bluuebunny/crossref_metadata_2025 huggingface dataset:
Definition of sampling units begets conclusions in ecology: the case of habitats for plant communities
Authors: Mörsdorf Martin A , Ravolainen Virve T. , Støvern Leif Einar , Yoccoz Nigel G. , Jónsdóttir Ingibjörg S. , Bråthen Kari Anne
Published: January 2018

In ecology, expert knowledge on habitat characteristics is often used to define sampling units such as study sites. Ecologists are especially prone to such approaches when prior sampling frames are not accessible. Here we ask to what extent can different approaches to the definition of sampling units influence the conclusions that are drawn from an ecological study? We do this by comparing a formal versus a subjective definition of sampling units within a study design which is based on well-articulated objectives and proper methodology. Both approaches are applied to tundra plant communities in mesic and snowbed habitats. For the formal approach, sampling units were first defined for each habitat in concave terrain of suitable slope using GIS. In the field, these units were only accepted as the targeted habitats if additional criteria for vegetation cover were fulfilled. For the subjective approach, sampling units were defined visually in the field, based on typical plant communities of mesic and snowbed habitats. For each approach, we collected information about plant community characteristics within a total of 11 mesic and seven snowbed units distributed between two herding districts of contrasting reindeer density. Results from the two approaches differed significantly in several plant community characteristics in both mesic and snowbed habitats. Furthermore, differences between the two approaches were not consistent because their magnitude and direction differed both between the two habitats and the two reindeer herding districts. Consequently, we could draw different conclusions on how plant diversity and relative abundance of functional groups are differentiated between the two habitats depending on the approach used. We therefore challenge ecologists to formalize the expert knowledge applied to define sampling units through a set of well-articulated rules, rather than applying it subjectively. We see this as instrumental for progress in ecology as only rules based on expert knowledge are transparent and lead to results reproducible by other ecologists.
Using network clustering to predict copy number variations associated with health disparities
Authors: Jiang Yi , Qin Hong HQ , Yang Li
Published: January 2018

Substantial health disparities exist between African Americans and Caucasians in the United States. Copy number variations (CNVs) are one form of human genetic variations that have been linked with complex diseases and often occur at different frequencies among African Americans and Caucasian populations. Here, we aimed to investigate whether CNVs with differential frequencies can contribute to health disparities from the perspective of gene networks. We inferred network clusters from human gene/protein networks based on two different data sources. We then evaluated each network cluster for the occurrences of known pathogenic genes and genes located in CNVs with different population frequencies, and used false discovery rates to rank network clusters. This approach let us identify five clusters enriched with known pathogenic genes and with genes located in CNVs with different frequencies between African Americans and Caucasians. These clustering patterns predict two candidate causal genes located in four population-specific CNVs that play potential roles in health disparities
Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen
Authors: Simeonov Kamen P. , Himmelstein Daniel S.
Published: January 2018

The atmospheric concentration of oxygen, a driver of free radical damage and tumorigenesis, decreases sharply with rising elevation. To understand whether ambient oxygen concentrations play a role in human carcinogenesis, we characterized age-adjusted cancer incidence (compiled by the National Cancer Institute from 2005–2009) across counties of the elevation-varying Western United States and compared trends displayed by respiratory cancer (lung) and non-respiratory cancers (breast, colorectal, and prostate). To adjust for important demographic and cancer-risk factors, 8–12 covariates were considered for each cancer. We produced sensible regression models that captured known risks. Models demonstrated that elevation strongly, negatively associates with lung cancer incidence (p < 10−16), but not with incidence of non-respiratory cancers. For every 1000 meter rise in elevation, lung cancer incidence decreased by 7.23 [99% CI: 5.18–9.29] cases per 100,000 individuals, equivalent to 12.7% of the mean incidence, 56.8. As a predictor of lung cancer incidence, elevation was second only to smoking prevalence in terms of significance and effect size. Furthermore, no evidence of uncontrolled confounding or ecological fallacy was detected: the lung cancer association was robust to varying regression models, county stratification, and population subgrouping; additionally seven environmental correlates of elevation, such as exposure to sunlight and fine particulate matter, could not capture the association. Overall, our findings suggest the presence of an inhaled carcinogen inherently and inversely tied to elevation, offering epidemiological support for oxygen-driven tumorigenesis. Finally, highlighting the need to consider elevation in studies of lung cancer, we demonstrated that previously reported inverse lung cancer associations with radon and UVB became insignificant after accounting for elevation.
Interethnic diversity of the CD209 (rs4804803) gene promoter polymorphisms in African but not American sickle cell disease
Authors: Noble Jenelle A , Duru Kimberley C , Guindo Aldiouma , Yi Li , Diallo Dapa A , Thomas Bolaji
Published: January 2018

