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https://www.readbyqxmd.com/read/28334284/genomic-diversity-guides-conservation-strategies-among-rare-terrestrial-orchid-species-when-taxonomy-remains-uncertain
#1
Collin W Ahrens, Megan A Supple, Nicola C Aitken, David J Cantrill, Justin O Borevitz, Elizabeth A James
Background and Aims: Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia...
March 15, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334086/pseudoalignment-for-metagenomic-read-assignment
#2
L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter
Motivation: Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains...
February 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333497/not-all-nonnormal-distributions-are-created-equal-improved-theoretical-and-measurement-precision
#3
Harry Joo, Herman Aguinis, Kyle J Bradley
We offer a four-category taxonomy of individual output distributions (i.e., distributions of cumulative results): (1) pure power law; (2) lognormal; (3) exponential tail (including exponential and power law with an exponential cutoff); and (4) symmetric or potentially symmetric (including normal, Poisson, and Weibull). The four categories are uniquely associated with mutually exclusive generative mechanisms: self-organized criticality, proportionate differentiation, incremental differentiation, and homogenization...
March 23, 2017: Journal of Applied Psychology
https://www.readbyqxmd.com/read/28333488/the-hierarchical-taxonomy-of-psychopathology-hitop-a-dimensional-alternative-to-traditional-nosologies
#4
Roman Kotov, Robert F Krueger, David Watson, Thomas M Achenbach, Robert R Althoff, R Michael Bagby, Timothy A Brown, William T Carpenter, Avshalom Caspi, Lee Anna Clark, Nicholas R Eaton, Miriam K Forbes, Kelsie T Forbush, David Goldberg, Deborah Hasin, Steven E Hyman, Masha Y Ivanova, Donald R Lynam, Kristian Markon, Joshua D Miller, Terrie E Moffitt, Leslie C Morey, Stephanie N Mullins-Sweatt, Johan Ormel, Christopher J Patrick, Darrel A Regier, Leslie Rescorla, Camilo J Ruggero, Douglas B Samuel, Martin Sellbom, Leonard J Simms, Andrew E Skodol, Tim Slade, Susan C South, Jennifer L Tackett, Irwin D Waldman, Monika A Waszczuk, Thomas A Widiger, Aidan G C Wright, Mark Zimmerman
The reliability and validity of traditional taxonomies are limited by arbitrary boundaries between psychopathology and normality, often unclear boundaries between disorders, frequent disorder co-occurrence, heterogeneity within disorders, and diagnostic instability. These taxonomies went beyond evidence available on the structure of psychopathology and were shaped by a variety of other considerations, which may explain the aforementioned shortcomings. The Hierarchical Taxonomy Of Psychopathology (HiTOP) model has emerged as a research effort to address these problems...
March 23, 2017: Journal of Abnormal Psychology
https://www.readbyqxmd.com/read/28332571/profiling-protein-expression-in-circulating-tumour-cells-using-microfluidic-western-blotting
#5
Elly Sinkala, Elodie Sollier-Christen, Corinne Renier, Elisabet Rosàs-Canyelles, James Che, Kyra Heirich, Todd A Duncombe, Julea Vlassakis, Kevin A Yamauchi, Haiyan Huang, Stefanie S Jeffrey, Amy E Herr
Circulating tumour cells (CTCs) are rare tumour cells found in the circulatory system of certain cancer patients. The clinical and functional significance of CTCs is still under investigation. Protein profiling of CTCs would complement the recent advances in enumeration, transcriptomic and genomic characterization of these rare cells and help define their characteristics. Here we describe a microfluidic western blot for an eight-plex protein panel for individual CTCs derived from estrogen receptor-positive (ER+) breast cancer patients...
March 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28331536/an-efficient-algorithm-for-testing-the-compatibility-of-phylogenies-with-nested-taxa
#6
Yun Deng, David Fernández-Baca
BACKGROUND: Semi-labeled trees generalize ordinary phylogenetic trees, allowing internal nodes to be labeled by higher-order taxa. Taxonomies are examples of semi-labeled trees. Suppose we are given collection [Formula: see text] of semi-labeled trees over various subsets of a set of taxa. The ancestral compatibility problem asks whether there is a semi-labeled tree that respects the clusterings and the ancestor/descendant relationships implied by the trees in [Formula: see text]. The running time and space usage of the best previous algorithm for testing ancestral compatibility depend on the degrees of the nodes in the trees in [Formula: see text]...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28331398/taxonomy-of-the-african-large-carpenter-bees-of-the-genus-xylocopa-latreille-1802-subgenus-xenoxylocopa-hurd-moure-1963-hymenoptera-apidae
#7
Jonathan R Mawdsley
The taxonomy of the genus Xylocopa Latreille, 1802, subgenus Xenoxylocopa Hurd & Moure, 1963, is reviewed. There is a single valid species in this subgenus, Xylocopa (Xenoxylocopa) inconstans Smith, 1874, which is widely distributed throughout sub-Saharan Africa, from Senegal to Ethiopia and south to northern Republic of South Africa. Synonyms of Xylocopa inconstans include Xylocopa abyssinica Radoszkowski, 1899, proposed for a male specimen from Ethiopia, as well as three names proposed for females with yellow (rather than white) dorsal pubescence: Mesotrichia chiyakensis Cockerell, 1908 (new synonym), Xylocopa inconstans var...
