bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunodeficiency and severe gastrointestinal manifestations in a patient with novel DKC1 mutations causing Hoyeraal–Hreidarsson syndrome
Authors: Marcus Nufar 
Published: July 2016

Background: Hoyeraal–Hreidarsson syndrome (HHS) is considered a clinically severe variant of dyskeratosis congenita (DKC) and represents the extreme phenotype caused by aberrant telomere biology. Unlike patients with DKC who present later in life, most cases of HHS present in the first years of life. Clinical features include intrauterine growth restriction and microcephaly, which are universal but not pathognomonic, as well as gastrointestinal, immunological and neurological manifestations. The immunological profile is varied as a result of cellular immunodeficiency, humoral defects, or both, and may be the presenting symptom of these patients. Moreover, the immunological phenotype can change over time, making HHS a diagnostic challenge. Methods: This case report highlights the clinical presentation and immune investigations of a male patient with a novel mutation in DKC1, causing HHS. Results: Here, we describe a patient with HHS who presented with Pneumocystis jiroveci pneumonia and low T cells, which is typical of severe combined immunodeficiency. Over time, he developed agammaglobulinemia whereas T-cell function improved. He also presented with extremely severe gastrointestinal manifestations, and died at 3 years of age. Conclusion: This case report highlights a novel compound heterozygous mutation in DKC1, and the need to consider HHS as the differential diagnosis of patients with combined immunodeficiency. Statement of novelty: The case reports on a novel mutation in DKC1.
The influence of morphological variation on migration performance in a trans-hemispheric migratory songbird
Authors: Lam Lawrence , McKinnon Emily A. , Ray James D. , Pearman Myrna , Hvenegaard Glen T. , Mejeur James , Moscar Lauren , Pearson Mackenzie , Applegate Kelly , Mammenga Paul , Tautin John , Fraser Kevin C. 
Published: July 2016

AbstractFor long-distance migratory songbirds,
morphological traits such as longer wings and a smaller
body size are predicted to increase migration efficiency.
Due to previous limitations in our ability to track the
long-distance journeys of small-bodied birds, the
relationship between morphology and start-to-finish
migration performance has never been fully tested in
free-living songbirds. Using direct-tracking data obtained
from light-level geolocators, we examined the effects of
morphological factors (wing and body size) on spring
and fall migration performance (flight speed, duration of
stopovers, total stopovers taken) of a widely distributed,
trans-hemispheric migratory songbird, the purple martin
(Progne subis) (n = 120). We found that smaller-bodied
birds spent fewer days at stopovers along fall migration,
but larger-bodied birds spent fewer days at stopover and
took fewer stopovers during spring migration. More of the
variation in fall migration performance was explained
by morphology, as compared to spring migration, possibly indicating a larger influence of environmental
conditions on spring performance. Overall, our results
partially support long-standing and previously untested
predictions regarding the influence of intrinsic factors on
migration performance. Future research should examine
the influence of environmental variation on migration
performance as well as additional morphological traits
that may contribute to migration performance.
High occurrence of Acanthamoeba genotype T4 in soil sources from Bolívar State, Venezuela
Authors: Wagner Carolina , Reyes-Batlle María , Hernán Aurora , Rojas Elsy , Pérez Gladymar , López-Arencibia Atteneri , Sifaoui Ines , Martínez-Carretero Enrique , Piñero José E. , Valladares Basilio , Lorenzo-Morales Jacob 
Published: July 2016

AbstractPathogenic strains of
A new species of Ergasilus (Copepoda: Ergasilidae) from Geophagus altifrons and G. argyrostictus (Perciformes: Cichlidae) in the Brazilian Amazon
Authors: Taborda Naraiana Lopes , Paschoal Fabiano , Luque José Luis 
Published: July 2016

AbstractA new species of ergasilid copepod,
First survey of parasitic helminths of goats along the Han River in Hubei Province, China
Authors: Yang Xin , Gasser Robin B. , Fang Rui , Zeng Jinrong , Zhu Kaixiang , Qi Mingwei , Zhang Zongze , Tan Li , Lei Weiqiang , Zhou Yanqin , Zhao Junlong , Hu Min 
Published: July 2016

