bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology
Authors: Asif Muhammad , Martiniano Hugo F. M. C. M. , Vicente Astrid M. , Couto Francisco M.
Published: November 2018

Identifying disease genes from a vast amount of genetic data is one of the most challenging tasks in the post-genomic era. Also, complex diseases present highly heterogeneous genotype, which difficult biological marker identification. Machine learning methods are widely used to identify these markers, but their performance is highly dependent upon the size and quality of available data.

In this study, we demonstrated that machine learning classifiers trained on gene functional similarities, using Gene Ontology (GO), can improve the identification of genes involved in complex diseases. For this purpose, we developed a supervised machine learning methodology to predict complex disease genes. The proposed pipeline was assessed using Autism Spectrum Disorder (ASD) candidate genes. A quantitative measure of gene functional similarities was obtained by employing different semantic similarity measures. To infer the hidden functional similarities between ASD genes, various types of machine learning classifiers were built on quantitative semantic similarity matrices of ASD and non-ASD genes. The classifiers trained and tested on ASD and non-ASD gene functional similarities outperformed previously reported ASD classifiers. For example, a Random Forest (RF) classifier achieved an AUC of 0. 80 for predicting new ASD genes, which was higher than the reported classifier (0.73). Additionally, this classifier was able to predict 73 novel ASD candidate genes that were were enriched for core ASD phenotypes, such as autism and obsessive-compulsive behavior. In addition, predicted genes were also enriched for ASD co-occurring conditions, including Attention Deficit Hyperactivity Disorder (ADHD).

We also developed a KNIME workflow with the proposed methodology which allows users to configure and execute it without requiring machine learning and programming skills. Machine learning is an effective and reliable technique to decipher ASD mechanism by identifying novel disease genes, but this study further demonstrated that their performance can be improved by incorporating a quantitative measure of gene functional similarities. Source code and the workflow of the proposed methodology are available at https://github.com/Muh-Asif/ASD-genes-prediction.
Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord
Authors: Delile Julien , Rayon Teresa , Melchionda Manuela , Edwards Amelia , Briscoe James , Sagner Andreas
Published: November 2018

The coordinated spatial and temporal regulation of gene expression in the vertebrate neural tube determines the identity of neural progenitors and the function and physiology of the neurons they generate. Progress has been made deciphering the gene regulatory programmes responsible for this process, however, the complexity of the tissue has hampered the systematic analysis of the network and the underlying mechanisms. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions of the developing mouse neural tube between embryonic days (e)9.5-e13.5. We confirmed the data accurately recapitulates neural tube development, allowing us to identify new markers for specific progenitor and neuronal populations. In addition, the analysis highlighted a previously underappreciated temporal component to the mechanisms generating neuronal diversity and revealed common features in the sequence of transcriptional events that lead to the differentiation of specific neuronal subtypes. Together the data provide a compendium of gene expression for classifying spinal cord cell types that will support future studies of neural tube development, function, and disease.
Sexual segregation in a highly pagophilic and sexually dimorphic marine predator
Authors: Barbraud Christophe , Delord Karine , Kato Akiko , Bustamante Paco , Cherel Yves
Published: November 2018

Abstract

Sexual segregation is common in many species and has been attributed to intra-specific competition, sex-specific differences in foraging efficiency or in activity budgets and habitat choice. However, very few studies have simultaneously quantified sex-specific foraging strategies, at sea distribution, habitat use, and trophic ecology. Moreover, these studies come from low latitude areas reflecting a lack of evidence for polar species. We investigated sexual segregation in snow petrelsPagodroma niveaand combined movement, foraging trip efficiency, stable isotope and oceanographic data to test whether sexual segregation results from sex-specific habitat use. Breeding birds foraging in the Dumont d’Urville sea, Antarctica, were tracked during incubation. Some similarities between males and females foraging characteristics did not support the sexual segregation hypothesis. Indeed, space-use sharing and utilization distribution, δ13C values and foraging trip performances (trip duration, length, speed and directions, mass gain, proportion mass gain) were similar between males and females.. However, there was support for sexual segregation in foraging characteristics linked to foraging habitats. Females foraged less than males in areas with higher sea ice concentration (SIC >70%) and had lower δ15N values in plasma, blood cells and feathers. Foraging efficiency (proportionate daily mass gain while foraging), was greater for females than for males, and was greater for larger females with deeper bills. Females were more efficient than males during short (<2 days) foraging trips, and for females, but not for males, mass gain, proportion mass gain and body condition at return from a foraging trip were positively correlated to SIC of the foraging areas. Together, these results suggest an absence of sexual segregation at large spatial scales in snow petrels during incubation, but strongly support habitat segregation between high (>70%) more profitable SIC (males) and low SIC areas (females), probably driven by intraspecific competition. Therefore, male and female snow petrels segregate at small spatial scales mainly determined by habitat (SIC) characteristics.
Recombination within theCepaea nemoralissupergene is confounded by incomplete penetrance and epistasis
Authors: Gonzalez Daniel Ramos , Aramendia Amaia Caro , Davison Angus
Published: November 2018

