bluuebunny/crossref_metadata_2025 huggingface dataset:
Posttransplant Lymphoproliferative Disorders in Irish Renal Transplant Recipients: Insights From a National Observational Study
Authors: O'Regan John A. , Prendeville Susan , McCaughan Jennifer Anne , Traynor Carol , O'Brien Frank J. , Ward Francis L. , O'Donovan Denis , Kennedy Claire , Berzan Ecaterina , Kinsella Sinead , Williams Yvonne , O'Kelly Patrick , Deady Sandy , Comber Harry , Leader Mary , Conlon Peter J.
Published: April 2016

Background

Posttransplant lymphoproliferative disorders (PTLD) are a common malignancy after renal transplantation with a high incidence of PTLD described in the first posttransplant year. We sought to determine incidence and risk determinants of PTLD in Irish kidney transplant recipients.

Methods

Retrospective observational study of 1996 adult first kidney transplant recipients between 1991 and 2010 in the Republic of Ireland. Recipients were cross-referenced with the National Cancer Registry to determine incidence of PTLD. Kaplan-Meier analysis was performed for PTLD-free survival, allograft survival, and patient survival after PTLD. Cox proportional hazards models were used to identify independent risk factors for PTLD in our population.

Results

We identified 31 cases of PTLD during the study period. Histological subgroups included: early lesions (n = 1); polymorphic PTLD (n = 1); monomorphic PTLD (n = 27), Hodgkin disease (n = 2). Median time to PTLD diagnosis was 8.3 (range, 1.2-13.9) years. Cumulative incidence (95% CI) of PTLD at 1, 2, 3, 5, 10, and 15 years was 0%, 0.16% (0.05-0.5%), 0.21% (0.08-0.57%), 0.21% (0.08-0.57%), 1.76% (1.15-2.69%), and 3.07% (2.1-4.43%), respectively. Allograft survival after PTLD diagnosis was 94.4% (66.6-99.2%) at 5 years. Patient survival after PTLD diagnosis was 64% at 1 year, 53% at 2 years, 48% at 5 years, and 37% at 10 years. No risk factors for PTLD were identified.

Conclusions

We found a paucity of early onset PTLD in our cohort with no cases in the first posttransplant year. Potential contributing factors included a high prevalence of previous Epstein-Barr virus exposure and a relatively low immunological risk profile in our recipient cohort compared with prior studies. Further studies are required to reevaluate the epidemiology of PTLD in the modern era of transplant immunosuppression.
Tree diversity reduces pest damage in mature forests across Europe
Authors: Guyot Virginie , Castagneyrol Bastien , Vialatte Aude , Deconchat Marc , Jactel Hervé
Published: April 2016

Forest pest damage is expected to increase with global change. Tree diversity could mitigate this impact, but unambiguous demonstration of the diversity–resistance relationship is lacking in semi-natural mature forests. We used a network of 208 forest plots sampled along two orthogonal gradients of increasing tree species richness and latitudes to assess total tree defoliation in Europe. We found a positive relationship between tree species richness and resistance to insect herbivores: overall damage to broadleaved species significantly decreased with the number of tree species in mature forests. This pattern of associational resistance was frequently observed across tree species and countries, irrespective of their climate. These findings confirm the greater potential of mixed forests to face future biotic disturbances in a changing world.
Long-term effect of yolk carotenoid levels on testis size in a precocial bird
Authors: Giraudeau Mathieu , Ziegler Ann-Kathrin , Tschirren Barbara
Published: April 2016

Conditions experienced during prenatal development can have long-lasting organizational effects on offspring. Maternal carotenoids deposited in the eggs of birds and other oviparous species play an important role during fast embryonic growth and chick development through their antioxidant properties. However, the long-term consequences of variation in maternal carotenoid transfer for the offspring have seldom been considered. Since plasma carotenoid levels at adulthood are known to influence testis size and yolk carotenoid levels influence the ability to extract carotenoids later in life, we hypothesized that maternally transmitted carotenoids might influence gonad size at adulthood. Here, we showed that male Japanese quail (Coturnix japonica) originating from a carotenoid-enriched egg had smaller testes than control individuals at adulthood. This result shows that yolk carotenoids have long-term organizational effects. In addition, given that carotenoid intake at sexual maturity increases sperm quality and that a decreased testis size is associated with a lower sperm production, we propose that carotenoid exposure during embryo development might influence a trade-off between ejaculate size and sperm quality.
Stay tuned: active amplification tunes tree cricket ears to track temperature-dependent song frequency
Authors: Mhatre Natasha , Pollack Gerald , Mason Andrew
Published: April 2016

Tree cricket males produce tonal songs, used for mate attraction and male–male interactions. Active mechanics tunes hearing to conspecific song frequency. However, tree cricket song frequency increases with temperature, presenting a problem for tuned listeners. We show that the actively amplified frequency increases with temperature, thus shifting mechanical and neuronal auditory tuning to maintain a match with conspecific song frequency. Active auditory processes are known from several taxa, but their adaptive function has rarely been demonstrated. We show that tree crickets harness active processes to ensure that auditory tuning remains matched to conspecific song frequency, despite changing environmental conditions and signal characteristics. Adaptive tuning allows tree crickets to selectively detect potential mates or rivals over large distances and is likely to bestow a strong selective advantage by reducing mate-finding effort and facilitating intermale interactions.
Microscopic and infrared spectroscopic comparison of the underwater adhesives produced by germlings of the brown seaweed speciesDurvillaea antarcticaandHormosira banksii
Authors: Dimartino Simone , Savory David M. , Fraser-Miller Sara J. , Gordon Keith C. , McQuillan A. James
Published: April 2016

