bluuebunny/crossref_metadata_2025_split huggingface dataset:
Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
Authors: Sczyrba Alexander , Hofmann Peter , Belmann Peter , Koslicki David , Janssen Stefan , Dröge Johannes , Gregor Ivan , Majda Stephan , Fiedler Jessika , Dahms Eik , Bremges Andreas , Fritz Adrian , Garrido-Oter Ruben , Jørgensen Tue Sparholt , Shapiro Nicole , Blood Philip D. , Gurevich Alexey , Bai Yang , Turaev Dmitrij , DeMaere Matthew Z. , Chikhi Rayan , Nagarajan Niranjan , Quince Christopher , Meyer Fernando , Balvoit Monika , Hansen Lars Hestbjerg , Sørensen Søren J. , Chia Burton K. H. , Denis Bertrand , Froula Jeff L. , Wang Zhong , Egan Robert , Kang Dongwan Don , Cook Jeffrey J. , Deltel Charles , Beckstette Michael , Lemaitre Claire , Peterlongo Pierre , Rizk Guillaume , Lavenier Dominique , Wu Yu-Wei , Singer Steven W. , Jain Chirag , Strous Marc , Klingenberg Heiner , Meinicke Peter , Barton Michael , Lingner Thomas , Lin Hsin-Hung , Liao Yu-Chieh , Silva Genivaldo Gueiros Z. , Cuevas Daniel A. , Edwards Robert A. , Saha Surya , Piro Vitor C. , Renard Bernhard Y. , Pop Mihai , Klenk Hans-Peter , Göker Markus , Kyrpides Nikos C. , Woyke Tanja , Vorholt Julia A. , Schulze-Lefert Paul , Rubin Edward M. , Darling Aaron E. , Rattei Thomas , McHardy Alice C. 
Published: January 2017

AbstractIn metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.
Automatic classification of diatoms of Merja fouarate
Authors: Chahboune Nouzha , Mehdi Mohamed , Douira Allal 
Published: January 2017

RESUMEObjective:This work consists of developing an automatic method of form analysis and classification of diatoms through processing of scanned images. The fundamental objective is to determine to what extent two diatoms are similar from the images stored in a database, and to conclude to what classes they belong. To do so, a comparison is made between a manual identification and an automatic identification, based on the ultimate points and the Freeman Chain Code.
Developing organizations: a system of enquiry, action and learning
Authors: Graham Wayne 
Published: January 2017

Purpose
This paper aims to demonstrate the applicability of an action learning model to improve organizational outcomes.

Design/methodology/approach
This paper extends previous work by applying the system of enquiry, action and learning (SEAL) model using an action research methodology to a small business operating in the health services industry.

Findings
The SEAL model is a useful approach to introduce small business practitioners to the principles of organizational development (OD).

Research limitations/implications
The application is limited to one small business, and subsequent studies could apply the model to more organizations that operate in industries other than health services.

Practical implications
Business owners from this study and previous studies have found the model to be useful in the improvement of organizational outcomes.

Originality/value
The SEAL model is a simplified model that introduces principles of OD and has provided value to the business owners of this study.
Developing your career: harnessing the power of the internet for “digital career management”
Authors: Hooley Tristram 
Published: January 2017

PurposeThis paper aims to discuss the role of the internet in framing individual’s career building. It argues that the 7 Cs of digital career literacy offer a useful framework for those working in learning and development in organizations. Every individual needs to engage with the internet when thinking about how to manage and future-proof their careers. Learning and development (L&D) professionals can support employees to harness the power of the internet and learn how to make use of the new opportunities of “digital career management”.Design/methodology/approachThis paper highlights steps that every individual needs to take for “digital career management” and pulls out the role of L&D professionals in addressing the developing internet context.FindingsSets out “7 C’s” for proactively managing a “digital career profile”.Originality/valueThe internet has shifted the context for career building and learning how to maximize the opportunities now offered is the central task for anyone wishing to carve out their future careers.
University students in the workplace strategies for successful industry placement experiences
Authors: Burdett Jane , Barker Sandy 
Published: January 2017

Purpose
Increasing numbers of university students in USA, UK and Australia are undertaking industry placements to gain workplace experience. However, outcomes are not always as expected. This paper aims to identify challenges for universities and host organizations in delivering quality student industry placement and presents strategies to achieve successful learning outcomes.

