bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signatures of selection in Charolais beef cattle identified by genome‐wide analysis
Authors: Jahuey‐Martínez Francisco Joel , Parra‐Bracamonte Gaspar Manuel , Sifuentes‐Rincón Ana María , Moreno‐Medina Victor Ricardo 
Published: April 2019

AbstractCharolais cattle are one of the most important breeds for meat production worldwide; in México, its selection is mainly made by live weight traits. One strategy for mapping important genomic regions that might influence productive traits is the identification of signatures of selection. This type of genomic features contains loci with extended linkage disequilibrium (LD) and homozygosity patterns that are commonly associated with sites of quantitative trait locus (QTL). Therefore, the objective of this study was to identify the signatures of selection in Charolais cattle genotyped with the GeneSeek Genomic Profiler Bovine HD panel consisting of 77 K single nucleotide polymorphisms (SNPs). A total 61,311 SNPs and 819 samples were used for the analysis. Identification of signatures of selection was carried out using the integrated haplotype score (iHS) methodology implemented in the rehh R package. The top ten SNPs with the highest piHS values were located on BTA 4, 5, 6 and 14. By identifying markers in LD with top ten SNPs, the candidate regions defined were mapped to 52.8–59.3 Mb on BTA 4; 67.5–69.3 on BTA 5; 39.5–41.0 Mb on BTA 6; and 26.4–29.6 Mb on BTA 14. The comparison of these candidate regions with the bovine QTLdb effectively confirmed the association (p < 0.05) with QTL related to growth traits and other important productive traits. The genomic regions identified in this study indicated selection for growth traits on the Charolais population via the conservation of haplotypes on various chromosomes. These genomic regions and their associated genes could serve as the basis for haplotype association studies and for the identification of causal genes related to growth traits.
Parasitism offers large rewards but carries high risks: Predicting parasitic strategies under different life history conditions in lampreys
Authors: Evans Thomas M. , Limburg Karin E. 
Published: April 2019

AbstractThe loss of parasitism in metazoan lineages is often seen as unlikely, but it has occurred in some lineages (e.g., leeches, lampreys). How and why parasitism is lost is aptly addressed by studying lampreys, because extant species include a range of feeding modes and parasitism has been lost repeatedly. An individual‐based model was developed to determine whether variations in survival and growth rates in the larval and juvenile stages could favour parasitic or nonparasitic strategies. A realization of the model for a Lampetra spp. population, a genus which includes parasitic and nonparasitic animals, indicated that both strategies could be successful. A different model realization of the nonparasitic species Lethenteron appendix also agreed with expectations, and only nonparasitic strategies were successful. Modelling anadromous Petromyzon marinus produced only parasitic animals, as expected, but suggested two different adult sizes should appear in the population, which has not been reported in the literature. Finally, a realization of an Ichthyomyzon castaneus population, known to be parasitic only, rarely selected for parasitism (c. 7% of model iterations), possibly because the population used to parameterize the model was unusual for the species. The results suggest that nonparasitic lineages in lampreys are common because parasitism, while offering better growth, also has lower survival. Additionally, nonparasitic species may be generated at different rates because growth and survival thresholds in the model favouring parasitism are close to observed estimates in some populations. Loss of parasitism can occur when life stages have different trade‐offs in growth and survivability.
Aflatoxins in almonds: Monitoring and exposure assessment
Authors: Kanik Tugce , Kabak Bulent 
Published: April 2019

