bluuebunny/crossref_metadata_2025 huggingface dataset:
What is the extent and distribution of evidence on effectiveness of systematic conservation planning around the globe? A systematic map protocol
Authors: McIntosh Emma J. , McKinnon Madeleine C. , Pressey Robert L. , Grenyer Richard
Published: July 2016

Background

Systematic conservation planning involves the prioritisation of conservation actions to optimise biodiversity conservation outcomes whilst considering implementation challenges such as minimising costs. Thousands of systematic conservation plans have been developed around the globe (a popular software package, ‘Marxan’, has over 4200 active users from more than 180 countries). However, the effects of systematic approaches on conservation actions and outcomes are not generally known, nor are the factors which distinguish effective from ineffective plans. Previous reviews of conservation planning outcomes have been limited in scope and to narrow time intervals, and have revealed very few formal evaluations of plans. Given systematic approaches are widely perceived to offer the best chance to rapidly and efficiently achieve biodiversity protection targets, a thorough, up-to-date synthesis of the evidence is required.

Methods

This protocol outlines the methodology for a systematic mapping exercise to identify retrospective studies measuring the effects of systematic conservation planning on biodiversity conservation at regional, national and subnational scales. Our primary research question is: what is the extent and distribution of evidence on the conservation outcomes of systematic conservation planning? Outcomes will be categorised according to types of capital: natural, financial, social, human and institutional, given the range of potential direct and indirect effects of systematic conservation planning on conservation outcomes. A comprehensive and repeatable search strategy will be undertaken, utilising a wide range of sources including grey literature sources and targeted searches of organisational websites and databases. Sources will be restricted to English language publications between 1983 and 2016. The resultant studies will be screened using standardised inclusion and exclusion criteria and data from included studies will be categorised according to a standardised data extraction form. Information about the study design of relevant articles will be recorded to determine study robustness. A searchable database of studies will be made publicly accessible and available for updating in future. The results will be published in this journal and also presented as an interactive online resource to aid conservation planners in identifying impacts and outcomes of conservation plans.
Bitter gourd (Momordica charantia L.) seed oil as a naturally rich source of bioactive compounds for nutraceutical purposes
Authors: Yoshime Luciana Tedesco , de Melo Illana Louise Pereira , Sattler José Augusto Gasparotto , de Carvalho Eliane Bonifácio Teixeira , Mancini-Filho Jorge
Published: July 2016

Background

Characterization of food lipids has triggered the development of applications for the food and health industries. Thus, the lipid profiles of an increasing number of fruits and their seeds have been characterized and numerous bioactive components have been isolated. The bitter gourd seed oil has aroused great interest because it contains relevant amounts of conjugated fatty acid α-eleostearic acid (C18:3 9c11t13t), a positional and geometric isomer of α-linolenic acid. The aim of this paper was to evaluate the phytochemical composition and quality parameters of the seed oil of bitter gourd grown in Brazil.

Methods

Bitter gourd was purchased from CEAGESP (Brazilian company of fresh food storages and warehouses). Seeds were lyophilized, and their oil was extracted using the Soxhlet and Folch extraction methods. The profiles of fatty acids and phytosterols were analyzed by gas chromatography, and the acidity and peroxide values were evaluated by methods of the American Oil Chemists’ Society (AOCS).

Results

The Soxhlet extraction (40 % w/w) resulted in a higher yield of bitter gourd seed oil than the Folch extraction (16 % w/w). For both methods, α-eleostearic acid (56 and 58 %) was the major lipid in bitter gourd seed oil, followed by stearic acid (C18:0; 32 and 27 %). The oil displayed high content of phytosterols (886 mg/100 g), mainly β-sitosterol, and low acidity and peroxide values.

Conclusions

Bitter gourd seed oil from Brazil is an oil of good quality and its high contents of α-eleostearic acid and phytosterols with potential health-beneficial properties make it an attractive plant byproduct.
Toxicity-Related Factors Associated With Use of Services Among Community Oncology Patients
Authors: Harrison Jordan M. , Stella Philip J. , LaVasseur Beth , Adams Paul T. , Swafford Lauren , Lewis JoAnn , Mendelsohn-Victor Kari , Friese Christopher R.
Published: July 2016

Purpose:

Community oncology practices frequently manage chemotherapy-associated toxicities, which may disrupt treatment, impair quality of life, and induce unplanned service use. We sought to understand the patterns and correlates of unplanned health care service use among patients receiving first-cycle chemotherapy at five community-based ambulatory oncology practices.