Although the land snailCepaea nemoralisis one of the most thoroughly investigated colour polymorphic species, there have been few recent studies on the inheritance of the shell traits. Previously, it has been shown that the shell polymorphism is controlled by a series of nine or more loci, of which five make a single ‘supergene’ containing tightly linked colour and banding loci and more loosely linked pigmentation, spread band and punctate loci. However, one limitation of earlier work was that putative instances of recombination between loci within the supergene were not easily verified. We therefore generated a new set ofC. nemoraliscrosses that segregate for colour, banding and pigmentation, and several other unlinked shell phenotype loci. The snails were genotyped using a set of RAD-seq loci that flank the supergene, and instances of recombination tested by comparing inferred supergene genotype against RAD-marker genotype. We found no evidence that suspected ‘recombinant’ individuals are recombinant within the supergene - point estimates of recombination between both colour/banding, and colour/pigmentation loci are zero, with upper limits of 0.8 and 1.8%. Incomplete penetrance and epistasis are a better explanation for the apparent ‘recombinant’ phenotypes. Overall, this work therefore provides a resource for fine mapping of the supergene and other major shell phenotype loci. It also shows that the architecture of the supergene may not be as previously supposed.
Supporting learners’ STEM-oriented career pathways with digital badges
Authors: Pitt Caroline R. , Bell Adam , Strickman Rose , Davis Katie
Published: November 2018

Purpose

This paper aims to investigate the potential for digital badges to support alternate learning and career pathways in formal and informal learning environments. Stakeholder groups in higher education and industry discussed how digital badges might transform current processes of admitting undergraduate students and hiring young professionals.

Design/methodology/approach

This research uses a thematic analysis of in-depth interviews with 30 stakeholders in higher education and the technology industry.

Findings

Interview participants expressed optimism about the potential for digital badges to make learning pathways visible to learners and external audiences and to promote equity in STEM (STEM: science, technology, engineering, and mathematics) education and careers. Participants noted several obstacles, largely focused on issues of credibility and logistics of working with badges across settings.

Research limitations/implications

Though the research approach is limited in geographic scope, the findings have broad applicability and insight for the use of digital badges in general.

Practical implications

Education policymakers, employers and scholars will be able to use the insights from this investigation in their efforts to find innovative ways to expand and diversify the STEM workforce, as well as support a wider range of learners than is currently supported by initiatives aligned with the school-to-workforce pipeline metaphor.

Originality/value

This paper directly confronts issues of real-world applications of digital badges by discussing practical implications with college admissions officers and employers. The current study fills a need for research that investigates the use of digital badges across – as opposed to within – contexts.
Design and optimization of heating, cooling and lightening systems for a residential villa at Saman city, Iran
Authors: Riahi Zaniani Javad , Taghipour Ghahfarokhi Shahab , Jahangiri Mehdi , Alidadi Shamsabadi Akbar
Published: November 2018

Purpose

This paper, using energy softwares, designed of Iran and optimized a residential villa in Saman city located in Chaharmahal and Bakhtiari Province.

Design/methodology/approach

Having used the ideas of Climate Consultant software, the basic designing was conducted by Design Builder Software, and the cooling and heating loads and lighting tools and equipment were calculated. Then, the amount of consuming of heating, cooling and lighting load of the building was optimized through insulation of walls and ceiling, using green roof, double glazing UPVC windows, light intensity sensor and variable refrigerant flow (VRF) system.

Findings

Simulation results for the stated scenarios showed an annual reduction in energy consumption of 21.1, 7.9, 26.41, 27.3 and 72.3 per cent, respectively. Also, by combining all the five scenarios, an optimal state was achieved which, from the results, brought about an annual reduction of 86.9 per cent in the energy consumption.

Originality/value

The authors hope that the results of the current paper could be helpful for designers and engineers in reduction of energy consumption for designing a building in similar climatic conditions.
Nutritional and sensory quality of complementary foods developed from bulla, pumpkin and germinated amaranth flours
Authors: Tadesse Abebe Yimer , Ibrahim Ali Mohammed , Forsido Sirawdink Fikreyesus , Duguma Haile Tesfaye
Published: November 2018

Purpose

Traditionally prepared enset-based products like bulla are characterised by low protein and vitamin contents and are highly viscous; this causes protein-energy malnutrition especially in infants and young children. This paper aims to improve the nutritional and sensory qualities of enset-based food with pumpkin and amaranth.

Design/methodology/approach

Sixteen formulations of composite flour were generated using a D-optimal constrained mixture design with a range of 50-80 per cent bulla, 10-25 per cent pumpkin and 10-40 per cent amaranth flour. Nutritional and sensory qualities of the formulations were investigated using standard methods.