AbstractDiseases caused by parasitic helminths cause considerable production and economic losses in livestock worldwide. Understanding the epidemiology of these parasites has important implications for controlling them. The main purpose of the present study was to estimate the prevalence of key parasitic helminths in goats along the Han River in Zhanggang, Hubei Province (from January to December 2014). We used faecal flotation and sedimentation techniques as well as PCR-based DNA sequencing to detect and identify helminths. Results showed that the prevalence of helminths was high throughout the year, particularly for gastrointestinal nematodes. These first findings provide useful baseline information for goat helminths in Zhanggang, and a starting point for the implementation of control programs. With an increased expansion of the goat industry in China, the findings also emphasise the need to undertake prevalence surveys in other regions of China where extensive farming practices are used.
A new species of Acanthocotyle Monticelli, 1888 (Platyhelminthes: Monogenea: Acanthocotylidae) from the ventral skin of the banded stingaree, Urolophus cruciatus (Lacépède, 1804), from Tasmania, Australia
Authors: Kearn Graham , Whittington Ian , Chisholm Leslie , Evans-Gowing Richard 
Published: July 2016

Abstractsp. nov. is described from the skin of the banded stingaree,
A new feather mite of the genus Trouessartia Canestrini 1899 (Acariformes: Trouessartiidae) from the Seychelles magpie-robin, Copsychus sechellarum (Passeriformes: Muscicapidae)
Authors: Mironov Sergey V. , Palma Ricardo L. 
Published: July 2016

AbstractA new feather mite species,
Genomic and phylogenetic analysis of Ceramium cimbricum (Ceramiales, Rhodophyta) from the Atlantic and Pacific Oceans supports the naming of a new invasive Pacific entity Ceramium sungminbooi sp. nov.
Authors: Hughey Jeffery R. , Boo Ga Hun 
Published: July 2016

Abstract
The filamentous marine red alga Ceramium cimbricum was described from Denmark, but the name has since been applied to populations worldwide. To determine if C. cimbricum from the Pacific is conspecific with C. cimbricum from the Atlantic, we (1) deciphered an authentic rbcL sequence for the lectotype specimen of C. cimbricum, (2) performed phylogenetic analysis on Pacific and Atlantic C. cimbricum, and (3) assembled and analyzed the complete mitochondrial and plastid genomes of specimens of C. cimbricum from Denmark and California. The lectotype sequence of C. cimbricum was unique and fully resolved with other Atlantic Ceramium species, however, the specimens of C. cimbricum from Denmark, Norway, California, Oregon, and Korea formed a clade with Pacific species. The plastid and mitochondrial genomes of C. cimbricum from Denmark and California were similar in length and gene content, differing by only 67 SNPs and nine gaps for the plastid, and by 100 SNPs and 31 gaps for the mitochondrial genomes. These results support the continued application of the name C. cimbricum to specimens from Denmark, and warrant the naming of a new species, Ceramium sungminbooi sp. nov., native to Asia and introduced to the northeastern Pacific and Europe.
Order of blood draw: Opinion Paper by the European Federation for Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for the Preanalytical Phase (WG-PRE)
Authors: Cornes Michael , van Dongen-Lases Edmée , Grankvist Kjell , Ibarz Mercedes , Kristensen Gunn , Lippi Giuseppe , Nybo Mads , Simundic Ana-Maria 
Published: July 2016

