bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory
Authors: Kozyreva Varvara K. , Truong Chau-Linda , Greninger Alexander L. , Crandall John , Mukhopadhyay Rituparna , Chaturvedi Vishnu 
Published: February 2017

AbstractBackgroundPublic health microbiology laboratories (PHL) are at the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards.Objectives1) Establish the performance specifications of WGS applications used in PHL to conform with CLIA (Clinical Laboratory Improvements Act) guidelines for laboratory developed tests (LDT), 2) Develop quality assurance (QA) and quality control (QC) measures, 3) Establish reporting language for end users with or without WGS expertise, 4) Create a validation set of microorganisms to be used for future validations of WGS platforms and multi-laboratory comparisons and, 5) Create modular templates for the validation of different sequencing platforms.MethodsMiSeq Sequencer and Illumina chemistry (Illumina, Inc.) were used to generate genomes for 34 bacterial isolates with genome sizes from 1.8 to 4.7 Mb and wide range of GC content (32.1%-66.1%). A customized CLCbio Genomics Workbench - shell script bioinformatics pipeline was used for the data analysis.ResultsWe developed a validation panel comprising tenEnterobacteriaceaeisolates, five gram-positive cocci, five gram-negative non-fermenting species, nineMycobacterium tuberculosis, and five miscellaneous bacteria; the set represented typical workflow in the PHL. The accuracy of MiSeq platform for individual base calling was >99.9% with similar results shown for reproducibility/repeatability of genome-wide base calling. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from MLST and genotyping tests were 100%. A test report format was developed for the end users with and without WGS knowledge.ConclusionWGS was validated for routine use in PHL according to CLIA guidelines for LDTs. The validation panel, sequencing analytics, and raw sequences will be available for future multi-laboratory comparisons of WGS in PHL. Additionally, the WGS performance specifications and modular validation template are likely to be adaptable for the validation of other platforms and reagents kits.
What shapes the continuum of reproductive isolation? Lessons fromHeliconiusbutterflies
Authors: Mérot C. , Salazar C. , Merrill R. M. , Jiggins C. , Joron M. 
Published: February 2017

AbstractThe process by which species evolve can be illuminated by investigating barriers that limit gene flow between taxa. Recent radiations, such asHeliconiusbutterflies, offer the opportunity to compare isolation between pairs of taxa at different stages of ecological, geographic and phylogenetic divergence. We carry out a comparative analysis of existing and novel data in order to quantify the strength and direction of isolating barriers within a well-studied clade ofHeliconius. Our results highlight that increased divergence is associated with the accumulation of stronger and more numerous barriers to gene flow. Wing pattern is both under natural selection for Müllerian mimicry and involved in mate choice, and therefore underlies several isolating barriers. However, pairs which share a similar wing pattern, also display strong reproductive isolation mediated by traits other than wing pattern. This suggests that, while wing pattern is a key factor for early stages of divergence, it is not essential at a higher level. Additional factors including habitat isolation, hybrid sterility and chemically-mediated mate choice are associated with complete speciation. Therefore, although most previous work has emphasised the role of wing pattern, our comparative results highlight that speciation is a multidimensional process, whose completion is stabilized by many factors.
An efficient FLP-based toolkit for spatiotemporal control of gene expression inCaenorhabditis elegans
Authors: Muñoz-Jiménez Celia María , Ayuso Cristina , Dobrzynska Agnieszka , Torres Antonio , de la Cruz Ruiz Patricia , Askjaer Peter 
Published: February 2017