Findings

Ash, fat and protein contents increased from 1.1-2.8 g/100 g (p < 0.001), 1.7-3.9 g/100 g (p < 0.001) and 6.1-9.0 g/100 g (p < 0.001) respectively with the increased amaranth flour. Crude fibre content increased with increasing percentage of the amaranth and pumpkin flours. On the other hand, carbohydrate content increased from 78.2 to 84.3 per cent (p < 0.001) with an increase of bulla flour. A significant increase in Fe, Zn and Ca from 6.8-10.5 (p < 0.01), 1.5-3.0 (p = 0.022) and 1.8-148.5 mg/g (p < 0.001) respectively was achieved with an increase in amaranth ratio in flour. The total carotenoid content increased with increase in the percentage of pumpkin flour. The best sensory attributes of the developed product were around the centre point of the three ingredients.

Originality/value

The study showed that a product with good nutritional value and sensory acceptability could be prepared from enset-based ingredients and the optimal product was obtained by blending 57.8 per cent bulla, 18.9 per cent pumpkin and 23.3 per cent amaranth flour. The enriched flour can have application for snack food preparation.
Artisan food production, small family business and the Scottish food paradox
Authors: Quinn Bernie , Seaman Claire
Published: November 2018

Purpose

This paper aims to draw together three strands of work currently being carried out at Queen Margaret University in Edinburgh to take an overview of food in Scotland and on-going local interventions. The provision of “artisan” food, defined here as food that forms part of the established tradition of its local area, usually produced on a relatively small scale, has become prominent in Scotland in recent years and is seen by many as part of a developing food culture that begins to address the Scottish food paradox.

Design/methodology/approach

A review of current research that considers artisanal food production and work that researches small and family enterprises was undertaken.

Findings

Small business support within the UK and indeed tailored support for businesses owned and managed by families is in a developmental phase at present. While there are numerous sources from which businesses can seek support, there are also acknowledged challenges for businesses in identifying the most appropriate sources of support, and the opportunity cost of engaging with business support agencies remains a serious concern for many. Further, much business support prioritises high-growth businesses, effectively de-prioritizing artisanal food producers.

Research limitations/implications

The development and promotion of appropriate business support systems tailored to artisanal food production is an area that would merit further development.

Originality/value

The value of this piece lies in its blending of two distinct areas of work, considering both the challenges faced by artisanal food producers and recent research in family and smaller enterprises.
Genomic analysis of the mesophilic Thermotogae genus Mesotoga reveals phylogeographic structure and genomic determinants of its distinct metabolism
Authors: Nesbø Camilla L. , Charchuk Rhianna , Pollo Stephen M. J. , Budwill Karen , Kublanov Ilya V. , Haverkamp Thomas H. A. , Foght Julia
Published: November 2018

The genus Mesotoga, the only described mesophilic Thermotogae lineage, is common in mesothermic anaerobic hydrocarbon‐rich environments. Besides mesophily, Mesotoga displays lineage‐specific phenotypes, such as no or little H2 production and dependence on sulfur‐compound reduction, which may influence its ecological role. We used comparative genomics of 18 Mesotoga strains (pairwise 16S rRNA identity >99%) and a transcriptome of M. prima to investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage‐specific metabolism. We propose that Mesotoga accomplish H2 oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase‐complex and that a pyruvate:ferredoxin oxidoreductase acquired from Clostridia is responsible for oxidizing acetate. Phylogenetic analysis revealed three distinct Mesotoga lineages (89.6%–99.9% average nucleotide identity [ANI] within lineages, 79.3%–87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra‐lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important for Mesotoga than hyperthermophilic Thermotoga and we hypothesize that distribution of Mesotoga is constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expanded Mesotoga habitats and dispersal capabilities.
Diazotrophic community and associated dinitrogen fixation within the temperate coral Oculina patagonica
Authors: Bednarz Vanessa N. , van de Water Jeroen A. J. M. , Rabouille Sophie , Maguer Jean‐François , Grover Renaud , Ferrier‐Pagès Christine
Published: November 2018

Dinitrogen (N2) fixing bacteria (diazotrophs) are an important source of new nitrogen in oligotrophic environments and represent stable members of the microbiome in tropical corals, while information on corals from temperate oligotrophic regions is lacking. Therefore, this study provides new insights into the diversity and activity of diazotrophs associated with the temperate coral Oculina patagonica from the Mediterranean Sea by combining metabarcoding sequencing of amplicons of both the 16S rRNA and nifH genes and 15N2 stable isotope tracer analysis to assess diazotroph‐derived nitrogen (DDN) assimilation by the coral. Results show that the diazotrophic community of O. patagonica is dominated by autotrophic bacteria (i.e. Cyanobacteria and Chlorobia). The majority of DDN was assimilated into the tissue and skeletal matrix, and DDN assimilation significantly increased in bleached corals. Thus, diazotrophs may constitute an additional nitrogen source for the coral host, when nutrient exchange with Symbiodinium is disrupted (e.g. bleaching) and external food supply is limited (e.g. oligotrophic summer season). Furthermore, we hypothesize that DDN can facilitate the fast proliferation of endolithic algae, which provide an alternative carbon source for bleached O. patagonica. Overall, O. patagonica could serve as a good model for investigating the importance of diazotrophs in coral recovery from bleaching.
Orthologous peramine and pyrrolopyrazine‐producing biosynthetic gene clusters in Metarhizium rileyi, Metarhizium majus and Cladonia grayi
Authors: Berry Daniel , Mace Wade , Rehner Stephen A. , Grage Katrin , Dijkwel Paul P. , Young Carolyn A. , Scott Barry
Published: November 2018

