bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving allele dosage in duplicated loci using genotyping‐by‐sequencing data: A path forward for population genetic analysis
Authors: McKinney Garrett J. , Waples Ryan K. , Pascal Carita E. , Seeb Lisa W. , Seeb James E. 
Published: February 2018

AbstractWhole‐genome duplications have occurred in the recent ancestors of many plants, fish and amphibians. Signals of these whole‐genome duplications still exist in the form of paralogous loci. Recent advances have allowed reliable identification of paralogs in genotyping‐by‐sequencing (GBS) data such as that generated from restriction‐site‐associated DNA sequencing (RADSeq); however, excluding paralogs from analyses is still routine due to difficulties in genotyping. This exclusion of paralogs may filter a large fraction of loci, including loci that may be adaptively important or informative for population genetic analyses. We present a maximum‐likelihood method for inferring allele dosage in paralogs and assess its accuracy using simulated GBS, empirical RADSeq and amplicon sequencing data from Chinook salmon. We accurately infer allele dosage for some paralogs from a RADSeq data set and show how accuracy is dependent upon both read depth and allele frequency. The amplicon sequencing data set, using RADSeq‐derived markers, achieved sufficient depth to infer allele dosage for all paralogs. This study demonstrates that RADSeq locus discovery combined with amplicon sequencing of targeted loci is an effective method for incorporating paralogs into population genetic analyses.
Impacts of licensed premises trading hour policies on alcohol‐related harms
Authors: Atkinson Jo‐An , Prodan Ante , Livingston Michael , Knowles Dylan , O'Donnell Eloise , Room Robin , Indig Devon , Page Andrew , McDonnell Geoff , Wiggers John 
Published: February 2018

AbstractBackground and aimEvaluations of alcohol policy changes demonstrate that restriction of trading hours of both ‘on’‐ and ‘off’‐licence venues can be an effective means of reducing rates of alcohol‐related harm. Despite this, the effects of different trading hour policy options over time, accounting for different contexts and demographic characteristics, and the common co‐occurrence of other harm reduction strategies in trading hour policy initiatives, are difficult to estimate. The aim of this study was to use dynamic simulation modelling to compare estimated impacts over time of a range of trading hour policy options on various indicators of acute alcohol‐related harm.MethodsAn agent‐based model of alcohol consumption in New South Wales, Australia was developed using existing research evidence, analysis of available data and a structured approach to incorporating expert opinion. Five policy scenarios were simulated, including restrictions to trading hours of on‐licence venues and extensions to trading hours of bottle shops. The impact of the scenarios on four measures of alcohol‐related harm were considered: total acute harms, alcohol‐related violence, emergency department (ED) presentations and hospitalizations.ResultsSimulation of a 3 a.m. (rather than 5 a.m.) closing time resulted in an estimated 12.3 ± 2.4% reduction in total acute alcohol‐related harms, a 7.9 ± 0.8% reduction in violence, an 11.9 ± 2.1% reduction in ED presentations and a 9.5 ± 1.8% reduction in hospitalizations. Further reductions were achieved simulating a 1 a.m. closing time, including a 17.5 ± 1.1% reduction in alcohol‐related violence. Simulated extensions to bottle shop trading hours resulted in increases in rates of all four measures of harm, although most of the effects came from increasing operating hours from 10 p.m. to 11 p.m.ConclusionsAn agent‐based simulation model suggests that restricting trading hours of licensed venues reduces rates of alcohol‐related harm and extending trading hours of bottle shops increases rates of alcohol‐related harm. The model can estimate the effects of a range of policy options.
Exploring wildlife predation in the Limpopo Province of South Africa: A double‐hurdle approach
Authors: Schepers Anché , Matthews Nicolette , van Niekerk Hermias Nieuwoudt 
Published: February 2018