Adhesives from marine organisms are often the source of inspiration for the development of glues able to create durable bonds in wet environments. In this work, we investigated the adhesive secretions produced by germlings of two large seaweed species from the South Pacific,Durvillaea antarctica, also named ‘the strongest kelp in the word’, and its close relativeHormosira banksii. The comparative analysis was based on optical and scanning electron microscopy imaging as well as Fourier transform infrared (FTIR) spectroscopy and principal component analysis (PCA). For both species, the egg surface presents peripheral vesicles which are released soon after fertilization to discharge a primary adhesive. This is characterized by peaks representative of carbohydrate molecules. A secondary protein-based adhesive is then secreted in the early developmental stages of the germlings. Energy dispersive X-ray, FTIR and PCA indicate thatD. antarcticasecretions also contain sulfated moieties, and become cross-linked with time, both conferring strong adhesive and cohesive properties. On the other hand,H. banksiisecretions are complemented by the putative adhesive phlorotannins, and are characterized by a simple mechanism in which all constituents are released with the same rate and with no apparent cross-linking. It is also noted that the release of adhesive materials appears to be faster and more copious inD. antarcticathan inH. banksii. Overall, this study highlights that both quantity and quality of the adhesives matter in explaining the superior attachment ability ofD. antarctica.
Can a linguistic serial founder effect originating in Africa explain the worldwide phonemic cline?
Authors: Fort Joaquim , Pérez-Losada Joaquim
Published: April 2016

It has been proposed that a serial founder effect could have caused the present observed pattern of global phonemic diversity. Here we present a model that simulates the human range expansion out of Africa and the subsequent spatial linguistic dynamics until today. It does not assume copying errors, Darwinian competition, reduced contrastive possibilities or any other specific linguistic mechanism. We show that the decrease of linguistic diversity with distance (from the presumed origin of the expansion) arises under three assumptions, previously introduced by other authors: (i) an accumulation rate for phonemes; (ii) small phonemic inventories for the languages spoken before the out-of-Africa dispersal; (iii) an increase in the phonemic accumulation rate with the number of speakers per unit area. Numerical simulations show that the predictions of the model agree with the observed decrease of linguistic diversity with increasing distance from the most likely origin of the out-of-Africa dispersal. Thus, the proposal that a serial founder effect could have caused the present observed pattern of global phonemic diversity is viable, if three strong assumptions are satisfied.
A meta-analysis of relationships between polychlorinated biphenyl exposure and performance across studies of free-ranging tree swallows (Tachycineta bicolor)
Authors: Bonier Frances
Published: April 2016

Habitats worldwide are increasingly being degraded by human activities, with environmental pollution representing a significant threat to species and ecosystems. The presence of persistent organic chemicals, such as polychlorinated biphenyls (PCBs), has generated concern. Captive experiments and field studies have reported some evidence for detrimental effects of PCB exposure, but also significant variation across studies and species. Here, I use a meta-analytical approach to combine findings across 10 studies investigating effects of PCBs on performance (e.g. reproductive success, offspring growth) in free-ranging tree swallows, a common bioindicator species that accumulates high levels of PCBs at some contaminated sites. Contrary to predictions, five complementary analyses revealed no significant negative association between PCB exposure and performance in tree swallows. In fact, in one analysis, increased PCB exposure was associated with improved reproductive success. Possible explanations for these findings include several limitations of field studies, variation in the toxicity of different PCB congener mixtures found across sites included in the analysis, and variation in the degree of tolerance of PCB exposure among species (with high tolerance found in tree swallows). At this point, the available evidence from field studies does not demonstrate negative impacts of PCB exposure on tree swallow performance.
Tracking urban activity growth globally with big location data
Authors: Daggitt Matthew L. , Noulas Anastasios , Shaw Blake , Mascolo Cecilia
Published: April 2016

In recent decades, the world has experienced rates of urban growth unparalleled in any other period of history and this growth is shaping the environment in which an increasing proportion of us live. In this paper, we use a longitudinal dataset from Foursquare, a location-based social network, to analyse urban growth across 100 major cities worldwide. Initially, we explore how urban growth differs in cities across the world. We show that there exists a strong spatial correlation, with nearby pairs of cities more likely to share similar growth profiles than remote pairs of cities. Subsequently, we investigate how growth varies inside cities and demonstrate that, given the existing local density of places, higher-than-expected growth is highly localized while lower-than-expected growth is more diffuse. Finally, we attempt to use the dataset to characterize competition between new and existing venues. By defining a measure based on the change in throughput of a venue before and after the opening of a new nearby venue, we demonstrate which venue types have a positive effect on venues of the same type and which have a negative effect. For example, our analysis confirms the hypothesis that there is large degree of competition between bookstores, in the sense that existing bookstores normally experience a notable drop in footfall after a new bookstore opens nearby. Other place types, such as museums, are shown to have a cooperative effect and their presence fosters higher traffic volumes to nearby places of the same type.
Anthropogenic impacts drive niche and conservation metrics of a cryptic rattlesnake on the Colorado Plateau of western North America
Authors: Douglas M. R. , Davis M. A. , Amarello M. , Smith J. J. , Schuett G. W. , Herrmann H.-W. , Holycross A. T. , Douglas M. E.
Published: April 2016

