bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex inter‐island colonization and peripatric founder speciation promote diversification of flightless Pachyrhynchus weevils in the Taiwan–Luzon volcanic belt
Authors: Tseng Hui‐Yun , Huang Wen‐San , Jeng Ming‐Luen , Villanueva Reagan Joseph T. , Nuñeza Olga M. , Lin Chung‐Ping 
Published: November 2017

AbstractAimWe investigated the spatial and temporal patterns of diversification among colourful and flightless weevils, the Pachyrhynchus orbifer complex, to test the stepping‐stone hypothesis of colonization across the Taiwan–Luzon volcanic belt.LocationSoutheast Asia.MethodsThe phylogeny of the P. orbifer complex was reconstructed from a multi‐locus data set of mitochondrial and nuclear genes using maximum likelihood in RAxML and Bayesian inference in MRBAYES. Likelihood‐based tests in CONSEL were used to evaluate alternative tree topologies. Divergence times were estimated in beast based on a range of mutation rates. Ancestral range and biogeographical history were reconstructed using Bayesian binary MCMC (BBM) methods in RASP and in BioGeoBEARS. Demographic histories were inferred using the extended Bayesian skyline plot (EBSP). Species boundaries were tested using BPP.ResultsThe phylogeny of the P. orbifer complex indicated strong support for seven reciprocally monophyletic lineages grouped by current island boundaries (Camiguin, Fuga, Dalupiri, Calayan, Babuyan, Orchid and Yaeyama Islands), except for a sister Green + Itbayat lineage. Complex and stochastic colonization of P. orbifer was inferred to have involved both northward and southward directions with short‐ and long‐distance dispersal events, which are strongly inconsistent with the strict stepping‐stone hypothesis. Divergence time estimates for all extant island lineages (<1 Myr of Middle Pleistocene) are much more recent than the geological ages (22.4–1.7 Myr) and subaerial existence (c. 3 Myr) of the islands. The statistically delimited seven cryptic species imply that the diversity of Pachyrhynchus from small peripheral islands continues to be largely under‐estimated.Main conclusionsThe non‐linear, more complex spatial and temporal settings of the archipelago and stochastic dispersal were probable key factors shaping the colonization history of the P. orbifer complex. Speciation of the P. orbifer complex may have occurred only between islands, indicating that peripatric speciation through the founders of stochastic dispersals was the major evolutionary driver.
Contrasting phylogeography of two Western Palaearctic fish parasites despite similar life cycles
Authors: Perrot‐Minnot Marie‐Jeanne , Špakulová Marta , Wattier Rémi , Kotlík Petr , Düşen Serdar , Aydoğdu Ali , Tougard Christelle 
Published: November 2017

AbstractAimWe used comparative phylogeography of two intestinal parasites of freshwater fish to test whether similarity in life cycle translates into concordant phylogeographical history. The thorny‐headed wormsPomphorhynchus laevisandP. tereticollis(Acanthocephala) were formerly considered as a single species with a broad geographical and host range within the Western Palaearctic.LocationCentral and eastern parts of Northern Mediterranean area, Western and Central Europe, Ponto‐Caspian Europe.MethodsA mitochondrial marker (COI) was sequenced for 111P. laevisand 50P. tereticollisindividuals and nuclearITS1 andITS2 sequences were obtained for 37P. laevisand 21P. tereticollis. Genetic divergence, phylogenetic relationships and divergence time were estimated for various lineages within each species, and their phylogeographical patterns were compared to known palaeogeographical events in Western Palaearctic. Biogeographical histories of each species were inferred.ResultsThe two species show very different phylogeographical patterns. Five lineages were identified inP. laevis, partially matching several major biogeographical regions defined in the European riverine fish fauna. The early stages ofP. laevisdiversification occurred in the peri‐Mediterranean area, during the Late Miocene. Subsequent expansion across Western Europe and Russia was shaped by dispersal and vicariant events, from Middle Pliocene to Middle Pleistocene. By contrast,P. tereticollishas differentiated more recently within the Western and Central parts of Europe, and shows weak geographical and genetic structuring.ConclusionOur study highlights weak to moderate similarity in the phylogeographical pattern of these acanthocephalan parasites compared to their amphipod and fish hosts. The observed differences in the timing of dispersion and migration routes taken may reflect the use of a range of final hosts with different ecologies and dispersal capabilities. By using a group underrepresented in phylogeographical studies, our study is a valuable contribution to revealing the biogeography of host–parasite interactions in continental freshwaters.
Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics
Authors: Bell Nicholas , Griffin Philippa C. , Hoffmann Ary A. , Miller Adam D. 
Published: November 2017