Peramine is a non‐ribosomal peptide‐derived pyrrolopyrazine (PPZ)‐containing molecule with anti‐insect properties. Peramine is known to be produced by fungi from genus Epichloë, which form mutualistic endophytic associations with cool‐season grass hosts. Peramine biosynthesis has been proposed to require only the two‐module non‐ribosomal peptide synthetase (NRPS) peramine synthetase (PerA), which is encoded by the 8.3 kb gene perA, though this has not been conclusively proven. Until recently, both peramine and perA were thought to be exclusive to fungi of genus Epichloë; however, a putative perA homologue was recently identified in the genome of the insect‐pathogenic fungus Metarhizium rileyi. We use a heterologous expression system and a hydrophilic interaction chromatography‐based analysis method to confirm that PerA is the only pathway‐specific protein required for peramine biosynthesis. The perA homologue from M. rileyi (MR_perA) is shown to encode a functional peramine synthetase, establishing a precedent for distribution of perA orthologs beyond genus Epichloë. Furthermore, perA is part of a larger seven‐gene PPZ cluster in M. rileyi, Metarhizium majus and the stalked‐cup lichen fungus Cladonia grayi. These PPZ genes encode proteins predicted to derivatize peramine into more complex PPZ metabolites, with the orphaned perA gene of Epichloë spp. representing an example of reductive evolution.
Developing the therapeutic conversation: a conversation analysis of information giving in Family Domains Therapy
Authors: Pethica Stefania , Hill Jonathan , Jones Katy , Tranter Paul , Riley Steve , Lee Heather , Swales Michaela
Published: November 2018

Family Domains Therapy is an intervention based on the work of Hill et al. (2014). A key feature of Family Domains Therapy is the provision of information on the model that underpins the therapy. This study is the first to use applied conversation analysis (CA) to explore the interactional impact of giving information regarding a therapeutic model during therapy sessions. Using techniques of conversation analysis this paper offers a description of the four formats therapists used to give information in this therapeutic setting (non‐technical scenarios, ‘if X then Y’ format, technical paraphrase and formulation format). Additional turn‐by‐turn conversation analysis uncovered how families were more likely to give extended responses when information was given using the format of non‐technical scenarios. Implications of the use of this type of applied conversation analysis for the study of therapeutic processes for future research and clinical practice are discussed.

Practitioner points

Practitioners can use different ways of providing information in order to open up or close down topics of conversation

Using everyday terminology often leads to family members sharing additional information

Using the terminology of the domains model often leads to minimal acknowledgement from family members

Corroborating findings from other settings suggest that therapists could use these ways of interacting strategically to structure therapy sessions
Information Retrieval in Food Science Research: A Bibliographic Database Analysis
Authors: Urhan Tuba Karaarslan , Rempel Hannah Gascho , Meunier‐Goddik Lisbeth , Penner Michael H.
Published: November 2018

The aim of the present research was to ascertain the importance of electronic bibliographic database selection and multiple database usage during the information retrieval phase of research in the food sciences. Six commonly recommended databases were compared with respect to overall journal coverage and journal overlap. Databases were also evaluated with respect to coverage of food science‐based journals and the extent of article coverage therein. A case study approach, focused on bile acid/dietary fiber interactions, was used to illustrate the ramifications of database selection/usage when dealing with specific research topics. Databases differed with respect to the breadth of disciplines covered, the total number of journals indexed, the number of food science discipline‐specific journals indexed, and the number of articles included per indexed journal. All of the databases contained citations that were unique to the given database. The data resulting from the case study provide an example of the extent to which relevant information may be missed if pertinent databases are not mined. In the present case, over half of the articles retrieved on the focus research topic were unique to a single database. The combined data from this study point to the importance of thoughtful database selection and multiple database usage when comprehensively assessing knowledge in the food sciences.