Abstract
It has been well reported over recent years that most errors within the total testing process occur in the pre-analytical phase (46%–68.2%), an area that is usually outside of the direct control of the laboratory and which includes sample collection (phlebotomy). National and international (WHO, CLSI) guidelines recommend that the order of draw of blood during phlebotomy should be blood culture/sterile tubes, then plain tubes/gel tubes, then tubes containing additives. This prevents contamination of sample tubes with additives from previous tubes that could cause erroneous results. There have been a number of studies recently looking at whether order of draw remains a problem with modern phlebotomy techniques and materials, or it is an outdated practice followed simply because of historical reasons. In the following article, the European Federation of Clinical Chemistry and Laboratory Medicine Working Group for the Preanalytical Phase (EFLM WG-PRE) provides an overview and summary of the literature with regards to order of draw in venous blood collection. Given the evidence presented in this article, the EFLM WG-PRE herein concludes that a significant frequency of sample contamination does occur if order of draw is not followed during blood collection and when performing venipuncture under less than ideal circumstances, thus putting patient safety at risk. Moreover, given that order of draw is not difficult to follow and knowing that ideal phlebotomy conditions and protocols are not always followed or possible, EFLM WG-PRE supports the continued recommendation of ensuring a correct order of draw for venous blood collection.
Complex manifolds with maximal torus actions
Authors: Ishida Hiroaki 
Published: July 2016

Abstract
In this paper, we introduce the notion of maximal actions of compact tori on smooth manifolds and study compact connected complex manifolds equipped with maximal actions of compact tori. We give a complete classification of such manifolds, in terms of combinatorial objects, which are triples

(
Δ
,
𝔥
,
G
)

{(\Delta,\mathfrak{h},G)}

of nonsingular complete fan Δ in

𝔤

{\mathfrak{g}}

, complex vector subspace

𝔥

{\mathfrak{h}}

of

𝔤
ℂ

{\mathfrak{g}^{\mathbb{C}}}

and compact torus G satisfying certain conditions. We also give an equivalence of categories with suitable definitions of morphisms in these families, like toric geometry. We obtain several results as applications of our equivalence of categories; complex structures on moment-angle manifolds, classification of holomorphic nondegenerate

ℂ
n

{\mathbb{C}^{n}}

-actions on compact connected complex manifolds of complex dimension n, and construction of concrete examples of non-Kähler manifolds.
DNA barcoding increases resolution and changes structure in Canadian boreal shield lake food webs
Authors: Bartley Timothy J. , Braid Heather E. , McCann Kevin S. , Lester Nigel P. , Shuter Brian J. , Shuter Brian J. , Hanner Robert H. 
Published: July 2016

AbstractFood webs are important in understanding the structure, function, and behaviour of ecosystems, but, due to methodological limitations, are often poorly resolved in ways that impact food-web properties. Although DNA barcoding has proven useful in determining the diet of consumers, few studies have used this technique to determine food-web structure. These studies report mixed impacts on various food-web properties, but are limited by their taxonomic focus and their failure to evaluate DNA barcoding for both diet analysis and food-web structure. In this study, we show that, when compared to a morphological approach, DNA barcoding increases foodweb resolution by increasing the number and frequency of prey species identified in the stomach contents of eight species of Canadian boreal shield predatory fishes. In addition, we observed differences in food-web structure, such as increased generalism, habitat coupling, and omnivory, that have strong implications for food-web stability and dynamics. We conclude that DNA barcoding is a powerful tool to evaluate how resolution impacts foodweb properties and can help further our understanding of how food webs are structured by identifying feeding interactions in an unprecedented and highly detailed manner.
An exploration of sufficient sampling effort to describe intraspecific DNA barcode haplotype diversity: examples from the ray-finned fishes (Chordata: Actinopterygii)
Authors: Phillips Jarrett D. , Gwiazdowski Rodger A. , Ashlock Daniel , Hanner Robert 
Published: July 2016

AbstractEstimating appropriate sample sizes to measure species abundance and richness is a fundamental problem for most biodiversity research. In this study, we explore a method to measure sampling sufficiency based on haplotype diversity in the ray-finned fishes (Animalia: Chordata: Actinopterygii). To do this, we use linear regression and hypothesis testing methods on haplotype accumulation curves from DNA barcodes for 18 species of fishes, in the statistics platform R. We use a simple mathematical model to estimate sampling sufficiency from a sample-number based prediction of intraspecific haplotype diversity, given an assumption of equal haplotype frequencies. Our model finds that haplotype diversity for most of the 18 fish species remains largely unsampled, and this appears to be a result of small sample sizes. Lastly, we discuss how our overly simple model may be a useful starting point to develop future estimators for intraspecific sampling sufficiency in studies using DNA barcodes.
Status of DNA Barcoding Coverage for the Tropical Western Atlantic Shorefishes and Reef Fishes
Authors: Victor Benjamin C. , Valdez-Moreno Martha , Vásquez-Yeomans Lourdes 
Published: July 2016

