Do we have infraspecific taxa of Salvia macrosiphon Boiss. (Lamiaceae) in Iran?

BACKGROUND: Salvia macrosiphon is an aromatic perennial species of Lamiaceae family that grows naturally in different parts of Iran. This herb is widely used in folk and modern medicine. Although in Flora Iranica and Flora of Iran, no infraspecific taxonomic rank has been detected for S. macrosiphon, some infraspecific taxonomic ranks have been reported. In the current study, we evaluated the genetic diversity and structure of 11 populations of this species to detect inter and intrapopulation genetic diversity and to survey the possibility of infraspecific taxonomic ranks in this species. METHODS AND RESULTS: We utilized the modified C-TAB protocol for DNA extraction and amplified the genomes using several SCoT molecular markers. We calculated of genetic diversity and polymorphism parameters using GenAlex 6.4, Geno-Dive ver.2, PopGene, PopART and Structure 2.3.4. The parameters of genetic polymorphism differed between the populations. Moreover, a low rate of gene flow supported a moderate level of population's genetic diversity and differentiation. According to haplotypes network (TCS) analysis, a high level of genetic mutation has occurred among the individuals of some populations leading to high intrapopulation diversity. On the basis of structure analysis and Nei's genetic distance, the examined populations were classified into four genotypes. CONCLUSIONS: The clustering pattern of the populations in each group was not related to geographical distance or phytogeography. It seems that the wide geographic distribution, a small gene flow rate and the occurrence of a high level of genetic mutation lead to infraspecific genetic differentiation in the species and we suppose some infraspecific ranks exist for it.

Folk classification of wild mushrooms from San Isidro Buensuceso, Tlaxcala, Central Mexico.

BACKGROUND: An ethnomycological study was conducted to describe the fungus concept and the traditional fungus classification system for the Nahuas of San Isidro Buensuceso, in central Mexico. The study which provides information on the co-existence of various forms of classification, based on both cultural and biological characteristics. METHODS: The research included conducting community interviews and forest forays in the company of mushroom pickers. The triad technique, pile sorting, and fresh mushroom sampling methods were used. Traditional names were analyzed to describe the Nahua classification system for fungi. RESULTS AND CONCLUSION: The triad technique with non-utilitarian stimuli allowed the fungi to be identified as an independent group of plants and animals. The Nahua people of San Isidro classify fungi primarily based on their use, where they grow, and by humoral characteristics. The analysis of the names revealed a classification based on the criteria proposed by Brent Berlin. This study identified the detailed knowledge of fungi in this Nahua community. The criteria used for the recognition of the species are very reliable, since they use organoleptic, ecological, phenological, and morphological characteristics.

Secondary metabolites of Tilia tomentosa Moench inflorescences collected in Central Italy: chemotaxonomy relevance and phytochemical rationale of traditional use.

In this paper, the phytochemical analysis on the inflorescences (flowers and bracts) of a sample of Tilia tomentosa collected from an isolated population in Central Italy, was reported for the first time. Thirteen compounds (oleanolic acid, maslinic acid, apigenin, luteolin, kaempferol, quercetin, kaempferol-3-O-glucoside, quercetin-3-O-glucoside, rutin, tiliroside, ellagic acid, shikimic acid and quinic acid), belonging to several different classes of natural products, were identified on the basis of spectroscopic and spectrometric analysis. This sample was found to be mainly composed by flavonoids, followed by organic acids and pentacyclic triterpenes. The chemosystematic aspects of the identified components were also discussed, together with their pharmacologic relevance with respect to the traditional medicinal uses of this plant material.

Microscopic techniques used for the identification of medicinal plants: A case study of Senna.

BACKGROUND: The use of quality control tool for adulteration of Senna (Cassia aungustifolia) a pharmaceutically very important. They were used for multiple health disorders such as constipation, indigestion, epilepsy, asthma, piles, migraine, and heart problems. Two different species of same family or same genus used commercially in Indo-Pak using the same medicine name Senna. One named as Senna (C. aungustifolia) and its adulterant named as Sickle Senna (Cassia obtusifolia). METHODOLOGY: These two plants were analyzed using classical microscopic techniques light microscopy and the modern chemotaxonomic traits scanning electron microscopy, fluorescence studies and phytochemical studies. RESULTS: The C. aungustifolia L. had found to be a perennial herb with trilobed pollen, diacytic, paracytic, and anisocytic stomata having smooth walled epidermal cells, whereas the C. obtusifolia stands out as a perennial shrub with spheroidal and circular pollen and paracytic type of stomata having irregular shaped epidermal cells. The powdered drug of C. aungustifolia is dark grayish green, whereas the powdered drug of C. obtusifolia is light green in color. Investigation and other techniques used in this project provided the basis for the authentication of this species.