Practical Application

This paper provides insights into article database usage for food science‐relevant information retrieval. Online information retrieval is an efficient way to assess current knowledge in any of the food science disciplines. Acquired knowledge in turn is the underpinning of effective problem solving; whether it be private sector‐ or academic/government‐based research.
Consumers’ Opinion on Dried Pomegranate Arils to Determine the Best Processing Conditions
Authors: Cano‐Lamadrid Marina , Vázquez‐Araújo Laura , Sánchez‐Rodríguez Lucía , Wodyło Aneta , Carbonell‐Barrachina Ángel A.
Published: November 2018

Consumers’ preference is essential to improve processed food products quality, but small companies sometimes lacks knowledge or tools to develop consumer studies. The aim of the present study was to investigate consumers’ insight to recommend the best drying methodology for pomegranate arils. With the aim of providing information that industry can correlate to the drivers of liking, descriptive sensory characteristics, and volatile compounds of the samples were determined and related with consumers’ responses. A total of 19 volatiles of dehydrated pomegranate arils were determined using solid‐phase microextraction and gas chromatography–mass spectrometry. Partial least square regression (PLS) results indicated that consumers overall liking was positively correlated with “pom ID”, “sweet”, and “fruity” attributes, and also volatile compounds of the esters family. Overall liking was negatively correlated with the “off‐flavor” and “burnt” attributes, related to the furan compounds family. Penalty analysis indicated that the sample corresponding with the current commercial product needed improvement on the “pom ID”, “fruity”, and “sweetness” parameters. All the samples processed using the proposed new drying techniques were more liked than the commercial sample, highlighting a sample dried using pre‐osmotic dehydration in Wonderful concentrate pomegranate juice.

Practical Application

Consumers’ preference is essential to improve processed food products quality, but small companies sometimes lack knowledge or tools to conduct consumer studies. The present study provides useful information to understand consumers’ preferences of a healthy product such as pomegranate dehydrated arils. Also, the link of physico‐chemical and sensory tools is clearly described, providing information about possible sensory quality indicators.
Low‐density lipoprotein net charge is a risk factor for atherosclerosis in lupus patients independent of lipid concentrations
Authors: Rodríguez Marina , Guardiola Montse , Oliva Iris , Carles Vallvé Joan , Ferré Raimon , Masana Lluís , Parra Sandra , Ribalta Josep , Castro Antoni
Published: November 2018

Aims

Patients with systemic lupus erythematosus (SLE) suffer from accelerated atherosclerosis. Their most common cause of death is a cardiovascular disease (CVD), in spite of the presence of moderate lipid alterations and normal cardiovascular risk scores. However, cholesterol still accumulates in the arteries of SLE patients, so we aim to identify additional factors that may help explain the residual risk that exists in these patients. We focus on investigating whether the net charge contributes significantly to both the development and the progression of atherosclerosis in patients with SLE.

Methods

The lipoproteins from 78 patients with SLE and 32 controls were isolated via sequential ultracentrifugation. Lipoprotein subclasses distributions were analyzed via nuclear magnetic resonance spectroscopy and the net charges of very low‐density lipoprotein (VLDL), intermediate‐density lipoprotein (IDL), low‐density lipoprotein (LDL) and high‐density lipoprotein (HDL) were measured using a Zetasizer Nano‐ZS. The degree of atherosclerosis (carotid intima‐media thickness [cIMT]) was determined in all the participants.

Results

Each lipoprotein class exhibited a negative net charge. IDL and LDL net charge correlated negatively with cIMT (r = −0.274, P = 0.034; r = −0.288; P = 0.033, respectively) in patients with SLE. This effect was independent of age, body mass index (BMI), gender, tobacco consumption, high‐sensitivity C‐reactive protein (hsCRP), lipid concentration and lipoprotein particle number. LDL net charge explained 4% of the cIMT variability among these patients; this contribution was also independent of age, BMI, gender, tobacco consumption, lipids levels, apolipoproteins and hsCRP.

Conclusions

Low‐density lipoprotein net charge may be considered a new independent contributor to subclinical atherosclerosis in SLE patients. The observed relationship was independent of lipid concentrations and extends the prominent role that IDL and LDL play in cardiovascular risk.
Skill Specificity and Attitudes toward Immigration
Authors: Pardos‐Prado Sergi , Xena Carla
Published: November 2018

Labor market competition theories explaining anti‐immigrant attitudes have received limited or no empirical validation in recent literature. This has led researchers to highlight education and cultural values as the main, if not the sole, drivers of attitudes toward immigration. We present a new labor market competition theory focusing on job availability rather than foreign labor supply. This theory predicts that individuals with low transferable skills in the labor market will articulate a subjective sense of job insecurity and higher hostility toward migrants. Our cross‐classified, longitudinal, and difference‐in‐differences models reveal that skill specificity is a strong driver of anti‐immigrant attitudes, and they suggest that economic competition theories cannot be dismissed. By shifting the attention from supply to demand in the labor market, and from actual to potential competition with migrants, we show that the highly educated are far from immune to anti‐immigrant attitudes.
Systematic review with meta‐analysis: portal vein recanalisation and transjugular intrahepatic portosystemic shunt for portal vein thrombosis
Authors: Rodrigues Susana G. , Sixt Sebastian , Abraldes Juan G. , De Gottardi Andrea , Klinger Christoph , Bosch Jaime , Baumgartner Iris , Berzigotti Annalisa
Published: November 2018

Background

Transjugular intrahepatic portosystemic shunt has been increasingly used in patients with portal vein thrombosis to obtain patency, but evidenced‐based decisions are challenging.

Aim

To evaluate published data on efficacy and safety of endovascular therapy in portal vein thrombosis.