AbstractSite-specific recombinases are potent tools to regulate gene expression. In particular, the Cre and FLP enzymes are widely used to either activate or inactivate genes in a precise spatiotemporal manner. Both recombinases work efficiently in the popular model organismCaenorhabditis elegansbut their use in this nematode is still only sporadic. To increase the utility of the FLP system inC. eleganswe have generated a series of single-copy transgenic strains that stably express an optimized version of FLP in specific tissues or by heat induction. We show that recombination efficiencies reach 100 percent in several cell types, such as muscles, intestine and serotonin producing neurons. Moreover, we demonstrate that most promoters drive recombination exclusively in the expected tissues. As examples of the potentials of the FLP lines we describe novel tools for induced cell ablation by expression of the PEEL-1 toxin and a versatile FLP-out cassette for generation of GFP-tagged conditional knockout alleles. Together with other recombinase-based reagents created by theC. eleganscommunity this toolkit increases the possibilities for detailed analyses of specific biological processes at developmental stages inside intact animals.
Chromosome Number of the Monarch Butterfly,Danaus plexippus(Linnaeus 1758) and the Danainae
Authors: Hamm Christopher A. 
Published: February 2017

AbstractThe monarch butterfly,Danaus plexippus(Linnaeus 1758) is a charismatic butterfly known for its multi-generational migration in Eastern North America, and is emerging as an important system in the study of evolutionary genetics. Assigning genes or genetic elements to chromosomes is an important step when considering how genomes evolved. The monarch butterfly has a reported haploid chromosome number of 30. The specimens that this count is based on are from Madras, India whereD. plexippusdoes not occur. As a consequence the reported haplotype for theD. plexippusis incorrect. A literature review revealed that the specimens this count was based on were most likelyDanaus genutia(Cramer 1779), which Linnaeus and others conflated withD. plexippus. In a 1954 Opinion (#282) the International Code of Zoological Nomenclature decided that the nameD. genutiarefers to specimens originating from the Orient andD. plexippusto those from North America. To clarify the haplotype number ofD. plexippusfrom North America I conducted chromosome squashes of male 5th instar larvae. All specimens examined had a haploid chromosome count of n = 28. Following these new data, I then reconstructed the evolution of haplotypes throughout the Danainae subfamily to provide a testable hypothesis on the evolution of chromosome number for this group.
Dichotomising dementia: is there another way?
Authors: McParland Patricia , Kelly Fiona , Innes Anthea 
Published: February 2017

AbstractThis article discusses the reduction of the complex experience of dementia to a dichotomised ‘tragedy’ or ‘living well’ discourse in contemporary Western society. We explore both discourses, placing them in the context of a successful ageing paradigm, highlighting the complex nature of dementia and the risks associated with the emergence of these arguably competing discourses. Specifically, we explore this dichotomy in the context of societal understandings and responses to dementia. We argue for an acceptance of the fluid nature of the dementia experience, and the importance of an understanding that recognises the multiple realities of dementia necessary for social inclusion to occur. Such an acceptance requires that, rather than defend one position over another, the current discourse on dementia is challenged and problematised so that a more nuanced understanding of dementia may emerge; one that fully accepts the paradoxical nature of this complex condition.
When walking becomes wandering: representing the fear of the fourth age
Authors: Brittain Katherine , Degnen Cathrine , Gibson Grant , Dickinson Claire , Robinson Louise 
Published: February 2017

AbstractDementia is linked to behavioural changes that are perceived as challenging to care practices. One such behavioural change is ‘wandering’, something that is often deeply feared by carers and by people with dementia themselves. Understanding how behavioural changes like wandering are experienced as problematic is critically important in current discussions about the behavioural and psychological symptoms of dementia. In this article we draw on our secondary analysis of qualitative interviews and focus groups with carers of people with dementia to critically question ‘when does walking become wandering’? Drawing on theoretical perspectives from anthropology, sociology and human geography to explore experiences of carers and of people with dementia, we argue that a conceptual shift occurs in how pedestrian activity, usually represented as something purposeful, meaningful and healthy (walking) is seen as something threatening that needs managing (wandering). We demonstrate how this shift is connected to cultural assumptions about the mind‐body relationship in both walking and in dementia. We further argue that the narratives of carers about wandering challenge the notion of ‘aimless’ walking in the fourth age. This is because, as these narratives show, there are often pronounced links to specific areas and meaningful places where people with dementia walk to.
Ageing, dementia and the social mind: past, present and future perspectives
Authors: Higgs Paul , Gilleard Chris 
Published: February 2017