Ethnotaxonomy of sharks from tropical waters of Brazil.

BACKGROUND: Accessing folk knowledge from small-scale fishers is an affordable and reliable approach to understand the dynamic and diversity of shark species worldwide, especially of those eventually caught. In this context, ethnotaxonomy (folk identification and classification) may represent an alternative to support sharks fisheries management, especially in data-poor places. This study aimed to investigate fishing and ethnotaxonomy of the main shark species caught by small-scale fisheries from the coastal waters of the Brazilian Northeast. METHODS: Semi-structured and structured interviews were conducted with fishers targeting general aspects of fishing activities and specific topics regarding ethnotaxonomy, capture, and commercialization of sharks. For species identification, an ethnobiological systematic perspective was used to analyze the folk nomenclature and classification criteria. Non-parametric statistical tests were used to verify associations between species caught, fishing gear, and harvest period. RESULTS: Fishers mentioned 73 binomial names, 21 main folk species, and eight synonymies. Some species belonging to the same scientific genus are often named and grouped by the same folk name, with no distinction between species by fishers. Sharks are most landed as bycatch and correspond to less than 5% of the total commercial fisheries in the communities, with socioeconomic value for subsistence consumption and local commercialization. Sharks were said to be mainly caught with hand line and surface long line during the rainy season, while gillnet captures were associated to the dry season. At least three of the species most mentioned by fishers are currently classified as vulnerable and endangered worldwide. CONCLUSIONS: Even though landed sharks account for a small proportion of the fishing catches, their biological and life history features place sharks among the most vulnerable organisms globally. Such an ethnobiological approach towards shark identification may contribute to generate basic information on species caught, their frequency in the landings, and how different species belonging to the same genus can be landed and sold together. This type of information can generate subsidies to the development of conservation and management plans for these fishing resources, where knowledge is scarce.

Proposal of an Extended Taxonomy of Serious Games for Health Rehabilitation.

OBJECTIVE: Serious Games is a field of research that has evolved substantially with valuable contributions to many application domains and areas. Patients often consider traditional rehabilitation approaches to be repetitive and boring, making it difficult for them to maintain their ongoing interest and assure the completion of the treatment program. Since the publication of our first taxonomy of Serious Games for Health Rehabilitation (SGHR), many studies have been published with game prototypes in this area. Based on literature review, our goal is to propose an updated taxonomy taking into account the works, updates, and innovations in game criteria that have been researched since our first publication in 2010. In addition, we aim to present the validation mechanism used for the proposed extended taxonomy. MATERIALS AND METHODS: Based on a literature review in the area and on the analysis of the contributions made by other researchers, we propose an extended taxonomy for SGHR. For validating the taxonomy proposal, a questionnaire was designed to use on a survey among experts in the area. RESULTS: An extended taxonomy for SGHR was proposed. As we have identified that, in general, and besides the mechanisms associated with the adoption of a given taxonomy, there were no reported validation mechanisms for the proposals, we designed a mechanism to validate our proposal. The mechanism uses a questionnaire addressed to a sample of researchers and professionals with experience and expertise in domains of knowledge interrelated with SGHR, such as Computer Graphics, Game Design, Interaction Design, Computer Programming, and Health Rehabilitation. CONCLUSION: The extended taxonomy proposal for health rehabilitation serious games provides the research community with a tool to fully characterize serious games. The mechanism designed for validating the taxonomy proposal is another contribution of this work.

Towards the use of similarity distances to music genre classification: A comparative study.

Music genre classification is a challenging research concept, for which open questions remain regarding classification approach, music piece representation, distances between/within genres, and so on. In this paper an investigation on the classification of generated music pieces is performed, based on the idea that grouping close related known pieces in different sets -or clusters- and then generating in an automatic way a new song which is somehow "inspired" in each set, the new song would be more likely to be classified as belonging to the set which inspired it, based on the same distance used to separate the clusters. Different music pieces representations and distances among pieces are used; obtained results are promising, and indicate the appropriateness of the used approach even in a such a subjective area as music genre classification is.