Methods

Systematic search of PubMed, ISI, Scopus, and Embase for studies (in English, until October 2017) reporting feasibility, safety, 12‐month portal vein recanalisation, transjugular intrahepatic portosystemic shunt patency, and survival in patients with benign portal vein thrombosis undergoing endovascular treatment. An independent extraction of articles using predefined data fields and quality indicators was used; pooled analyses based on random‐effects models; heterogeneity assessment by Cochran's Q, I2 statistic, subgroup analyses, and meta‐regression.

Results

Thirteen studies including 399 patients (92% cirrhosis; portal vein thrombosis: complete 46%, chronic 87%, cavernous transformation 17%, superior mesenteric vein involvement 55%) were included. Transjugular intrahepatic portosystemic shunt was technically feasible in 95% (95% CI: 89%‐98%) with heterogeneity (I2 = 57%, P < 0.001) explained by cavernous transformation. Major complications occurred in 10% (95% CI: 6.0%‐18.0%; I2 = 52%, P = 0.55). Additional catheter‐directed thrombolysis was associated with more complications compared to transjugular intrahepatic portosystemic shunt alone or plus thrombectomy (17.6% vs 3.3%). Twelve‐month portal vein recanalisation was 79% (95% CI: 67%‐88%; I2 = 78%, P < 0.01). Shunt patency at 12 months was 84% (95% CI: 76%‐90%; I2 = 62%, P < 0.01). Overall 12‐month survival rate was 89%, with no heterogeneity.

Conclusions

Transjugular intrahepatic portosystemic shunt for portal vein thrombosis recanalisation was highly feasible, effective, and safe. Cavernous transformation was the main determinant of technical failure. Additional catheter‐directed thrombolysis was associated with higher risk of severe complications.
A Smoothing-Based Goodness-of-Fit Test of Covariance for Functional Data
Authors: Chen Stephanie T. , Xiao Luo , Staicu Ana-Maria
Published: November 2018

Functional data methods are often applied to longitudinal data as they provide a more flexible way to capture dependence across repeated observations. However, there is no formal testing procedure to determine if functional methods are actually necessary. We propose a goodness-of-fit test for comparing parametric covariance functions against general nonparametric alternatives for both irregularly observed longitudinal data and densely observed functional data. We consider a smoothing-based test statistic and approximate its null distribution using a bootstrap procedure. We focus on testing a quadratic polynomial covariance induced by a linear mixed effects model and the method can be used to test any smooth parametric covariance function. Performance and versatility of the proposed test is illustrated through a simulation study and three data applications.
An augmented reality‐based learning approach to enhancing students’ science reading performances from the perspective of the cognitive load theory
Authors: Lai Ah‐Fur , Chen Chih‐Hung , Lee Gon‐Yi
Published: November 2018

Reading has been regarded as a medium for learning science, revealing the importance of enhancing learners’ reading competence in science education. The critical features of science texts are their multiple representations, such as text and visual elements, which assist the representation of science concepts. A multimedia learning environment can present relevant materials in various formats and help students to process the materials in meaningful ways, for example, by integrating learning materials with relevant prior concepts, and organizing them into a consistent and coherent cognitive structure. However, some issues with multimedia instructional design have been proposed, such as students’ cognitive load and learning motivations. In this study, an augmented reality‐based science learning system was developed based on the contiguity principle of multimedia learning in order to promote students’ science learning. Moreover, an experiment was conducted on a natural science course in an elementary school to assess the effectiveness of the implemented system on students’ learning. The experimental results display that the students learning with this approach found made significant gains in their learning achievements and motivations compared to those learning science with conventional multimedia science learning; moreover, their perceptions of extraneous cognitive load were significantly reduced during the learning activity.
Tablet‐based AR technology: Impacts on students’ conceptions and approaches to learning mathematics according to their self‐efficacy
Authors: Cai Su , Liu Enrui , Yang Yang , Liang Jyh‐Chong
Published: November 2018

Most studies of Augmented Reality (AR) in education have considered students’ learning outcomes and motivation. Previous studies have revealed that AR has the potential to help students learn abstract conceptions in mathematics. In this paper, a series of statistics and probability lessons using AR installed on tablets was designed and developed to examine the effect of the AR technology by comparing the conceptions and learning approaches of junior high school students with different levels of self‐efficacy. A total of 101 students were divided into two groups based on their mathematics learning self‐efficacy. The analysis of the results shows that AR applications in mathematics courses can help students with higher self‐efficacy to pay closer attention to higher level conceptions. It can also help higher self‐efficacy students to apply more advanced strategies when learning mathematics.
Rapid tools to gain insights into the interaction dynamics of new 8‐hydroxyquinolines with few fungal lines
Authors: Joaquim Angélica Rocha , Pippi Bruna , de Cesare Maycon Antonio , Rocha Débora Assumpção , Boff Roberta Taufer , Staudt Keli Jaqueline , Ruaro Thaís Carine , Zimmer Aline Rigon , de Araújo Bibiana Verlindo , Silveira Gustavo Pozza , Martins Andreza Francisco , Teixeira Mario Lettieri , dos Santos Francisco Paulo , Fuentefria Alexandre Meneghello , de Andrade Saulo Fernandes
Published: November 2018