Design/methodology/approach
The reflections, evaluation and feedback data received from stakeholders, namely, university students, host organizations and faculty mentors in a large Australian university were used to formulate strategies.

Findings
Lessons learned from the authors’ experience in industry placement programs over 5 years with 180 students in 127 organizations indicate that careful planning and management of placements is needed to achieve successful learning outcomes.

Research limitations/implications
Further research into the application of these strategies in other universities would be valuable.

Practical implications
Lessons learned and recommendations offered provide strategies to assist in planning and management of industry placements.

Originality/value
Given the growing popularity of work experience in university programs, this should be of interest to faculty and organizations.
Essential Oils Against Pathogen and Spoilage Microorganisms of Fruit Juices: Use of Versatile Antimicrobial Delivery Systems
Authors: Trinetta Valentina , Morgan Mark T. , Coupland John N. , Yucel Umut 
Published: January 2017

AbstractEssential oils (EO) are increasingly used as natural antimicrobial compounds, however the effect of delivery system to enhance their antimicrobial activity has not been widely studied. Limonene (0 to 10 μL/mL) was added to microbial suspensions (∼105 CFU/mL) of selected foodborne pathogens (Listeria monocytogenes Scott A, Salmonella enterica Typhimurium, Escherichia coli and Staphylococcus aureus), and spoilage microorganisms (Lactobacillus plantarum, Saccharomyces cerevisiae, and Candida albicans). S. aureus was found to be the most sensitive foodborne pathogen while Salmonella enterica showed continued growth under all concentrations. Stable nanoemulsions and solid lipid nanoparticles (SLN) (d ∼ 170 nm) were prepared using an alkane carrier oil (n‐tetradecane and n‐eicosane, respectively). Interfacial effects and homogenous distribution of limonene in nanoemulsions improved its (8 and 12 μL/mL) antimicrobial effect against S. aureus. Higher aqueous concentrations as a result of expulsion from SLN further enhanced the antimicrobial activity pronounced at higher limonene concentrations. Therefore, our findings confirm that the emulsion‐based delivery systems are able to effectively distribute limonene inside a microbial suspension to improve its antimicrobial activity.
Formation and Characterization of Green Tea Extract Loaded Liposomes
Authors: Dag Damla , Oztop Mecit Halil 
Published: January 2017

AbstractGreen tea extract was encapsulated into liposomes to enhance bioavailability and stability of catechins by protecting their functional properties simultaneously. Encapsulation was achieved by dispersing 1% (w/v) soy lecithin through high pressure homogenization (microfluidization) and ultrasonication. Effects of homogenization type and pH of the dispersing medium on the physical properties and stability of the liposomes during 1‐mo storage period were investigated. Mean particle size, total phenolic content by Folin–Ciocalteu method and antioxidant activity by 2‐diphenyl‐1‐picrylhydrazyl radical scavenging and ferric reducing‐antioxidant power methods, and transmission electron microscopy (TEM) experiments were conducted for characterization. Green tea extract loaded liposomes prepared by microfluidization in distilled water were determined as the most stable system which demostrated no significant difference (P > 0.05) on mean particle size, total phenolic content, and antioxidant activity between the first and final day of 1‐mo storage time. Additionally, uniform size and shape in TEM images supported the results.
Fish and Invertebrate Flow‐Biology Relationships to Support the Determination of Ecological Flows for North Carolina
Authors: Phelan Jennifer , Cuffney Tom , Patterson Lauren , Eddy Michele , Dykes Robert , Pearsall Sam , Goudreau Chris , Mead Jim , Tarver Fred 
Published: January 2017