AbstractAflatoxins (AFs) are naturally occurring contaminants classified as human carcinogens. This article describes presence and concentrations of AFs in both raw and roasted almonds collected from Turkey from September 2017 to February 2018. Long‐term exposure to AFs was then calculated using the per capita consumption of almonds and the concentration of AFs in almonds. AFs were determined by high performance liquid chromatography coupled to fluorescence detector (HPLC‐FLD). The analytical method fulfilled the requirements on method performance according to Commission Regulation (EC) No 401/2006. AFs were detected in 15% of almonds, but at levels far below the European Union (EU) maximum levels (MLs). The long‐term mean exposure to AFB1 and total AFs via the consumption of almonds for Turkish consumer were calculated as 0.0019 and 0.0021 ng kg−1 b.w. day−1 at the lower bound, and 0.0043 and 0.0067 ng kg−1 b.w. day−1 at the upper bound, respectively.Practical applicationsThe present work was focused on aflatoxins (AFB1, AFB2, AFG1, and AFG2) contamination levels of raw and roasted almond kernels consumed in Turkey. The exposure assessment of general Turkish population to AFs through the consumption of almonds was also assessed. This study underlines the importance of periodic monitoring studies to provide a high level of food safety. This is the first report on exposure to AFs through the consumption of almond kernels for Turkish consumers.
Evaluation of the effectiveness and usability of an educational portion size tool, ServARpreg, for pregnant women
Authors: Brown H. M. , Collins C. E. , Bucher T. , Rollo M. E. 
Published: April 2019

AbstractBackgroundElevated blood glucose levels in pregnancy increases the risk of adverse pregnancy outcomes. Modifying consumption of carbohydrate‐rich foods is important for blood glucose regulation; however, the tools commonly used to assist in guiding portion control are impractical. The present study aimed to evaluate usability of ServARpreg, a mobile phone‐based nutrition tool, and its effectiveness with respect to improving carbohydrate and standard serve size knowledge in pregnant women.MethodsA baseline survey assessed knowledge of carbohydrates and standard serve sizes of pregnant women. A subset of women living in Newcastle were invited to use ServARpreg, containing pregnancy nutrition information and augmented reality guidance on portion control. A follow‐up survey was sent to all women 4 weeks after baseline and women who received ServARpreg also received a process evaluation survey after 10 weeks.ResultsResponses were received from 186 pregnant women for the baseline survey, with 97 completing the follow‐up (52.2%). Of the 56 women eligible to receive ServARpreg in the sub‐study, 47 accepted (83.9%) and, of these, 40 completed the process evaluation survey (85.1%). At follow‐up, there was a significant group × time interaction in favour of the ServARpreg group for carbohydrate quantification knowledge (F1,279 = 9.705, P = 0.002). Standard serve size knowledge did not change between groups. In the process evaluation survey, 80% strongly agreed/agreed that ServARpreg made them more aware of how much they ate and 72.5% found ServARpreg easy to use.ConclusionsServARpreg has shown potential to educate pregnant women about carbohydrate quantification and increase portion size awareness. Further refinement of the tool and evaluation is needed to improve standard serve size knowledge.
What Became of Bruce the Shark? From Man‐Eating Monster to Savable Subject in Forty Years of Conservation
Authors: Nason Patrick 
Published: April 2019

AbstractForty years after Jaws, sharks have become savable subjects. Through public advocacy and personal adventures, shark conservationists claim these animals are not monstrous, but misunderstood. On rare occasions, the success of their advocacy is tempered by a fatal encounter, or “attack.” When this happens, multiple intentionalities emerge around the aesthetic category of the monstrous. Drawing on ethnographic and archival research in Western Australia, New England, and South Florida, this article examines these ways of being‐toward‐sharks in ongoing colonial contexts, and asks what is at stake when humans enter the sea alongside these large predatory animals.
The impact of the Affordable Care Act on provision of endodontic services within a dental school setting in Oregon
Authors: Peck Joseph , Sedgley Christine M. , Schwarz Eli , Replogle Karan J. 
Published: April 2019