Moving Past the Systematics Wars.

It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting to a practice-oriented view of methodology, centered on the trajectory of mathematization in systematics, demonstrates problems with the common view that one camp (cladistics) straightforwardly "won" over the other (phenetics). In particular, we critique David Hull's historical account in Science as a Process by demonstrating exactly the sort of intermediate level of positive sharing between phenetic and cladistic theories that undermines their mutually exclusive individuality as conceptual systems over time. It is misleading, or at least inadequate, to treat them simply as holistically opposed theories that can only interact by competition to the death. Looking to the future, we suggest that the concept of workflow provides an important new perspective on the history of mathematization and computerization in biology after World War II.

Development and Validation of a Taxonomy for Characterizing Measurements in Health Self-Quantification.

BACKGROUND: The use of wearable tools for health self-quantification (SQ) introduces new ways of thinking about one's body and about how to achieve desired health outcomes. Measurements from individuals, such as heart rate, respiratory volume, skin temperature, sleep, mood, blood pressure, food consumed, and quality of surrounding air can be acquired, quantified, and aggregated in a holistic way that has never been possible before. However, health SQ still lacks a formal common language or taxonomy for describing these kinds of measurements. Establishing such taxonomy is important because it would enable systematic investigations that are needed to advance in the use of wearable tools in health self-care. For a start, a taxonomy would help to improve the accuracy of database searching when doing systematic reviews and meta-analyses in this field. Overall, more systematic research would contribute to build evidence of sufficient quality to determine whether and how health SQ is a worthwhile health care paradigm. OBJECTIVE: The aim of this study was to investigate a sample of SQ tools and services to build and test a taxonomy of measurements in health SQ, titled: the classification of data and activity in self-quantification systems (CDA-SQS). METHODS: Eight health SQ tools and services were selected to be examined: Zeo Sleep Manager, Fitbit Ultra, Fitlinxx Actipressure, MoodPanda, iBGStar, Sensaris Senspod, 23andMe, and uBiome. An open coding analytical approach was used to find all the themes related to the research aim. RESULTS: This study distinguished three types of measurements in health SQ: body structures and functions, body actions and activities, and around the body. CONCLUSIONS: The CDA-SQS classification should be applicable to align health SQ measurement data from people with many different health objectives, health states, and health conditions. CDA-SQS is a critical contribution to a much more consistent way of studying health SQ.

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.

Identification of drug targets and mechanism of action (MoA) for new and uncharacterized anticancer drugs is important for optimization of treatment efficacy. Current MoA prediction largely relies on prior information including side effects, therapeutic indication, and chemoinformatics. Such information is not transferable or applicable for newly identified, previously uncharacterized small molecules. Therefore, a shift in the paradigm of MoA predictions is necessary toward development of unbiased approaches that can elucidate drug relationships and efficiently classify new compounds with basic input data. We propose here a new integrative computational pharmacogenomic approach, referred to as Drug Network Fusion (DNF), to infer scalable drug taxonomies that rely only on basic drug characteristics toward elucidating drug-drug relationships. DNF is the first framework to integrate drug structural information, high-throughput drug perturbation, and drug sensitivity profiles, enabling drug classification of new experimental compounds with minimal prior information. DNF taxonomy succeeded in identifying pertinent and novel drug-drug relationships, making it suitable for investigating experimental drugs with potential new targets or MoA. The scalability of DNF facilitated identification of key drug relationships across different drug categories, providing a flexible tool for potential clinical applications in precision medicine. Our results support DNF as a valuable resource to the cancer research community by providing new hypotheses on compound MoA and potential insights for drug repurposing. Cancer Res; 77(11); 3057-69. ©2017 AACR.

Taxonomic examination of longgu (Fossilia Ossis Mastodi, "dragon bone") and a related crude drug, longchi (Dens Draconis, "dragon tooth"), from Japanese and Chinese crude drug markets.