AbstractA method was developed to characterize fish and invertebrate responses to flow alteration in the state of North Carolina. This method involved using 80th percentile linear quantile regressions to relate six flow metrics to the diversity of riffle‐run fish and benthic Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness. All twelve flow‐biology relationships were found to be significant, with both benthos and fish showing negative responses to ecodeficits and reductions in flow. The responses of benthic richness to reduced flows were consistent and generally greater than that of fish diversity. However, the riffle‐run fish guild showed the greatest reductions in diversity in response to summer ecodeficits. The directional consistency and differential seasonal sensitivities of fish and invertebrates to reductions in flow highlight the need to consider seasonality when managing flows. In addition, all relationships were linear, and therefore do not provide clear thresholds to support ecological flow determinations and flow prescriptions to prevent the degradation of fish and invertebrate communities in North Carolina rivers and streams. A method of setting ecological flows based on the magnitude of change in biological condition that is acceptable to society is explored.
Sofosbuvir‐based treatment regimens: real life results of 14 409 chronic HCV genotype 4 patients in Egypt
Authors: Elsharkawy A. , Fouad R. , El Akel W. , El Raziky M. , Hassany M. , Shiha G. , Said M. , Motawea I. , El Demerdash T. , Seif S. , Gaballah A. , El Shazly Y. , Makhlouf M. A. M. , Waked I. , Abdelaziz A. O. , Yosry A. , El Serafy M. , Thursz M. , Doss W. , Esmat G. 
Published: January 2017

SummaryBackgroundChronic hepatitis C virus infection is one of the most important health problems in Egypt. The Ministry of Health's National Treatment Programme introduced sofosbuvir‐based therapy in October 2014.AimTo assess the clinical effectiveness and predictors of response to SOF‐based treatment regimens, either dual therapy, with SOF/ribavirin (RBV) for 6 months or triple therapy with SOF/peg‐IFN‐alfa‐2a/RBV for 3 months, in a cohort of patients treated in National Treatment Programme affiliated centres in Egypt.MethodsBetween October 2014 and end of 2014, patients who were eligible for treatment were classified according to their eligibility for interferon therapy: Group 1 (interferon eligible) were treated with triple therapy for 12 weeks and Group 2 (interferon ineligible) were treated with dual therapy for 24 weeks. Difficult to treat patients included those with F3‐F4 on Metavir score, Fib‐4 >3.25, albumin ≤3.5, total Bilirubin >1.2 mg/dL, INR >1.2 and platelet count <150 000 mm3.ResultsTwelve weeks post‐treatment data were available on 14 409 patients; 8742 in group 1 and 5667 in group 2. In group 1, the sustained virological response at week 12 (SVR12) was 94% and in group 2 the SVR12 was 78.7%. Multivariate logistic regression analysis in which treatment failure is the dependent variable was done. Male gender, being a difficult to treat patient and previous interferon therapy were significant predictors of nonresponse in both treatment groups.ConclusionResults of sofosbuvir‐based therapies in Egypt achieved similar rates of SVR12 as seen in phase III efficacy studies.
Faithful vertical transmission but ineffective horizontal transmission of bacterial endosymbionts during sexual reproduction of the black bean aphid, Aphis fabae
Authors: VORBURGER CHRISTOPH , SIEGRIST GABRIELLE , RHYNER NICOLA 
Published: January 2017

1. Insects are commonly infected with bacterial endosymbionts. In addition to the costs and benefits associated with harbouring these symbionts, their rates of vertical and horizontal transmission are important determinants of symbiont prevalence.2. Aphids are cyclical parthenogens and show virtually perfect maternal transmission of endosymbionts during asexual reproduction. Less clear is the role of the annual sexual generation, during which overwintering eggs are produced. Data from pea aphids (Acyrthosiphon pisum Harris) suggest that maternal transmission failures and horizontal transmission via males may occur under sexual reproduction at least occasionally. No such data exist for other aphid species.3. In the present study, the rates of maternal and paternal transmission of facultative endosymbionts during sexual reproduction in the black bean aphid, Aphis fabae (Scopoli) were examined. Crosses were performed between clones infected with Hamiltonella defensa, clones infected with Regiella insecticola and clones without facultative endosymbionts, and eggs were overwintered under three different conditions.4. Only one of 205 offspring from crosses testing for maternal transmission failed to inherit the symbiont present in the maternal clone, and in crosses testing for horizontal transmission, only one of 412 offspring acquired a facultative symbiont from the father.5. These results show that in A. fabae, maternal transmission of H. defensa and R. insecticola is extremely reliable also during sexual reproduction, indicating that maternal transmission failures are unlikely to exert a significant influence on frequencies of infection in the field. Paternal transmission of endosymbionts was exceedingly rare, suggesting that this route of horizontal transmission may be less important than hitherto assumed.
Two microcrustaceans affect microbial and macroinvertebrate‐driven litter breakdown
Authors: Chambord Sophie , Tackx Michèle , Chauvet Eric , Escolar Guillaume , Colas Fanny 
Published: January 2017