AbstractObjectivesIn January 2014 implementation of the Medicaid expansion of the Affordable Care Act (EACA) in Oregon increased the number of children and adults qualifying for the Oregon Health Plan (OHP). Simultaneously, dental care benefits for adult Medicaid members were restored in Oregon after a period of noncoverage. This study evaluated the impact of these changes on the receipt of endodontic services in the Graduate Endodontic Clinic (GEC) at Oregon Health & Science University.MethodsA retrospective electronic health records (EHRs) database review was conducted from July 2010 through June 2017, a seven‐year period covering 3.5 years before (pre–EACA) and 3.5 years after (post–EACA) implementation of EACA. The number of completed anterior, premolar and molar non‐surgical root canal therapies (NS‐RCT) was retrieved from de‐identified EHRs by targeting dental codes. Pre– and post–EACA frequencies were compared and analyzed by patient age [<21 years (children) versus adults], payer mix [OHP versus non‐Medicaid (self‐pay and private insurance)], and tooth type (anterior, premolar and molar) using Chi‐square tests (P < 0.05).ResultsThe number of procedures provided for patients covered by OHP post–EACA compared to pre–EACA was increased by 363 percent. There was an 18 percent decline in NS‐RCT provided for non‐OHP patients (P < 0.0001). Post–EACA increases in frequency applied to anterior, premolar, and molar NS‐RCT (P < 0.0001), with the greatest increase in frequency post–EACA occurring for premolar NS‐RCT procedures (666 percent).ConclusionsBy eliminating barriers to care greater numbers of vulnerable people in Oregon sought and received endodontic services at the GEC.
Simultaneously inhibiting undecaprenyl phosphate production and peptidoglycan synthases promotes rapid lysis in Escherichia coli
Authors: Jorgenson Matthew A. , MacCain William J. , Meberg Bernadette M. , Kannan Suresh , Bryant Joseph C. , Young Kevin D. 
Published: April 2019

SummaryPeptidoglycan (PG) is a highly cross‐linked polysaccharide that encases bacteria, resists the effects of turgor and confers cell shape. PG precursors are translocated across the cytoplasmic membrane by the lipid carrier undecaprenyl phosphate (Und‐P) where they are incorporated into the PG superstructure. Previously, we found that one of our Escherichia coli laboratory strains (CS109) harbors a missense mutation in uppS, which encodes an enzymatically defective Und‐P(P) synthase. Here, we show that CS109 cells lacking the bifunctional aPBP PBP1B (penicillin binding protein 1B) lyse during exponential growth at elevated temperature. PBP1B lysis was reversed by: (i) reintroducing wild‐type uppS, (ii) increasing the availability of PG precursors or (iii) overproducing PBP1A, a related bifunctional PG synthase. In addition, inhibiting the catalytic activity of PBP2 or PBP3, two monofunctional bPBPs, caused CS109 cells to lyse. Limiting the precursors required for Und‐P synthesis in MG1655, which harbors a wild‐type allele of uppS, also promoted lysis in mutants lacking PBP1B or bPBP activity. Thus, simultaneous inhibition of Und‐P production and PG synthases provokes a synergistic response that leads to cell lysis. These findings suggest a biological connection that could be exploited in combination therapies.
Characterizing standard genetic parts and establishing common principles for engineering legume and cereal roots
Authors: Feike Doreen , Korolev Andrey V. , Soumpourou Eleni , Murakami Eiichi , Reid Dugald , Breakspear Andrew , Rogers Christian , Radutoiu Simona , Stougaard Jens , Harwood Wendy A. , Oldroyd Giles E. D. , Miller J. Benjamin 
Published: April 2019

