder heterogeneity, and low reliability. HiTOP has made inroads to addressing these problems, but its prognostic validity is uncertain. The present study sought to test the prediction of long-term outcomes in psychotic disorders was improved when the HiTOP dimensional approach was considered along with traditional (ie, DSM) diagnoses. We analyzed data from the Suffolk County Mental Health Project (N = 316), an epidemiologic study of a first-admission psychosis cohort followed for 20 years. We compared 5 diagnostic groups (schizophrenia/schizoaffective, bipolar disorder with psychosis, major depressive disorder with psychosis, substance-induced psychosis, and other psychoses) and 5 dimensions derived from the HiTOP thought disorder spectrum (reality distortion, disorganization, inexpressivity, avolition, and functional impairment). Both nosologies predicted a significant amount of variance in most outcomes. However, except for cognitive functioning, HiTOP showed consistently greater predictive power across outcomes-it explained 1.7-fold more variance than diagnoses in psychiatric and physical health outcomes, 2.1-fold more variance in community functioning, and 3.4-fold more variance in neural responses. Even when controlling for diagnosis, HiTOP dimensions incrementally predicted almost all outcomes. These findings support a shift away from the exclusive use of categorical diagnoses and toward the incorporation of HiTOP dimensions for better prognostication and linkage with neurobiology.

Towards omics-based predictions of planktonic functional composition from environmental data

Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes through a network-based approach and detect 233,756 protein functional clusters, from which 15% are functionally unannotated. We investigate all clusters' distributions across the global ocean through machine learning, identifying biogeographical provinces as the best predictors of protein functional clusters' abundance. The abundances of 14,585 clusters are predictable from the environmental context, including 1347 functionally unannotated clusters. We analyze the biogeography of these 14,585 clusters, identifying the Mediterranean Sea as an outlier in terms of protein functional clusters composition. Applicable to any set of sequences, our approach constitutes a step towards quantitative predictions of functional composition from the environmental context.

Characterization and Phylogenetic Analysis of the Mitochondrial Genome Sequence of Nisia fuliginosa (Hemiptera: Fulgoroidea: Meenoplidae)

We explored characterization of the mitochondrial genome (mitogenome or mtGenome) and phylogenetic analysis between 32 Fulgoroid species by sequencing and analyzing the mitogenome of Nisia fuliginosa Yang and Hu, 1985 (Hemiptera: Fulgoroidea: Meenoplidae), thereby making it the first determined mitogenome from the family Meenoplidae. The mitogenome was found to be 15,754 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, two ribosomal RNA genes (rRNAs), and a control region. All PCGs started with typical ATN codons, except for nad1, which used GTG as the start codon. Canonical TAA termination codons were found in 10 PCGs and the remaining three genes (cox2, nad6, and nad1) had incomplete stop codons T. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnC, trnV, and trnS1. Additionally, we compared the AT and GC skews of 13 PCGs of 32 Fulgoroidea mitogenomes, on the L-strand, the AT and GC skews were negative and positive, respectively. However, on the H-strand, the AT skew could be positive or negative and the GC skew was always negative. Phylogenetic results showed that the eight families of Fulgoroidea were divided into two large groups. Delphacidae formed a monophyletic group sister to a clade comprising Meenoplidae and other six families (Fulgoridae, Ricaniidae, Flatidae, Issidae, Caliscelidae, and Achilidae). Meenoplidae was located near the clade of Delphacidae, and Fulgoridae was located near the clade of Meenoplidae. Furthermore, Caliscelidae, Issidae, Ricaniidae, and Flatidae are closely related and they collectively formed a sister group to Achilidae.

DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the 'DKFZ Sarcoma Classifier'

