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.].

Country-level pandemic risk and preparedness classification based on COVID-19 data: A machine learning approach

In this work we present a three-stage Machine Learning strategy to country-level risk classification based on countries that are reporting COVID-19 information. A K% binning discretisation (K = 25) is used to create four risk groups of countries based on the risk of transmission (coronavirus cases per million population), risk of mortality (coronavirus deaths per million population), and risk of inability to test (coronavirus tests per million population). The four risk groups produced by K% binning are labelled as 'low', 'medium-low', 'medium-high', and 'high'. Coronavirus-related data are then removed and the attributes for prediction of the three types of risk are given as the geopolitical and demographic data describing each country. Thus, the calculation of class label is based on coronavirus data but the input attributes are country-level information regardless of coronavirus data. The three four-class classification problems are then explored and benchmarked through leave-one-country-out cross validation to find the strongest model, producing a Stack of Gradient Boosting and Decision Tree algorithms for risk of transmission, a Stack of Support Vector Machine and Extra Trees for risk of mortality, and a Gradient Boosting algorithm for the risk of inability to test. It is noted that high risk for inability to test is often coupled with low risks for transmission and mortality, therefore the risk of inability to test should be interpreted first, before consideration is given to the predicted transmission and mortality risks. Finally, the approach is applied to more recent risk levels to data from September 2020 and weaker results are noted due to the growth of international collaboration detracting useful knowledge from country-level attributes which suggests that similar machine learning approaches are more useful prior to situations later unfolding.

Isolation of Picrotoxanes from Austrobuxus carunculatus Using Taxonomy-Based Molecular Networking

A unique collection of 292 extracts from 107 New Caledonian Euphorbiaceae species sensu lato was profiled by LC-MS² and the metabolite content organized by molecular networking. Based on the assumption that taxon-specific molecules are more likely to be structurally novel, taxonomic data were mapped on spectral networks to detect genus-specific clusters. Using this approach, a group of compounds unique to the genus Austrobuxus was highlighted. The subsequent MS-guided purification of the fruit EtOAc extract of Austrobuxus carunculatus led to the isolation of 13 new monolactone and "norditerpene" picrotoxanes (2-14), along with the known tutin (1). The structures of the new compounds were elucidated by HRESIMS and NMR spectroscopic data analysis, and the absolute configurations of compounds 1, 3, 7, 11, 12, and 14 were determined by single-crystal X-ray diffraction analysis. The relative and absolute configurations of compounds 4 and 5 were ascertained by chemical transformation of compound 3. The absolute configurations of other members of the series have been proposed on the basis of biogenetic considerations and specific rotation values of similar sign and magnitude. Compounds 1-14 were evaluated for their antiproliferative activities against HCT116 colon, U87-MG glioblastoma, and A549 lung human cancer cell lines. Compounds bearing an acyl chain at C-2 (i.e., 2, 4, and 13) showed IC₅₀ values in the micromolar range for the three cell lines used.

Kant, Linnaeus, and the economy of nature

Ecology arguably has roots in eighteenth-century natural histories, such as Linnaeus's economy of nature, which pressed a case for holistic and final-causal explanations of organisms in terms of what we'd now call their environment. After sketching Kant's arguments for the indispensability of final-causal explanation merely in the case of individual organisms, and considering the Linnaean alternative, this paper examines Kant's critical response to Linnaean ideas. I argue that Kant does not explicitly reject Linnaeus's holism. But he maintains that the indispensability of final-causal explanation depends on robust modal connections between types of organism and their functional parts; relationships in Linnaeus's economy of nature, by contrast, are relatively contingent. Kant's framework avoids strong metaphysical assumptions, is responsive to empirical evidence, and can be fruitfully compared with some contemporary approaches to biological organization.

Integrative taxonomy identifies a new stingray species of the genus Hypanus Rafinesque, 1818 (Dasyatidae, Myliobatiformes), from the Tropical Southwestern Atlantic

An integrative approach by the congruence of genetics, morphology and ecological niche modelling (ENM) was used to delimit a new species of Hypanus (Rafinesque, 1818), a recently resurrected genus of marine stingrays comprising eight species, five of which occur in the western Atlantic. The species with the widest distribution, Hypanus americanus (Hildebrand and Schroeder, 1928), from the northeastern coast of the United States to southeastern Brazil, was demonstrated to be paraphyletic based on protein-coding mitochondrial genome analyses. This data set also indicates that the genetic distance between the new species Hypanus berthalutzae sp. nov. and its three closely related species (H. americanus, H. longus and H. rudis) varies from 0.82% to 3.14%. In addition, Bayesian Analysis of Population Similarity using the mitochondrial gene mt-nd2 supports the separation of H. berthalutzae sp. nov. (southwestern Atlantic) from its sister species H. rudis (eastern Atlantic). Similarly, morphological and morphometric analyses corroborated four morphotypes within the H. americanus species group and indicated the ventral caudal fold height and length and interspiracular and interorbital lengths as useful measurements to distinguish among them. Claspers of adult males also exhibit morphological differences among species. The ENM agreed with molecular and morphological analyses and delimits the distribution of H. berthalutzae sp. nov. to shallow areas close to shore along the Brazilian coast, from the mouth of the Amazon River to São Paulo State, including the northeastern oceanic islands, suggesting that the great outflow of fresh water and sediments and the Mid-Atlantic Ridge might act as barriers. The integration of these data to describe a new species provides information relevant to their conservation status, because all species of the H. americanus species group are under the "data-deficient" status.

No vagina, one vagina, or multiple vaginae? An integrative study of Pseudaxine trachuri (Monogenea, Gastrocotylidae) leads to a better understanding of the systematics of Pseudaxine and related genera

The presence/absence and number of vaginae is a major characteristic for the systematics of the Monogenea. Three gastrocotylid genera share similar morphology and anatomy but are distinguished by this character: Pseudaxine Parona & Perugia, 1890 has no vagina, Allogastrocotyle Nasir & Fuentes Zambrano, 1983 has two vaginae, and Pseudaxinoides Lebedev, 1968 has multiple vaginae. In the course of a study of Pseudaxine trachuri Parona & Perugia 1890, we found specimens with structures resembling "multiple vaginae"; we compared them with specimens without vaginae in terms of both morphology and molecular characterisitics (COI barcode), and found that they belonged to the same species. We also investigated the male copulatory organ (MCO) of this species, the accuracy of the original description of which is known to be a matter of debate. We found that the genital atrium is armed with 12 hooks arranged as a single circle and a central hollow stylet which is probably involved in traumatic insemination. We redescribed Pseudaxine trachuri based on newly collected specimens from off the coast of Algeria and Museum specimens from off France. Specimens from the type-host, Trachurus trachurus, were found to be similar, for both molecular sequences and morphology, to those found on Boops boops. We can therefore confirm, for the first time with molecular evidence, that B. boops is a host of this parasite. We consider that Pseudaxinoides was erected on the basis of an erroneous interpretation of structures which are not vaginae and, consequently, propose the transfer of most of its species to Pseudaxine, as P. australis (Lebedev, 1968) n. comb., P. bychowskyi (Lebedev, 1977) n. comb., P. caballeroi (Lebedev, 1977) n. comb., P. cariacoensis (Nasir & Fuentes-Zambrano, 1983) n. comb., and P. vietnamensis (Lebedev, Parukhin & Roitman, 1970) n. comb. We also propose Allogastrocotyle dillonhargisorum nom. nov. for Pseudaxine bivaginalis Dillon & Hargis, 1965 to avoid a secondary homonymy.

