bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protective immunity against severe malaria is associated with antibodies to a conserved repertoire of PfEMP1 variants
Authors: Tessema Sofonias K. , Nakajima Rie , Jasinskas Algis , Monk Stephanie L. , Lekieffre Lea , Lin Enmoore , Kiniboro Benson , Proietti Carla , Siba Peter , Felgner Philip L. , Doolan Denise L. , Mueller Ivo , Barry Alyssa E. 
Published: November 2018

AbstractExtreme diversity of the major surface antigen and virulence determinant of the malaria parasite Plasmodium falciparum, Erythrocyte Membrane Protein-1 (PfEMP1), poses a major barrier to identifying targets of protective immunity. To overcome this problem, we developed a PfEMP1 protein microarray containing 456 DBLα domains, which was used to characterize the immunome of a cohort of semi-immune children and to identify variants associated with protective immune responses. Children with high mean antibody levels to DBLα group 2 had a 26-36% reduced risk of uncomplicated (clinical) malaria, however only 8 diverse DBLα variants were weakly associated with protection from clinical malaria and had low predictive accuracy. On the other hand, children with high mean antibodies to DBLα groups 1 and 2 (which are markers for pathogenic “Type A” PfEMP1) and elevated antibodies to 85 (18.6%) of individual DBLα variants had a 70 −100% reduced risk of severe malaria. Of the top 20 predictive variants for severe disease protection, 17 were strongly associated with protection (86 - 100% reduction in risk of severe malaria) and had high predictive accuracy for severe disease risk. Many variants were conserved and had highly correlated antibody responses, including the three highest-ranking variants, which were linked to EPCR-binding CIDR domains. The results suggest that while immunity to uncomplicated malaria is characterised by antibodies to a diverse repertoire of PfEMP1, immunity to severe malaria requires antibodies to a limited subset of antigenically conserved variants. These findings provide new insights into antimalarial immunity and potential biomarkers for tracking disease risk.
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

AbstractIdentifying 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

ABSTRACTThe 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

AbstractSexual 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

AbstractAlthough 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

SummaryThe 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

SummaryDinitrogen (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

SummaryPeramine 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