Diagnosing bone and soft tissue neoplasms remains challenging because of the large number of subtypes, many of which lack diagnostic biomarkers. DNA methylation profiles have proven to be a reliable basis for the classification of brain tumours and, following this success, a DNA methylation-based sarcoma classification tool from the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg has been developed. In this study, we assessed the performance of their classifier on DNA methylation profiles of an independent data set of 986 bone and soft tissue tumours and controls. We found that the 'DKFZ Sarcoma Classifier' was able to produce a diagnostic prediction for 55% of the 986 samples, with 83% of these predictions concordant with the histological diagnosis. On limiting the validation to the 820 cases with histological diagnoses for which the DKFZ Classifier was trained, 61% of cases received a prediction, and the histological diagnosis was concordant with the predicted methylation class in 88% of these cases, findings comparable to those reported in the DKFZ Classifier paper. The classifier performed best when diagnosing mesenchymal chondrosarcomas (CHSs, 88% sensitivity), chordomas (85% sensitivity), and fibrous dysplasia (83% sensitivity). Amongst the subtypes least often classified correctly were clear cell CHSs (14% sensitivity), malignant peripheral nerve sheath tumours (27% sensitivity), and pleomorphic liposarcomas (29% sensitivity). The classifier predictions resulted in revision of the histological diagnosis in six of our cases. We observed that, although a higher tumour purity resulted in a greater likelihood of a prediction being made, it did not correlate with classifier accuracy. Our results show that the DKFZ Classifier represents a powerful research tool for exploring the pathogenesis of sarcoma; with refinement, it has the potential to be a valuable diagnostic tool.

A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis

Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group-Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.

Establishment of Aedes (Ochlerotatus) scapularis (Diptera: Culicidae) in Mainland Florida, With Notes on the Ochlerotatus Group in the United States

Aedes scapularis (Rondani), a widespread neotropical vector mosquito species, has been included in the mosquito fauna of Florida on the basis of just three larval specimens that were collected in the middle Florida Keys in 1945. Here, we report numerous recent collections of immature and adult Ae. scapularis from multiple locations in two counties of southern Florida. These specimens represent the first records of Ae. scapularis from mainland Florida and the first records of the species in the state since the initial detection of the species 75 yr ago. Collections of both larvae and adults across several years indicate that Ae. scapularis is now established in Broward and Miami-Dade Counties. These contemporary records of this species in Florida may represent novel dispersal and subsequent establishment events from populations outside the United States or a recent reemergence of undetected endemic populations. To confirm morphological identification of Ae. scapularis specimens from Florida, the DNA barcoding region of the cytochrome c oxidase subunit I gene (COI) was sequenced and compared to all other Ochlerotatus Group species from the United States, specifically Aedes condolescens Dyar and Knab (Diptera: Culicidae), Aedes infirmatus Dyar and Knab (Diptera: Culicidae), Aedes thelcter Dyar (Diptera: Culicidae), Aedes tortilis (Theobald) (Diptera: Culicidae), and Aedes trivittatus (Coquillett) (Diptera: Culicidae). Molecular assays and sequencing confirm morphological identification of Ae. scapularis specimens. Maximum likelihood phylogenetic analysis of COI and ITS2 sequences place Florida Ae. scapularis in a distinct clade, but was unable to produce distinct clades for Florida specimens of Ae. condolescens and Ae. tortilis.

Data integration enables global biodiversity synthesis

The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.

Exploring the participation of young citizen scientists in scientific research: The case of iNaturalist

Online citizen science projects have broadened options for accessing science and enabled different forms of participation in scientific research for adult and young volunteers. Yet, little is known regarding participation patterns among youth participants. Quantitative approaches were used to investigate the contribution of 183 young volunteers to citizen science on the iNaturalist platform and the participation behaviour that relates to their contribution. The participants accessed and used iNaturalist as part of one-day field-based events (bioblitzes) facilitated by museums. Compared to the observation behaviour of all iNaturalist users, as documented on the platform, the young volunteers observe fewer plants and birds, and more molluscs, arachnids and insects. The average daily contributions of young volunteers were found to be positively associated with a large proportion of active days on iNaturalist and a systematic contribution behaviour, yet negatively related to a long duration on the platform. This study enhances our understanding of young volunteers' contributions to citizen science and provides insights for research on participation in online citizen science. Our findings have implications on how museums design the field-based events to encourage follow-up systematic participation and maintain active contribution.

A Revision of Parasecia (Trombidiformes: Trombiculidae) With a Description of a New Species, a New Genus and a Key to Species

Chiggers of the genus Parasecia Loomis parasitize birds, mammals, and reptiles in the Nearctic and Neotropical regions. In the present review, we examined 18 species previously included in the genus, 15 of them being retained in the genus Parasecia, one genus is created, Nahuacarus bulbocalcarn. gen. (Trombidiformes: Trombiculidae), and new combinations are proposed for two species: Lorillatum lasiurusn. comb. and Lorillatum orphanan. comb. (Trombidiformes: Trombiculidae). In addition, Parasecia kansasensis (Loomis) (Trombidiformes: Trombiculidae) is synonymized with Parasecia gurneyi (Ewing) (Trombidiformes: Trombiculidae), Parasecia gilbetoin. sp. (Trombidiformes: Trombiculidae) is described and new locality and host records are added for Parasecia chara (Wharton), Parasecia longicalcar (Brennan and Jones), Parasecia manueli (Brennan and Jones), and Parasecia thalurania (Brennan) (Trombidiformes: Trombiculidae).