Molecular characterization of ascaridoid parasites from captive wild carnivores in China using ribosomal and mitochondrial sequences

BACKGROUND

Despite the public health importance of toxocariasis/toxascariasis, only a few species of these ascaridoid parasites from wild canine and feline carnivores have been studied at the molecular level so far. Poor understanding of diversity, host distribution and the potential (zoonotic) transmission of the ascaridoid species among wild animals negatively affects their surveillance and control in natural settings. In this study, we updated previous knowledge by profiling the genetic diversity and phylogenetic relationships of ascaridoid species among eleven wild canine and feline animals on the basis of a combined analysis of the ribosomal internal transcribed spacer region (ITS) gene and the partial mitochondrial cytochrome c oxidase subunit 2 (cox2) and NADH dehydrogenase subunit 1 (nad1) genes.

RESULTS

In total, three genetically distinct ascaridoid lineages were determined to be present among these wild carnivores sampled, including Toxocara canis in Alopex lagopus and Vulpes vulpes, Toxocara cati in Felis chaus, Prionailurus bengalensis and Catopuma temmincki and Toxascaris leonina in Canis lupus, Panthera tigris altaica, Panthera tigris amoyensis, Panthera tigris tigris, Panthera leo and Lynx lynx. Furthermore, it was evident that T. leonina lineage split into three well-supported subclades depending on their host species, i.e. wild felids, dogs and wolves and foxes, based on integrated genetic and phylogenetic evidence, supporting that a complex of T. leonina other than one species infecting these hosts.

CONCLUSIONS

These results provide new molecular insights into classification, phylogenetic relationships and epidemiological importance of ascaridoids from wild canids and felids and also highlight the complex of the taxonomy and genetics of Toxascaris in their wild and domestic carnivorous hosts.

Taxonomic Triangulation of Care in Healthcare Protocols: Mapping of Diagnostic Knowledge From Standardized Language

Taxonomic triangulation is a data mining technique for the management of care knowledge. This technique uses standardized languages, such as North American Nursing Diagnosis Association International, Nursing Outcomes Classification, and Nursing Interventions Classification, as well as logic. Its purpose is to find patterns in the data and identify care diagnoses. Triangulation can be applied to databases (clinical records) or to bibliographic sources (eg, protocols). The objective of this study is to identify the care diagnoses implicit in the nursing care protocols of the Community of Madrid. The method followed has three phases: knowledge extraction for mapping of variables, linking to diagnoses, and triangulation with analysis. The study analyzes six protocols, and 344 variables (167 assessment, 29 planning, and 148 intervention) and 6118 links have been extracted. Triangulation identified 165 NANDA diagnoses (68.48%), and only 25 labels were not revealed through this process. As a limitation, the results depend on the knowledge presented in protocols and change with language editions. Some labels included in the sample are recent and are not included in the links with nursing outcomes classification and nursing interventions classification. In conclusion, taxonomic triangulation makes it possible to manage knowledge, discover data patterns, and represent care situations.

Phage S144, A New Polyvalent Phage Infecting Salmonella spp. and Cronobacter sakazakii

Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. In total, 32 ORFs coding for structural proteins were confirmed by ESI-MS/MS analysis, whereas 45 gene products were functionally annotated within DNA metabolism, packaging, nucleotide biosynthesis and phage morphogenesis. Transmission electron microscopy showed that phage S144 is a myovirus, with a prolate head and short tail fibers. The putative S144 tail fiber structure is, overall, similar to the tail fiber of phage Mu and the C-terminus shows amino acid similarity to tail fibers of otherwise unrelated phages infecting Cronobacter. Since all phages in the Loughboroughvirus genus encode tail fibers similar to S144, we suggest that phages in this genus infect Cronobacter sakazakii and are polyvalent.

Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

BACKGROUND

Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics.

METHODS

To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms.

RESULTS

The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers.

CONCLUSIONS

This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

Characterization of gut contractility and microbiota in patients with severe chronic constipation

Chronic constipation (CC) is one of the most common gastrointestinal disorders worldwide. Its pathogenesis, however, remains largely unclear. The purpose of the present work was to gain an insight into the role of contractility and microbiota in the etiology of CC. To this end, we studied spontaneous and evoked contractile activity of descending colon segments from patients that have undergone surgery for refractory forms of CC. The juxta-mucosal microbiota of these colon samples were characterized with culture-based and 16S rRNA sequencing techniques. In patients with CC the spontaneous colonic motility remained unchanged compared to the control group without dysfunction of intestinal motility. Moreover, contractions induced by potassium chloride and carbachol were increased in both circular and longitudinal colonic muscle strips, thus indicating preservation of contractile apparatus and increased sensitivity to cholinergic nerve stimulation in the constipated intestine. In the test group, the gut microbiota composition was assessed as being typically human, with four dominant bacterial phyla, namely Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, as well as usual representation of the most prevalent gut bacterial genera. Yet, significant inter-individual differences were revealed. The phylogenetic diversity of gut microbiota was not affected by age, sex, or colonic anatomy (dolichocolon, megacolon). The abundance of butyrate-producing genera Roseburia, Coprococcus, and Faecalibacterium was low, whereas conventional probiotic genera Lactobacillus and Bifidobacteria were not decreased in the gut microbiomes of the constipated patients. As evidenced by our study, specific microbial biomarkers for constipation state are absent. The results point to a probable role played by the overall gut microbiota at the functional level. To our knowledge, this is the first comprehensive characterization of CC pathogenesis, finding lack of disruption of motor activity of colonic smooth muscle cells and insufficiency of particular members of gut microbiota usually implicated in CC.

Identification of Cartilage Microbial DNA Signatures and Associations With Knee and Hip Osteoarthritis

OBJECTIVE

Alterations of the gut microbiota have been implicated in many forms of arthritis, but an examination of cartilage microbial patterns has not been performed. This study was undertaken to characterize the microbial DNA profile of articular cartilage and determine changes associated with osteoarthritis (OA).

METHODS

We performed 16S ribosomal RNA gene deep sequencing on eroded and intact cartilage samples from knee OA patients (n = 21 eroded and 21 intact samples) and hip OA patients (n = 34 eroded and 33 intact samples) and cadaver controls (n = 10 knee samples and 10 hip samples). Microbial DNA diversity was assessed, groups were compared, and metagenomic profiles were reconstructed. Confirmation was performed in an independent cohort by clade-specific quantitative polymerase chain reaction. Findings in human cartilage were compared to those in cartilage from OA-susceptible C57BL/6 (B6) mice and OA-resistant MRL/MpJ (MRL) mice. Germ-free B6 mouse cartilage was analyzed as a methodologic control.