Elucidating the genomic diversity of CD209 gene promoter polymorphisms could assist in clarifying disease pathophysiology as well as contribution to co-morbidities. CD209 gene promoter polymorphisms have been shown to be associated with susceptibility to infection. We hypothesize that CD209 mutant variants occur at a higher frequency among Africans and in sickle cell disease. We analyzed the frequency of the CD209 gene (rs4804803) in healthy control and sickle cell disease (SCD) populations and determined association with disease. We obtained genomic DNA from 145 SCD and 244 control Africans (from Mali), 331 SCD and 379 control African Americans and 159 Caucasians. Comparative analysis among and between groups was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Per ethnic diversification, we found significant disparity in genotypic (23.4% versus 16.9% versus 3.2%) and allelic frequencies (36.1% versus 25.1% versus 11.6%) of the mutant variant of the CD209 (snp 309A/G) gene promoter between Africans, African Americans and Caucasians respectively. Surprisingly, there was a wide disparity in the genotypic and allelic frequencies among African SCD versus healthy controls (10.4% versus 23.4% (genotypes) and 25.2% versus 36.1% (alleles), which is completely absent among African Americans. Comparing SCD groups, there was no difference between Africans and Americans, implying a lack of association between CD209 polymorphisms and sickle cell disease in either population. The higher frequency of CD209 mutant variants in the non-SCD group reveals an impaired capacity to mount an immune response to infectious diseases. We conclude that CD209 polymorphism play a major role in susceptibility to infectious pathogens and could potentially delineate susceptibility to and severity of co-morbidities.
Continued Dispensing: What medications do patients believe should be available?
Authors: Abukres Salem Hasn , Hoti Kreshnik. , Hughes Jeffery David
Published: January 2018

Background. Continued Dispensing (CD) is a new medication supply method for certain medications in Australia. It aims to prevent treatment interruption as a result of patients’ inability to obtain a new valid prescription. The only currently eligible patients for this service are statin and oral contraceptive users who are: using these medications for 6 months or more, did not utilise the CD method during the last 12 months, and cannot obtain an immediate appointment with the prescriber in order to get a new prescription. This study aimed to investigate patients’ attitudes towards potential extension and expansion of this medication supply method. Methods. A randomly selected 301 users of these medications from all Australian States were recruited using Computer Assisted Telephone Interview (CATI). Result. The majority of the participants (73.3%) did not agree with current restriction on CD utilisation frequency. They also supported, to varying degrees, inclusion of all the proposed medications (support ranged from 44.2 - 78.4%). Participants who suffered from a specific disease did not differ significantly from those without the disease except in case of patients with depression (p= 0.001 ). Conclusions. Participants of this study strongly supported both CD extension and expansion. A critical review of the current version of CD is highly recommended in order to enhance CD capability to achieve its goals.
Socioeconomic status and health inequalities among older people from Bangladeshi ethnic minority group in England
Authors: Hossain Muhammad Z
Published: January 2018

The study aims to examine what socio-economic, health and psychological problems of older Bangladeshi (55 years and older) experience in later life and what members of the Bangladeshi community perceive to be the reasons for these difficulties. It also aims at finding out the extent to which gerontological theories, that highlight the problems associated with later life, reflect the experiences of older people across ethnic and cultural differences in the United Kingdom. The research has been carried out in the London Borough of Croydon where a small number of
Bangladeshi communities live. Semi-structured interviews were conducted with older people from the mixer of men and women so as to answer the above research question i.e. the problems and the effects of ageing process far from home where they made their later life abode. In a qualitative semi - structured interview study in the London Borough of Croydon, 17 older persons from the Bangladeshi communities were asked about their problems of ageing and how they feel about living and growing old in a western country.
Combining Weight-Length Relationships and condition factors to estimate the population structure for Skipjack tuna in the Western and Central Pacific Ocean
Authors: Jin Shaofei , Yan Xiaodong , Zhang Heng , Fan Wei
Published: January 2018

The arguments between Weight-Length Relationship (WLR) and Condition Factor (K) have been lasted since the day they occurred. This paper described WLRs and Ks of Skipjack tuna (Katsuwonus pelamis) samples in Purse Seine fisheries from three cruises (August-September cruise (A-S) in 2009, November-December cruise (N-D) in 2012, and June-July cruise (J-J) in 2013) in the Central and Western Pacific Ocean (CWPO). The results showed that fork length of more than 70% of specimen was below 60 cm (76% in A-S, 87% in N-D, and 73% in J-J). b values of WLRs in class of fork length > 60cm were below 3 significantly (P = 0.062), while b values when fork length < 60 cm were > 3 significantly (P = 0.028). Moreover, K values in different fork length classes for each cruises had one turning point: 60-65cm for J-J, 60-65cm for N-D, and 55-60cm for A-S, and K values were still significantly larger than those of fork length < 40cm (P = 0.06). However, b values at larger fishes were significantly smaller than those of fork length <40cm. We suggest to combine WLRs and K values at different growth phases for evaluating population structure for skipjack tuna.
Predictors of health care utilization in young children with recurrent pain – a population-based study
Authors: Hirschfeld Gerrit , Wager Julia , Zernikow Boris
Published: January 2018