Ecosystems transition quickly in the Anthropocene, whereas biodiversity adapts more slowly. Here we simulated a shifting woodland ecosystem on the Colorado Plateau of western North America by using as its proxy over space and time the fundamental niche of the Arizona black rattlesnake (Crotalus cerberus). We found an expansive (= end-of-Pleistocene) range that contracted sharply (= present), but is blocked topographically by Grand Canyon/Colorado River as it shifts predictably northwestward under moderate climate change (= 2080). Vulnerability to contemporary wildfire was quantified from available records, with forested area reduced more than 27% over 13 years. Both ‘ecosystem metrics' underscore how climate and wildfire are rapidly converting the Plateau ecosystem into novel habitat. To gauge potential effects onC. cerberus, we derived a series of relevant ‘conservation metrics' (i.e. genetic variability, dispersal capacity, effective population size) by sequencing 118 individuals across 846 bp of mitochondrial (mt)DNA-ATPase8/6. We identified five significantly different clades (net sequence divergence = 2.2%) isolated by drainage/topography, with low dispersal (FST = 0.82) and small sizes (2Nef = 5.2). Our compiled metrics (i.e. small-populations, topographic-isolation, low-dispersal versus conserved-niche, vulnerable-ecosystem, dispersal barriers) underscore the susceptibility of this woodland specialist to a climate and wildfire tandem. We offer adaptive management scenarios that may counterbalance these metrics and avoid the extirpation of this and other highly specialized, relictual woodland clades.
New insights on equid locomotor evolution from the lumbar region of fossil horses
Authors: Jones Katrina Elizabeth
Published: April 2016

The specialization of equid limbs for cursoriality is a classic case of adaptive evolution, but the role of the axial skeleton in this famous transition is not well understood. Extant horses are extremely fast and efficient runners, which use a stiff-backed gallop with reduced bending of the lumbar region relative to other mammals. This study tests the hypothesis that stiff-backed running in horses evolved in response to evolutionary increases in body size by examining lumbar joint shape from a broad sample of fossil equids in a phylogenetic context. Lumbar joint shape scaling suggests that stability of the lumbar region does correlate with size through equid evolution. However, scaling effects were dampened in the posterior lumbar region, near the sacrum, which suggests strong selection for sagittal mobility in association with locomotor–respiratory coupling near the lumbosacral joint. I hypothesize that small-bodied fossil horses may have used a speed-dependent running gait, switching between stiff-backed and flex-backed galloping as speed increased.
The colonization history of British water vole (Arvicola amphibius(Linnaeus, 1758)): origins and development of the Celtic fringe
Authors: Brace Selina , Ruddy Mark , Miller Rebecca , Schreve Danielle C. , Stewart John R. , Barnes Ian
Published: April 2016

The terminal Pleistocene and Early Holocene, a period from 15 000 to 18 000 Before Present (BP), was critical in establishing the current Holarctic fauna, with temperate-climate species largely replacing cold-adapted ones at mid-latitudes. However, the timing and nature of this process remain unclear for many taxa, a point that impacts on current and future management strategies. Here, we use an ancient DNA dataset to test more directly postglacial histories of the water vole (Arvicola amphibius, formerlyA.terrestris), a species that is both a conservation priority and a pest in different parts of its range. We specifically examine colonization of Britain, where a complex genetic structure can be observed today. Although we focus on population history at the limits of the species' range, the inclusion of additional European samples allows insights into European postglacial colonization events and provides a molecular perspective on water vole taxonomy.
Crossing fitness valleys: empirical estimation of a fitness landscape associated with polymorphic mimicry
Authors: Arias Mónica , le Poul Yann , Chouteau Mathieu , Boisseau Romain , Rosser Neil , Théry Marc , Llaurens Violaine
Published: April 2016

Characterizing fitness landscapes associated with polymorphic adaptive traits enables investigation of mechanisms allowing transitions between fitness peaks. Here, we explore how natural selection can promote genetic mechanisms preventing heterozygous phenotypes from falling into non-adaptive valleys. Polymorphic mimicry is an ideal system to investigate such fitness landscapes, because the direction of selection acting on complex mimetic colour patterns can be predicted by the local mimetic community composition. Using more than 5000 artificial butterflies displaying colour patterns exhibited by the polymorphic Müllerian mimicHeliconius numata, we directly tested the role of wild predators in shaping fitness landscapes. We compared predation rates on mimetic phenotypes (homozygotes at the supergene controlling colour pattern), intermediate phenotypes (heterozygotes), exotic morphs (absent from the local community) and palatable cryptic phenotypes. Exotic morphs were significantly more attacked than local morphs, highlighting predators' discriminatory capacities. Overall, intermediates were attacked twice as much as local homozygotes, suggesting the existence of deep fitness valleys promoting strict dominance and reduced recombination between supergene alleles. By including information on predators' colour perception, we also showed that protection on intermediates strongly depends on their phenotypic similarity to homozygous phenotypes and that ridges exist between similar phenotypes, which may facilitate divergence in colour patterns.
Pan-cancer analysis of the metabolic reaction network
Authors: Gatto F. , Nielsen J.
Published: April 2016