AbstractAccompanying the ageing of contemporary ageing societies is an increase in age associated morbidity, with dementia having an important impact. Mental frailty in later life is a source of fear for many and a major policy concern to all those concerned with health and welfare services. This introduction to the special issue on ‘Ageing, dementia and the social mind’ situates the selected papers within the context of debates about dementia and its social relations. In particular it draws attention to the importance of the social imaginary of the fourth age and what this means for the issue of personhood, care, social representations of dementia and its social contextualisation. The papers illuminating these themes draw on a variety of disciplines and approaches; from the social sciences to the humanities and from the theoretical to the empirical in order to help orientate future researchers to the complexities of dementia and the social and cultural matrix in which it exists. This paper provides an introduction to the potential for a more extended sociology of dementia; one which could combine the insights from medical sociology with the concerns of social gerontology.
Preterm birth prevention in twin pregnancies with progesterone, pessary, or cerclage: a systematic review and meta‐analysis
Authors: Jarde A , Lutsiv O , Park CK , Barrett J , Beyene J , Saito S , Dodd JM , Shah PS , Cook JL , Biringer AB , Giglia L , Han Z , Staub K , Mundle W , Vera C , Sabatino L , Liyanage SK , McDonald SD 
Published: February 2017

BackgroundAbout half of twin pregnancies deliver preterm, and it is unclear whether any intervention reduces this risk.ObjectivesTo assess the evidence for the effectiveness of progesterone, cerclage, and pessary in twin pregnancies.Search strategyWe searched Medline, EMBASE, CINAHL, Cochrane Central Register of Controlled Trials, and ISI Web of Science, without language restrictions, up to 25 January 2016.Selection criteriaRandomised controlled trials of progesterone, cerclage, or pessary for preventing preterm birth in women with twin pregnancies, without symptoms of threatened preterm labour.Data collection and analysisTwo independent reviewers extracted data using a piloted form. Study quality was appraised with the Cochrane Risk of Bias tool. We performed pairwise inverse variance random‐effects meta‐analyses.Main resultsWe included 23 trials (all but three were considered to have a low risk of bias) comprising 6626 women with twin pregnancies. None of the interventions significantly reduced the risk of preterm birth overall at <34 or <37 weeks of gestation, or neonatal death, our primary outcomes, compared to a control group. In women receiving vaginal progesterone, the relative risk (RR) of preterm birth <34 weeks of gestation was 0.82 (95% CI 0.64–1.05, seven studies, I2 36%), with a significant reduction in some key secondary outcomes, including very low birthweight (<1500 g, RR 0.71, 95% CI 0.52–0.98, four studies, I2 46%) and mechanical ventilation (RR 0.61, 95% CI 0.45–0.82, four studies, I2 22%).ConclusionIn twin gestations, although no overarching intervention was beneficial for the prevention of preterm birth and its sequelae, vaginal progesterone improved some important secondary outcomes.Tweetable abstractVaginal progesterone may be beneficial in twin pregnancies, but not 17‐OHPC, cerclage, or pessary.
Harnessing the Potential of Blood Proteins as Functional Ingredients: A Review of the State of the Art in Blood Processing
Authors: Lynch Sarah A. , Mullen Anne Maria , O'Neill Eileen E. , García Carlos Álvarez 
Published: February 2017

AbstractBlood is generated in very large volumes as a by‐product in slaughterhouses all around the world. On the one hand, blood generation presents a serious environmental issue because of its high pollutant capacity; however, on the other hand, blood has the potential to be collected and processed to generate high‐added‐value food ingredients based on its exceptional nutritive value and its excellent functional properties. In this paper, we review the current state of the art for blood processing, from collection to final recovery of protein isolates, the functional properties of blood, impact of processing on functional properties, and potential applications as food ingredients. Furthermore, future challenges are outlined for this underutilized and abundant product from the meat industry.
Antimicrobials from Mushrooms for Assuring Food Safety
Authors: Shen Heng‐Sheng , Shao Suqin , Chen Jun‐Chen , Zhou Ting 
Published: February 2017