2017: ZooKeys
https://www.readbyqxmd.com/read/28331396/catalog-of-the-neotropical-trichoptera-caddisflies
#8
Ralph W Holzenthal, Adolfo R Calor
The Neotropical caddisfly (Trichoptera) fauna is cataloged from a review of over 1,000 literature citations through 2015 (partial 2016) to include 3,262 currently recognized, valid species-group names in 25 families and 155 extant genera. Fourteen subspecies are included in the total as well as 35 fossil species and 1 fossil genus. The region covered includes all of Mexico, Central America, the Caribbean, and South America. Genus-group and species-group synonyms are listed. For each nominal species, information on the type locality, type depository, sex of type, distribution by country, and other pertinent taxonomic or biological information is included...
2017: ZooKeys
https://www.readbyqxmd.com/read/28331387/taxonomy-of-the-leptogenys-modiglianii-species-group-from-southeast-asia-hymenoptera-formicidae-ponerinae
#9
Kôichi Arimoto
Leptogenys brevilobasp. n., Leptogenys curvasp. n., Leptogenys itoisp. n., Leptogenys kanaoisp. n., Leptogenys malayanasp. n., and Leptogenys modiglianii Emery, 1900 are described from southeast Asia. The Leptogenys modiglianii species group is proposed on the basis of similarities among the six species. An identification key to species in this group from southeast Asia is provided.
2017: ZooKeys
https://www.readbyqxmd.com/read/28330330/a-combined-chloroplast-atpb-rbcl-and-trnl-f-phylogeny-unveils-the-ancestry-of-balsams-impatiens-spp-in-the-western-ghats-of-india
#10
P P Shajitha, N R Dhanesh, P J Ebin, Joseph Laly, Devassy Aneesha, John Reshma, Jomy Augustine, Mathew Linu
Only a few Impatiens spp. from South India (one of the five centers of diversity for Impatiens species) were included in the published datum of molecular phylogeny of the family Balsaminaceae. The present investigation is a novel attempt to reveal the phylogenetic association of Impatiens species of South India, by placing them in the global phylogeny of Impatiens based on a combined analysis of two chloroplast genes. Thirty species of genus Impatiens were collected from different locations of South India. Total genomic DNA was extracted from fresh plant leaf, and polymerase chain reaction was carried out using atpB-rbcL and trnL-F intergenic spacer-specific forward and reverse primers...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329020/how-a-collaborative-integrated-taxonomic-effort-has-trained-new-spongiologists-and-improved-knowledge-of-martinique-island-french-antilles-eastern-caribbean-sea-marine-biodiversity
#11
Thierry Pérez, Maria-Cristina Díaz, César Ruiz, Baslavi Cóndor-Luján, Michelle Klautau, Eduardo Hajdu, Gisele Lobo-Hajdu, Sven Zea, Shirley A Pomponi, Robert W Thacker, Sophie Carteron, Guillaume Tollu, Adeline Pouget-Cuvelier, Philippe Thélamon, Jean-Philippe Marechal, Olivier P Thomas, Alexander V Ereskovsky, Jean Vacelet, Nicole Boury-Esnault
Although sponges are important components of benthic ecosystems of the Caribbean Sea, their diversity remained poorly investigated in the Lesser Antilles. By organizing a training course in Martinique, we wanted both to promote taxonomy and to provide a first inventory of the sponge diversity on this island. The course was like a naturalist expedition, with a field laboratory and a classroom nearby. Early-career scientists and environmental managers were trained in sponge taxonomy. We gathered unpublished data and conducted an inventory at 13 coastal sites...
2017: PloS One
https://www.readbyqxmd.com/read/28328931/x-ray-microtomography-for-ant-taxonomy-an-exploration-and-case-study-with-two-new-terataner-hymenoptera-formicidae-myrmicinae-species-from-madagascar
#12
Francisco Hita Garcia, Georg Fischer, Cong Liu, Tracy L Audisio, Gary D Alpert, Brian L Fisher, Evan P Economo
We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrog sp. n. and T. nymeria sp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution maps for both new species...