RESULTS

Alpha diversity was reduced in human OA versus control samples (P < 0.0001), and in hip versus knee samples (P < 0.0001). Numerous clades were different in human OA versus control samples, and similar findings were noted in comparisons of murine B6 versus MRL mice. Hip samples were microbiologically distinct from knee samples. OA microbial DNA demonstrated increased gram-negative constituents (P = 0.02). Functional analysis demonstrated increases in lipopolysaccharide production (P = 9.9 × 10-3 ), phosphatidylinositol signaling (P = 4.2 × 10-4 ), and nitrogen metabolism (P = 8 × 10-3 ) and decreases in sphingolipid metabolism (P = 7.7 × 10-4 ) associated with OA.

CONCLUSION

Our study reveals a microbial DNA signature in human and mouse cartilage. Alterations in this signature, including increases in gram-negative constituents, occur during the development and progression of human OA. Furthermore, our findings indicate that strain-specific signatures exist within mouse cartilage that mirror human patterns. Further study of the establishment and potential pathogenic role of these DNA signatures is needed.

Effects of octylphenol exposure on the lipid metabolism and microbiome of the intestinal tract of Rana chensinensis tadpole by RNAseq and 16s amplicon sequencing

Octylphenol (OP) is a widely distributed endocrine disrupting chemical (EDC), and can be commonly found in various and diverse environmental media. Previous studies have reported that OP exposure could cause many adverse effects on aquatic animals. However, knowledge concerning the impact of OP on lipid metabolism in amphibians was still limited. In our study, Rana chensinensis tadpoles were exposed to different OP concentrations (0, 10^-8, 10^-7 and 10^-6 mol/L) from the Gosner stage (Gs) 25-38. The RNA-seq analysis of tadpole intestines was explored by RNA-seq, and six differentially expressed genes (DEGs) related to the fat digestion and absorption were validated by RT-qPCR. Moreover, we used 16s amplicon sequencing to evaluate effects of OP on intestinal microbiome in tadpoles, further determining the variations of lipid metabolism. Our results revealed that OP exposure influenced gene expression levels related to fat digestion and absorption and led to alteration of structure and composition of intestinal microbiome. At the phylum level, the Firmicutes/Bacteroidetes ratio was gradually decreased in OP exposure groups, which disrupted lipid metabolism. According to the results of intestinal microbial functional prediction, OP exposure interfered with metabolic function and increased risk of disease. These data provide us with powerful resources to assess the effects of OP on lipid metabolism by integrating RNAseq and 16s amplicon sequencing analysis of intestinal tract and intestinal microbiome.

Cuscuta seeds: Diversity and evolution, value for systematics/identification and exploration of allometric relationships

Cuscuta (dodders) is a group of parasitic plants with tremendous economic and ecological significance. Their seeds are often described as "simple" or "unspecialized" because they do not exhibit any classical dispersal syndrome traits. Previous studies of seed morphology and/or anatomy were conducted on relatively few species. We expanded research to 101 species; reconstructed ancestral character states; investigated correlations among seed characters and explored allometric relationships with breeding systems, the size of geographical distribution of species in North America, as well as the survival of seedlings. Seed morphological and anatomical characters permit the separation of subgenera, but not of sections. Identification of Cuscuta species using seed characteristics is difficult but not impossible if their geographical origin is known. Seeds of subg. Monogynella species, exhibit the likely ancestral epidermis type consisting of elongated and interlocked cells, which are morphologically invariant, uninfluenced by dryness/wetness. Subgenera Cuscuta, Pachystigma and Grammica have evolved a seed epidermis with isodiametric cells that can alternate their morphology between two states: pitted when seeds are dry, and papillose after seed imbibition. A seed coat with double palisade architecture throughout the entire seed has also apparently evolved in subgenera Cuscuta, Pachystigma and Grammica, but several species in two clades of the latter subgenus reverted to a single palisade layer outside the hilum area. The same latter species also evolved a peculiar, globose embryo, likely having a storage role, in contrast to the ancestral filiform and coiled embryo present throughout the remainder of the genus. Autogamous species had on average the highest number of seeds per capsule, whereas fully xenogamous taxa had the lowest. No correlation was revealed between the size of the seeds and the size of their geographical distribution in North America, but seedlings of species with larger seeds survived significantly longer than seedlings resulted from smaller seeds. Diversity and evolution of seed traits was discussed in relationship with their putative roles in dormancy, germination and dispersal.

Cognitive phenotypes in temporal lobe epilepsy utilizing data- and clinically driven approaches: Moving toward a new taxonomy

OBJECTIVE

To identify cognitive phenotypes in temporal lobe epilepsy (TLE) and test their reproducibility in a large, multi-site cohort of patients using both data-driven and clinically driven approaches.

METHOD

Four-hundred seven patients with TLE who underwent a comprehensive neuropsychological evaluation at one of four epilepsy centers were included. Scores on tests of verbal memory, naming, fluency, executive function, and psychomotor speed were converted into z-scores based on 151 healthy controls (HCs). For the data-driven method, cluster analysis (k-means) was used to determine the optimal number of clusters. For the clinically driven method, impairment was defined as >1.5 standard deviations below the mean of the HC, and patients were classified into groups based on the pattern of impairment.

RESULTS

Cluster analysis revealed a three-cluster solution characterized by (a) generalized impairment (29%), (b) language and memory impairment (28%), and (c) no impairment (43%). Based on the clinical criteria, the same broad categories were identified, but with a different distribution: (a) generalized impairment (37%), (b) language and memory impairment (30%), and (c) no impairment (33%). There was a 82.6% concordance rate with good agreement (κ = .716) between the methods. Forty-eight patients classified as having a normal profile based on cluster analysis were classified as having generalized impairment (n = 16) or an isolated language/memory impairment (n = 32) based on the clinical criteria. Patients with generalized impairment had a longer disease duration and patients with no impairment had more years of education. However, patients demonstrating the classic TLE profile (ie, language and memory impairment) were not more likely to have an earlier age at onset or mesial temporal sclerosis.

SIGNIFICANCE

We validate previous findings from single-site studies that have identified three unique cognitive phenotypes in TLE and offer a means of translating the patterns into a clinical diagnostic criteria, representing a novel taxonomy of neuropsychological status in TLE.

Pollen morphology of Polish species from the genus Rubus L. (Rosaceae) and its systematic importance

The genus Rubus L. (Rosaceae) not been investigated satisfactorily in terms of palynology. This genus is taxonomically very difficult due to the large number of species and problems with their delimitation, as well as very different distribution areas of particular species. The aim of this study was to investigate pollen morphology and for the first time the ranges of intrageneric and interspecific variability of Rubus species, as well as verify the taxonomic usefulness of these traits in distinguishing studied taxa from this genus. The selected species of the genus Rubus were analysed for 11 quantitative pollen characteristics and the following qualitative ones: exine ornamentation, pollen outline and shape, as well as bridge structure. Analyses were conducted on a total of 1740 pollen grains, which represent 58 blackberry species belonging to a majority of subgenera and all the sections and series found in Poland. The most important characters included exine ornamentation (exine ornamentation type, width and direction of grooves and striae, number and diameter of perforations) and length of the polar axis (P). The arrangement of the examined species on the dendrogram does not corroborate division of the genus Rubus into subgenera, sections and series currently adopted in taxonomy. This fact is not surprising because the taxonomy of the genus was not based on pollen characters. Pollen features should be treated in taxonomy as auxiliary, because they fail to differentiate several (10) individual species, while the other ones create groups with similar pollen traits.