Summary

Leaf litter degradation in fresh waters is a fundamental ecosystem process performed by a wide array of decomposers. The meiofauna is an important component of aquatic heterotrophic assemblages, which can provide a trophic link between plant detritus and associated microbial and macroinvertebrate communities, but their contribution to leaf breakdown remains poorly understood.

We hypothesised that, through their feeding activity, microcrustaceans influence the structure of fungal assemblages and consequently microbially mediated litter breakdown. Litter‐associated microcrustaceans were predicted to change the pathways of energy transfer in the food web according to the positive (e.g. complementarity) or negative (e.g. predation) interactions with macroinvertebrate detritivore taxa.

We evaluated experimentally in the laboratory, over 6 and 13 days, the potential contribution of two freshwater microcrustaceans (a cladoceran and a copepod) to litter breakdown in the presence of microfungi (aquatic hyphomycetes), with and without macroinvertebrate detritivores (a trichopteran and a gammarid amphipod).

The presence of microcrustaceans enhanced leaf mass loss by 62 and 22% in treatments with fungi or trichopteran alone, respectively, while no significant effect was observed for treatments with the amphipod. Microcrustaceans strongly increased the production of fine particulate organic matter, particularly in treatments with fungi alone (+637%). The leaf consumption rate by the amphipod significantly decreased (−61%) at 13 days in the presence of microcrustaceans, likely due to predation on cladocerans.

Our study supports the potential role of microcrustaceans in the detrital food web of streams and rivers. Interestingly, microcrustaceans may interact with microbial and macroinvertebrate decomposers in either positive or negative ways. Therefore, microcrustaceans add complexity to detrital food webs by increasing vertical diversity and modulating biotic interactions with important consequences for carbon and energy transfers in stream ecosystems.
Recurrent NAB2–STAT6 gene fusions and oestrogen receptor‐α expression in pulmonary adenofibromas
Authors: Fusco Nicola , Guerini‐Rocco Elena , Augello Claudia , Terrasi Andrea , Ercoli Giulia , Fumagalli Caterina , Vacirca Davide , Braidotti Paola , Parafioriti Antonina , Jaconi Marta , Runza Letterio , Ananthanarayanan Vijayalakshmi , Pagni Fabio , Bosari Silvano , Barberis Massimo , Ferrero Stefano 
Published: January 2017

AimsPulmonary adenofibromas are rare benign fibroepithelial tumours of the lung with unknown histogenesis and an indolent clinical behaviour. Their stroma resembles that of solitary fibrous tumours, whereas the glands are composed of respiratory epithelium organized in a phyllodes‐like architecture. Differentiation of pulmonary adenofibromas from other more aggressive intrathoracic tumours is clinically relevant. However, their biology is unknown. Here, we sought to characterize pulmonary adenofibromas at a clinicopathological level and to define whether they could be underpinned by a highly recurrent somatic genetic alteration akin to tumours with similar morphology.Methods and resultsSeven pulmonary adenofibromas were subjected to immunohistochemical analysis for thyroid transcription factor 1 (TTF1), napsin A, cytokeratin 7, E‐cadherin, CD99, CD34, CD31, STAT6, oestrogen receptor (ER), progesterone receptor, androgen receptor, bcl‐2, and vimentin, as well as electron microscopy and capillary sequencing on microdissected samples to evaluate the presence of NAB2–STAT6 fusion genes and MED12 exon 2 mutations in their discrete components. A control group comprising pulmonary solitary fibrous tumours, pulmonary hamartomas and breast fibroadenomas was also analysed. We confirmed that the stromal elements of pulmonary adenofibromas pertain to the fibroblastic lineage, and show ER overexpression in 71% of cases, whereas the epithelium consists of TTF1‐positive, E‐cadherin positive bronchiolar elements. A highly recurrent NAB2–STAT6 fusion variant (exon 4–exon 2) was detected in the stroma but not in the epithelium. No MED12 mutations were identified.ConclusionsHere, we demonstrate that pulmonary adenofibromas are neoplastic lesions harbouring the molecular hallmark of solitary fibrous tumours.
The effect of calcium chloride and calcium lactate pretreatment concentration on peach cell integrity after high‐pressure processing
Authors: Techakanon Chukwan , Barrett Diane M. 
Published: January 2017