Background: Recurrent pain is a common experience in childhood, but only few children with recurrent pain attend a physician. Previous small-scale studies yielded conflicting findings with regard to predictors of health care utilization in children with recurrent pain. Methods: The present study analyzes a subset of the data from the German Health Interview and Examination Survey for Children and Adolescents (KiGGS) study. Specifically, our sample comprised n= 2,149 young children (3-10 years old) with recurrent pain to find robust predictors. We used multiple logistic regressions to investigate age, gender, SES, migration background, pain intensity, pain frequency, pain-related disability, somatic symptoms, HRQL, as predictors for visiting a doctor due to pain. Additionally we investigated the variability of the predictors to assess the sample size needed to make reliable claims about predictors of health-care utilization. Results: Overall, 1144 (53%) children consulted a physician due to recurrent pain. Young girls with high pain-related disability, -intensity, –frequency, and migration background were more likely to attend a physician. Pain-related disability had the largest impact. Socioeconomic status, health-related quality of life and somatic symptoms were not systematically related to health care utilization. An analysis of the variability of these results indicated that several hundred participants are needed until the results stabilize. Conclusions: Our findings highlight the importance of pain-related disability and frequency in assessing the severity of recurrent pain. Generic predictors and demographic variables are of lesser relevance to children with recurrent pain. On a methodological level our results show that large-scale population-based studies are need to reliably identify predictors of health care utilization.
Validating the use of a dumbbell to measure body sway in female Olympic air pistol shooting
Authors: Mon Daniel , Zakynthinaki Maria , Cordente-Martinez Carlos A.
Published: January 2018

The present study validates use of a dumbbell to simulate the air pistol in female Olympic shooting, examining, at the same time, the relation between body sway and performance. The study’s participants were 23 senior female Olympic pistol shooters who competed at a Spanish air pistol championship. The participants’ performance was measured at competition while their COP movements were recorded during two static bipodal balance tests which were performed the day previous to the competition, during the official training time and at the training stands. During one of the tests a 1.5 kg dumbbell was used to simulate the pistol. The calculated Pearson product moment correlations for all variables that refer to the movement of the COP revealed statistically significant correlations between the two tests. Statistically significant inverse linear correlations were also found between performance and COP movements regarding both tests: strong correlations regarding COP movement amplitudes and moderate correlations regarding COP velocities. The study concludes that a) a dumbbell can be validly used to simulate the pistol in female Olympic air pistol shooting, and b) specific balance training programs should be taken into account in order to improve performance in female air pistol shooting.
The biter bit? Investigation of possible in-ovo self-envenomation in an Egyptian saw-scaled viper using region of interest X-ray microtomography
Authors: Johnston Richard E , Mulley John
Published: January 2018

Proven examples of self-envenomation by venomous snakes, and especially instances of death as a result of these events, are extremely rare, if not non-existent. Here we use Region of Interest X-ray microtomography to investigate a putative case of fatal in-ovo self-envenomation in the Egyptian saw-scaled viper, Echis pyramidum. Our analyses have provided unprecedented insight into the skeletal anatomy of a late-stage embryonic snake and the disposition of the fangs without disrupting or destroying a unique biological specimen.
Comparing size of morphospace occupation among extant and cretaceous fossil freshwater mussels using Elliptical Fourier Analysis
Authors: Burton-Kelly Matt , Hartman Joseph H
Published: January 2018

Background. Freshwater mussels of superfamily Unionoidea are a diverse group with an evolutionary history of at least 360 million years. Many fossil and modern species exhibit a generally unsculptured, roughly elliptical shell outline. Such morphology results in difficulties when attempting to identify or classify fossil material, as only hard parts are preserved. Several latest-Cretaceous fossil localities over a small geographic area in southwestern North Dakota contain poorly preserved edentulous freshwater mussels that effectively lack all but shell outlines. This paper discusses methods that were used to attempt to determine how many fossil taxa were present in one of these assemblages. Methods. Elliptical Fourier Analysis was performed on two-dimensional shell outlines of both edentulous fossils and modern taxa to create Fourier scores representing outline shape. Morphospace occupation, or the amount of variation within a sample of shell outlines, was calculated using two methods: within-group dispersion and sum of variance. Morphospace occupation was compared among each of the modern taxa (at both generic and specific levels) and fossil assemblage using confidence intervals, ANOVA, and Tukey’s HSD tests. Results. The amount of outline variation within the fossil assemblage tested is more than some modern genera and species and less than others. Morphospace occupation and confidence intervals are defined for the modern taxa (nine genera and 24 species) that were examined. Discussion. Although results were inconclusive, discussion points are presented to drive future research. Methodological improvements are suggested including choice of extant (comparative) genera, ontogeny and size, morphological plasticity, phenotypic convergence, taphonomic deformation, and general geometric morphometrics.
Comment on “Chemically mediated behavior of recruiting corals and fishes: A tipping point that may limit reef recovery”
Authors: Baird Andrew H , Cumbo Vivian R , Figueiredo Joana , Harii Saki , Hata Tom , Madin Joshua S
Published: January 2018