The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

Virus taxonomy emerged as a discipline in the middle of the twentieth century. Traditionally, classification by virus taxonomists has been focussed on the grouping of relatively closely related viruses. However, during the past few years, the International Committee on Taxonomy of Viruses (ICTV) has recognized that the taxonomy it develops can be usefully extended to include the basal evolutionary relationships among distantly related viruses. Consequently, the ICTV has changed its Code to allow a 15-rank classification hierarchy that closely aligns with the Linnaean taxonomic system and may accommodate the entire spectrum of genetic divergence in the virosphere. The current taxonomies of three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus and herpes simplex virus 1 are used to illustrate the impact of the expanded rank structure. This new rank hierarchy of virus taxonomy will stimulate further research on virus origins and evolution, and vice versa, and could promote crosstalk with the taxonomies of cellular organisms.

Endemism patterns are scale dependent

Areas of endemism are important in biogeography because they capture facets of biodiversity not represented elsewhere. However, the scales at which they are relevant to research and conservation are poorly analysed. Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE) separately for all birds and amphibians across the globe. We show that scale dependence is widespread for both indices and manifests across grain sizes, spatial extents and taxonomic treatments. Variations in taxonomic opinions-whether species are treated by systematic 'lumping' or 'splitting'-can profoundly affect the allocation of WE hotspots. Global patterns of PE can provide insights into complex evolutionary processes but this congruence is lost at the continental to country extents. These findings are explained by environmental heterogeneity at coarser grains, and to a far lesser extent at finer resolutions. Regardless of scale, we find widespread deficits of protection for endemism hotspots. Our study presents a framework for assessing areas for conservation that are robust to assumptions on taxonomy, spatial grain and extent.

Gait pattern analysis and clinical subgroup identification: a retrospective observational study

To identify basic gait features and abnormal gait patterns that are common to different neurological or musculoskeletal conditions, such as cerebral stroke, Parkinsonian disorders, radiculopathy, and musculoskeletal pain.In this retrospective study, temporal-spatial, kinematic, and kinetic gait parameters were analyzed in 424 patients with hemiplegia after stroke, 205 patients with Parkinsonian disorders, 216 patients with radiculopathy, 167 patients with musculoskeletal pain, and 316 normal controls (total, 1328 subjects). We assessed differences according to the condition and used a community detection algorithm to identify subgroups within each condition. Additionally, we developed a prediction model for subgroup classification according to gait speed and maximal hip extension in the stance phase.The main findings can be summarized as follows. First, there was an asymmetric decrease of the knee/ankle flexion angles in hemiplegia and a marked reduction of the hip/knee range of motion with increased moment in Parkinsonian disorders. Second, three abnormal gait patterns, including fast gait speed with adequate maximal hip extension, fast gait speed with inadequate maximal hip extension, and slow gait speed, were found throughout the conditions examined. Third, our simple prediction model based on gait speed and maximal hip extension angle was characterized by a high degree of accuracy in predicting subgroups within a condition.Our findings suggest the existence of specific gait patterns within and across conditions. Our novel subgrouping algorithm can be employed in routine clinical settings to classify abnormal gait patterns in various neurological disorders and guide the therapeutic approach and monitoring.

Optimal Feature Selection for Big Data Classification: Firefly with Lion-Assisted Model

In this article, the proposed method develops a big data classification model with the aid of intelligent techniques. Here, the Parallel Pool Map reduce Framework is used for handling big data. The model involves three main phases, namely (1) feature extraction, (2) optimal feature selection, and (3) classification. For feature extraction, the well-known feature extraction techniques such as principle component analysis, linear discriminate analysis, and linear square regression are used. Since the length of feature vector tends to be high, the choice of the optimal features is complex task. Hence, the proposed model utilizes the optimal feature selection technology referred as Lion-based Firefly (L-FF) algorithm to select the optimal features. The main objective of this article is projected on minimizing the correlation between the selected features. It results in providing diverse information regarding the different classes of data. Once, the optimal features are selected, the classification algorithm called neural network (NN) is adopted, which effectively classify the data in an effective manner with the selected features. Furthermore, the proposed L-FF+NN model is compared with the traditional methods and proves the effectiveness over other methods. Experimental analysis shows that the proposed L-FF+NN model is 92%, 28%, 87%, 82%, and 78% superior to the state-of-art models such as GA+NN, FF+NN, PSO+NN, ABC+NN, and LA+NN, respectively.

Question classification based on Bloom's taxonomy cognitive domain using modified TF-IDF and word2vec

The assessment of examination questions is crucial in educational institutes since examination is one of the most common methods to evaluate students’ achievement in specific course. Therefore, there is a crucial need to construct a balanced and high-quality exam, which satisfies different cognitive levels. Thus, many lecturers rely on Bloom’s taxonomy cognitive domain, which is a popular framework developed for the purpose of assessing students’ intellectual abilities and skills. Several works have been proposed to automatically handle the classification of questions in accordance with Bloom’s taxonomy. Most of these works classify questions according to specific domain. As a result, there is a lack of technique of classifying questions that belong to the multi-domain areas. The aim of this paper is to present a classification model to classify exam questions based on Bloom’s taxonomy that belong to several areas. This study proposes a method for classifying questions automatically, by extracting two features, TFPOS-IDF and word2vec. The purpose of the first feature was to calculate the term frequency-inverse document frequency based on part of speech, in order to assign a suitable weight for essential words in the question. The second feature, pre-trained word2vec, was used to boost the classification process. Then, the combination of these features was fed into three different classifiers; K-Nearest Neighbour, Logistic Regression, and Support Vector Machine, in order to classify the questions. The experiments used two datasets. The first dataset contained 141 questions, while the other dataset contained 600 questions. The classification result for the first dataset achieved an average of 71.1%, 82.3% and 83.7% weighted F1-measure respectively. The classification result for the second dataset achieved an average of 85.4%, 89.4% and 89.7% weighted F1-measure respectively. The finding from this study showed that the proposed method is significant in classifying questions from multiple domains based on Bloom’s taxonomy.

Shelter in Smoleń III - A unique example of stratified Holocene clastic cave sediments in Central Europe, a lithostratigraphic stratotype and a record of regional paleoecology

A cave site Shelter in Smoleń III (southern Poland) contains an approximately 2-m-thick stratified sequence of Upper Pleistocene and Holocene clastic sediments, unique for Central Europe. The sequence contents abundant fossil fauna, including mollusk, rodent and bat remains. The cave sites with long profiles of subfossil fauna present a great value for reconstructions of regional terrestrial paleoenvironment. We explore the stratigraphy of this site through analyses of the lithology and geochemistry of sediments, radiocarbon dating of faunal and human remains and charcoals, and archaeological study, as well as the paleoecology derived from the taxonomic composition of fossil faunal assemblages. Our data show that the entire period of the Holocene is recorded in the rockshelter, which makes that site an exceptional and highly valuable case. We present paleoenvironmental reconstructions of regional importance, and we propose to regard Shelter in Smoleń III as a regional stratigraphic stratotype of Holocene clastic cave sediments.

