SciCombinator

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Concept: Carl Linnaeus

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Hymenoptera, the insect order that includes sawflies, bees, wasps, and ants, exhibits an incredible diversity of phenotypes, with over 145,000 species described in a corpus of textual knowledge since Carolus Linnaeus. In the absence of specialized training, often spanning decades, however, these articles can be challenging to decipher. Much of the vocabulary is domain-specific (e.g., Hymenoptera biology), historically without a comprehensive glossary, and contains much homonymous and synonymous terminology. The Hymenoptera Anatomy Ontology was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy, as well as provide support for domain experts so they may actively benefit from the anatomy ontology development. As part of HAO development, an active learning, dictionary-based, natural language recognition tool was implemented to facilitate Hymenoptera anatomy term discovery in literature. We present this tool, referred to as the ‘Proofer’, as part of an iterative approach to growing phenotype-relevant ontologies, regardless of domain. The process of ontology development results in a critical mass of terms that is applied as a filter to the source collection of articles in order to reveal term occurrence and biases in natural language species descriptions. Our results indicate that taxonomists use domain-specific terminology that follows taxonomic specialization, particularly at superfamily and family level groupings and that the developed Proofer tool is effective for term discovery, facilitating ontology construction.

Concepts: Evolution, Insect, Taxonomy, Controlled vocabulary, Wasp, Ant, Hymenoptera, Carl Linnaeus

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Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples.

Concepts: DNA, Life, Genome, Natural environment, Nature, Natural history, Museum, Carl Linnaeus

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The British Museum, based in Montague House, Bloomsbury, opened its doors on 15 January 1759, as the world’s first state-owned public museum. The Museum’s collection mostly originated from Sir Hans Sloane (1660-1753), whose vast holdings were purchased by Parliament shortly after his death. The largest component of this collection was objects of natural history, including a herbarium made up of 265 bound volumes, many of which were classified according to the late seventeenth-century system of John Ray (1627-1705). The 1750s saw the emergence of Linnaean binomial nomenclature, following the publication of Carl Linnaeus' Species Plantarum (1753) and Systema Naturae (1758). In order to adopt this new system for their collections, the Trustees of the British Museum chose to employ the Swedish naturalist and former student of Linnaeus, Daniel Solander (1733-1782) to reclassify the collection. Solander was ordered to devise a new system for classifying and cataloguing Sloane’s natural history collection, which would allow both Linnaeans and those who followed earlier systems to access it. Solander’s work was essential for allowing the British Museum to realize its aim of becoming a public centre of learning, adapting the collection to reflect the diversity of classificatory practices which were existent by the 1760s. This task engaged Solander until 1768, when he received an offer from Joseph Banks (1743-1820) to accompany him on HMS Endeavour to the Pacific.

Concepts: Natural history, Museum, Royal Society, Carl Linnaeus, Systema Naturae, British Museum, Hans Sloane, Natural History Museum

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The natural history of non-functioning pituitary macroadenomas (NFPMA) after surgical resection is variable, with guidelines unable to define the duration of radiological follow up. In this first Australian series, we identify risk factors for regrowth/recurrence of NFPMA to assist with guiding recommendations for long-term follow-up.

Concepts: Risk, The Canon of Medicine, Avicenna, Sequence, Nature, Algebra, Baseball, Carl Linnaeus

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HIV-1-infected persons spontaneously controlling viremia without treatment (SCV) are rare. Gender and race effects on prevalence and outcome are poorly defined, and it is unclear whether SCV qualitatively or quantitatively differs from typical infection. These issues are examined.

Concepts: Disease, Natural environment, Nature, History of science, Natural science, Natural history, Spontaneous human combustion, Carl Linnaeus

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This review reflects the trajectory of my career in hematopathology, and my personal reflections on scientific advances in the field. During the course of more than 40 years, the approach to classification of hematological malignancies has evolved from descriptive approaches, based on either cytological or clinical features, to a modern approach, which incorporates cutting-edge technologies. My philosophy has focused on defining individual diseases, an approach that can best lead to an understanding of molecular pathogenesis. To quote Carolus Linnaeus (1, p. 19), the father of taxonomy, “The first step in wisdom is to know the things themselves; this notion consists in having a true idea of the objects; objects are distinguished and known by classifying them methodically and giving them appropriate names. Therefore, classification and name-giving will be the foundation of our science.” Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease Volume 12 is January 24, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Concepts: Immune system, Cancer, Disease, Pathology, Hematological malignancy, Linnaean taxonomy, Carl Linnaeus, Carolus Linnaeus the Younger