Metabolic reprogramming is considered a hallmark of malignant transformation. However, it is not clear whether the network of metabolic reactions expressed by cancers of different origin differ from each other nor from normal human tissues. In this study, we reconstructed functional and connected genome-scale metabolic models for 917 primary tumors based on the probability of expression for 3,765 reference metabolic genes in the sample. This network-centric approach revealed that tumor metabolic networks are largely similar in terms of accounted reactions, despite diversity in the expression of the associated genes. On average, each network contained 4,721 reactions, of which 74% were core reactions (present in >95% of all models). Whilst 99.3% of the core reactions were classified as housekeeping also in normal tissues, we identified reactions catalyzed byARG2, RHAG, SLC6andSLC16family gene members, andPTGS1andPTGS2as core exclusively in cancer. The remaining 26% of the reactions were contextual reactions. Their inclusion was dependent in one case (GLS2) on the absence ofTP53mutations and in 94.6% of cases on differences in cancer types. This dependency largely resembled differences in expression patterns in the corresponding normal tissues, with some exceptions like the presence of theNANP-encoded reaction in tumors not from the female reproductive system or of theSLC5A9-encoded reaction in kidney-pancreatic-colorectal tumors. In conclusion, tumors expressed a metabolic network virtually overlapping the matched normal tissues, raising the possibility that metabolic reprogramming simply reflects cancer cell plasticity to adapt to varying conditions thanks to redundancy and complexity of the underlying metabolic networks. At the same time, the here uncovered exceptions represent a resource to identify selective liabilities of tumor metabolism.
Convergent evolution of sperm gigantism and the developmental origins of sperm size variability inCaenorhabditisnematodes
Authors: Vielle Anne , Callemeyn-Torre Nicolas , Gimond Clotilde , Poullet Nausicaa , Gray Jeremy C. , Cutter Asher D. , Braendle Christian
Published: April 2016

Sperm cells provide crucial, if usually diminutive, ingredients to successful sexual reproduction as the source of centrioles and half the diploid genome. Despite this essential conserved function, sperm competition and coevolution with female traits can drive spectacular change in size and shape of these motile cells. Here we characterize four repeated instances of convergent evolution of sperm gigantism inCaenorhabditisnematodes using phylogenetic comparative methods on 26 species. Species at the extreme end of the 50-fold range of sperm-cell volumes across the genus have sperm capable of comprising up to 5% of egg-cell volume, representing severe attenuation of the magnitude of anisogamy. Exploring potential genetic and developmental determinants ofCaenorhabditissperm size variation, we uncover significant differences in mean and variance of sperm size among genotypes, between sexes of androdioecious species, as well as within and between individuals of identical genotypes. We demonstrate that the developmental basis of sperm size variation, both within and between species, becomes established during an early stage of sperm development, i.e. at the formation of primary spermatocytes while subsequent meiotic divisions contribute little further sperm size variability. These findings provide first insights into the developmental determinants of inter-and intraspecific sperm size differences inCaenorhabditis. Together, our results provide a novel integrative view on the developmental and evolutionary origins ofCaenorhabditissperm size variation. We hypothesize that life history and/or ecological differences among species favoured the evolution of alternative sperm competition strategies toward either many smaller sperm or fewer larger sperm, with gigantic sperm potentially providing a means of paternal care via gametic provisioning or as a potent vehicle for sexual conflict over offspring development.
Comparative analysis of protein evolution and RNA structural changes in the genome of pre-epidemic and epidemic Zika virus
Authors: Ramaiah Arunachalam , Dai Lei , Contreras Deisy , Sinha Sanjeev , Sun Ren , Arumugaswami Vaithilingaraja
Published: April 2016

Zika virus (ZIKV) infection is associated with microcephaly, neurological disorders and poor pregnancy outcome1-3and no vaccine is available. Although ZIKV was first discovered in 1947, the exact mechanism of virus replication and pathogenesis still remains unknown. Recent outbreaks of Zika virus in the Americas clearly suggest a better adaptation of viral strains to human host. Understanding the conserved and adaptive features in the evolution of ZIKV genome will reveal the molecular mechanism of virus replication and host adaptation. Here, we show comprehensive analysis of protein evolution and changes in RNA secondary structures of ZIKV strains including the current 2015-16 outbreak. To identify the constraints on ZIKV evolution, selection pressure at individual codons, immune epitopes, co-evolving sites, and RNA structures were analyzed. The proteome of current 2015/16 epidemic ZIKV strains of Asian genotype is found to be genetically conserved due to genome-wide negative selection on codons, with limited positive selection. Predicted RNA structures at the 5’ and 3’ ends of ZIKV strains reveal substantial changes such as an additional stem loop which makes it similar to that of Yellow Fever Virus. Concisely, the targeted changes at both the amino acid and the RNA levels contribute to the better adaptation of ZIKV strains to human host with an enhanced neurotropism.
C19ORF66 is an Interferon-Stimulated Gene (ISG) which Inhibits Human Immunodeficiency Virus-1
Authors: Xiong Weidong , Contreras Deisy , Ignatius Irudayam Joseph , Ali Ayub , Yang Otto O. , Arumugaswami Vaithilingaraja
Published: April 2016