A unique framework for the Persian clinical guidelines: addressing an evidence-based CDSS development need

BACKGROUND AND AIM

One of the prerequisites to develop Computerised Decision Support Systems is Clinical Practice Guidelines (CPGs) which provide a systematic aid to make complex medical decisions. In order to provide an automated CPG, it is needed to have a unique structure for the CPGs. This study aims to propose a unique framework for the Persian guidelines.

MATERIALS AND METHODS

20 Persian CPGs were selected and divided into the creation and validation sets (n=10 for each). The first group was studied independently and their headings were listed; wherever possible, the headings were merged into a new heading that was applicable to all the guidelines. The developed framework was validated by the second group of the guidelines.

RESULTS

Studied guidelines had a very heterogeneous structure. The number of original headings was 249; they were reduced to 14 main headings with 16 subheadings in a unique developed framework. The framework is able to represent and cover 100% of the guidelines.

CONCLUSION

The heterogeneity of guidelines was high as they were not developed based on the unique framework. The proposed framework provides a layout for designing the CPGs with a homogeneous structure. Guideline developers can use this framework to develop structured CPGs. This will facilitate the integration of the guidelines into electronic medical records as well as clinical decision support systems.

A new species of Cambeva (Siluriformes, Trichomycteridae) from the Rio Ivaí basin, Upper Rio Paraná basin, Paraná State, Brazil

A new species of Cambeva endemic to the Rio Ivaí basin, Upper Paraná basin, is described combining morphological and molecular data. This new species is distinguished from all congeners by characters related to the number of pectoral-fin rays, to the colour pattern of the dorsal and lateral surface of the body, to the presence of diffuse blotches in the ventral surface of body, to the presence of a pelvic-fin and pelvic girdle, to the number of odontodes in the inter-opercular and opercular patches, to the number of dorsal and ventral procurrent rays. In addition, the analysis of mitochondrial DNA sequences identified a satisfactory genetic distance between this new species and its congeners. The new species from the Rio Ivaí reinforces its characteristics as an area of endemism for fishes in the Upper Rio Paraná basin.

Spectral sensitivity of L2 biotype in the Thrips tabaci cryptic species complex

The onion thrips, Thrips tabaci (Lindeman, 1889), is a cosmopolitan pest of economic importance on a wide range of crops. Despite being one of the most studied thrips species, there is very limited knowledge available about its ability to perceive light. The T. tabaci cryptic species complex consists of a tobacco-associated (T) and two leek-associated (L1, L2) biotypes. We made electroretinogram recordings on the most widespread thelytokous (where unfertilized eggs produce females) T. tabaci L2 biotype and measured attraction to light sources in this biotype as a function of wavelength in behavioural experiments. The spectral sensitivity of the T. tabaci L2 biotype shows a unimodal curve peaking at λ_max = 521 nm. Contrary to this spectral sensitivity curve, L2 biotype attraction in an arena is bimodal with local maxima at 368 nm (UV) and 506-520 nm (green) being practically of the same magnitude. Although being similar to the arrhenotokous (where unfertilized eggs produce males) L1 biotype in phototaxis, significant differences regarding photoreceptor cell responses emerged. This study contributes to our understanding of light perception in Thysanoptera as well as to the development of more effective monitoring tools for this economically important pest species.

Sutterella faecalis sp. nov., isolated from human faeces

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119^T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691^T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119^T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119^T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C_18:1ω9c and C_16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119^T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119^T (= KCTC 15823^T = NBRC 114254^T).

Noasaurids are a component of the Australian 'mid'-Cretaceous theropod fauna

The diversity of Australia's theropod fauna from the 'mid'-Cretaceous (Albian-Cenomanian) is distinctly biased towards the medium-sized megaraptorids, despite the preponderance of abelisauroids in the younger but latitudinally equivalent Patagonian theropod fauna. Here, we present new evidence for the presence of ceratosaurian, and specifically abelisauroid, theropods from the Cenomanian Griman Creek Formation of Lightning Ridge, New South Wales. A partial cervical vertebra is described that bears a mediolaterally concave ventral surface of the centrum delimited by sharp ventrolateral ridges that contact the parapophyses. Among theropods, this feature has been reported only in a cervical vertebra attributed to the noasaurid Noasaurus. We also reappraise evidence recently cited against the ceratosaurian interpretation of a recently described astragalocalcaneum from the upper Barremian-lower Aptian San Remo Member of the upper Strzelecki Group in Victoria. Inclusion of the Lightning Ridge cervical vertebra and Victorian astragalocalcaneum into a revised phylogenetic analysis focused on elucidating ceratosaurian affinities reveals support for placement of both specimens within Noasauridae, which among other characters is diagnosed by the presence of a medial eminence on the ascending process of the astragalus. The Lightning Ridge and Victorian specimens simultaneously represent the first noasaurids reported from Australia and the astragalocalcaneum is considered the earliest known example of a noasaurid in the world to date. The recognition of Australian noasaurids further indicates a more widespread Gondwanan distribution of the clade outside of South America, Madagascar and India consistent with the timing of the fragmentation of the supercontinent.

Taxonomy of the yeast genus Vanderwaltozyma and proposal of Vanderwaltozyma meishanica sp. nov., Vanderwaltozyma huisunica sp. nov., and Vanderwaltozyma molinica sp. nov

Using electrophoretic karyotyping, RAPD fingerprinting and phylogenetic analysis of ribosomal RNA gene sequences, twenty-six Vanderwaltozyma strains were studied. Out of 19 strains isolated in mountainous areas of Taiwan, eighteen strains were isolated from soil and one strain was isolated from the fruiting body of mushroom, six were identified as V. polyspora and three as V. verrucispora. Based on the results of a multigene sequence analysis (D1/D2, ITS and mitochondrial COX II gene) and DNA-DNA reassociation, three new ascosporic members of the genus Vanderwaltozyma are formally described: V. huisunica sp. nov. (GA1S06^T = CBS 12250^T = BCRC 23260^T), V. meishanica sp. nov. (EN4S02^T = CBS 12249^T = BCRC 23255^T) and V. molinica sp. nov. (GJ8S05^T = CBS 12251^T = BCRC 23264^T), and the holotypes of these novel species are assigned as BCRC 23260^T, BCRC 23255^T and BCRC 23264^T, respectively.

A new species of Hyphessobrycon (Characiformes, Characidae) from the upper Rio Jequitinhonha basin, Minas Gerais, Brazil, with comments on morphological similarities with Stethaprioninae species from headwater environments

A new species of Hyphessobrycon is described from a marshland area in the headwaters of Rio Jequitinhonha basin, Minas Gerais, Brazil. The new species differs from congeners by presenting a single well-delimited conspicuous humeral blotch, rounded to vertically oval, restricted to the area dorsal to the lateral-line row of scales, without a narrower downward extension, greatest body depth anterior to dorsal-fin origin, bony processes in anal and pectoral-fin rays of males and four teeth in the inner row of the premaxillary bone. The new species presents a set of morphological features shared by some species currently assigned to Hasemania, Myxiops and to the Astyanax scabripinnis complex. Some of these features are discussed.