Dixson et al. (2014) report that coral larvae navigate towards chemical cues associated with healthy reefs and avoid cues from degraded reefs. However, the swimming capabilities of coral larvae and well-established patterns of recruitment and reef hydrodynamics indicate that coral larvae will not be able to use these cues to recruit to healthy reefs. Perfuming degraded reefs, as suggested by Dixson et al (2014), will not enhance recovery rather it will distract from the difficult task of reducing fishing effort and improving water quality.
Malaria prevalence and incidence in an isolated, meso-endemic area of Mozambique
Authors: Charlwood Jacques Derek D , Tomás Erzelia V.E. , Bragança Mauro , Cuamba Nelson , Alifrangis Michael , Kelly-Hope Louise , Stanton Michelle
Published: January 2018

If malaria can be eliminated from anywhere it is from isolated areas such as the 2x7 km peninsula of Linga Linga in southern Mozambique. Currently available control strategies include bed nets impregnated with pyrethroid insecticides (long-lasting insecticidal bed nets; LLINs), artemisinin combination therapy (ACT) for treatment and rapid diagnostic tests (RDTs) for diagnosis. When these became available, they were applied and their effects on malaria prevalence measured over the years 2007 – 2011. Following a census of the population and mapping of 500 households, five annual all age prevalence surveys were conducted over the years 2007 – 2011. Information on LLIN use, house construction, and animal ownership was obtained. Mean prevalence varied from 16% (in 2007) to 65% (in 2009) according to the season in which the surveys were performed. The 5 – 9 year old age group had the highest prevalence rate in the first three surveys (2007 – 2009). A spatially structured generalised additive model indicated that malaria risk was greatest towards the northern end of the peninsula. The effect on the incidence of malaria of a clinic providing RDT’s for diagnosis and ACT’s for treatment was also monitored from March 2009 to May 2011. Malaria was diagnosed in 31% of the 4321 visits from residents attending the clinic and 72% of those tested were positive. People with confirmed malaria were younger than the median age of people attending the clinic. People with a fever were more likely to have malaria than people without a fever but bednet use did not affect the likelihood of having malaria. People living further away from the health post were less likely to attend. The number of attendees diagnosed with malaria decreased significantly from 35% (399 of 1144 attendees) in 2009 to 24% (271 of 1150 attendees) in 2011 (Chi sq = 19.1, p> 0.0001). In order to reduce malaria prevalence in an area such as Linga Linga further measures of vector control need to be considered if reductions in malaria prevalence are to be achieved.
Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance
Authors: Ezewudo Matthew N. , Joseph Sandeep , Castillo-Ramirez Santiago , Dean Deborah , Del Rio Carlos , Didelot Xavier , Dillon Jo-Anne R. , Selden Richard F , Shafer William M. , Turingan Rosemary S. , Unemo Magnus , Read Timothy D.
Published: January 2018

Neisseria gonorrhoeae is the causative agent of gonorrhea, a sexually transmitted infection (STI) of major importance. As a result of antibiotic resistance, there are now limited options for treating patients. We collected whole genome sequences and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. The population structure and evolutionary forces within the pathogen population were analyzed. Our results indicated a cosmopolitan gonoccocal population mainly made up of five subgroups. The estimated ratio of recombination to mutation (r/m=2.2) from our data set indicates an appreciable level of recombination occurring in the population. Strains with resistance phenotypes to more recent antibiotics (azithromycin and cefixime) were mostly found in two of the five population subgroups.
Temporal profiling of the bacterial and fungal communities in ΔF508 adult cysticfibrosis sputum
Authors: Nelson Andrew , Perry Audrey , Stewart Christopher J , Lanyon Clare V , Perry John D , Bourke Stephen J , De Soyza Anthony , Cummings Stephen P
Published: January 2018

Aims: The purpose of this study was to analyse the bacterial and fungal turnover in the lungs of cystic fibrosis patients who were ΔF508 homo- and hetero-zygotes. Further to this we wanted to identify the effects that Intravenous (IV) antibiotic perturbations had on the community and most importantly, whether exacerbations in these patients could be attributed to microbial species or communities. Methods: A total of 149 samples were collected from 18 adult CF patients attending a clinic at the RVI hospital, Newcastle upon Tyne. The samples were subject to DNA extraction followed by bacterial and fungal community DGGE analysis as well as qPCR analysis of the bacterial load. Results: We have found that bacterial and fungal communities present in the CF lung are not different when patients are suffering an exacerbation. Further to this, we have found that bacterial communities in the CF lung are disturbed by IV antibiotic administration and cause increased species turnover. We have shown that fungal taxa are capable of chronically colonising the CF lung. Conclusions: Our study adds further evidence to the assertion that changes in bacterial communities are not the cause of CF exacerbations. However, we were able to demonstrate that acquisition of new bacterial taxa was strongly associated with exacerbations in one patient. This study is the first to illustrate that fungi can persist in the CF lung but are not associated with clinical status.
Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions
Authors: Fernandes Humberto , Leen Eoin N , Cromwell Jnr Hamlet , Pfeil Marc-Philipp , Curry Stephen
Published: January 2018