The combination of tools such as time‐kill assay with subsequent application of mathematical modeling can clarify the potential of new antimicrobial compounds, since minimal inhibitory concentration (MIC) value does not provide a very detailed characterization of antimicrobial activity. Recently, our group has reported that the 8‐hydroxy‐5‐quinolinesulfonic acid presents relevant antifungal activity. However, its intrinsic acidity could lead to an ionization process, decreasing fungal cell permeability. To overcome this potential problem and enhance activity, the purpose of this study was to synthesize and evaluate a novel series of hybrids between the 8‐hydroxyquinoline core and sulfonamide and to prove their potential using broth microdilution method, obtaining the pharmacodynamic parameters of the most active derivatives combining time‐kill studies and mathematical modeling and evaluating their toxicity. Compound 5a was the most potent, being active against all the fungal species tested, with low toxicity in normal cells. 5a and 5b have presented important antibacterial activity against Staphylococcus aureus strain. The EC50 values obtained by combination of time‐kill studies with mathematical model were similar to those of MIC, which confirms the potential of compounds. In addition, these derivatives are non‐irritant molecules with the absence of topical toxicity. Finally, 5a and 5b are promising candidates for treatment of dermatomycosis and candidiasis.
Pretend Play and Fantasy: What if Montessori Was Right?
Authors: Lillard Angeline S. , Taggart Jessica
Published: November 2018

Pretend play and fantasy are staples of childhood, supported by adults’ provision of encouraging tools (like dress‐up clothing and play kitchens) and by media. Decades ago, Maria Montessori developed a system of education based on close observation of children, and she concluded that pretend play and fantasy were not as helpful for children's development as the zeitgeist suggested (and still suggests). In this article, we present her views and relevant evidence, and ask: What if she was right? What if, as a culture, we are putting great effort and faith into activities and contexts for children that we believe help development but that might actually be less helpful than engaging in the real world?
Reliability of scores obtained from standardized patient and instructor assessments
Authors: Taşdelen Teker Gülşen , Odabaşı Orhan
Published: November 2018

Introduction

To obtain more reliable results from observation‐based assessments, high‐quality raters are key. Although this quality can be obtained by using instructors, extra workload can be a burden on them. To overcome this problem, one alternative to instructor raters can be standardized patients (SPs).

Method

In this study, the students carried out an SP interview related to communication with an applicant/patient in the context of clinical skills training course. SPs rated student interviews just after interview and after watching a recording. Instructors rated students just by watching the recordings. To determine the appropriateness of use of SPs as raters, ratings of SPs and instructors were compared by using mean scores given to the interview performances of students’ communication skills. Moreover, G theory was used to determine the reliability of scores.

Results

Standardized patients’ ratings immediately after the interviews showed the highest scores, and these ratings were statistically different from the SPs’ and instructors’ ratings done while watching recordings. Besides, the G coefficient for the 4 instructors was 0.71, while that for the 12 SPs was estimated as 0.73. However, even when using 12 SPs, the obtained reliability coefficient of 0.73 brings into question the reliability of their ratings. Moreover, it was found that the one who contributed the most to reliability among instructors was the most experienced person in subject area.

Conclusions

If SPs are to be used as raters, they will need more comprehensive training. More importantly, regardless of who the rater is, rater training is one of the most important factors in achieving more reliable and valid results. Moreover, having experience and knowledge about assessed topic is another crucial point of performance assessment by means of obtaining reliable results.
Frequency and etiology of pulmonary hypertension in patients with myeloproliferative neoplasms
Authors: Brabrand Mette , Hansen Knud Nørregaard , Laursen Christian B. , Larsen Thomas Stauffer , Vestergaard Hanne , Abildgaard Niels
Published: November 2018

Objective

Pulmonary hypertension (PH) has been reported to be associated with myeloproliferative neoplasms (MPN), affecting 5%‐48% of MPN patients. With the aims to describe the prevalence of PH in Ph‐MPN patients and explore the cause in identified subjects, we performed a prospective cohort study of Ph‐MPN patients.

Method

Transthoracic echocardiography (TTE) was performed on all patients. When the TTE was abnormal, further investigations were performed according to current guidelines from the European Society of Cardiology. The primary endpoint was the frequency of PH. The secondary endpoint was causes of PH.

Results

We included 158 patients, median age was 65 years. Fifty percent had polycythemia vera, 34% essential thrombocytosis, and 11% primary myelofibrosis, 3% post‐ET‐myelofibrosis, and 2% post‐PV‐myelofibrosis. Only six patients (3.8%) were found to have a high probability of PH. They were all examined with right heart catheterization and all met the invasive criteria for PH. In all six patients other causes than MPN for PH were identified, although some contribution from the MPN could not be ruled out in three patients.