NCBI Taxonomy: a comprehensive update on curation, resources and tools

The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy.

Evidence of a landlocked reproducing population of the marine pejerrey Odontesthes argentinensis (Actinopterygii; Atherinopsidae)

In South America, the order Atheriniformes includes the monophyletic genus Odontesthes with 20 species that inhabit freshwater, estuarine and coastal environments. Pejerrey Odontesthes argentinensis is widely distributed in coastal and estuarine areas of the Atlantic Ocean and is known to foray into estuaries of river systems, particularly in conditions of elevated salinity. However, to our knowledge, a landlocked self-sustaining population has never been recorded. In this study, we examined the pejerrey population of Salada de Pedro Luro Lake (south-east of Buenos Aires Province, Argentina) to clarify its taxonomic identity. An integrative taxonomic analysis based on traditional meristic, landmark-based morphometrics and genetic techniques suggests that the Salada de Pedro Luro pejerrey population represents a novel case of physiological and morphological adaptation of a marine pejerrey species to a landlocked environment and emphasises the environmental plasticity of this group of fishes.

Taxonomic revision of Hypostomus albopunctatus (Siluriformes: Loricariidae) reveals a new piece of the Hypostomus jigsaw in the upper Rio Paraná basin

Hypostomus albopunctatus was described from the Rio Piracicaba, a tributary of the Rio Tietê, upper Rio Paraná basin. Nevertheless, specimens attributed to this species are commonly found throughout other river systems in the upper Rio Paraná basin and present varying degrees of morphological variation. A taxonomic review of H. albopunctatus based on large series of specimens from many localities throughout the upper Rio Paraná basin was carried out. Results support H. lexi, H. niger and H. scaphyceps as junior synonyms. Hypostomus albopunctatus differs from all congeners except H. heraldoi by having pectoral-fin spine equal to or shorter than pelvic-fin spine (v. longer); it differs from H. heraldoi by having white or light yellow spots on the body and fins (v. dark brown or black spots). Despite conspicuous variation related to the shape and size of the spots and snout morphology, both spot and snout patterns overlapped among the examined populations, thus this variation was inferred to be intraspecific within a widely distributed H. albopunctatus.

A new species of spiny driftwood catfish Spinipterus (Siluriformes: Auchenipteridae) from the Amazon basin

An expedition to the middle Rio Purus basin uncovered a remarkable new species of the genus Spinipterus. The new species has a very distinct and conspicuous colour pattern resembling a jaguar and it is almost four times larger than Spinipterus acsi, a small specimen (32 mm L_S ) from Caño Santa Rita, a right bank tributary of Río Nanay in Peru and a second specimen was reported from Rio Juruá, Amazonas State, Brazil. Although the new species is more similar in size and colour pattern to Liosomadoras, it shares the synapomorphies for Spinipterus. The new species differs from the congener by the following characters: (a) colour pattern with large black rosette-like spots over a light yellow to brown background (v. brown background with small dark blotches over the body); (b) adult body size reaching 104.5 mm L_S (v. maximum known size 37.1 mm L_S ); (c) posterior process of cleithrum short, never reaching vertical through the dorsal-fin origin (v. posterior process long, surpassing vertical through the dorsal-fin origin); (d) seven soft pectoral-fin rays (v. six); (e) caudal fin truncated (v. caudal fin rounded).

Oreonectes guilinensis (Teleostei, Cypriniformes, Nemacheilidae), a new loach species from Guangxi, China

A new loach Oreonectes guilinensis sp. nov. is described from Guangxi Zhuang Autonomous Region, China. It is the second surface-dwelling fish identified in the genus Oreonectes after the type species Oreonectes platycephalus. This new species can be distinguished from other species within the genus by the combination of the following features: a round caudal fin, 13-14 branched rays, an incomplete lateral line with 4-6 pores, a short pelvic fin located some distance from the anus, a scale-covered body, a stout build (body width 14.0%-16.7% of standard length), a posterior chamber of well-developed airbladder and a yellowish-brown body with a lateral dark brown strip. The maximum likelihood phylogenetic analysis based on cytb gene recovered this new species in a well-supported clade with the type species O. platycephalus, sister to the Lefua clade. Morphological comparisons as well as our phylogenetic tree support Oreonectes shuilongensis, Oreonectes daqikongensis, Oreonectes jiarongensis as species of Troglonectes. Based on our results there are 6 valid species in the genus Oreonectes.

Phylogenetic re-evaluation of the Grosmannia penicillata complex (Ascomycota, Ophiostomatales), with the description of five new species from China and USA

The Grosmannia penicillata complex (Ophiostomatales, Ascomycota) is one of the major species complexes in Leptographium sensu lato. Most of these are wood staining fungi associated with conifer-infesting bark beetles, and the complex encompasses the type species of the genus Grosmannia. Yet the phylogenetic relationships of species within the complex is unresolved. The aim of this study was to re-evaluate the circumscriptions of all known species in the G. penicillata complex, as well as isolates resembling G. penicillata obtained from a recent survey in China. Phylogenetic analyses of four gene regions: Internal transcribed spacer 2 and large subunit (ITS2-LSU), beta-tubulin (TUB), calmodulin (CAL), and translation elongation factor 1 alpha (TEF-1α) resolved the relationships of 15 species, including four new species (Grosmannia xianmiense sp nov., Grosmannia purpurea sp. nov., Grosmannia crassifolia sp. nov. and Grosmannia maixiuense sp. nov.), from China. Some isolates from pine in the USA that had previously been identified as Grosmannia abietina, represented a distinct taxon that is described here as Grosmannia xeno-abietina sp. nov.

Dataset for file fragment classification of textual file formats

OBJECTIVES

Classification of textual file formats is a topic of interest in network forensics. There are a few publicly available datasets of files with textual formats. Therewith, there is no public dataset for file fragments of textual file formats. So, a big research challenge in file fragment classification of textual file formats is to compare the performance of the developed methods over the same datasets.

DATA DESCRIPTION

In this study, we present a dataset that contains file fragments of five textual file formats: Binary file format for Word 97-Word 2003, Microsoft Word open XML format, portable document format, rich text file, and standard text document. This dataset contains the file fragments in three different languages: English, Persian, and Chinese. For each pair of file format and language, 1500 file fragments are provided. So, the dataset of file fragments contains 22,500 file fragments.