Noroviruses are positive-sense single-stranded RNA viruses. They encode an NS6 protease that cleaves a viral polyprotein at specific sites to produce mature viral proteins. In an earlier study we obtained crystals of murine norovirus (MNV) NS6 protease in which crystal contacts were mediated by specific insertion of the C-terminus of one protein (which contains residues P5-P1 of the NS6-7 cleavage junction) into the peptide binding site of an adjacent molecule, forming an adventitious protease-product complex. We sought to reproduce this crystal form to investigate protease-substrate complexes by extending the C-terminus of NS6 construct to include residues on the C-terminal (P´) side of the cleavage junction. We report the crystallization and crystal structure determination of inactive mutants of murine norovirus NS6 protease with C-terminal extensions of one, two and four residues from the N-terminus of the adjacent NS7 protein (NS6 1´, NS6 2´, NS6 4´). We also determined the structure of a chimeric extended NS6 protease in which the P4 P4′ sequence of the NS6-7 cleavage site was replaced with the corresponding sequence from the NS2-3 cleavage junction (NS6 4´ 2|3).

The constructs NS6 1′ and NS6 2′ yielded crystals that diffracted anisotropically. We found that, although the uncorrected data could be phased by molecular replacement, refinement of the structures stalled unless the data were ellipsoidally truncated and corrected with anisotropic B-factors. These corrections significantly improved phasing by molecular replacement and subsequent refinement.

The refined structures of all four extended NS6 proteases are very similar in structure to the mature MNV NS6 — and in one case reveal additional details of a surface loop. Although the packing arrangement observed showed some similarities to those observed in the adventitious protease-product crystals reported previously, in no case were specific protease-substrate interactions observed.
The mechanisms of intertidal fish coexistence: a model
Authors: Barrett Chris J , Johnson Magnus L , Hull Susan L
Published: January 2018

Research into the ecology of intertidal fishes of the U.K. appears to be lacking, reportedly due to the mobility and cryptic nature of the more common species. However, some intertidal fishes contribute to the diets of commercially important species such as cod (Gadus morhua), haddock (Melanogrammus aeglefinus) and near-threatened European otter (Lutra lutra). The current study contains the first comprehensive research into the ecology of intertidal fishes from the English, Yorkshire coast and Welsh, Anglesey coast, identifying and addressing the mechanisms which allow for their coexistence. Seven mechanisms were identified which promote interspecific fish coexistence. It was found that coexistence can occur when: (I) fish diversity on a shore is low, thus minimising high degrees of co-occurrence within pools, (II) co-occurrence on shores (at tidal height level) is minimal and when fishes do co-occur, they are of similar sizes thus reducing size-dominated hierarchies, (III) the significant variables which predict fish presences differ, (IV) there is an abundance of shelter/protection readily available, which reduces the competition to access such features, (V) morphology is such, that for the majority of the year, it is more profitable for the piscivorous fishes to predate on food items other than fish, (VI) competition for prey items is reduced, when variability of resources is high, and (VII) there is a difference in the most targeted prey items between fish species, despite some overlap in targeted prey items.
Validation of reference genes for gene expression studies in non viruliferous and viruliferous Frankliniella occidentalis (Thysanoptera: Thripidae)
Authors: Yang Chunxiao Chunxiao , Li Hui , Pan Huipeng , Ma Yabin , Zhang Deyong , Liu Yong , Zhang Zhanhong , Zheng Changying , Chu Dong
Published: January 2018

Quantitative real-time PCR (qRT-PCR) is a powerful technique for measuring and evaluating gene expressions during different biological processes. To facilitate gene expression studies, normalization with respect to stable housekeeping genes (HKGs) is mandatory. The western flower thrips, Frankliniella occidentalis (Thysanoptera: Thripidae), the main vector of Tomato spotted wilt virus (TSWV), is a very destructive invasive species. In this study, expression profiles of 11 candidate HKGs, including β-actin (Actin), α-tubulin (Tubulin), elongation factor 1 α (EF1A), vacuolar-typeH+-ATPase (ATPase), NADH-ubiquinone oxidoreductase (NADH), heat shock protein 60 (HSP60), heat shock protein 70 (HSP70), heat shock protein 90 (HSP90), ribosomal protein l32 (RPL32), 28S ribosomal RNA (28S), and 18S ribosomal RNA (18S), from no nviruliferous and viruliferous F. occidentalis were investigated. Four distinct algorithms, geNorm, Normfinder, BestKeeper, and the ΔCt method, were employed to determine the performance of these genes as endogenous controls under the virus condition. Based on RefFinder, which integrates all four analytical algorithms to compare and rank the candidates, HSP70 , HSP60, EF1A, and RPL32 were the most stable housekeeping genes. This work is the initial first step to establish a standardized qRT-PCR analysis in F. occidentalis. Additionally, this study lays a foundation for the research in the interactions between TSWV and F. occidentalis.
An assessment of fracture resistance of three composite resin core build-up materials on three prefabricated non-metallic posts, cemented in endodontically treated teeth: An in vitro study
Authors: Kumar Lalit , Pal Bhupinder , Pujari Prashant
Published: January 2018