AbstractPredation is a well‐known problem in South Africa with large losses in the small and large livestock sectors. Predation in the wildlife ranching industry has also become more of a concern, as the financial losses due to predation on valuable antelope species are large. Predation data for small, large, and scarce/colour‐variant antelope species were collected using a structured questionnaire from wildlife ranchers in the Limpopo province, South Africa. We explore the factors that influence predation on these species by determining whether the perceptions of predation and consequent managerial decisions affect predation. The use of nonlethal control methods can be successfully employed to reduce the probability of predation occurrences, however, a combination of lethal and nonlethal control methods were used to reduce the level of predation. The type of antelope species will determine the type of predation control method to be employed. Therefore, the antelope species should be taken into account when making predation management decisions.
A camera trap assessment of the forest mammal community within the transitional savannah‐forest mosaic of the Batéké Plateau National Park, Gabon
Authors: Hedwig Daniela , Kienast Ivonne , Bonnet Matthieu , Curran Bryan K. , Courage Amos , Boesch Christophe , Kühl Hjalmar S. , King Tony 
Published: February 2018

AbstractMonitoring populations in areas of ecological transition is crucial to understanding species distributions, but also a critical conservation tool. We used camera trapping to investigate the forest mammal community in the Batéké Plateau National Park (BPNP) in Gabon, a transitional landscape that experiences severe poaching. We compiled a species inventory, investigated group sizes and activity patterns of observed species, and conducted an initial test to evaluate whether ecological gradients within this landscape influence species occurrence. Based on 6612 images and videos recorded at 40 locations during 5,902 camera days, we identified 31 mammal species, including eight classified as threatened according to the IUCN. We detected lion (Panthera leo, Linnaeus), which was thought to be extinct in Gabon, and mandrill (Mandrillus sphinx, Linnaeus), for which BPNP was thought to be outside of their natural range. Our findings suggest that BPNP supports a low species richness compared to more forested protected areas. We found no changes in species composition of the forest mammal community with increasing distance from the continuous Gabonese rainforest, but a potential decrease in abundance for some species. Continued survey efforts need to be combined with detailed ecological data collection and effective law enforcement in the region.
An intriguing, new planarian species from Tasmania, with a discussion on protandry in triclad flatworms (Platyhelminthes, Tricladida)
Authors: Sluys Ronald , Vila‐Farré Miquel , Rink Jochen , Rasko John E. J. 
Published: February 2018

AbstractAn account is given of an unusual new species of freshwater planarian from the Hartz Mountains in Tasmania, Australia, Romankenkius flaccidus Sluys, sp. nov. The species is characterized, among other features, by an asymmetrical penis papilla, an extremely large, elongated copulatory bursa, and by the absence of testes in animals with fully developed male and female copulatory apparatus. Instigated by the sexual cycle of this new species, the study opportunely reviews whether planarian flatworms generally are simultaneous or sequential—in particular protandrous—hermaphrodites. It is concluded that real protandry does not occur in triclads and that even less extreme cases of sexual segregation, such as complete reduction of the testes or the more or less complete separation of male and female functionality as present in some species, have only sparsely and convergently evolved within the group of the triclad flatworms.
Placental structures and their association with matrotrophy and superfetation in poeciliid fishes
Authors: Olivera‐Tlahuel Claudia , Moreno‐Mendoza Norma A. , Villagrán‐Santa Cruz Maricela , Zúñiga‐Vega J. Jaime 
Published: February 2018

AbstractBoth matrotrophy, the maternal provisioning of nutrients to developing embryos after fertilization, and superfetation, the simultaneous presence of two or more groups of embryos at different stages of development, occur at varying degrees among species of the fish family Poeciliidae. However, it is still unclear if these two reproductive modes depend on the presence of relatively complex placentas. We describe the ultrastructure of the maternal follicular placenta of 11 poeciliid fishes using electron microscopy. In addition, we quantified six ultrastructure characteristics that reflect the degree of complexity (number of vesicles, area of vesicles, number of microvilli, microvilli length, thickness of the maternal follicle and follicular area). Using phylogenetic comparative methods, we evaluated the relationship between degree of matrotrophy and placental characteristics. We also analysed the potential effect of the presence of superfetation on placental complexity. We found a positive relationship between the degree of matrotrophy and follicular area, number of microvilli and number and area of vesicles. Similarly, follicular area and number of microvilli were larger in species with superfetation than in those without superfetation. We conclude that high degrees of matrotrophy and superfetation are associated with placental characteristics that increase the efficiency of nutrient transfer between mother and embryos.
Functional interplay between liver X receptor and AMP‐activated protein kinase α inhibits atherosclerosis in apolipoprotein E‐deficient mice − a new anti‐atherogenic strategy
Authors: Ma Chuanrui , Zhang Wenwen , Yang Xiaoxiao , Liu Ying , Liu Lipei , Feng Ke , Zhang Xiaomeng , Yang Shu , Sun Lei , Yu Miao , Yang Jie , Li Xiaoju , Hu Wenquan , Miao Robert Q , Zhu Yan , Li Luyuan , Han Jihong , Chen Yuanli , Duan Yajun 
Published: February 2018