The Culex Mosquitoes (Diptera: Culicidae) of French Guiana: A Comprehensive Review With the Description of Three New Species

The taxonomically intricate genus Culex Linnaeus includes numerous known vector species of parasites and viruses to humans. The aim of this article is to comprehensively review the Culex species which occur in French Guiana to provide a stronger taxonomic foundation for future studies on this genus in South America. The occurrence of Culex species was investigated in light of current taxonomic knowledge through an extensive examination of voucher specimens deposited in the entomological collections of four French depositories and additional specimens recently collected at various localities in French Guiana. Based on this review, 104 Culex species classified in eight subgenera are confirmed to occur in French Guiana. Compared to the most recent checklist, 18 species are added, and 10 species excluded, resulting in a total number of 242 valid mosquito species known to occur in French Guiana. Three nominal species are synonymized, three others are newly described, and a last one is transferred to another informal infrasubgeneric group. Overall, this review also highlights the limits of the use of only bibliographic data when dealing with taxonomically complex groups of insects.

Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra

The clingfish (Gobiesocidae) genus Gouania Nardo, 1833 is endemic to the Mediterranean Sea and inhabits, unlike any other vertebrate species in Europe, the harsh intertidal environment of gravel beaches. Following up on a previous phylogenetic study, we revise the diversity and taxonomy of this genus by analysing a comprehensive set of morphological (meristics, morphometrics, microcomputed tomography imaging), geographical and genetic (DNA-barcoding) data. We provide descriptions of three new species, G. adriatica sp. nov., G. orientalis sp. nov. and G. hofrichteri sp. nov., as well as redescriptions of G. willdenowi (Risso, 1810) and G. pigra (Nardo, 1827) and assign neotypes for the latter two species. In addition to elucidating the complex taxonomic situation of Gouania, we discuss the potential of this enigmatic clingfish genus for further ecological, evolutionary and biodiversity studies that might unravel even more diversity in this unique Mediterranean fish radiation.

Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies

The family-level relationships within Plecoptera have been a focused area of research for a long time. Its higher classification remains unstable, and the phylogenetic relationships within Plecoptera should be re-examined. Here, we sequenced and analyzed two complete mitochondrial genomes (mitogenomes) of Paraleuctra cercia and Perlomyia isobeae of the family Leuctridae. We reconstructed the phylogeny of Plecoptera based on 13 protein-coding genes (PCGs) from published stoneflies. Our results showed that the Bayesian inference and maximum-likelihood tree had similar topological structures except for the positions of two families, Peltoperlidae and Scopuridae. The Plecoptera is divided into two clades, the suborder Antarctoperlaria and the suborder Arctoperlaria. The two suborders subsequently formed two groups, Eusthenioidea and Gripopterygoidea, and Euholognatha and Systellognatha, which is consistent with the results of morphological studies. In addition, the Leuctridae is the earliest branch within the superfamily Nemouroidea. But the monophyly of Perloidea and Pteronarcyoidea are still not well supported.

Knowing what you need to know in advance: The neural processes underpinning flexible semantic retrieval of thematic and taxonomic relations

Semantic retrieval is flexible, allowing us to focus on subsets of features and associations that are relevant to the current task or context: for example, we use taxonomic relations to locate items in the supermarket (carrots are a vegetable), but thematic associations to decide which tools we need when cooking (carrot goes with peeler). We used fMRI to investigate the neural basis of this form of semantic flexibility; in particular, we asked how retrieval unfolds differently when participants have advanced knowledge of the type of link to retrieve between concepts (taxonomic or thematic). Participants performed a semantic relatedness judgement task: on half the trials, they were cued to search for a taxonomic or thematic link, while on the remaining trials, they judged relatedness without knowing which type of semantic relationship would be relevant. Left inferior frontal gyrus showed greater activation when participants knew the trial type in advance. An overlapping region showed a stronger response when the semantic relationship between the items was weaker, suggesting this structure supports both top-down and bottom-up forms of semantic control. Multivariate pattern analysis further revealed that the neural response in left inferior frontal gyrus reflects goal information related to different conceptual relationships. Top-down control specifically modulated the response in visual cortex: when the goal was unknown, there was greater deactivation to the first word, and greater activation to the second word. We conclude that top-down control of semantic retrieval is primarily achieved through the gating of task-relevant 'spoke' regions.