Endodontically treated teeth with excessive loss of tooth structure would require to be restored with post and core to enhance the strength and durability of the tooth and to achieve retention for the restoration. The non-metallic posts have of a superior esthetic quality. Various core materials can be used to build-up cores on the posts placed in endodontically treated teeth. The core materials would show variation in their bonding with the non-metallic posts and the remaining tooth structure. They will also have an effect on the strength and resistance to fracture of the remaining tooth structure. Aims: The aim of the study was to assess the fracture resistance of three composite resin core build-up materials on three prefabricated non-metallic posts, cemented in extracted endodontically treated teeth. Material and methods: Forty five freshly extracted maxillary central incisors of approximately of the same size and shape were selected for the study. Student’s unpaired ‘t’ test was also used to analyse and compare each group with the other groups individually, and decide whether their comparisons were statistically significant. Results: Luxacore showed the highest fracture resistance among the three core build-up materials with all the three posts systems. Ti-core had intermediate values of fracture resistance and Lumiglass had least values of fracture resistance.
A β-mannanase from Fusarium oxysporum SS-25 via solid state fermentation on brewer spent grain: Medium optimization by statistical tools, kinetic characterization and its applications
Authors: Rana Susheel Singh , Janveja Chetna , Soni Sanjeev Kumar
Published: January 2018

This study concerned with the optimization of fermentation parameters for the hyper production of mannanase from Fusarium oxysporum SS-25 employing two step statistical strategy and kinetic characterization of crude enzyme preparation. The Plackett-Burman design was first used to screen out the important factors in the culture medium which were found to be: 20% (w/w) wheat bran, 2% (w/w) each of potato peels, soybean meal, malt extract, 1% tryptone, 0.14% NH4SO4, 0.2% KH2PO4, 0.0002% ZnSO4, 0.0005% FeSO4, 0.01% MnSO4, 0.012% SDS, 0.03% NH4Cl, 0.1% NaNO3 in brewer’s spent grain based medium with 50% moisture content, inoculated with 2.8×107 spores and incubated at 30oC for 6 days. Out of twenty seven factors, four variables including soybean meal, FeSO4, MnSO4 and NaNO3 were selected to study the interactive effects and optimum level of these variables in central composite design of response surface methodology. The final mannanase yield was 193 IU/g which was active at broader temperature and pH range and could result in 26.6% reduction in kappa number with 4.93% higher tear index and 1% increase in brightness when used to treat the wheat straw based kraft pulp. The hydrolytic potential of enzyme was demonstrated on both locust bean gum and guar gum.
DCEMRI.jl: A fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis
Authors: Smith David S , Li Xia , Arlinghaus Lori R , Yankeelov Thomas E , Welch E. Brian
Published: January 2018

We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10-20x speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 x 192 breast image, we achieved run times of < 1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N1.9), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise.
A workflow for characterizing nanoparticle monolayers for biosensors: Machine learning on real and artificial SEM images
Authors: Hughes Adam S , Liu Zhaowen , Raftari Maryam , Reeves Marke M. E.
Published: January 2018

A persistent challenge in materials science is the characterization of a large ensemble of heterogeneous nanostructures in a set of images. This often leads to practices such as manual particle counting, and sampling bias of a favorable region of the “best” image. Herein, we present the open-source software, imaging criteria and workflow necessary to fully characterize an ensemble of SEM nanoparticle images. Such characterization is critical to nanoparticle biosensors, whose performance and characteristics are determined by the distribution of the underlying nanoparticle film. We utilize novel artificial SEM images to objectively compare commonly-found image processing methods through each stage of the workflow: acquistion, preprocessing, segmentation, labeling and object classification. Using the semi- supervised machine learning application, Ilastik, we demonstrate the decomposition of a nanoparticle image into particle subtypes relevant to our application: singles, dimers, flat aggregates and piles. We outline a workflow for characterizing and classifying nanoscale features on low-magnification images with thousands of nanoparticles. This work is accompanied by a repository of supplementary materials, including videos, a bank of real and artificial SEM images, and ten IPython Notebook tutorials to reproduce and extend the presented results.
Sex-specific predation risk and the evolution of sexual dimorphism in immunocompetence: a theoretical analysis
Authors: Fanson Benjamin , Søvik Eirik
Published: January 2018