Longgu ("dragon bone," Ryu-kotsu, Fossilia Ossis Mastodi, or Os Draconis) is the only fossil crude drug listed in the Japanese Pharmacopoeia. All longgu in the current Japanese market is imported from China, where its resources are being depleted. Therefore, effective countermeasures are urgently needed to prevent resource depletion. One possible solution is the development of a substitute made from bones of contemporary animals that are closely related to the original animal source of the current longgu. However, no research has been conducted on the original animal source of longgu, except for a report on the longgu specimens present in the Shosoin Repository. Taxonomic examination was performed on the fossil specimens related to longgu which are owned by the Museum of Osaka University, Japan. In total, 20,939 fossil fragments were examined, of which 20,886 were mammalian fossils, and 246 of these fossils were classified into nine families. The longgu specimens from the Japanese market belonged to a relatively smaller variety of taxa than those from the Chinese market. Despite the variety of taxa in longgu, medical doctors using Kampo preparations with longgu have not reported any problems due to the presence of impurities in the original animal source. These results suggest that the effect of longgu is independent of its origin as long as it is closely related to the origin of the current longgu. Thus, despite the considerable effects of fossilization, our results could help in developing an optimal substitute for longgu.

From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories.

Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of taxonomic identifications in occurrence data repositories and to provide a filtering mechanism which can considerably reduce the number of voucher specimens that need critical revision, in this case from 4,672 to about 100.

Towards an international taxonomy of integrated primary care: a Delphi consensus approach.

BACKGROUND: Developing integrated service models in a primary care setting is considered an essential strategy for establishing a sustainable and affordable health care system. The Rainbow Model of Integrated Care (RMIC) describes the theoretical foundations of integrated primary care. The aim of this study is to refine the RMIC by developing a consensus-based taxonomy of key features. METHODS: First, the appropriateness of previously identified key features was retested by conducting an international Delphi study that was built on the results of a previous national Delphi study. Second, categorisation of the features among the RMIC integrated care domains was assessed in a second international Delphi study. Finally, a taxonomy was constructed by the researchers based on the results of the three Delphi studies. RESULTS: The final taxonomy consists of 21 key features distributed over eight integration domains which are organised into three main categories: scope (person-focused vs. population-based), type (clinical, professional, organisational and system) and enablers (functional vs. normative) of an integrated primary care service model. CONCLUSIONS: The taxonomy provides a crucial differentiation that clarifies and supports implementation, policy formulation and research regarding the organisation of integrated primary care. Further research is needed to develop instruments based on the taxonomy that can reveal the realm of integrated primary care in practice.

Classification of self-driven mental tasks from whole-brain activity patterns.

During wakefulness, a constant and continuous stream of complex stimuli and self-driven thoughts permeate the human mind. Here, eleven participants were asked to count down numbers and remember negative or positive autobiographical episodes of their personal lives, for 32 seconds at a time, during which they could freely engage in the execution of those tasks. We then examined the possibility of determining from a single whole-brain functional magnetic resonance imaging scan which one of the two mental tasks each participant was performing at a given point in time. Linear support-vector machines were used to build within-participant classifiers and across-participants classifiers. The within-participant classifiers could correctly discriminate scans with an average accuracy as high as 82%, when using data from all individual voxels in the brain. These results demonstrate that it is possible to accurately classify self-driven mental tasks from whole-brain activity patterns recorded in a time interval as short as 2 seconds.

N-gram support vector machines for scalable procedure and diagnosis classification, with applications to clinical free text data from the intensive care unit.

BACKGROUND: Existing risk adjustment models for intensive care unit (ICU) outcomes rely on manual abstraction of patient-level predictors from medical charts. Developing an automated method for abstracting these data from free text might reduce cost and data collection times. OBJECTIVE: To develop a support vector machine (SVM) classifier capable of identifying a range of procedures and diagnoses in ICU clinical notes for use in risk adjustment. MATERIALS AND METHODS: We selected notes from 2001-2008 for 4191 neonatal ICU (NICU) and 2198 adult ICU patients from the MIMIC-II database from the Beth Israel Deaconess Medical Center. Using these notes, we developed an implementation of the SVM classifier to identify procedures (mechanical ventilation and phototherapy in NICU notes) and diagnoses (jaundice in NICU and intracranial hemorrhage (ICH) in adult ICU). On the jaundice classification task, we also compared classifier performance using n-gram features to unigrams with application of a negation algorithm (NegEx). RESULTS: Our classifier accurately identified mechanical ventilation (accuracy=0.982, F1=0.954) and phototherapy use (accuracy=0.940, F1=0.912), as well as jaundice (accuracy=0.898, F1=0.884) and ICH diagnoses (accuracy=0.938, F1=0.943). Including bigram features improved performance on the jaundice (accuracy=0.898 vs 0.865) and ICH (0.938 vs 0.927) tasks, and outperformed NegEx-derived unigram features (accuracy=0.898 vs 0.863) on the jaundice task. DISCUSSION: Overall, a classifier using n-gram support vectors displayed excellent performance characteristics. The classifier generalizes to diverse patient populations, diagnoses, and procedures. CONCLUSIONS: SVM-based classifiers can accurately identify procedure status and diagnoses among ICU patients, and including n-gram features improves performance, compared to existing methods.