Cryptosporidium ratti n. sp. (Apicomplexa: Cryptosporidiidae) and genetic diversity of Cryptosporidium spp. in brown rats (Rattus norvegicus) in the Czech Republic

The diversity and biology of Cryptosporidium that is specific for rats (Rattus spp.) are not well studied. We examined the occurrence and genetic diversity of Cryptosporidium spp. in wild brown rats (Rattus norvegicus) by microscopy and polymerase chain reaction (PCR)/sequencing targeting the small subunit rDNA (SSU), actin and HSP70 genes. Out of 343 faecal samples tested, none were positive by microscopy and 55 were positive by PCR. Sequence analysis of SSU gene revealed the presence of Cryptosporidium muris (n = 4), C. andersoni (n = 3), C. ryanae (n = 1), C. occultus (n = 3), Cryptosporidium rat genotype I (n = 23), Cryptosporidium rat genotype IV (n = 16) and novel Cryptosporidium rat genotype V (n = 5). Spherical oocysts of Cryptosporidium rat genotype I obtained from naturally-infected rats, measuring 4.4-5.4 μm × 4.3-5.1 μm, were infectious to the laboratory rats, but not to the BALB/c mice (Mus musculus) nor Mongolian gerbils (Meriones unguiculatus). The prepatent period was 3 days post infection and the patent period was longer than 30 days. Naturally- and experimentally-infected rats showed no clinical signs of disease. Percentage of nucleotide similarities at the SSU, actin, HSP70 loci between C. ratti n. sp. and the rat derived C. occultus and Cryptosporidium rat genotype II, III, IV, and V ranged from 91.0 to 98.1%. These genetic variations were similar or greater than that observed between closely related species, i.e. C. parvum and C. erinacei (93.2-99.5%). Our morphological, genetic and biological data support the establishment of Cryptosporidium rat genotype I as a new species, Cryptosporidium ratti n. sp.

It is marine: distinguishing a new species of Catatropis (Digenea: Notocotylidae) from its freshwater twin

The morphology of sexual adults is the cornerstone of digenean systematics. In addition, life cycle data have always been significant. The integration of these approaches, supplemented with molecular data, has allowed us to detect a new species that many researchers may have previously seen, but not recognized. Sexual adults from common eiders that we found in northern European seas were extremely similar to other notocotylids, but the discovery of their intermediate host, a marine snail, revealed the true nature of this material. Here we describe sexual adults, rediae and cercariae of Catatropis onobae sp. nov. We discuss how 'Catatropis verrucosa' should be regarded, justify designation of the new species C. onobae for our material and explain why it can be considered a cryptic species. The phylogenetic position of C. onobae within Notocotylidae, along with other evidence, highlights the challenges for the taxonomy of the family, for which two major genera appear to be polyphyletic and life cycle data likely undervalued.

Evidence for the taxonic latent structure for DSM-5 intermittent explosive disorder in adults

BACKGROUND

Identification of individuals with clinically significant aggressive behavior is critical for the prevention and management of human aggressive behavior. A previous population-based taxometric study reported that the Diagnostic and Statistical Manual of Mental Disorders-4th Edition (DSM-IV) intermittent explosive disorder (IED) belongs to its own discrete class (taxon) rather than existing along a continuum.

METHODS

This study sought to extend previous population-based findings in a clinical research sample of adults with DSM-5 IED (n = 346), adults with non-aggressive DSM-5 disorders (n = 293), and adults without any DSM-5 disorder (n = 174), using standardized assessments of DSM-5 diagnoses, aggression, and other related measures not available in past studies.

RESULTS

Analyses revealed a taxonic latent structure that overlapped with the DSM-5 diagnosis of IED. Within the sample, taxon group members had higher scores on a variety of measures of psychopathology than did the complement members of the sample. Comorbidity of other diagnoses with IED did not affect these results.