Background and PurposeThe liver X receptor (LXR) agonist T317 reduces atherosclerosis but induces fatty liver. Metformin activates energy metabolism by activating AMPKα. In this study, we determined if interactions between metformin and T317 could inhibit atherosclerosis without activation of hepatic lipogenesis.Experimental ApproachApolipoprotein E‐deficient mice were treated with T317, metformin or both agents, in a high‐fat diet for 16 weeks. Then, samples of aorta, liver, macrophage and serum were collected to determine atherosclerotic lesions, fatty liver, lipid profiles and expression of related proteins. Techniques used included immunohistochemistry, histology, qRT‐PCR and Western blot.Key ResultsT317 inhibited en face and aortic root sinus lesions, and the inhibition was further enhanced by addition of metformin. Co‐treatment with metformin and T317 increased lesion stability, by increasing collagen content, and reducing necrotic cores and calcification. Formation of macrophages/foam cells and their accumulation in arterial wall were inhibited by the co‐treatment, which was accompanied by increased ABCA1/ABCG1 expression, reduced monocyte adhesion and apparent local proliferation of macrophages. Metformin blocked T317‐induced fatty liver by inhibiting T317‐induced hepatic LXRα nuclear translocation and expression of lipogenic genes and by activating AMPKα. Moreover, co‐treatment with T317 and metformin improved triglyceride metabolism by inducing expression of adipose triglyceride lipase, hormone‐sensitive lipase, PPARα and carnitine acetyltransferase and by inhibiting acyl‐CoA:diacylglycerol acyltransferase 1 expression.Conclusions and ImplicationsCo‐treatment with T317 and metformin inhibited the development of atherosclerosis without activation of lipogenesis, suggesting that combined treatment with T317 and metformin may be a novel approach to inhibition of atherosclerosis.
Cell cycle‐related and expression‐elevated protein in tumor overexpression is associated with proliferation behaviors and poor prognosis in non‐small‐cell lung cancer
Authors: Li Weimiao , Zheng Guoxu , Xia Jinghua , Yang Guang , Sun Jianyong , Wang Xuejiao , Wen Miaomiao , Sun Ying , Zhang Zhipei , Jin Faguang 
Published: February 2018

The cell cycle‐related and expression‐elevated protein in tumor (CREPT) is overexpressed in several human malignancies. However, the clinical relevance of CREPT expression and its biological role in non‐small‐cell lung cancer (NSCLC) remains unclear. In this study, we detected the expression of CREPT in both NSCLC tissues and cell lines by immunohistochemistry, Western blot analysis, and RT‐PCR. The correlation between CREPT expression and clinicopathologic features was analyzed in 271 NSCLC patients. The prognostic value of CREPT expression was evaluated by Kaplan–Meier analysis and Cox regression analysis. CREPT was overexpressed in Calu‐1 cell lines by using plasmid vector and its biological function was explored both in vitro and in vivo. We found that CREPT was significantly overexpressed in NSCLC compared with paired adjacent non‐tumor tissues, and the expression level of CREPT was correlated with tumor differentiation, lymph node metastasis, and clinical stage. Kaplan–Meier analysis showed that the recurrence‐free survival and overall survival of high CREPT expression groups were significantly shorter than those of the low CREPT expression group. Multivariate analysis identified that CREPT might be an independent biomarker for the prediction of NSCLC prognosis. Overexpression of CREPT increased cell proliferation and enhanced the migration and invasion ability of Calu‐1 cells (a human NSCLC cell line with relative low CRPET expression) in vitro. Moreover, CREPT overexpression promoted tumor growth in a nude mice model. These results suggest that CREPT is closely relevant to the proliferation of NSCLC cells and it might be a potential prognostic marker in NSCLC patients.
Topical fluoride use: Knowledge, attitudes and practices of undergraduate dental students of three Dental Colleges in South India
Authors: Muralidharan D. , Pocha S. , Paul A. 
Published: February 2018