Sexual dimorphism in immunocompetence, with males having lower immune function, is a prevalent pattern in nature. The main evolutionary explanation for this pattern is that males preferentially allocate resources away from immune function and towards reproductive effort to increase their competitiveness for limited females. However, the role of differential predation risk between the sexes has not been considered, despite predation risk being a major driver of life history strategies and male sexual traits often having associated predation costs. It is unclear whether increased predation risk should increase or decrease investment in immune function, as males have been shown to utilize both behavioural (e.g. decrease foraging activity) and/or life-history (e.g. decrease investment in sexual trait) defense strategies to manage predation risk. Here, we modelled optimal resource acquisition and allocation towards immune function under differential predation risk with multiple defense strategies. If males have limited defense strategies, increasing predation risk caused males to trade-off immune function for reproductive effort, leading to reduced immunocompetence. In contrast, if males can only decrease predation risk through reduction of reproductive effort (e.g. decrease colouration or calling rates), then increasing predation risk causes immune function to increase. If males can utilize multiple defense strategies and sexual selection is low, then males maintain a constant immune function as predation risk increases. Sexual selection robustly resulted in decreased immunocompetence. Overall, our results suggest that predation plays an important role in the evolution of sexual dimorphism in immunocompetence, but predicting its effect requires understanding the integrated defense strategies available.
Sexual selection studies: a NESCent catalyst meeting
Authors: Roughgarden Joan , Adkins-Regan Elizabeth , Akçay Erol , Crawford Jeremy Chase , Gadagkar Raghavendra , Griffith Simon C. , Hinde Camilla A. , Hoquet Thierry , O’Connor Cailin , Prokop Zofia M. , Prum Richard O. , Shafir Sharoni , Snow Samuel S. , Taylor Daniel , Van Cleve Jeremy , Weisberg Michael
Published: January 2018

A catalyst meeting on sexual selection studies was held in July 2013 at the facilities of the National Evolutionary Synthesis Center (NESCent) in Durham, NC. This article by a subcommittee of the participants foregrounds some of the topics discussed at the meeting. Topics mentioned here include the relevance of heritability estimates to assessing the presence of sexual selection, whether sexual selection is distinct from natural selection, and the utility of distinguishing sexual selection from fecundity selection. A possible definition of sexual selection is offered based on a distinction between sexual selection as a frequency-dependent process and fecundity selection as a density-dependent process. Another topic highlighted is a deep disagreement among participants in the reality of good-genes, sexy-sons, and run-away processes. Finally, the status of conflict in political-economic theory is contrasted with the status accorded to conflict in evolutionary behavioral theory, and the professional responsibility of sexual-selection workers to consider the ethical dimension of their research is underscored.
Blood serum and BSA, but neither red blood cells nor hemoglobin can support vitellogenesis and egg production in the dengue vector Aedes aegypti
Authors: Gonzales Kristina K , Tsujimoto Hitoshi , Hansen Immo A
Published: January 2018

Aedes aegypti is the major vector of dengue, yellow fever and chikungunya viruses that put millions of people in endemic countries at risk. Mass rearing of this mosquito is crucial for strategies that use modified insects to reduce vector populations and transmission of pathogens, such as sterile insect technique or population replacement. A major problem for vector mosquito mass rearing is the requirement of vertebrate blood for egg production since it poses significant costs as well as potential health hazards. Also regulations for human and animal use as blood source can pose a significant obstacle. A completely artificial diet that supports egg production in vector mosquitoes can solve this problem. In this study, we compared different blood fractions as dietary protein sources for mosquito egg production. We also tested artificial diets made from commercially available blood proteins (bovine serum albumin (BSA) and hemoglobin). We found that Ae. aegypti performed vitellogenesis and produced eggs when given whole bovine blood, serum, or an artificial diet containing BSA. Conversely, egg production was impaired after feeding of the red blood cell fraction or an artificial diet containing only hemoglobin. Our results indicate that serum proteins, not hemoglobin, may replace vertebrate blood in artificial diets for mass mosquito rearing.
Staff attitudes and beliefs around LGBTQ issues at the Children's Hospital of Eastern Ontario
Authors: Sampson Margaret , Potter Marnie , Bragg Heather , Langill Corrine
Published: January 2018

Introduction: Pediatric specialty hospitals may be experiencing increases in the number of lesbian, gay, bisexual transgender and queer (LGBTQ) patients and parents seen. There is no published information on the attitudes, beliefs and information needs of the broad range of staff and physicians that provide care in a hospital context, although recent surveys have considered individual professional groups. We undertook such a hospital-wide survey to assess the climate and information needs of care providers. Methods: A web-based survey was opened to all staff and physicians at a tertiary care pediatric hospital in Ottawa, Canada in June 2013. Results: 315 completed surveys were analyzed. Most respondents identified as heterosexual and none identified as transgender. Approximately half were directly involved in patient care. Approximately 90% were fully comfortable around LGBTQ patients and coworkers and most felt the hospital provided fair and equitable care for all. LGBTQ-identified respondents were somewhat less positive about the climate than heterosexual respondents, and front line staff less positive than managers. Many respondents identified knowledge deficits and were receptive to additional training. Conclusions: In the context of a socially and legally liberal jurisdiction, most pediatric hospital staff are accepting of LGBTQ clientele and co-workers while some identify areas where knowledge and skill could be improved and are willing to undergo additional training in working with LGBTQ clientele. Survey results can inform policy and procedural changes as well as training initiatives.
Illustrating a free, open-source method for quantifying locomotor performance with sprinting Aegean wall lizards
Authors: Donihue Colin , Kazez Ben
Published: January 2018