SummaryThe objective of this study was to determine the effect of calcium chloride and calcium lactate pretreatments at different concentrations (1, 1.5 and 2% w/v) on enzymatic browning of clingstone and freestone peaches following high‐pressure processing (HPP) at 200 MPa for 10 min. Proton nuclear magnetic resonance (1H‐NMR) relaxometry indicated that following calcium pretreatment and HPP, both peach types had lower percentages of water in the vacuole compartment and a simultaneous increase in the percentage of water in the cytoplasm compartment. Calcium pretreatment of freestone peaches did not affect the development of browning, regardless of the form of calcium or the concentration, whereas calcium lactate pretreatment undesirably enhanced clingstone peach discoloration. Calcium pretreatments have the potential to reduce the loss of cell integrity that results from HPP; however, in this study, the effect was not sufficient to inhibit the interaction between the polyphenol oxidase enzyme that catalyses browning and its substrates.
Kinetics of phase formation in the Ln–O–S (Ln=La, Gd, Y) systems during oxide sulfidation in ammonium thiocyanate vapor
Authors: Bakovets Vladimir V. , Sotnikov Aleksandr V. , Korolkov Ilya V. 
Published: January 2017

AbstractKinetics and mechanism of phase formation in the Ln–O–S (Ln=La, Gd, Y) systems during Ln2O3 sulfidation in ammonium thiocyanate vapor and the identified sequence of transformations of obtained phases in the temperature range 873‐1273 K have been studied. The kinetic dependencies for the reactions involved were fitted by the Jander equation for topochemical heterogeneous reactions with a squared correlation coefficient R2=.99. The reaction rate constants, pre‐exponential factors, and effective activation energies for the reaction formation of compounds have been calculated, and approximate times and low temperatures for the formation of particular phases have been found.
A systematic review of evidence relating to clinical supervision for nurses, midwives and allied health professionals
Authors: Pollock Alex , Campbell Pauline , Deery Ruth , Fleming Mick , Rankin Jean , Sloan Graham , Cheyne Helen 
Published: January 2017

AbstractAimThe aim of this study was to systematically review evidence relating to clinical supervision for nurses, midwives and allied health professionals.BackgroundSince 1902 statutory supervision has been a requirement for UK midwives, but this is due to change. Evidence relating to clinical supervision for nurses and allied health professions could inform a new model of clinical supervision for midwives.DesignA systematic review with a contingent design, comprising a broad map of research relating to clinical supervision and two focussed syntheses answering specific review questions.Data sourcesElectronic databases were searched from 2005 ‐ September 2015, limited to English‐language peer‐reviewed publications.Review methodsSystematic reviews evaluating the effectiveness of clinical supervision were included in Synthesis 1. Primary research studies including a description of a clinical supervision intervention were included in Synthesis 2. Quality of reviews were judged using a risk of bias tool and review results summarized in tables. Data describing the key components of clinical supervision interventions were extracted from studies included in Synthesis 2, categorized using a reporting framework and a narrative account provided.ResultsTen reviews were included in Synthesis 1; these demonstrated an absence of convincing empirical evidence and lack of agreement over the nature of clinical supervision. Nineteen primary studies were included in Synthesis 2; these highlighted a lack of consistency and large variations between delivered interventions.ConclusionDespite insufficient evidence to directly inform the selection and implementation of a framework, the limited available evidence can inform the design of a new model of clinical supervision for UK‐based midwives.