AbstractObjectivesFor effective utilisation of topical fluorides in caries prevention, dental professionals should have adequate knowledge regarding its appropriate use. The decision regarding preventive treatments like topical fluorides is influenced by knowledge acquired during undergraduate training. The aim of this study was to assess the knowledge, attitudes and practices of undergraduate dental students in the use of topical fluorides.MethodologyA descriptive cross‐sectional questionnaire study was conducted from June to August 2015 following ethical clearance. Three willing Dental Colleges from 3 states of South India participated. Information regarding the knowledge, attitudes and practices of students in the use of topical fluorides was collected using a validated questionnaire.ResultsNine hundred and seventy‐two dental students (79.6% females, 20.4% males) participated. Freshers and preclinical batches had poor overall knowledge of fluorides, which did not show substantial improvement by internship. Self‐applied topical fluoride use (fluoridated toothpaste) was seen in more than 90% of interns, and majority had “positive fluoride attitude.” Having knowledge of topical fluorides and positive attitudes to topical fluorides did not result in “good oral self‐care behaviour” nor appropriate clinical use of topical fluorides. Students who used topical fluorides for persons with history of caries had highest odds of brushing twice a day (OR = 2.7, 95% CI = 1.54, 4.12) and a “positive fluoride attitude” (OR = 1.2, 95% CI = 0.21, 1.57).ConclusionDental students showed deficiencies in their knowledge and understanding of topical fluorides. Dental education in India needs emphasis on topical fluorides across all years, with a special focus on caries risk‐based topical fluoride use.
Challenges in the transition to clinical training in dentistry: An ADEE special interest group initial report
Authors: Serrano C. M. , Botelho M. G. , Wesselink P. R. , Vervoorn J. M. 
Published: February 2018

AbstractIntroductionCurricular integration in higher education has been widely supported in the educational literature. As a result, several health care and specifically dental curricula have evolved from compartmentalised disciplinary training to integrated modalities; however, in many courses, a pre‐clinical‐clinical watershed remains a barrier to integration in dental education. This article introduces a general description of the pre‐clinical‐clinical transition in dentistry according to the outcomes of the discussion held during the first working group session of the “Transition to Clinical Training” Special Interest Group during the 2016 annual meeting of the Association for Dental Education in Europe.Materials and MethodsAn online questionnaire was made available before the meeting to survey the curricular characteristics of the participants’ schools. During the meeting, a working session related to the pre‐clinical‐clinical transition occurred. Conclusions from the discussion are summarised in this article.ResultsFourteen dental schools from 12 countries participated in the online survey. The included programmes had an average duration of 5.3 years (SD = 0.48), with high school or the local equivalent as the required entrance level for dentistry. The hybrid curriculum was the leading curriculum design (n = 9) followed by competence‐based curricula (n = 3), with patient treatment as the core of clinical training in every included programme.ConclusionThe pre‐clinical‐clinical transition in dentistry is a recognisable matter in dental education that requires assessment and research to ease the management of a stage with relevant influence on educational outcomes. This article presents an initial framework for further research and educational intervention.
Neuronal oscillations on an ultra‐slow timescale: daily rhythms in electrical activity and gene expression in the mammalian master circadian clockwork
Authors: Belle Mino D. C. , Diekman Casey O. 
Published: February 2018

AbstractNeuronal oscillations of the brain, such as those observed in the cortices and hippocampi of behaving animals and humans, span across wide frequency bands, from slow delta waves (0.1 Hz) to ultra‐fast ripples (600 Hz). Here, we focus on ultra‐slow neuronal oscillators in the hypothalamic suprachiasmatic nuclei (SCN), the master daily clock that operates on interlocking transcription‐translation feedback loops to produce circadian rhythms in clock gene expression with a period of near 24 h (< 0.001 Hz). This intracellular molecular clock interacts with the cell's membrane through poorly understood mechanisms to drive the daily pattern in the electrical excitability of SCN neurons, exhibiting an up‐state during the day and a down‐state at night. In turn, the membrane activity feeds back to regulate the oscillatory activity of clock gene programs. In this review, we emphasise the circadian processes that drive daily electrical oscillations in SCN neurons, and highlight how mathematical modelling contributes to our increasing understanding of circadian rhythm generation, synchronisation and communication within this hypothalamic region and across other brain circuits.
Antibacterial properties of silver nanoparticles as a root canal irrigant against Enterococcus faecalis biofilm and infected dentinal tubules
Authors: Rodrigues C. T. , de Andrade F. B. , de Vasconcelos L. R. S. M. , Midena R. Z. , Pereira T. C. , Kuga M. C. , Duarte M. A. H. , Bernardineli N. 
Published: February 2018