2017: PloS One
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#13
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28326054/dynamical-constants-and-time-universals-a-first-step-toward-a-metrical-definition-of-ordered-and-abnormal-cognition
#14
REVIEW
Mark A Elliott, Naomi du Bois
From the point of view of the cognitive dynamicist the organization of brain circuitry into assemblies defined by their synchrony at particular (and precise) oscillation frequencies is important for the correct correlation of all independent cortical responses to the different aspects of a given complex thought or object. From the point of view of anyone operating complex mechanical systems, i.e., those comprising independent components that are required to interact precisely in time, it follows that the precise timing of such a system is essential - not only essential but measurable, and scalable...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28326048/developing-a-taxonomy-of-dark-triad-triggers-at-work-a-grounded-theory-study-protocol
#15
Annika Nübold, Josef Bader, Nera Bozin, Romil Depala, Helena Eidast, Elisabeth A Johannessen, Gerhard Prinz
In past years, research and corporate scandals have evidenced the destructive effects of the dark triad at work, consisting of narcissism (extreme self-centeredness), psychopathy (lack of empathy and remorse) and Machiavellianism (a sense of duplicity and manipulativeness). The dark triad dimensions have typically been conceptualized as stable personality traits, ignoring the accumulating evidence that momentary personality expressions - personality states - may change due to the characteristics of the situation...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28325881/probabilistic-models-of-species-discovery-and-biodiversity-comparisons
#16
Stewart M Edie, Peter D Smits, David Jablonski
Inferring large-scale processes that drive biodiversity hinges on understanding the phylogenetic and spatial pattern of species richness. However, clades and geographic regions are accumulating newly described species at an uneven rate, potentially affecting the stability of currently observed diversity patterns. Here, we present a probabilistic model of species discovery to assess the uncertainty in diversity levels among clades and regions. We use a Bayesian time series regression to estimate the long-term trend in the rate of species description for marine bivalves and find a distinct spatial bias in the accumulation of new species...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28325441/a-review-of-fuzzy-cognitive-maps-in-medicine-taxonomy-methods-and-applications
#17
REVIEW
Abdollah Amirkhani, Elpiniki I Papageorgiou, Akram Mohseni, Mohammad R Mosavi
BACKGROUND AND OBJECTIVE: A high percentage of medical errors, committed because of physician's lack of experience, huge volume of data to be analyzed, and inaccessibility to medical records of previous patients, can be reduced using computer-aided techniques. Therefore, designing more efficient medical decision-support systems (MDSSs) to assist physicians in decision-making is crucially important. Through combining the properties of fuzzy logic and neural networks, fuzzy cognitive maps (FCMs) are among the latest, most efficient, and strongest artificial intelligence techniques for modeling complex systems...
April 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28324166/redescription-of-chloromyxum-ellipticum-li-nie-1973-myxosporea-chloromyxidae-infecting-the-gall-bladder-of-grass-carp-ctenopharyngodon-idellus-valenciennes-1844-supplemented-by-morphological-and-molecular-characteristics
#18
J Y Zhang, Y L Zhao, M D Batueva, D Luo, Z F Xing, Q Q Zhang, X H Liu
The traditional taxonomy of the genus Chloromyxum Mingazzini, 1890 has been intensively challenged to be paraphyletic by recent ribosomal DNA (rDNA)-based phylogenetic analysis. Undersampling to get rich sequence data to infer more scientific phylogenetic relationships makes scientists conservatively assign all non-marine elasmobranch-infecting species as Chloromyxum sensu lato. Although complex ridge pattern on the spore surface observed by scanning electron microscopy was thought to be critical for the identification of Chloromyxum species, insufficient data also prevent this ultrastructural data to be a valid taxonomic feature for this genus...
March 21, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28322728/phlebotomine-sandflies-of-botswana-a-taxonomic-review-and-a-faunistic-update-with-the-first-record-of-genus-phlebotomus
#19
Andreas Krüger
The first records of phlebotomine sandflies from Botswana have been published only recently, comprising of four species of genus Sergentomyia. This update presents the first record of genus Phlebotomus, namely Ph. (Anaphlebotomus) rodhaini Parrot, which is also the first detection of a putative vector of leishmaniasis in Botswana. In addition, records of the Sergentomyia "bedfordi (Newstead) group" are reviewed, and the molecular taxonomy of all taxa known from Botswana is analysed based on three mitochondrial gene fragments (mtDNA)...
March 18, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28322330/distribution-of-bathyarchaeota-communities-across-different-terrestrial-settings-and-their-potential-ecological-functions
#20
Xing Xiang, Ruicheng Wang, Hongmei Wang, Linfeng Gong, Baiying Man, Ying Xu
High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database...
March 21, 2017: Scientific Reports
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