AbstractThe interest in discovering and developing natural antimicrobials has significantly increased due to consumer preferences for foods that are free of chemical preservatives while still microbiologically safe. One of the best sources of natural antimicrobials is certain mushrooms (fungi) as many of them not only have nutraceutical functions but also possess antimicrobial properties. This article reviews the available information on mushroom antimicrobials for food safety control. It includes available resources, extraction procedures, antimicrobial activities, and the status of their applications to food safety. The review indicates that there are great potential benefits to be gained from mushroom antimicrobials in food production, processing, and preservation as a biosolution to meet the increasing demands for food quality and safety.
Sensory Profile and Consumer Acceptability of Prebiotic White Chocolate with Sucrose Substitutes and the Addition of Goji Berry (Lycium barbarum)
Authors: Morais Ferreira Janaína Madruga , Azevedo Bruna Marcacini , Luccas Valdecir , Bolini Helena Maria André 
Published: February 2017

AbstractFunctional food is a product containing nutrients that provide health benefits beyond basic nutrition. The objective of the present study was to evaluate the descriptive sensory profile and consumers’ acceptance of functional (prebiotic) white chocolates with and without the addition of an antioxidant source (goji berry [GB]) and sucrose replacement. The descriptive sensory profile was determined by quantitative descriptive analysis (QDA) with trained assessors (n = 12), and the acceptance test was performed with 120 consumers. The correlation of descriptive and hedonic data was determined by partial least squares (PLS). The results of QDA indicated that GB reduces the perception of most aroma and flavor attributes, and enhances the bitter taste, bitter aftertaste, astringency, and most of the texture attributes. The consumers’ acceptance of the chocolates was positive for all sensory characteristics, with acceptance scores above 6 on a 9‐point scale. According to the PLS regression analysis, the descriptors cream color and cocoa butter flavor contributed positively to the acceptance of functional white chocolates. Therefore, prebiotic white chocolate with or without the addition of GB is innovative and can attract consumers, due to its functional properties, being a promising alternative for the food industry.
Characterization of Antibiotic Resistance Genes from Lactobacillus Isolated from Traditional Dairy Products
Authors: Guo Huiling , Pan Lin , Li Lina , Lu Jie , Kwok Laiyu , Menghe Bilige , Zhang Heping , Zhang Wenyi 
Published: February 2017

AbstractLactobacilli are widely used as starter cultures or probiotics in yoghurt, cheese, beer, wine, pickles, preserved food, and silage. They are generally recognized as safe (GRAS). However, recent studies have shown that some lactic acid bacteria (LAB) strains carry antibiotic resistance genes and are resistant to antibiotics. Some of them may even transfer their intrinsic antibiotic resistance genes to other LAB or pathogens via horizontal gene transfer, thus threatening human health. A total of 33 Lactobacillus strains was isolated from fermented milk collected from different areas of China. We analyzed (1) their levels of antibiotic resistance using a standardized dilution method, (2) their antibiotic resistance gene profiles by polymerase chain reaction (PCR) using gene‐specific primers, and (3) the transferability of some of the detected resistance markers by a filter mating assay. All Lactobacillus strains were found to be resistant to vancomycin, but susceptible to gentamicin, linezolid, neomycin, erythromycin, and clindamycin. Their susceptibilities to tetracycline, kanamycin, ciprofloxacin, streptomycin, quinupristin/dalfopristin, trimethoprim, ampicillin, rifampicin, and chloramphenicol was different. Results from our PCR analysis revealed 19 vancomycin, 10 ciprofloxacin, and 1 tetracycline‐resistant bacteria that carried the van(X), van(E), gyr(A), and tet(M) genes, respectively. Finally, no transferal of the monitored antibiotic resistance genes was observed in the filter mating assay. Taken together, our study generated the antibiotic resistance profiles of some milk‐originated lactobacilli isolates and preliminarily assessed their risk of transferring antibiotic gene to other bacteria. The study may provide important data concerning the safe use of LAB.
Preparation and Characterization of an Olive Flounder (Paralichthys olivaceus) Skin Gelatin and Polylactic Acid Bilayer Film
Authors: Lee Ka‐Yeon , Song Kyung Bin 
Published: February 2017