Locomotion is an important characteristic of many animals’ natural history. With the increasing availability of high-speed video cameras, videography is a powerful tool for analyzing fast or subtle motions with unprecedented resolution. However, the programs currently available for analyzing these videos are either dauntingly time intensive or prohibitively expensive. We have developed a free, open-source video analysis program, SAVRA, that enables the quick capture of scaled position data. Here we demonstrate its use with an analysis of several videos of the Aegean wall lizard (Podarcis erhardii). We hope making this program freely available will facilitate the analysis of video data across taxa, not just in laboratory settings but also in natural contexts.
Experimental food supplementation increases reproductive effort in an antbird in subtropical Brazilian Atlantic Forest fragments
Authors: Roper James J , Lima André M. X. , Uejima Angélica M. K.
Published: January 2018

Food limitation may interact with nest predation and influence nesting patterns, such as breeding season length and renesting intervals. If so, reproductive effort should change with food availability. Thus, when food is limited, birds should have fewer attempts and shorter seasons than when food is not limiting. Here we experimentally test that increased food availability results in increased reproductive effort in a fragmented landscape in the Variable Antshrike (Thamnophilus caerulescens) in southern Brazil. We followed nesting pairs in five natural fragments (4, 23, 24, 112, 214 ha) in which food was supplemented for half of those pairs, beginning with the first nest. Nest success in the largest (214 ha) fragment was 59%, compared to 5% in the 112 ha fragment and no nest was successful in the smallest (24 ha) fragment. Birds were seen, but evidence of nesting was never found in the two smallest fragments. Pairs with supplemented food were more likely to increase clutch size from two to three eggs, tended to renest sooner (20 d on average) than control pairs. Also, fragment size interacted with breeding and pairs in the largest fragment had greater daily nest survival rates, and so nests tended to last longer, and so these pairs had fewer nesting attempts than those in the 112 ha fragment while more than those in the smallest fragment with nesting (24 ha). Clearly, pairs increased their reproductive effort when food was supplemented in comparison to control pairs and fragment size seems to influence both predation risk and food abundance.
Weak effects of fire, large herbivores, and their interaction on regrowth of harvested trees in two West African savannas
Authors: Tredennick Andrew , Karembé Moussa , Dembélé Fadiala , Dohn Justin , Hanan Niall
Published: January 2018

Theory and empirical evidence for the impacts of fire and herbivory in savannas is well established – they are top-down disturbances that maintain savannas in disequilibrium states away from potential tree cover. In African savannas the demand for fuelwood is extremely high, so tree harvest likely also has an impact, both directly and indirectly, on tree cover, density, and biomass. Many savanna trees resprout vigorously from the base after harvest. However, harvested trees regenerate as saplings susceptible to fire and browsing, so harvest may have important demographic consequences. Here, we report the effects of tree harvest, and its interaction with fire and herbivory, on savanna dynamics by analyzing woody regrowth following a harvest in arid Sahelian and mesic Guinean savannas in Mali, West Africa. Tree harvest resulted in an overall reduction in wood production per tree compared to growth in non-harvested trees. Regrowth, either biomass or height, did not differ among fire and herbivory treatments. Our results suggest that the resprouting abilities that savanna trees have evolved to cope with frequent fire are essential for surviving tree harvest and subsequent disturbance. In these savannas, regrowth is rapid enough in the first growing season to escape the impact of dry season fires.
Autonomous Sensory Meridian Response (ASMR): A flow-like mental state
Authors: Barratt Emma L , Davis Nick J
Published: January 2018

Autonomous Sensory Meridian Response (ASMR) is a previously unstudied sensory phenomenon, in which individuals experience a tingling, static-like sensation across the scalp, back of the neck and at times further areas in response to specific triggering audio and visual stimuli. This sensation is widely reported to be accompanied by feelings of relaxation and wellbeing. The current study identifies several common triggers used to achieve ASMR, including whispering, personal attention, crisp sounds and slow movements. Data obtained also illustrates temporary improvements in symptoms of depression and chronic pain in those who engage in ASMR. A high prevalence of synaesthesia (5.9%) within the sample suggests a possible link between ASMR and synaesthesia, similar to that of misophonia. Links between number of effective triggers and heightened flow state suggest that flow may be necessary to achieve sensations associated with ASMR.