A computational study of mental health awareness campaigns on social media

As public discourse continues to progress online, it is important for mental health advocates, public health officials, and other curious parties and stakeholders, ranging from researchers, to those affected by the issue, to be aware of the advancing new mediums in which the public can share content ranging from useful resources and self-help tips to personal struggles with respect to both illness and its stigmatization. A better understanding of this new public discourse on mental health, often framed as social media campaigns, can help perpetuate the allocation of sparse mental health resources, the need for educational awareness, and the usefulness of community, with an opportunity to reach those seeking help at the right moment. The objective of this study was to understand the nature of and engagement around mental health content shared on mental health campaigns, specifically #MyTipsForMentalHealth on Twitter around World Mental Health Awareness Day in 2017. We collected 14,217 Twitter posts from 10,805 unique users between September and October 2017 that contained the hashtag #MyTipsForMentalHealth. With the involvement of domain experts, we hand-labeled 700 posts and categorized them as (a) Fact, (b) Stigmatizing, (c) Inspirational, (d) Medical/Clinical Tip, (e) Resource Related, (f) Lifestyle or Social Tip or Personal View, and (g) Off Topic. After creating a "seed" machine learning classifier, we used both unsupervised and semi supervised methods to classify posts into the various expert identified topical categories. We also performed a content analysis to understand how information on different topics spread through social networks. Our support vector machine classification algorithm achieved a mean cross-validation accuracy of 0.81 and accuracy of 0.64 on unseen data. We found that inspirational Twitter posts were the most spread with a mean of 4.17 retweets, and stigmatizing content was second with a mean of 3.66 retweets. Classification of social media-related mental health interactions offers valuable insights on public sentiment as well as a window into the evolving world of online self-help and the varied resources within. Our results suggest an important role for social media-based peer support to not only guide information seekers to useful content and local resources but also illuminate the socially-insular aspects of stigmatization. However, our results also reflect the challenges of quantifying the heterogeneity of mental health content on social media and the need for novel machine learning methods customized to the challenges of the field.

Untangling the assembly of macrophyte metacommunities by means of taxonomic, functional and phylogenetic beta diversity patterns

Metacommunity ecology has broadened considerably with the recognition that measuring beta diversity beyond the purely taxonomic viewpoint may improve our understanding of the dispersal- and niche-based mechanisms across biological communities. In that perspective, we applied a novel multidimensional approach including taxonomic, functional and phylogenetic data to enhance our basic understanding of macrophyte metacommunity dynamics. For each beta diversity metric, we calculated the mean overall value and tested whether the mean value was different from that expected by chance using null models. We also employed evolutionary and spatially constrained models to first identify the degree to which the studied functional traits showed a phylogenetic signal, and then to estimate the relative importance of spatial and environmental effects on metacommunity structure. We first found that most individual ponds were inhabited by species that were merely random draws from the taxonomic and phylogenetic species pool available in the study region. Contrary to our expectations, not all measured traits were conserved along the phylogeny. We also showed that trait and phylogenetic dimensions strongly increased the amount of variation in beta diversity that can be explained by degree of environmental filtering and dispersal limitation. This suggests that accounting for functional traits and phylogeny in metacommunity ecology helps to explain idiosyncratic patterns of variation in macrophyte species distribution. Importantly, phylogenetic and functional analyses identified the influence of underlying mechanisms that would otherwise be missed in an analysis of taxonomic turnover. Together, these results let us conclude that macrophyte species have labile functional traits adapted to dispersal-based processes and some evolutionary trade-offs that drive community assembly via species sorting. Overall, our exploration of different facets of beta diversity showed how functional and phylogenetic information may be used with species-level data to test community assembly hypotheses that are more ecologically meaningful than assessments of environmental patterns based on the purely taxonomic viewpoint.

Dacentrurine stegosaurs (Dinosauria): A new specimen of Miragaia longicollum from the Late Jurassic of Portugal resolves taxonomical validity and shows the occurrence of the clade in North America

The stegosaur species Miragaia longicollum was erected based on a partial anterior skeleton from the Upper Jurassic of Portugal. Until then, almost all stegosaur specimens in Portugal and Spain had been identified as Dacentrurus armatus, the sister taxon of M. longicollum and only other member of the clade Dacentrurinae. The holotypes of the two species have little overlap, since the holotype of D. armatus is mostly a posterior skeleton, so the classification of other specimens to either species is unclear and the validity of M. longicollum has been questioned and debated. Here we describe a largely complete specimen of M. longicollum discovered in 1959 in Atouguia da Baleia, Peniche, Portugal, consisting of both anterior and posterior portions of the skeleton. Comparisons to the holotypes of dacentrurines and other stegosaurs shed light on the convoluted relationships of this group. We conclude that M. longicollum is valid and rather different from D. armatus, and provide a revised diagnosis of M. longicollum, as well as revised diagnoses for D. armatus, Dacentrurinae, and the first diagnosis of the genus Miragaia, granting stability to these taxa and allowing new considerations to be given on the classification of other Iberian stegosaurs. This new specimen is, to date, the most complete dinosaur described from Portugal and the most complete stegosaur described from Europe. Miragaia shared anatomical features that show a close affinity to Alcovasaurus longispinus, confirming this to be the first known dacentrurine stegosaur in America, coherent with the hypothesis of an ephemeral land bridge between North America and Iberia that allowed faunal exchange.

Habitat availability explains variation in climate-driven range shifts across multiple taxonomic groups

Range shifting is vital for species persistence, but there is little consensus on why individual species vary so greatly in the rates at which their ranges have shifted in response to recent climate warming. Here, using 40 years of distribution data for 291 species from 13 invertebrate taxa in Britain, we show that interactions between habitat availability and exposure to climate change at the range margins explain up to half of the variation in rates of range shift. Habitat generalists expanded faster than more specialised species, but this intrinsic trait explains less of the variation in range shifts than habitat availability, which additionally depends on extrinsic factors that may be rare or widespread at the range margin. Similarly, while climate change likely underlies polewards expansions, we find that more of the between-species variation is explained by differences in habitat availability than by changes in climatic suitability. A model that includes both habitat and climate, and their statistical interaction, explains the most variation in range shifts. We conclude that climate-change vulnerability assessments should focus as much on future habitat availability as on climate sensitivity and exposure, with the expectation that habitat restoration and protection will substantially improve species' abilities to respond to uncertain future climates.

Archaeospora ecuadoriana sp. nov. from a mountainous biodiversity hotspot area in Ecuador, and transfer of Palaeospora spainiae to Archaeospora, as A. spainiae comb. nov

A new glomeromycotan fungus, Archaeospora ecuadoriana sp. nov., was found in the south Ecuadorian mountain rainforest region, a global plant biodiversity hotspot. It was cultivated as single spore isolate originating from nursery-grown native tree seedlings inoculated with mixed soil from pristine forest and agricultural fields. The new species is known from the Loja area, southern Ecuador, at about 2100 m above mean sea level (mamsl) and has been detected in potato roots from an Andean region in Peru at 2658 mamsl by previous molecular data. The fungus forms small, colourless to frosted white, mainly globose spores, averaging 61 × 60 μm, formed singly or very rarely in clusters. There is no reaction to Melzer's reagent, other than a slight unspecific overall yellow iodine staining. The spores are very similar to those of Archaeospora trappei and A. schenckii. However, molecular phylogenetic analysis shows the species to be clearly separate from all other described Archaeospora species. The analysis of the available Archaeospora sequence data shows that sequences of Palaeospora spainiae, of the monospecific genus Palaeospora, cluster within the genus Archaeospora. Palaeospora therefore is synonymised with Archaeospora and P. spainiae is transferred to Archaeospora, as A. spainiae comb. nov.

Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex

Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.

A new computerized tomography classification to evaluate response to Denosumab in giant cell tumors in the extremities

Objectives

The aim of this study was to describe the cohort of patients who have been treated with Denosumab as neoadjuvant therapy prior to surgery for aggressive giant cell tumor of bone in the extremities, to evaluate the radiological responses to Denosumab comparing Choi criteria and a newly described computerized tomography (CT) classification, and to evaluate the risk of local recurrence after intralesional curettage or radical excision.