SummaryPlant synthetic biology and cereal engineering depend on the controlled expression of transgenes of interest. Most engineering in plant species to date has relied heavily on the use of a few, well‐established constitutive promoters to achieve high levels of expression; however, the levels of transgene expression can also be influenced by the use of codon optimization, intron‐mediated enhancement and varying terminator sequences. Most of these alternative approaches for regulating transgene expression have only been tested in small‐scale experiments, typically testing a single gene of interest. It is therefore difficult to interpret the relative importance of these approaches and to design engineering strategies that are likely to succeed in different plant species, particularly if engineering multigenic traits where the expression of each transgene needs to be precisely regulated. Here, we present data on the characterization of 46 promoters and 10 terminators in Medicago truncatula, Lotus japonicus, Nicotiana benthamiana and Hordeum vulgare, as well as the effects of codon optimization and intron‐mediated enhancement on the expression of two transgenes in H. vulgare. We have identified a core set of promoters and terminators of relevance to researchers engineering novel traits in plant roots. In addition, we have shown that combining codon optimization and intron‐mediated enhancement increases transgene expression and protein levels in barley. Based on our study, we recommend a core set of promoters and terminators for broad use and also propose a general set of principles and guidelines for those engineering cereal species.
Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection
Authors: Wu Shan , Wang Xin , Reddy Umesh , Sun Honghe , Bao Kan , Gao Lei , Mao Linyong , Patel Takshay , Ortiz Carlos , Abburi Venkata L. , Nimmakayala Padma , Branham Sandra , Wechter Pat , Massey Laura , Ling Kai‐Shu , Kousik Chandrasekar , Hammar Sue A. , Tadmor Yaakov , Portnoy Vitaly , Gur Amit , Katzir Nurit , Guner Nihat , Davis Angela , Hernandez Alvaro G. , Wright Chris L. , McGregor Cecilia , Jarret Robert , Zhang Xingping , Xu Yong , Wehner Todd C. , Grumet Rebecca , Levi Amnon , Fei Zhangjun 
Published: April 2019

SummaryYears of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.
Transcriptome analysis reveals regulation of gene expression during photoacclimation to high irradiance levels in Dunaliella salina (Chlorophyceae)
Authors: Li Yuanxiang , Gu Wenhui , Huang Aiyou , Xie Xiujun , Wu Songcui , Wang Guangce 
Published: April 2019

SUMMARYThe unicellular green alga Dunaliella salina is an attractive organism for studying photoacclimation responses. Changes in irradiance level during cell growth affect the organization and structure of the photosystem and the composition of pigments. In this study, D. salina was exposed to different irradiance levels, and cell growth, photosynthetic activity, pigments, and neutral lipids were analyzed. Photosystem II activity and chlorophyll content were reduced, carotenoids content and neutral lipids increased as light intensity increased, suggesting that photosynthetic apparatus was reduced and photoprotection mechanisms were activated. The RNA of D. salina was sequenced to investigate the transcriptomic response of the organism after transitioning from normal light conditions to higher light intensity. Genes encoding for enzymes involved in photosynthesis were downregulated, whereas genes involved in the metabolism of carotenoid and triacylglycerol were upregulated. Genes encoding for photoprotective enzymes related to reactive oxygen species scavenging and to the xanthophyll cycle were also upregulated at higher irradiance levels. The present transcriptomic study would assist in the comprehensive understanding of photoacclimation mechanisms of D. salina.
Secondary self‐deception
Authors: Jordan Maiya 
Published: April 2019

AbstractAccording to doxastic accounts of self‐deception, self‐deception that P yields belief that P. For doxastic accounts, the self‐deceiver really believes what he, in self‐deception, professes to believe. I argue that doxastic accounts are contradicted by a phenomenon that often accompanies self‐deception. This phenomenon – which I term ‘secondary deception’ – consists in the self‐deceiver's defending his professed (deceit‐induced) belief to an audience by lying to that audience. I proceed to sketch an alternative, non‐doxastic account of how we should understand self‐deception in terms of the self‐deceiver's misrepresentation of himself as believing that P.
Phylogenetic relationships in the genus Lethrus (Coleoptera: Geotrupidae) reveal contrasting evolutionary history in Europe
Authors: Tóth János P. , Bereczki Judit , Rácz Rita , Varga Zoltán , Barta Zoltán , Sramkó Gábor 
Published: April 2019