Patients and Methods:

A survey study examined the dichotomous outcome of unplanned service use, defined as oncologist visits, emergency department visits, and hospitalizations, resulting from toxicity-related factors. Newly diagnosed patients with breast, lung, head and neck, or colorectal cancer or non-Hodgkin lymphoma were recruited during the first chemotherapy cycle. Before beginning the second cycle of chemotherapy, patients completed a questionnaire that measured unplanned service use and overall distress, plus severity of nausea, vomiting, diarrhea, constipation, mouth sores, intravenous catheter problems, pain, fever and chills, extremity edema, and dyspnea on a 5-point scale (1, did not experience; 5, disabling). Medical record reviews captured chemotherapy doses, comorbid conditions, and supportive care interventions. Mixed-effects logistic regression was used to identify factors associated with unplanned service use, with random effects specified for each clinic.

Results:

Among 106 patients (white, 98%; female, 74.5%; mean age ± standard deviation, 60 ± 11 years), frequently reported toxicities were pain, nausea, diarrhea, and constipation. Thirty-six patients (34%) reported unplanned service use: 29% reported oncologist visits, 14% reported emergency department visits, and 8% reported hospitalizations. Factors significantly associated with unplanned service use were high patient-reported distress and receipt of colony-stimulating factor.

Conclusion:

Service use resulting from toxicity-related factors occurs frequently in community oncology settings. Monitoring toxicity patterns and outcomes can inform proactive symptom management approaches to reduce toxicity burden between scheduled visits.
Recovering signals in physiological systems with large datasets
Authors: Pendar Hodjat , Socha John J. , Chung Julianne
Published: July 2016

In many physiological studies, variables of interest are not directly accessible, requiring that they be estimated indirectly from noisy measured signals. Here, we introduce two empirical methods to estimate the true physiological signals from indirectly measured, noisy data. The first method is an extension of Tikhonov regularization to large-scale problems, using a sequential update approach. In the second method, we improve the conditioning of the problem by assuming that the input is uniform over a known time interval, and then use a least-squares method to estimate the input. These methods were validated computationally and experimentally by applying them to flow-through respirometry data. Specifically, we infused CO2 in a flow-through respirometry chamber in a known pattern, and used the methods to recover the known input from the recorded data. The results from these experiments indicate that these methods are capable of sub-second accuracy. We also applied the methods on respiratory data from a grasshopper to investigate the exact timing of abdominal pumping, spiracular opening, and CO2 emission. The methods can be used more generally for input estimation of any linear system.
Global and Local Calibrations to Predict Chemical and Physical Properties of a National Spatial Dataset of Scottish Soils from Their near Infrared Spectra
Authors: Pérez-Fernández Estefanía , Robertson A.H. Jean
Published: July 2016

Calibrations were developed to predict chemical and physical properties from near infrared spectra of an extensive spatial dataset of Scottish soils. For this purpose we used a spectral library of 1246 soil samples collected throughout Scotland in two campaigns: 546 samples collected in a 10 km grid between 1978 and 1988 (NSIS1); and 700 samples collected between 2007 and 2009 during a re-sample of the same sites but in a 20 km grid (NSIS2). The samples were split into validation ( N = 250) and calibration ( N = 996) sets, and global partial least squares regression (PLSR) was performed in combination with spectral pre-processing treatments, namely first or second derivative and, optionally, standard normal variate and de-trending or multiplicative scatter correction treatments. For the local model, the calibration set ( N = 996) was split into test ( N = 121) and library ( N = 875). Local calibration was performed using PLSR in batches that iteratively selected from the library between 75 and 425 reference spectra, in increments of 50, in combination with spectral preprocessing treatments. Both global and local models were validated on the same validation set ( N = 250). We succeeded in developing predictive calibrations with r2 of validation greater than 0.60 for total elemental C and N, loss on ignition (450°C and 900°C), exchangeable H and Mg, moisture content, pH (in H2O and CaCl2) and dry bulk density. Promising results were also achieved for the prediction of total P, aqua regia-extracted Mg and P, and ammonium oxalate-extracted Al and Si, although these calibrations were highly biased. Predictive results for exchangeable Ca, sand, silt, clay, K (aqua regia), mineralisable N and δ15N were very informative, but not robust enough for predictive purposes. The lowest performance was observed for exchangeable Al and K, δ13C, Na (exchangeable and aqua regia), P (ammonium oxalate) and in particular for Fe and Mn (both exchangeable and extracted in ammonium oxalate). We found that local calibration was superior to global, in terms of accuracy and number of soil attributes successfully calibrated, and we observed better results when first derivative was applied to pre-process the spectra. Further work, including the expansion of the dataset or testing alternative calibration methods or spectral ranges, will be pursued.
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
Authors: Ramiro-Garcia Javier , Hermes Gerben D. A. , Giatsis Christos , Sipkema Detmer , Zoetendal Erwin G. , Schaap Peter J. , Smidt Hauke
Published: July 2016

Background

Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises true meta-analyses, although this fact is often disregarded.