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data.

BACKGROUND: Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade. RESULTS: The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation' barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity. CONCLUSIONS: The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is available at https://github.com/naturalis/HTS-barcode-checker.

What is in a name? The need for accurate scientific nomenclature for plants.

ETHNOPHARMACOLOGICAL RELEVANCE: To avoid ambiguities and error, ethnopharmacological and any other research on plants requires precise and appropriate use of botanical scientific nomenclature. AIMS: This paper explores problems and impacts of ambiguous or erroneous use of botanical scientific nomenclature in ethnopharmacological studies. It suggests how the frequency and impact of such errors can be reduced. APPROACH AND METHODS: We assessed 214 articles published in the three first volumes of the Journal of Ethnopharmacology in 2012: 140(1) to 141 (3) and 214 articles in Phytomedicine (2012-2013): 19 (5) to 20 (7). RESULTS: Amongst the articles reviewed 308 articles cited plant names incorrectly. Among the articles studied 9178 Latin scientific names were cited and 3445 were incorrect in some respect. Simple principles applied in a systematic way and used together with open-access reference resources could help authors, referees and editors of ethnopharmacological, phytochemical, toxicological and clinical studies to reduce ambiguity about the identity and name of the species involved and thus significantly improve the quality of the final publication. CONCLUSIONS: We have identified a series of key steps needed to solve the taxonomic ambiguities and errors. Aside from reinforcing existing policies, journals will have to implement better tools to ensure the proper authentication of materials. The new electronic publishing environments offer novel ways to develop such botanical-taxonomic tools.

Classification of grass pollen through the quantitative analysis of surface ornamentation and texture.

Taxonomic identification of pollen and spores uses inherently qualitative descriptions of morphology. Consequently, identifications are restricted to categories that can be reliably classified by multiple analysts, resulting in the coarse taxonomic resolution of the pollen and spore record. Grass pollen represents an archetypal example; it is not routinely identified below family level. To address this issue, we developed quantitative morphometric methods to characterize surface ornamentation and classify grass pollen grains. This produces a means of quantifying morphological features that are traditionally described qualitatively. We used scanning electron microscopy to image 240 specimens of pollen from 12 species within the grass family (Poaceae). We classified these species by developing algorithmic features that quantify the size and density of sculptural elements on the pollen surface, and measure the complexity of the ornamentation they form. These features yielded a classification accuracy of 77.5%. In comparison, a texture descriptor based on modelling the statistical distribution of brightness values in image patches yielded a classification accuracy of 85.8%, and seven human subjects achieved accuracies between 68.33 and 81.67%. The algorithmic features we developed directly relate to biologically meaningful features of grass pollen morphology, and could facilitate direct interpretation of unsupervised classification results from fossil material.

Clasificación radiográfica de la cadera con desarrollo displásico / Radiographic classification of developmental dysplasia of the hip

Por más de una década, la férula en abducción de cadera ha sido el método de tratamiento del desarrollo displásico de caderas, en el Hospital Pediátrico Universitario Paquito González Cueto de Cienfuegos. El objetivo de este trabajo es exponer la clasificación dinámica para las caderas con desarrollo displásico, desde el punto de vista radiográfico. Para ilustrar la clasificación se utilizaron esquemas representativos y radiografías de pacientes portadores de diferentes grados de la afección. El comportamiento dinámico de los parámetros radiográficos utilizados en la clasificación, permite realizar agrupaciones diagnósticas antes, durante y después del tratamiento, en función de evaluar los resultados finales de este(AU)

For over a decade, abduction splinting has been the method of treatment for developmental dysplasia of the hip in the Paquito González Cueto University Pediatric Hospital. This paper is aimed at presenting the dynamic classification for this condition from a radiographic point of view. Representative schemes and radiographies of patients with various stages of developmental hip dysplasia were used for illustrating this classification. The dynamic behavior of the radiographic parameters used in the classification allows gathering diagnostic groups before, during and after treatment in order to assess its final results(AU)