Innate immunity is the first line of defense against invading microbes1. The type I interferon (IFN) pathway plays a key role in controlling Human Immunodeficiency Virus type 1 (HIV-1) replication2,3. We identified an IFN-α stimulated gene C19ORF66 that we term Suppressor of Viral Activity (SVA). Full length SVA-1 protein inhibits HIV-1 by blocking virion production. SVA splice variants truncated at the C-terminus and/or disrupted at the nuclear export signal (NES) lose antiviral activity and localize to nucleus, while full length SVA-1 co-localizes with HIV-1 p24 protein in the cytoplasmic compartment of infected cells. SVA-1 is structurally and functionally conserved across species, including mouse and chimpanzee. We provide the first description of the effector function of the gene SVA/C190RF66 as an innate immune factor with anti-HIV-1 activity.
Different speciation types meet in a Mediterranean genus: the biogeographic history ofCymbalaria(Plantaginaceae)
Authors: Carnicero Pau , Sáez Llorenç , Garcia-Jacas Núria , Galbany-Casals Mercè
Published: April 2016

Cymbalariais a Mediterranean genus including ten species and six subspecies growing on rocky habitats. A very fragmented distribution, the different ecologic preferences of partially sympatric species and the presence of different ploidy levels, suggest the role of allopatric, sympatric ecological and polyploid speciation in its evolution. The aims of this study are to verify the monophyly and to reconstruct the phylogenetic relationships ofCymbalaria, to infer its biogeographic history by estimating the lineage divergence dates and the ancestral areas of distribution, and to discuss the role of different types of speciation. To address these issues, we constructed a complete phylogeny of the genus with ITS, 3’ETS,ndhF andrpl32-trnL sequences. A time-calibrated phylogeny and an ancestral-area estimation were obtained from the nrDNA data. The evidence supported the genusCymbalariaas monophyletic. It originated ca. 5 Ma and three lineages segregated rapidly, one with the single extant taxaCymbalaria microcalyxsubsp.microcalyxand the other two corresponding to western and central-eastern species, respectively. The main diversification events occurred after the onset of the Mediterranean climate and during Pleistocene oscillations. Founder-event and sympatric speciation were supported by the biogeographic analyses, and chromosome data combined with our phylogeny supported at least two polyploidization events. We observed that the consequences of physical barriers were different amongst the different species.

Supplementary Material

Electronic Supplement (Figure S1, Table S1) are available in the Supplementary Data section of the online version of this article (http://www.ingentaconnect.com/content/iapt/tax).
Human infants’ understanding of social imitation: Inferences of affiliation from third party observations
Authors: Powell Lindsey J. , Spelke Elizabeth S.
Published: April 2016

Imitation is ubiquitous in positive social interactions. For adult and child observers, it also supports inferences about the participants in such interactions and their social relationships, but the origins of these inferences are obscure. Do infants attach social significance to this form of interaction? Here we test 4- to 5.5-month-old infants’ interpretation of imitation, asking if the imitative interactions they observe support inferences of social affiliation across 10 experimental conditions that varied the modality of the imitation (movement vs. sound), the roles of specific characters (imitators vs. targets), the number of characters in the displays (3 vs. 5), and the number of parties initiating affiliative test events (1 vs. 2). These experiments, together with one experiment conducted with 12-month-old infants, yielded three main findings. First, infants expect that characters who engaged in imitation will approach and affiliate with the characters whom they imitated. Second, infants show no evidence of expecting that characters who were targets of imitation will approach and affiliate with their imitators. Third, analyzing imitative interactions is difficult for young infants, whose expectations vary in strength depending on the number of characters to be tracked and the number of affiliative actors to be compared. These findings have implications for our understanding of social imitation, and they provide methods for advancing understanding of other aspects of early social cognitive development.
Pan-Retinal Characterisation of Light Responses from Ganglion Cells in the Developing Mouse Retina
Authors: Hilgen Gerrit , Pirmoradian Sahar , Pamplona Daniela , Kornprobst Pierre , Cessac Bruno , Hennig Matthias H. , Sernagor Evelyne
Published: April 2016