Conclusion

In the largest study ever reported, we found a lower prevalence of PH (3.8%) than previously reported. Screening for PH in unselected MPN patients is not justified.
Orchestration as a form of public action: The EU engagement with voluntary sustainability standards
Authors: Partiti Enrico
Published: November 2018

EU authorities have come to engage with transnational private standards in the domain of sustainability in forms which are different from the traditional interplay based on agency relations and incorporation by reference. This phenomenon is evident in the domain of global value chain sustainability where the employment of voluntary sustainability standards (VSS) is permitted in certain EU measures. This contribution depicts the main features of orchestration as a distinct form of public action involving transnational private regulation. It lays down the reasons underpinning public ‘use’ of forms of public authority, it highlights the potential for orchestration in publicising transnational private rules and it exposes the hidden dynamics stemming from the interplay between public and private rules. It discusses the conditions under which orchestration can enhance the effectiveness of public measures, and how orchestration can transform transnational private regimes by steering their substance and procedures.
Enhancing the high cycle fatigue life of high strength aluminum alloys for aerospace applications
Authors: Rama Krishna Lingamaneni , Madhavi Yarlagadda , Sahithi Thatipamula , Srinivasa Rao Dameracharla , Ijeri Vijaykumar Sharanappa , Prakash Om , Gaydos Stephen Paul
Published: November 2018

Hard anodized (HA) and micro arc oxidation (MAO) coatings of identical thickness were deposited on two different high strength aluminum (Al) alloys namely, 2024‐T3 and 7075‐T6. Further, as received Al alloys were also subjected to shot peening (SP) to induce subsurface compressive residual stresses followed by the MAO coating deposition (SP + MAO). The average velocity of particle‐in‐flight during the SP process was measured and utilized to calculate the kinetic energy of the peening particles. The bare and coated alloys were subjected to completely reversed stress (R = −1) rotating beam high cycle fatigue tests at five different stress levels. In addition, the bare and coated alloys were also evaluated for their tensile properties, elemental composition, phase constituents, surface, and cross‐sectional morphologies including the surface roughness (Ra, Rz) and correlated the same with the corresponding fatigue behavior. Irrespective of substrate alloy composition and stress levels investigated, the duplex SP + MAO treatment resulted in significant fatigue life enhancement over and above the fatigue life of corresponding bare (not shot peened) Al alloy, while the hard anodized and plain MAO (both without prior shot peening) continue to exhibit significant fatigue debit. Driven by the compressive residual stresses present beneath the subsurface region of SP + MAO coating interface, fractured surface examination of SP + MAO coatings clearly highlights the crack‐branching associated multiple crack deflection as the predominant operative mechanism responsible for diminishing the crack growth rate and therefore enhance the fatigue life as compared with the near linear crack extension without significant deflections leading to relative premature failure of plain MAO coated alloys.
Microbially influenced formation of Neoarchean ooids
Authors: Flannery David T. , Allwood Abigail C. , Hodyss Robert , Summons Roger Everett , Tuite Michael , Walter Malcolm R. , Williford Kenneth H.
Published: November 2018

Ooids are accretionary grains commonly reported from turbulent, shallow‐water environments. They have long been associated with microbially dominated ecosystems and often occur in close proximity to, or embedded within, stromatolites, yet have historically been thought to form solely through physicochemical processes. Numerous studies have revealed both constructive and destructive roles for microbes colonizing the surfaces of modern calcitic and aragonitic ooids, but there has been little evidence for the operation of these processes during the Archean and Proterozoic, when both ooids and microbially dominated ecosystems were more widespread. Recently described carbonate ooids from the 2.9 Ga Pongola Supergroup, South Africa, include well‐preserved examples composed of diagenetic dolomite interpreted to have formed from a high‐Mg‐calcite precursor. Spatial distributions of organic matter and elements associated with metabolic activity (N, S, and P) were interpreted as evidence for a biologically induced origin. Here, we describe exceptionally well‐preserved ooids composed of calcite, collected from Earth's oldest known carbonate lake system, the ~2.72 Ga Meentheena Member (Tumbiana Formation), Fortescue Group, Western Australia. We used optical microscopy, Raman spectroscopy, XRD, SEM‐EDS, LA‐ICP‐MS, EA‐IRMS, and a novel micro‐XRF instrument to investigate an oolite shoal deposited between stromatolites that preserve abundant evidence for microbial activity. We report an extremely fine, radial‐concentric, calcitic microfabric that is similar to the primary and early diagenetic fabrics of calcitic ooids reported from modern temperate lakes. Early diagenetic silica has trapped isotopically light and thermally mature organic matter. The close association of organic matter with mineral phases and microfabrics related to primary and early diagenetic processes suggest incorporation of organic matter occurred during accretion, likely due to the presence of microbial biofilms. We conclude that the oldest known calcitic ooids were likely formed through processes similar to those that mediate the accretion of ooids in similar environments today, including formation within a microbial biosphere.