AbstractOlive flounder skin gelatin (OSG) was used as a film base material. A bilayer film of OSG and polylactic acid (PLA) was prepared using solvent casting method to enhance the film properties. Physical properties of the OSG–PLA film were increased compared with the nonaugmented OSG film. In particular, the PLA lamination decreased water vapor permeability from 2.17 to 0.92 × 10−9 g·m/m2·s·Pa, as well as of the water solubility from 16.62% to 9.27%, in the bilayer film relative to the OSG film. The oxygen permeability of the OSG–PLA bilayer film was held low by the OSG film, compensating for the high oxygen permeability of the PLA layer. Therefore, the OSG–PLA bilayer film with its enhanced physical properties and high water and oxygen barrier properties can be applied as a food packaging material.
High‐throughput mining of E‐genome‐specific SNPs for characterizing Thinopyrum elongatum introgressions in common wheat
Authors: Lou Haijuan , Dong Lingli , Zhang Kunpu , Wang Da‐Wei , Zhao Maolin , Li Yiwen , Rong Chaowu , Qin Huanju , Zhang Aimin , Dong Zhenying , Wang Daowen 
Published: February 2017

AbstractDiploid Thinopyrum elongatum (EE, 2n = 2x = 14) and related polyploid species constitute an important gene pool for improving Triticeae grain and forage crops. However, the genomic and molecular marker resources are generally poor for these species. To aid the genetic, molecular, breeding and ecological studies involving Thinopyrum species, we developed a strategy for mining and validating E‐genome‐specific SNPs using Th. elongatum and common wheat (Triticum aestivum, AABBDD, 2n = 6x = 42) as experimental materials. By comparing the transcriptomes between Chinese Spring (CS, a common wheat variety) and the CS‐Th. elongatum octoploid, 35,193 candidate SNPs between E genome genes and their common wheat orthologs were computed. Through comparative genomic analysis, these SNPs were putatively assigned to the seven individual E genome chromosomes. Among 420 randomly selected SNPs, 373 could be validated. Thus, approximately 89% of the mined SNPs may be authentic with respect to their polymorphism and chromosomal location. Using 14 such SNPs as molecular markers, complex E genome introgressions were reliably identified in 78 common wheat‐Th. elongatum hybrids, and the structural feature of a novel recombinant chromosome formed by 6E and 7E was revealed. Finally, based on testing 33 SNPs assigned to chromosome 3E in multiple genotypes of Th. elongatum, Pseudoroegneria stipifolia (carrying the St genome related to E) and common wheat, we suggest that some of the SNP markers may also be applicable for genetic studies within and among the Thinopyrum species (populations) carrying E and/or St genomes in the future.
Cactivalva nebularia, gen. et sp. nov. (Lepidoptera: Gracillariidae): a new Weinmannia leaf miner from southern Brazil
Authors: Moreira Gilson Rudinei Pires , Pollo Pietro , Brito Rosângela , Gonçalves Gislene Lopes , Vargas Héctor A 
Published: February 2017

AbstractMale, female, pupa, larva and egg of a new genus and species of Gracillariidae (Ornixolinae), Cactivalva nebularia Moreira & Vargas gen. et sp. nov., from southern Brazil are described and illustrated with the aid of optical and scanning electron microscopy. A preliminary analysis of mitochondrial DNA sequences including members of related lineages is also provided. The immature stages are associated with Weinmannia paulliniifolia Pohl ex Ser. (Cunoniaceae) in high altitude cloud forest of northeast Rio Grande do Sul state. During the first two sap‐feeding instars, the larva forms a serpentine mine in the lowest layer of the spongy parenchyma of a leaflet. After moulting to the third instar, it moves to another leaflet, forming a blotch mine within which the last three tissue‐feeding instars complete development, feeding upon both spongy and palisade parenchyma. Pupation occurs outside the mine, within a cocoon built on the leaf surface. This is the third genus of gracillariid moths described from the Atlantic Forest, and the first gracillariid species ever known to be associated with the Cunoniaceae.