We have investigated the ontogeny of light-driven responses in mouse retinal ganglion cells (RGCs). Using a large-scale, high-density multielectrode array, we recorded from hundreds to thousands of RGCs simultaneously at pan-retinal level, including dorsal and ventral locations. Responses to different contrasts not only revealed a complex developmental profile for ON, OFF and ON-OFF RGC types, but also unveiled differences between dorsal and ventral RGCs. At eye-opening, dorsal RGCs of all types were more responsive to light, perhaps indicating an environmental priority to nest viewing for pre-weaning pups. The developmental profile of ON and OFF RGCs exhibited antagonistic behavior, with the strongest ON responses shortly after eye-opening, followed by an increase in the strength of OFF responses later on. Further, we found that with maturation receptive field (RF) center sizes decrease, responses to light get stronger, and centers become more circular while seeing differences in all of them between RGC types. These findings show that retinal functionality is not spatially homogeneous, likely reflecting ecological requirements that favour the early development of dorsal retina, and reflecting different roles in vision in the mature animal.
NGS-based assay for frequent newborn inherited diseases: from development to implementation
Authors: Simakova T. , Bragin A. , Zaytseva M. , Clemente C. , Lewicka M. , Machado J.C. , Costa J.L. , Hughes M. , Hertz-Fowler C. , Petrova N. , Polyakov A. , Zinchenko R. , Kondratyeva E. , Pavlov A.
Published: April 2016

NGS is a powerful tool for the diagnostics of inherited diseases. A number of studies devoted to the development and validation of targeted NGS panels are published. Here we present not only development and validation of an assay, but report our experience on introduction of a new approach into the real clinical practice. The assay is intended for the diagnostics of frequent newborn inherited diseases: cystic fibrosis, phenylketonuria and galactosemia. The analysis is performed on the Ion PGM™ sequencing platform and allows the detection of single-nucleotide variations as well as copy number variants. We developed the software performing data quality control, providing decision-support variant annotation and generating the medical report that enables clinical application of the assay. Analytical validation of the assay was performed by bi-directional Sanger sequencing of the most part of the targeted region. Clinical validation was performed by multicenter blind testing of clinical and control samples. Sensitivity and specificity of the assay are above 99%. We have developed statements for test ordering, test acquisition form and practical recommendations for the results interpretation. The test has been successfully applied for the confirmatory diagnostics in a clinical laboratory during a year. Thus, the developed assay is a comprehensive ready-to-use CE-IVD solution for clinical diagnostics.
Reconstructing contact network parameters from viral phylogenies
Authors: McCloskey Rosemary M. , Liang Richard H. , Poon Art F.Y.
Published: April 2016

Models of the spread of disease in a population often make the simplifying assumption that the population is homogeneously mixed, or is divided into homogeneously mixed compartments. However, human populations have complex structures formed by social contacts, which can have a significant influence on the rate of epidemic spread. Contact network models capture this structure by explicitly representing each contact which could possibly lead to a transmission. We developed a method based on kernel approximate Bayesian computation (kernel-ABC) for estimating structural parameters of the contact network underlying an observed viral phylogeny. The method combines adaptive sequential Monte Carlo for ABC, Gillespie simulation for propagating epidemics though networks, and a kernel-based tree similarity score. We used the method to fit the Barabási-Albert network model to simulated transmission trees, and also applied it to viral phylogenies estimated from five published HIV sequence datasets. On simulated data, we found that the preferential attachment power and the number of infected nodes in the network can often be accurately estimated. On the other hand, the mean degree of the network, as well as the total number of nodes, were not estimable with kernel-ABC. We observed substantial heterogeneity in the parameter estimates on real datasets, with point estimates for the preferential attachment power ranging from 0.06 to 1.05. These results underscore the importance of considering contact structures when performing phylodynamic inference. Our method offers the potential to quantitatively investigate the contact network structure underlying viral epidemics.
AyurvedicAmalaki Rasayanapromotes improved stress tolerance and thus has anti-aging effects inDrosophila melanogaster
Authors: Dwivedi Vibha , Lakhotia Subhash C.
Published: April 2016

Ethnopharmacological relevance

Amalaki Rasayana(AR) is a common Ayurvedic herbal formulation ofPhyllanthus emblicafruits and other ingredients and is used for general good health and healthy aging. We earlier reported it to improve life history traits and to suppress neurodegeneration as well as induced apoptosis inDrosophila.

Aim of the study

To examine effects of dietary AR supplement on cell stress responses inDrosophila melanogaster.

Materials and methods

Larvae/flies, reared on normal food or on that supplemented with 0.5% (w/v) AR, were exposed to crowding, thermal or oxidative stress and examined for survival, stress tolerance and levels of lipid peroxides, SOD and HSPs.

Results

Wild type larvae/flies reared on AR supplemented food survived the various cell stresses much better than those reared on normal food. AR-fed mutantpark13orDJ-1βDelta93(Parkinson’s disease model) larvae, however, showed only partial or no protection, respectively, against paraquat-induced oxidative stress, indicating essentiality ofDJ-1βfor AR mediated oxidative stress tolerance. AR feeding reduced the accumulation of reactive oxygen species (ROS) and lipid peroxidation even in aged (35 day old) wild type flies while enhancing superoxide dismutase (SOD) activity. We show for the first time that while Hsp70 or Hsp83 expression under normal or stress conditions was not differentially affected by AR feeding, Hsp27 levels were elevated in AR fed wild type control as well as heat shocked larvae. Therefore, besides the known anti-oxidant activity ofPhyllanthus emblicafruits, dietary AR also enhances cellular levels of Hsp27.