AbstractBackground: Barcode coverage is difficult to assess for large regions due to incomplete species lists, inaccurate identifications, and cryptic diversity. However, as coverage approaches completion, it becomes possible to critically evaluate identifications and validate barcode lineages. We collate the results of the FISH-BOL barcode project and assess coverage for each family of bony shorefishes and reef fishes from the tropical western Atlantic Ocean. Methodology: We identify to species the public and private barcode lineages from the region on BOLD, confirming identifications by vouchers, phylogeographic deduction, and the process of elimination. The lineages and BINs are assigned to species from a comprehensive species list for the region. Results: We estimate 1029 of 1311 total bony shorefish species in the region are barcoded (78.5%). For reef-associated fishes, 902 of 1083 species are barcoded (83.3%). About 70 of the 181 species not yet barcoded are endemic species from Florida/ Gulf of Mexico or Venezuela, leaving about 90% of the central Caribbean reef fish species barcoded to date. Most species are represented by one barcode lineage, but among the gobioids and blennioids there are many more lineages (BINs) than species, indicating substantial cryptic diversity. Conclusions: As barcode coverage for a region approaches completion, a robust assessment of coverage can be made. The reef fish fauna of the tropical western Atlantic now has the highest coverage for a large marine area, from about 80 to 90% depending on definitions and geographic limits.
A case study of the forensic application of DNA Barcoding to sharkfin identification in the Mexican Pacific
Authors: Espinosa Héctor , Lambarri Christian , Martínez Armando , Jiménez Andrea 
Published: July 2016

AbstractOne of the problems that arose from the meetings of the Barcode in Mexico project was the urgency of having a method in which Mexican authorities could trust for detecting shark finning. This study examined DNA barcoding as a method to identify 14 dried shark fins confiscated by the Mexican Government in two exportation shipments in Mazatlán and Manzanillo ports. Fins were DNA barcoded using the COI mitochondrial gene and provided matching sequences of six species: Prionace glauca, Carcharhinus falciformis, Carcharhinus limbatus, Alopias pelagicus, Mustelus henlei and Rhizoprionodon longurio. There is no information on DNA barcoding sharkfin trade in the Mexican Pacific and this is the first group effort with Mexican Government Agencies for the conservation of sharks.
Molecular identification of Leporinus from the south portion of South America
Authors: Avelino Gleisy S. , Britski Heraldo A. , Foresti Fausto , Oliveira Claudio 
Published: July 2016

AbstractAnostomidae is a widely distributed group that includes the species rich Leporinus. This genus is widespread in South America, including its south portion where they are mainly distributed in the São Francisco and La Plata basins. Here we obtained sequences of mitochondrial and nuclear genes of 19 species of Leporinus with the objective of testing our methods of molecular species identification and to test the similarities between species of Leporinus of the São Francisco and La Plata basins. Results show that two species pair have a genetic distance below 2% (L. paranensis x L. obtusidens and L. paranensis x L. aff. paranensis). Our results also show that a high genetic distance occurs in L. obtusidens and L. striatus suggesting a possible local differentiation of these species. An interesting finding of our study is that the genetic similarities observed among species does not corroborate the division of species of Leporinus in groups according to color patterns. Additionally, our results show that the species of Leporinus from the La Plata and São Francisco are not more similar among themselves than to species of other drainages which could be explained by the occurrence of recent fauna exchanges between these two basins and adjacent basins.
Species delimitation in Neoplecostomus (Siluriformes: Loricariidae) using morphologic and genetic approaches
Authors: Roxo Fábio F. , Ochoa Luz E. , Costa-Silva Guilherme J. , Oliveira Claudio 
Published: July 2016