Methods

We retrospectively evaluated 36 patients (20 females and 16 males; mean age at diagnosis 36 years (range, 18–64)) treated with neoadjuvant Denosumab therapy prior to surgery for aggressive giant cell tumor of bone in the extremities. The radiological responses to Denosumab treatment were analyzed on the preoperative images after the neoadjuvant course with the Choi criteria and with a newly proposed classification based on CT. All these images were independently reviewed by two of the researchers. Surgical intervention methods were noted and local recurrence rates were evaluated. The correlation between radiological response amount and local recurrence were analyzed for both Choi criteria and the new CT classification.

Results

Denosumab was administered for a mean of 21 weeks (range 7–133). Five patients also had a short postoperative course. According to Choi criteria there was a radiological response in 32 patients (89%), while the new CT classification identified responses in all the 36 patients (100%). The identification of changes after 7 weeks of treatment was higher using the CT classification compared to Choi criteria (p = 0.043 vs p = 0.462). The surgical interventions after Denosumab comprised curettage in 29 patients (74%) and resection in 7 (26%). Local recurrence was higher in patients managed with intralesional curettage than in those treated with en bloc resection (55.1% vs 0%, p < 0.001). At last follow up 19 patients (53%) required en bloc resections. Good responders to Denosumab (type 2C) had lower risk of local recurrence (p = 0.047) after either resection or curettage.

Conclusion

The new CT classification evaluated more accurately the response to Denosumab. Our experience suggests that the requirement for radical bone resection remains high despite the use of Denosumab.

Level of evidence

Level IV, Therapeutic Study.

Incidence of anatomical variations according to the International Frontal Sinus Anatomy Classification (IFAC) and their coincidence with radiological sings of opacification

BACKGROUND

The endonasal access to the frontal recess and sinus may be complicated by a variety of anatomical variations. Previous classifications of these variants were characterized by proper names or position information without anatomical reference. The IFAC is intended to simplify the classification of anatomical variations of the frontoethmoidal complex. The aim of this study was to analyse a representative number of sinus CT scans to assess the incidence of anatomical variations according to the IFAC and to compare the results with previous classifications. In addition, the coincidence of complex anatomical variations and radiological sings of opacification was investigated.

METHODOLOGY/PRINCIPAL

Two hundred and forty-nine sinus CT scans were analysed in multiplanar reconstructions. Exclusion criteria were previous operations on the paranasal sinuses, malignant diseases, and an insufficient image quality. All anatomical variants were analysed according to the IFAC criteria. In addition, the coincidence of radiological sings of opacification and the presence of anatomical variations of the frontal recess and sinus were investigated.

RESULTS

The analysis revealed Agger nasi cells in 95% of the CT scans. Supra agger cells (SACs) were detected in 49% and Supra agger frontal cells (SAFCs) in 25% of the data sets. Suprabulla cells (SBCs) were detected in 89% and Supra bulla frontal cells (SBFCs) in 27% of the scans. Supraorbital ethmoid cells (SECs) were detectable in 9% and interfrontal septal cells in 28% of the scans. Despite a partially strong narrowing of the frontal recess, no increased occurrence of radiological sings of opacification could be detected (p > 0.05).

CONCLUSIONS

Anatomical variations in the frontoethmoidal area are very common. According to the IFAC criteria, in 43% of the patients, cells could be detected with pneumatization to or into the frontal sinus. The IFAC is structured more clearly compared to previous classifications due to the anatomical aspect. It represents the most consistent classification regarding surgical planning. Further studies will demonstrate the scientific and clinical value of this classification.

Patent pledges, open IP, or patent pools? Developing taxonomies in the thicket of terminologies

Recently, a range of organisations, including car and consumer electronics manufacturers, have applied so-called patent pledges. A patent pledge is a publicly announced intervention by patent-owning entities (‘pledgers’) to out-license active patents to the restricted or unrestricted public free from or bound to certain conditions for a reasonable or no monetary compensation. Despite growing research to better understand this phenomenon, the underlying terminology remains contradictory. We apply an inductive research approach using qualitative coding to analyse 60 patent pledges made by 80 organisations. Based on this analysis, we propose a three-dimensional taxonomy that distinguishes eight types of patent pledges. Extending this taxonomy using case examples, we then propose a generalised patent licensing taxonomy. This second taxonomy can be used to distinguish patent licensing strategies, including other frequently used approaches, such as patent pools and cross-licenses. Finally, we use the patent pledge taxonomy to illustrate how patent owners change their licensing strategies over time and how it can support strategic decision processes within an organisation. We contribute to the field of patent management by building an ontology of patent pledges through proposing a definition and eight types. The patent licensing taxonomy enables organisations to devise and choose licensing strategies, and to illustrate licensing approaches of competitors, for instance.

Normative Social Role Concepts in Early Childhood

The current studies (N = 255, children ages 4-5 and adults) explore patterns of age-related continuity and change in conceptual representations of social role categories (e.g., "scientist"). In Study 1, young children's judgments of category membership were shaped by both category labels and category-normative traits, and the two were dissociable, indicating that even young children's conceptual representations for some social categories have a "dual character." In Study 2, when labels and traits were contrasted, adults and children based their category-based induction decisions on category-normative traits rather than labels. Study 3 confirmed that children reason based on category-normative traits because they view them as an obligatory part of category membership. In contrast, adults in this study viewed the category-normative traits as informative on their own (not only as a cue to obligations). Implications for continuity and change in representations of social role categories will be discussed.

Revisiting metazoan phylogeny with genomic sampling of all phyla

Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa-or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.

Mapping the Passions: Toward a High-Dimensional Taxonomy of Emotional Experience and Expression

What would a comprehensive atlas of human emotions include? For 50 years, scientists have sought to map emotion-related experience, expression, physiology, and recognition in terms of the "basic six"-anger, disgust, fear, happiness, sadness, and surprise. Claims about the relationships between these six emotions and prototypical facial configurations have provided the basis for a long-standing debate over the diagnostic value of expression (for review and latest installment in this debate, see Barrett et al., p. 1). Building on recent empirical findings and methodologies, we offer an alternative conceptual and methodological approach that reveals a richer taxonomy of emotion. Dozens of distinct varieties of emotion are reliably distinguished by language, evoked in distinct circumstances, and perceived in distinct expressions of the face, body, and voice. Traditional models-both the basic six and affective-circumplex model (valence and arousal)-capture a fraction of the systematic variability in emotional response. In contrast, emotion-related responses (e.g., the smile of embarrassment, triumphant postures, sympathetic vocalizations, blends of distinct expressions) can be explained by richer models of emotion. Given these developments, we discuss why tests of a basic-six model of emotion are not tests of the diagnostic value of facial expression more generally. Determining the full extent of what facial expressions can tell us, marginally and in conjunction with other behavioral and contextual cues, will require mapping the high-dimensional, continuous space of facial, bodily, and vocal signals onto richly multifaceted experiences using large-scale statistical modeling and machine-learning methods.