AbstractAimTo evaluate the antimicrobial action of an irrigant containing silver nanoparticles in an aqueous vehicle (AgNp), sodium hypochlorite and chlorhexidine against Enterococcus faecalis biofilm and infected dentinal tubules.MethodologyBovine dentine blocks were used for E. faecalis biofilm development for 21 days and irrigated with 94 ppm AgNp solution, 2.5% NaOCl and 2% chlorhexidine for 5, 15 and 30 min. For infection of dentinal tubules with E. faecalis, dentine specimens from bovine incisors were submitted to a contamination protocol over 5 days, with eight centrifugation cycles on every alternate day, and irrigated with the same solutions and time intervals used for the biofilm. The specimens were stained with the Live/Dead technique and evaluated using a confocal laser scanning microscope (CLSM). The bioImage_L software was used for measurement of the total biovolume of biofilm in μm3 and percentage of viable bacteria (green cells) in biofilm and in dentinal tubules found after the irrigation. Statistical analyses were performed using Kruskal–Wallis and Dunn's tests for quantification of viable cells in biofilm, the Friedman test for comparisons of viable bacteria in dentinal tubules in different areas of the root canal and the Mann–Whitney U‐test to compare the action of the irrigants between the two methods (P < 0.05).ResultsThe AgNp solution eliminated fewer bacteria, but was able to dissolve more biofilm compared with chlorhexidine (P < 0.05). NaOCl had the greatest antimicrobial activity and biofilm dissolution capacity. AgNp solution had less antimicrobial action in infected dentinal tubules compared with NaOCl (P < 0.05). The AgNp solution after 5 min was more effective in eliminating planktonic bacteria in dentinal tubules than in biofilm, but at 30 min fewer viable bacteria were observed in the biofilm compared with intratubular dentine (P < 0.05).ConclusionsAgNp irrigant was not as effective against E. faecalis compared to solutions commonly used in root canal treatment. NaOCl is appropriate as an irrigant because it was effective in disrupting biofilm and in eliminating bacteria in biofilms and in dentinal tubules.
Evaluation of the bioactivity of fluoride‐enriched mineral trioxide aggregate on osteoblasts
Authors: Proksch S. , Brossart J. , Vach K. , Hellwig E. , Altenburger M. J. , Karygianni L. 
Published: February 2018

AbstractAimTo investigate whether a combination of mineral trioxide aggregate (MTA) and fluoride compounds affects bone cells.MethodologyMineral trioxide aggregate (MTA) discs (ProRoot®, Dentsply Sirona, Ballaigues, Switzerland) with and without the addition of 0.1%, 0.25% and 0.5% sodium fluoride were characterized for their surface roughness by laser scanning microscopy and for the adhesion of human alveolar osteoblasts by scanning electron microscopy. Using eluates from fluoride‐enriched MTA discs, the cell proliferation was measured by monitoring the DNA incorporation of 5‐bromo‐2′‐deoxyuridine. Further, gene expression was evaluated by qPCR arrays, extracellular matrix mineralization was quantified by absorption measurement of Alizarin red stains, and effects were calculated with repeated measures analysis and post hoc P‐value adjustment.ResultsIrrespective of fluoride addition, cell adhesion was similar on MTA discs, of which the surface roughness was comparable. Control osteoblasts had a curvilinear proliferation pattern peaking at d5, which was levelled out by incubation with MTA. The addition of fluoride partly restored the MTA‐related reduction in the cellular proliferation rate in a dose‐dependent manner. At the mRNA level, both fluoride and MTA modulated a number of genes involved in osteogenesis, bone mineral metabolism and extracellular matrix formation. Although MTA significantly impaired extracellular matrix mineralization, the addition of fluoride supported the formation of mineralized nodules in a dose‐dependent manner.ConclusionThe addition of fluoride modulated the biocompatibility of MTA in terms of supporting bone cell proliferation and hard tissue formation. Hence, fluoride enrichment is a trend‐setting advancement for MTA‐based endodontic therapies.