Results

To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as the currently most frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed evaluating important factors of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 96%. On average 99.94% and 92.02% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.02% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not the case when samples were analysed using QIIME.

Conclusions

Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.
Vortioxetine: An antidepressant apart?
Authors: Greener Mark
Published: July 2016

Antidepressants remain a mainstay of treatment to alleviate the heavy economic, societal and human tolls imposed by depression. Nevertheless, the high rates of treatment failure and poor adherence underscore the need for novel treatments. Vortioxetine is a new antidepressant that has a different pharmacological profile to conventional antidepressants and a long half-life that reduces the risk of discontinuation symptoms. Vortioxetine appears to be effective for major depression in adults. Emerging data suggest that vortioxetine may have cognitive benefits that are independent of antidepressant efficacy. Vortioxetine appears to be relatively well tolerated. The National Institute for Health and Care Excellence (NICE) recommends vortioxetine for major depressive episodes in adults who responded inadequately to two antidepressants within the current episode. Further studies need to fully characterise and quantify vortioxetine's risks, benefits and place in the antidepressant armamentarium.
Thoughts and feelings associated with parasuicide: A thematic analysis
Authors: Asfaw Rhea Eleanor , Jones Russell
Published: July 2016

This article seeks to shed more light on what influences an individual to take their own life. By interviewing individuals who have presented at a general hospital with an act of attempted suicide, their recollections of events running up to the act have been analysed by the research team and described in this article. Nobody can be certain of an individuals' exact motives when being assessed following an act of self-harm, but by using a validated suicide intent scale and clinician judgement together, the research can reasonably claim to have included those patients whose actions were clearly intent on suicide rather than self-harm with no strong desire to end one's life. Seven in-depth interviews were conducted 7–14 days after the initial presentation, time enough to ensure recollections are accurate while not being too close to the initial act of attempted suicide as to be viewed as too soon to expect someone to reflect on a traumatic episode. A comprehensive literature search and discussion section in the article enables the reader to learn more about the issue of suicide, which is fair to say generates much debate among psychiatric, psychological, and social commentators alike.
D is for the Digestive system…
Authors: Hammond Paula , Lillie Stephen
Published: July 2016

This month, we continue our series that takes the form of an extended alphabetical adventure around the body, helping children to get to know themselves a little better.
Research roundup
Authors: Costello John
Published: July 2016

Synopses of a selection of recently published research articles of relevance to palliative care.
Internal Armature of the Hindgut of Pericapritermes nitobei (Shiraki)
Authors: Kanzaki Natsumi , Ohmura Wakako
Published: July 2016

The internal armature of the hindgut of Pericapritermes nitobei was examined under a light microscope. Termites were obtained from Iriomote Island, Okinawa Prefecture, Japan, identified based on the typological characters of soldiers and 12S (mitochondrial) ribosomal RNA sequencing, and dissected to examine hindgut morphology. The hindgut of P. nitobei could be separated into four parts, P1-P4, and P1-P3 had cuticular spines on the inner surface. P1 bore small triangular spines. P2 formed an enteric valve, composed of six finger-shaped enteric pads with triangular spines, and six marginal regions with small dot-like spines. P3 bore three different types of spines: relatively large star-shaped spines; thorn-like small spines, and long curved spines with brush-like tips.
Risk of local extinction and genetic diversity of Melipona quadrifasciata (Apidae: Meliponini) in a possible Northeastern limit of its distribution in Brazil
Authors: Araújo Edilson D , Oliveira Rosane Gomes , Calazans Higor Cesar Meneses , França Carina Caroline Silva , SANTOS Valdson , Jain Sona Arun , Batista Marcus Vinícius Aragão , Nunes Lorena Andrade , Ribeiro Genésio Tamara
Published: July 2016

Rapid loss of genetic diversity among eusocial bees, and extinction of their local population has become a major world concern. Populations of M. quadrifasciata have increasingly declined due to predatory extractivism and destruction of their habitat. Knowledge of their local population could give insights on the strategies for monitoring and conservation of this species. In this study, initially, 14 colonies (140 workers) from the Northern limit of the Northeastern sandbank of the Atlantic Forest were analyzed employing geometric morphometrics techniques. Then the cytochrome b gene sequences and ISSR primers were utilized for molecular analysis. The results were compared with the results of 30 M. quadrifasciata colonies (300 workers) found in the semiarid Caatinga region. The morphometrics and the molecular analysis suggested the formation of disjunct populations between the studied geographical zones. All the 14 colonies analyzed from the river São Francisco region were found on the Southern margin of the river São Francisco and they all belonged to one single haplotype. No colonies were found on the Northern bank of the river. We suggest that the river São Francisco is an effective georgraphical barrier for the distribution of this species and propose an urgent need for the development of a conservation program for the population of M. quadrifasciata as it represents a unique haplotype in the region. Also their nesting habit exclusively in the diseased coconut trees which probably will be replaced by new trees, create the risk of population extinction due to the lack of nesting site.
Estimation of Nuclear Genome Size of Three Species of Camponotus (Mayr, 1861) (Hymenoptera: Formicidae: Formicinae) and Their Cytogenetic Relationship
Authors: Aguiar Hilton Jeferson Alves Cardoso de , Barros Luísa Antônia Campos , Soares Fernanda Aparecida Ferrari , Carvalho Carlos Roberto de , Pompolo Silvia Das Graças
Published: July 2016