Conclusion

In the context of the reported “anti-aging” and “healthy-aging” effects of AR, the present in vivo study on a model organisms shows that AR feeding significantly improves tolerance to a variety of cell stresses through reduced ROS and lipid peroxidation and enhanced SOD activity and Hsp27. Such improved cellular defences following dietary AR provide better homeostasis and thereby improve the life-span and quality of organism’s life.
Mechanical design, multiple criteria decision making and Pareto optimality gap
Authors: Kaliszewski Ignacy , Kiczkowiak Tomasz , Miroforidis Janusz
Published: April 2016

Purpose

We present an approach to multiple criteria mechanical design problems, for cases where problem complexity precludes derivation of the whole Pareto front. For such problems we propose to limit search, and hence also derivation, of the Pareto front exclusively to regions of the direct designer’s interest, thus saving on computing efforts and gaining on tractable problem sizes.

Design/methodology/approach

To achieve the purpose, we frame the decision making process (design) into a combination of three specific concepts, namely decision maker's preference capture, local Pareto front search and approximate multiobjective optimization with assessments of the Pareto optimality gap.

We illustrate the approach with two small design problems, namely Pareto optimal round tube beam and Pareto optimal pneumatic high speed machine drive selection. We solve these problems in a setting which can be regarded as representative for problem solving in real environment.

Findings

On the decision making side, the proposed approach has turned out to be a versatile tool for selecting designs from the Pareto suboptimal ones, where each such a Pareto suboptimal design has an explicit assessment of the Pareto optimality gap. On the technical (optimization) side, it has been demonstrated that the approach seamlessly works with evolutionary computations, structured to the specific needs of the approach.

Research limitations/implications

It has been shown that the navigation over the Pareto front can be achieved with limited effort, both on the cognitive and the computing side. Moreover, navigation over the Pareto front can be focused from the very beginning of the design selection process on the regions of the Pareto front which are of the direct designer’s interest. This eliminates the need to derive (or only approximate) the whole Pareto front, a tangible asset as the derivation of that set is the main factor precluding scalability of design selection problems to higher dimensions (to higher problem sizes).

Practical implications

Because of the general formulation of the Pareto optimal design selection problem considered in the paper, the absence of any assumptions on its form and easiness of implementation of the underlying procedure of the proposed approach, the paper offers a clear option to approaches based on classical optimization computations.

Originality/value

The approach offers derivation of Pareto suboptimal designs with assessments of the Pareto optimality gap, whereas currently available multiobjective evolutionary optimization algorithms which derive Pareto suboptimal designs as well, offer no such assessments. Thus, the approach provides a firm ground to valuate designs resulting from approximate multiobjective optimization computations.
Generalized Finite Element Method in linear and nonlinear structural dynamic analyses
Authors: Piedade Neto Dorival , Baroncini Proenca Sergio Persival
Published: April 2016

Purpose

The purpose of this study is to evaluate the accuracy and numerical stability of the Generalized Finite Element Method (GFEM) for solving structural dynamic problems.

Design/methodology/approach

The GFEM is a numerical method based on the Partition of Unity (PU) concept. The method can be understood as an extension of the conventional Finite Element Method (FEM) for which the local approximation provided by the shape functions can be improved by means of enrichment functions. Polynomial enrichment functions are hereby used combined with an implicit time-stepping integration technique for improving the dynamical response of the models. Both consistent and lumped mass matrices techniques are tested. The method accuracy and stability are investigated through linear and nonlinear elastic problems.

Findings

The results indicate that the adopted strategies can provide stable and accurate responses for GFEM in dynamic analyses. Furthermore, the mass lumping technique provided remarkable reductions of the system of equation condition number, therefore leading to more stable numerical models.

Originality/value

The evaluated features of GFEM models for implicit time-stepping integration schemes represent new information of great deal of interest regarding linear and nonlinear dynamic analyses using such a method.
Hydromagnetic flow of heat absorbing and radiating fluid over exponentially stretching sheet with partial slip and viscous and Joule dissipation
Authors: Seth Gauri Shanker , Sharma Rohit , Kumbhakar Bidyasagar , Chamkha Ali J
Published: April 2016

Purpose

An investigation of hydromagnetic two dimensional boundary layer flow with heat transfer of a viscous, incompressible, electrically conducting, heat absorbing and optically thick heat radiating fluid over a permeable exponentially stretching sheet considering the effects of viscous and Joule dissipations in the presence of velocity and thermal slip is carried out.

Design/methodology/approach

Using similarity transform, governing differential equations representing mathematical model of the problem are solved with the help of fourth-order Runge-Kutta method along with shooting technique. Numerical solutions of fluid velocity and fluid temperature are depicted graphically for various values of pertinent flow parameters whereas numerical values of wall velocity gradient and wall temperature gradient are displayed graphically for various values of pertinent flow parameters.