AbstractIn the present study, we compare the results of alpha taxonomy (based on morphology), DNA Barcoding method with a 2% genetic divergence threshold, and the GMYC (General Model Yule Coalescent) technique to identify species clusters in Neoplecostomus. We used partial sequences of mitochondrial COI (Cytochrome oxidase subunit I) for 59 specimens representing 13 valid species (Neoplecostomus bandeirante, N. jaguari, N. langeanii, N. paranensis, N. yapo, N. botucatu, N. selenae, N. doceensis, N. corumba, N. ribeirensis, N. microps, N. espiritosantensis and N. franciscoensis) of Neoplecostomus collected in all its distribution area. For the analysis we used Bayesian inference of phylogeny with relaxed clock methods on an arbitrary timescale, using BEAST. The ultrametrics genes trees obtained for each tree prior evaluated (Yule, Birth-death and coalescent Population Size) were used in the GMYC analysis to identify a time in the tree when the branching rate shifts (in forward time) from Yule and Birth-Death (species) to a coalescent (population) process. We found that the GMYC model using the Yule prior identified 11 groups, closer to the current taxonomy (13 species). GMYC analyses using other ultrametric gene trees estimated under alternative prior such as Birth-Death and Coalescent Population Size, identified 9 groups, results observed in the traditional 2% genetic distance threshold, resulting in a low number of species recognized compared to the number of species identified with current taxonomy. Based on these results we conclude that the molecular approaches are helpful to distinguish species of Neoplecostomus, nevertheless it is important to combine molecular methodologies with current taxonomy in order to identify correctly species that recently originated.
Knodus moenkhausii (Characiformes: Characidae): one fish species, three hydrographic basins - a natural or anthropogenic phenomenon?
Authors: Souza Camila da Silva de , Oliveira Claudio , Pereira Luiz Henrique Garcia 
Published: July 2016

AbstractWe used the DNA barcoding technique (COI and CytB markers) combined with GMYC analysis to characterize the genetics of the widely distributed Neotropical fish species Knodus moenkhausii from three different isolated hydrographic basins. Despite the fact that most of the Neotropical hydrographic basins have been isolated for millions of years, species could be shared between basins due to natural events (stream capture) or anthropogenic activities. Recent surveys, however, have shown that many widely distributed species are actually species complexes divided into previously unrecognized cryptic species. In this study, we tested the hypothesis that K. moenkhausii from three hydrographic basins represent a single panmictic species and discuss the most likely explanation of its present geographical distribution. The GMYC analysis revealed that all specimens of K. moenkhausii represent a single species: the intra- and intergroup minimum K2P genetic distances for both genes were zero and haplotypes were shared among the three hydrographic basins. This suggests there has been recent interchange of K. moenkhausii throughout the three hydrographic basins. It is likely that this is due to recent human activities, either the transposition of natural barriers or intentional introduction or accidental escape due to the ornamental fish trade.
DNA Barcoding Indonesian freshwater fishes: challenges and prospects
Authors: Hubert Nicolas , Kadarusman  , Wibowo Arif , Busson Frédéric , Caruso Domenico , Sulandari Sri , Nafiqoh Nuna , Pouyaud Laurent , Rüber Lukas , Avarre Jean-Christophe , Herder Fabian , Hanner Robert , Keith Philippe , Hadiaty Renny K. 
Published: July 2016

AbstractWith 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.
Wahrnehmung und Explikation
Authors: Jardine James 
Published: July 2016

AbstractWithin the phenomenological tradition, one frequently finds the bold claim that interpersonal understanding is rooted in a sui generis form of intentional experience, most commonly labelled empathy (Einfühlung). The following paper explores this claim, emphasizing its distinctive character, and examining the phenomenological considerations offered in its defence by two of its main proponents, Edmund Husserl and Edith Stein. Having offered in section 2 some preliminary indications of how empathy should be understood, I then turn to some characterizations of its distinctive structure, considering, in section 3, the Husserlian claim that certain forms of empathy are perceptual in nature, and in section 4, Stein’s insistence that empathetic experience frequently involves explicating the other’s own intentional experiences. Section 5 will conclude by assessing the extent to which their analyses lend support to a conception of empathy as an intuitive experience of other minds.