CONCLUSION

These findings support the proposition that DSM-5 IED represents a distinct behavioral disorder rather than the severe end of an aggressive behavior continuum.

Perlidae (Plecoptera) from the Paranapiacaba Mountains, Atlantic Forest, Brazil: Diversity and implications of the integrative approach and teneral specimens on taxonomy

The study of complementary sources of biological variation (e.g. morphological, molecular) has allowed a better understanding of biodiversity through the construction of an integrative taxonomy. Using this approach, specimens from the Paranapiacaba Mountains, southeastern Brazil, were studied to update the knowledge on the stonefly family Perlidae from the region, characterize the species, and make associations between nymphs and adults using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. The study also discusses the implications of integrative taxonomy and teneral specimens for the study of South American Perlidae. The molecular data were analyzed using Bayesian inference, Neighbor-joining, and delimiting species methods. Our results revealed that, in general, there was a morphological and molecular congruence between species. In the Paranapiacaba Mountains, three genera and 15 species were recorded: Anacroneuria boraceiensis Froehlich 2004, A. debilis (Pictet 1841) (new record), A. fiorentini De Ribeiro and Froehlich 2007 (new record), A. flintorum Froehlich 2002, A. iporanga Bispo and Froehlich 2004, A. itajaimirim Bispo and Froehlich 2004, A. polita (Burmeister 1913), A. subcostalis Klapálek 1921, A. tupi Bispo and Froehlich 2004 (with a description of the nymph), Kempnyia auberti Froehlich 1996, K. colossica (Navás 1934), K. flava Klapálek 1916, K. neotropica (Jacobson and Bianchi 1905) (including its new junior synonym K. petersorum Froehlich 1996), Kempnyia sp., and Macrogynoplax veneranda Froehlich 1984. COI sequences were obtained for 11 species, five of which had nymphs associated with adults. Among the five associated nymphs, the nymph of A. tupi is described here. The results of this study indicate that the color of adult teneral specimens differs from that of mature specimens. Given this, the synonym of K. neotropica and K. petersorum was proposed since these species have high morphological and molecular similarities and differ only in color patterns. In addition, the previous record of A. petersi Froehlich 2002 from the Paranapiacaba Mountains was invalidated since it was considered a teneral specimen of A. flintorum. These results suggest that the development of an integrative taxonomy is essential to continue advancing the study of Perlidae diversity in South America.

Circular Complex-Valued GMDH-Type Neural Network for Real-Valued Classification Problems

Recently, applications of complex-valued neural networks (CVNNs) to real-valued classification problems have attracted significant attention. However, most existing CVNNs are black-box models with poor explanation performance. This study extends the real-valued group method of data handling (RGMDH)-type neural network to the complex field and constructs a circular complex-valued group method of data handling (C-CGMDH)-type neural network, which is a white-box model. First, a complex least squares method is proposed for parameter estimation. Second, a new complex-valued symmetric regularity criterion is constructed with a logarithmic function to represent explicitly the magnitude and phase of the actual and predicted complex output to evaluate and select the middle candidate models. Furthermore, the property of this new complex-valued external criterion is proven to be similar to that of the real external criterion. Before training this model, a circular transformation is used to transform the real-valued input features to the complex field. Twenty-five real-valued classification data sets from the UCI Machine Learning Repository are used to conduct the experiments. The results show that both RGMDH and C-CGMDH models can select the most important features from the complete feature space through a self-organizing modeling process. Compared with RGMDH, the C-CGMDH model converges faster and selects fewer features. Furthermore, its classification performance is statistically significantly better than the benchmark complex-valued and real-valued models. Regarding time complexity, the C-CGMDH model is comparable with other models in dealing with the data sets that have few features. Finally, we demonstrate that the GMDH-type neural network can be interpretable.

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

Dealing with dysnomia: Strategies for the cultivation of used concepts in social research

This article follows recent calls to turn social theory away from its fixations on intellectual history and toward the mechanics and craft of creating social theories in the research process. The subject of this article is a dilemma common to theorizing in social science: dysnomia, or the phenomenon in which some object is poorly named. Specifically, this article focuses on how social scientists distinguish original concepts from their equivalents in everyday speech. Three tactics for dealing with dysnomia are named-academic arcana, classification and sociologism-and considered in order to ascertain the strengths and weaknesses of each.

Repositories for Taxonomic Data: Where We Are and What is Missing

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].