Findings

Numerical results obtained in this paper are compared with earlier published results and are found to be in excellent agreement. Magnetic field and suction tend to enhance the wall velocity gradient whereas dimensionless co-ordinate, injection and velocity slip factor have reverse effect on it. Suction and heat absorption tend to enhance wall temperature gradient whereas magnetic field, velocity slip factor, injection, thermal radiation, thermal slip factor and viscous dissipation have reverse effect on it.

Originality/value

The investigation of this problem may have bearing in several engineering processes such as extrusion of plastic sheet, annealing and tinning of copper wire, paper production, crystal growing and glass blowing, continuous casting of metals and spinning of fibers.
Particle swarm optimization algorithm for suspendome structure under multiple loading cases
Authors: Liu Xuechun , Zhang Ailin , Zhang Xun , Tian Chen
Published: April 2016

Purpose

The purpose of the paper is to provide an optimization algorithm for a large-span suspendome which is a spatial prestressed structure with complex mechanical characteristics. The algorithm optimizes the cable tension, the dimension of components, the shape parameters of structure simultaneously.

Design/methodology/approach

With the span-to-rise ratio, the length of the strut, the cable tension, the cross-sectional area of the cables and the cross-sectional size of steel members as design variables and the gross mass of entire structure as the objective function, a mathematical optimization method was proposed in the paper based on the hybridization of full stress and particle swarm optimization.

Findings

By using the improved particle swarm optimization algorithm, the coupling problem of the three types of design variables was resolved: the cable tension and the size and shape of the structure were optimized simultaneously for a suspendome. A program was compiled according to this method and was used for a large-span suspendome. The optimization results of the suspendome demonstrates that the method proposed in the paper has the advantages of high efficiency, rapid convergence, and general applicability, which enable it to be used for the optimization of various types of prestressed steel structures.

Originality/value

The optimization program has more general parameters, which can be used to optimize suspendome with different spans, different lattice divisions and different cable-layouts. In addition to the strength of steel and cable, the integral stability of the members, the deformation of the structure and the geometrical and material nonlinearity were considered in this algorithm and program. The optimization result was compared to the design of an actual large-span suspendome engineering project.
Bi-direction multi-surrogate surrogate assisted global optimization
Authors: Wang Hu , Li Enying
Published: April 2016

Purpose

For global optimization, an important issue is a trade-off between exploration and exploitation within limited number of evaluations. Efficient Global Optimization (EGO) is an important algorithm considering such condition termed as Expected Improvement (EI). One of major bottlenecks of EGO is to keep the diversity of samples. Recently, Multi-Surrogate EGO (MSEGO) uses more samples generated by multiple surrogates to improve the efficiency. However, the total number of samples is commonly large. To overcome this bottleneck, a bi-direction multi-surrogate global optimization is suggested.

Design/methodology/approach

As the name implies, two different ways are used. The first way is to EI criterion to find better samples similar to EGO. The second way is to use the second term of EI to find accurate regions. Sequentially, the samples in these regions should be evaluated by multiple surrogates instead of exact function evaluations. To enhance the accuracy of these samples, Bayesian inference is employed to predicted the performance of each surrogate in each iteration and obtain the corresponding weight coefficients. The predicted response value of a cheap sample is evaluated by the weighted multiple surrogates combination. Therefore, both accuracy and efficiency can be guaranteed based on such frame.

Findings

According to the test functions, it empirically shows that the proposed algorithm is a potentially feasible method for complicated underlying problems.

Originality/value

A bi-direction sampling strategy is suggested. The first way is to use EI criterion to generate samples similar to the EGO. In this way, new samples should be evaluated by real functions or simulations called expensive samples. Another way is to search accurate region according to the second term of EI. To guarantee the reliability of samples, a sample selection scenario based on Bayesian theorem is suggested to select the cheap samples. We hope this strategy help us to construct more accurate model without increasing computational cost.
Filtering algorithm for eigenvalue bounds of fuzzy symmetric matrices
Authors: Mahato Nisha Rani , Chakraverty Snehashish
Published: April 2016

Purpose

The solution of dynamic problems of structures using finite element method leads to generalised eigenvalue problem. In general, if the material properties are crisp (exact) then we get crisp eigenvalue problem. But in actual practice, instead of crisp material properties we may have only bounds of values as a result of errors in measurements, observations and calculations or it may be due to maintenance induced error etc. Such bounds of values may be considered in terms of interval or fuzzy numbers. The purpose of this paper is to develop a fuzzy filtering procedure for finding real eigenvalue bounds of different structural problems.

Design/methodology/approach

The proposed fuzzy filtering algorithm has been developed in terms of fuzzy number to solve the fuzzy eigenvalue problem. The initial bounds of fuzzy eigenvalues are filtered to obtain precise eigenvalue bounds which are depicted by fuzzy (Triangular Fuzzy Number) plots using α-cut.

Findings

Previously, bounds of eigenvalues of interval matrices have been investigated by few authors. But when the structural problem consists of fuzzy material properties, then the interval eigenvalue bounds may be obtained for each interval of the fuzzy number. The proposed algorithm has been applied for standard fuzzy eigenvalue problems which may be extended to generalised fuzzy eigenvalue problems for obtaining filtered fuzzy bounds.

Originality/value

The developed fuzzy filtering method is found to be efficient for different structural dynamics problems with fuzzy material properties.