The chromosome variability among ant species is remarkable, and the processes generating such variation are still under discussion since polyploidy has been observed in some distinct taxa. The chromosome number of species belonging to the Camponotus, subgenera Myrmothrix and Myrmobrachys, are highly different, whereas, the first subgenus has double the number of chromosomes of the second. In order to test the hypothesis of chromosome number doubling through polyploidy, the genome sizes of Camponotus (Myrmothrix) rufipes, Camponotus (Myrmothrix) renggeri and Camponotus (Myrmobrachys) crassus were estimated by flow cytometry. The chromosome number of specimens from the nests studied was also defined. No significant variation was noted in the genome size among them. The mean haploid genome size value (1C) of workers for the three species was 286.16 Mpb (0.29 pg). The polyploidy hypothesis can be ruled out as an evolutionary step linking the karyotype variations among the three studied species since the genome size of C. crassus with 2n = 20 chromosomes was the same as that of C. rufipes and C. renggeri with 2n = 40. The lack of variation in the amount of DNA between the related species C. rufipes and C. renggeri also demonstrate that flow cytometry is not an adequate approach to distinguish them. Our results highlight the importance of combining distinct methods, DNA quantification, and cytogenetics from the same colony. Understanding the path of chromosome evolution of three species with distinct degrees of relatedness should provide further information in enriching our knowledge about the Minimum Interaction Theory.
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

For 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

Pathogenic strains of
New larval trematodes in Biomphalaria species (Planorbidae) from Northeastern Argentina
Authors: Fernández María Virginia , Hamann Monika Inés , de Núñez Margarita Ostrowski
Published: July 2016

Larval trematodes infecting
Prevalence and first molecular identification of Sarcocystis species in cattle and water buffaloes in India
Authors: Daptardar Monal , Singh Balbir Bagicha , Aulakh Rabinder Singh , Gill Jatinder Paul Singh
Published: July 2016

The importance 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

A 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

Diseases 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

sp. 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

A 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

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

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

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

Food 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

Estimating 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

Background: 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

One 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

Anostomidae 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

In 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

We 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

With 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

Within 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.
Ethik der Veränderung
Authors: Wille Katrin
Published: July 2016

Pragmatist ethics is not a special discipline. Human action and human experience as such have to be described and analysed in an ethical perspective. This means a reinterpretation of the whole idea of normative ethics. John Dewey’s philosophy provides a rich source for this task. In the article I show the interdependencies between a “logic of experience”, an “aesthetics of experience”, and an “ethics of experience”. The “logic of experience” offers a key to understanding and deepening our concrete experiences. If we study possible situations thoroughly (“aesthetics of experience”), we can see why and how a distinction between facts and norms becomes necessary. This brings up the question whether one’s own or others’ behaviour preserves the conditions of the variability of experience. It is the purpose of an “ethics of experience” to show the strength of this question for normative orientation and judgement.
Gibt es eine pragmatistische Ethik?
Authors: Hartmann Martin
Published: July 2016

It is commonly assumed that classical pragmatism has not developed an ethical outlook that deserves to be taken seriously despite the fact that John Dewey, in particular, has published several books on ethics. Major contemporary textbooks in ethics do not mention a possible pragmatist ethics. However, recently there have been various approaches in ethics and political philosophy that claim to base their normative accounts on pragmatist ideas (Philip Kitcher, Elizabeth Anderson). The article introduces these approaches and suggests that they adopt a methodological or proceduralist interpretation of pragmatism devoid of substantial ethical assumptions. It is then claimed that a purely methodological or procedural reading of pragmatism runs into problems that can only be solved if a closer look is taken at some of the more substantial ethical assumptions of pragmatism. Following a review of central elements of Dewey’s ethics, in particular his description of the role of the self in moral dilemmas, typical criticisms of these assumptions are discussed and partially rebutted. It is then suggested that one might conceptualise a pragmatist ethics as a “consequentialism of character”.