AbstractIn this study we analysed for the first time the phylogenetic relationships among the European Lethrus species based on mitochondrial (COI, 16S) and nuclear (H3, wingless) markers. The phylogenetic inference based on these genes indicated that the European Lethrus species form a monophyletic group with two main lineages. One of them is distributed in the central part of the Balkan Peninsula (North Macedonia, northwestern Greece and southwestern Bulgaria) and includes five species (L. perun, L. raymondi, L. strymonensis, L. halkidikiensis and L. elephas). Three species of the other clade (L. schaumii, L. ares and L. schneideri) occur in the eastern part of the Balkan Peninsula (southeastern Bulgaria and northeastern Greece) while its fourth member, L. apterus, could colonize much larger areas in central and eastern Europe. Despite its large geographic distribution, L. apterus proved to be a single species. By contrast, we found strong intraspecific differentiation in both L. schaumii and L. halkidikiensis in spite of their restricted distribution. Surprisingly, two highly divergent mitogroups were also detected within a single L. schneideri population. As the microsatellite markers did not show any differentiation between them, this finding is likely to be accounted for by a unidirectional hybridization event. These findings highlight that phylogenetic studies or species descriptions should not be based on mitochondrial markers alone. Our study clearly demonstrates that allopatric speciation is the most important speciation mechanism in the European species of the genus Lethrus, although we also hypothesize that other well‐known factors, such as hybridization or the glacial‐interglacial dynamics, could significantly affect the speciation patterns of certain lineages.
The historical topography of the Battle of Hastings: A geographical reconstruction
Authors: Hewitt Christopher Macdonald 
Published: April 2019

AbstractIn 1066, English and Norman forces engaged in a decisive battle near Hastings. The battlefield itself provides an example of the way in which physical geography can contribute to our understanding of historical events. According to historical accounts, the rolling landscape of the Hastings battle site was unquestionably an important factor in understanding the conflict. Yet surprisingly few analyses of the local terrain exist to test this proposition. In part, this is because historians of the battle have largely affirmed that the current battle site bears little or no physical resemblance to that present in 1066, and thus is unsuitable for contemporary analysis that might shed light on the outcome of the battle itself. By applying advanced geographical analysis using the RUSLE model, this study demonstrates that there is in fact considerable evidence to suggest that a limited amount of sediment was removed, hence the battlefield has in fact changed very little since the battle. This finding is significant, insofar as it opens the door to new research on the Battle of Hastings which may shed additional light on the events that occurred there and the factors that influenced the outcome of this key conflict in British history.
Retrospective evaluation of the route and timing of nutrition in dogs with septic peritonitis: 68 cases (2007–2016)
Authors: Smith Kristin M. , Rendahl Aaron , Sun Yiwen , Todd Jeffrey M. 
Published: April 2019

AbstractObjectiveTo determine the impact of route of nutrition on length of hospitalization and survival to discharge in dogs with septic peritonitis.DesignRetrospective study from 2007 to 2016.SettingUniversity teaching hospital.AnimalsSixty‐eight dogs with septic peritonitis that survived ≥48 hours.InterventionsNone.Measurements and Main ResultsNutritional strategy was categorized into 1 of 4 groups: voluntary, feeding tube, parenteral (PN), and combined feeding tube and PN. Body weight, body condition score, time without caloric intake before and during hospitalization, length of hospitalization, and percentage of resting energy requirements provided during the first 3 days of nutritional support were recorded. Overall, 54/68 dogs survived (79%). Survival Prediction Index 2 scores were not significantly different between groups. Dogs receiving PN only were less likely to survive than those receiving any enteral nutrition (OR 9.7; 95CI 1.84–58.75). Compared to dogs not receiving PN, dogs receiving any PN were significantly less likely to survive (OR 9.66; 95% CI 1.7–105.8), and were in hospital significantly longer (P = 0.025). Metabolic complications associated with PN were frequent but not associated with increased length of hospitalization or survival to discharge.ConclusionsDogs with septic peritonitis that received any PN were in hospital longer and less likely to survive but may have been sicker than those receiving other forms of nutritional support. Further studies are warranted to evaluate reasons for worse outcomes in dogs with septic peritonitis receiving PN.