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In Philosophia Botanica (1751), Carolus Linnaeus (1707-1778) presented a calculation of the number of plant genera that may be distinguished based on his taxonomic concepts. In order to derive that number, he relied upon the organs of fructification, which represent the flower and the fruit, by selecting over 30 elements from them, and then assuming that each could vary by four dimensions. However, while Linnaeus was good in counting stamens and pistils, he and many of his followers who edited or translated Philosophia Botanica were less careful, basing their calculations of the number of possible genera on flawed assumptions, or even introducing basic arithmetic errors. Furthermore, although mathematics was quite advanced in the eighteenth century, the gap between combinatorial and botanical thinking was too deep, preventing Linnaeus to seek a reasonable solution to the problem he raised. The authors demonstrate this by a historical analysis of 15 editions of Philosophia Botanica, plus many references to it, and conclude that the desired number almost always appeared in error during the past 265 years. The German botanist J. G. Gleditsch (1714-1786) was the most successful with respect to Linnaeus' original intention. Elementary mathematics demonstrates that if Linnaeus' assumptions were taken seriously, then the possible number of genera would be astronomical. The practice he followed in Genera Plantarum (1754) shows, however, that the fructification dimensions served as a universal set for Linnaeus from which he chose only the relevant ones for describing a particular genus empirically. Based on the corrections and modifications implemented in reworked editions, we suggest an evolutionary network for the historical and modern versions or translations of Philosophia Botanica.

Concepts: Mathematics, Species, Botany, Arithmetic, Binomial nomenclature, Elementary arithmetic, Botanical nomenclature, Carl Linnaeus

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During his 20-year career as a surgeon-naturalist with the British East India Company, Francis Buchanan (later Hamilton, known in botany as Buchanan-Hamilton and in ichthyology as Hamilton-Buchanan) undertook pioneering survey explorations in several diverse regions of the Indian subcontinent. A naturalist at heart, his collections of plants and animals are often the first from such regions, notably Nepal, Burma (Myanmar) and Bangladesh. Buchanan had wide-ranging interests beyond natural history, using his talent for observation and meticulous recording to amass a huge body of information on the lands and peoples he encountered. However, much of this information remains unpublished in his survey reports, journals and other manuscripts, and so his role in the building of knowledge for these areas has been under-appreciated. Although a keen and able botanist, it is ironic that his multitudinous botanical discoveries are particularly poorly known, with the vast majority of his material on this subject languishing unpublished in archival collections. These include his original records and working notes which show the methods he used when dealing with ‘information overload’ and arranging his syntheses ready for publication. Notable is his experimentation with Jussieu’s Natural System for classifying his Nepalese plants, and his recognition of biogeographic links of the Nepalese flora with Europe and Japan - both ahead of his fellow countrymen in Britain and India. The life of Francis Buchanan awaits the attention of a biographer who can do justice to his many interests, activities and influences. This is the first of two papers covering his life, providing an empirical baseline for future research and correcting misinformation that abounds in the literature. These papers outline Buchanan’s professional career, concentrating on his activities in the exploration of natural history, and placing them in the wider context of botanical research in India.

Concepts: Botany, India, Indian subcontinent, Buddhism, Nepal, British Empire, Carl Linnaeus, East India Company

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Dried plant parts used as culinary spices (CSs) in food are permitted as dietary ingredients in dietary supplements (DSs) within certain constraints in the United States. We reviewed the amounts, forms, and nutritional support (structure/function) claims of DSs that contain CS plants listed in the Dietary Supplement Label Database (DSLD) and compared this label information with trial doses and health endpoints for CS plants that were the subject of clinical trials listed in clinicaltrials.gov. According to the DSLD, the CS plants occurring most frequently in DSs were cayenne, cinnamon, garlic, ginger, pepper, rosemary, and turmeric. Identifying the botanical species, categorizing the forms used, and determining the amounts from the information provided on DS labels was challenging. CS plants were typically added as a component of a blend, as the powered biomass, dried extracts, and isolated phytochemicals. The amounts added were declared on about 55% of the labels, rendering it difficult to determine the amount of the CS plant used in many DSs. Clinicaltrials.gov provided little information about the composition of test articles in the intervention studies. When plant names were listed on DS labels and in clinical trials, generally the common name and not the Latin binomial name was given. In order to arrive at exposure estimates and enable researchers to reproduce clinical trials, the Latin binomial name, form, and amount of the CS plant used in DSs and tested in clinical trials must be specified.

Concepts: Clinical trial, Species, ClinicalTrials.gov, Dietary supplement, Food and Drug Administration, Nomenclature, Spice, Carl Linnaeus