AbstractAimThe alpine region of mainland Australia is one of the world's 187 biodiversity hotspots. Genetic analyses of Australian alpine fauna indicate high levels of endemism on fine spatial scales, unlike Northern Hemisphere alpine systems where shallow genetic differentiation is typically observed among populations. These discrepancies have been attributed to differences in elevation and influence from glacial activity, and point to a unique phylogeographic history affecting Australian alpine biodiversity. To test generality of these findings across Australian alpine biota, we assessed patterns of genetic structure across plant species.LocationThe Australian Alps, Victoria, eastern Australia.MethodsWe used an economical pooled genotyping‐by‐sequencing (GBS) approach to examine patterns of genetic diversity among seven widespread species including shrubs and forbs from 16 mountain summits in the Australian Alpine National Park. Patterns of genetic structure among summit populations for each species were inferred from an average of 2,778 independentSNPloci using Bayesian phylogenomic inference and clustering approaches.ResultsSNPresults were consistent across species in identifying deep evolutionary splits among summit communities from the Northern and Central Victorian Alpine regions. These patterns of genetic structure are also consistent with those previously reported for invertebrate and mammal taxa. However, local genetic structure was less pronounced in the plants, supporting the notion that population connectivity tends to be higher in plant species.Main conclusionThere is deep lineage diversification between the North and Central Victorian Alpine regions, reflecting a high level of endemism. These findings differ from those reported for alpine biodiversity from New South Wales and much of the Northern Hemisphere, and support the notion that genetic diversity is typically greatest in areas least affected by historical ice sheet formation. We discuss the implications of our findings in the context of conservation planning, and highlight the benefits of this rapid and cost‐effective genome scan approach for characterizing evolutionary processes at multispecies and landscape scales.
A Heuristic Screening Aid for Consequential Life Cycle Assessment
Authors: Rajagopal Deepak 
Published: November 2017

SummaryConsequential life cycle assessment (CLCA) is envisioned as a framework that combines the technological richness of attributional life cycle assessment (ALCA) with basic economic intuition to assess the potential environmental impact of an innovation. However, despite a growing literature, CLCA still lacks general guidelines for system boundary definition. Toward filling this gap, this article invents a new index of vulnerability of the life cycle impact of a product (or activity) to emissions arising from the impact of its large‐scale adoption on market prices. Using corn ethanol as an example, it is illustrated how such an index might aid in the selection of a small set of affected activities for formal consideration in a CLCA. The application to corn ethanol reveals that in addition to land‐cover change, there exist other sources of vulnerability that have not received attention in the context of biofuels. A general procedure for utilizing the vulnerability index as a screening aid for CLCA is outlined. The utility of the vulnerability index is independent of the type of modeling framework (such as multimarket partial equilibrium or computable general equilibrium) that might be employed for a formal CLCA. Finally, this work illustrates how the vulnerability index approach bridges ALCA and CLCA.
Amelogenesis imperfecta in the dentition of a wild chimpanzee
Authors: Towle Ian , Irish Joel D. , De Groote Isabelle 
Published: November 2017

AbstractThis report describes a case of amelogenesis imperfecta in the dentition of a female chimpanzee. Amelogenesis imperfecta is a group of rare genetic conditions that create severe enamel defects, which, although well researched in humans, has not yet been investigated in wild non‐human primates.
Incidence and cost of hospitalisation of children with injuries from playground equipment falls in New South Wales, Australia
Authors: Bierbaum Mia , Curtis Kate , Mitchell Rebecca 
Published: November 2017

AimsTo describe the epidemiological profile and cost of hospitalised injuries caused by playground equipment falls of children aged 0–14 years, in New South Wales, Australia.MethodsLinked New South Wales hospitalisation data from 1 January 2010 to 30 June 2014 were used to describe the incidence of hospitalisation for playground falls, the age‐standardised rate of hospitalisation per year, age group and gender, the characteristics of the injured children and the injury incident. Health outcomes, such as length of stay in hospital, and the hospital costs associated with the injuries were examined by age group. Negative binomial regression assessed the trend in hospitalisation rates over time.ResultsThere were 7795 hospitalisations of children for playground fall injuries. The highest hospitalisation rate was for the 5–9 year olds (220.7 per 100 000 population) and was higher in males than females (234.2 and 206.3 per 100 000 population, respectively). The majority of these injuries occurred in schools (17.1%) and homes (14.6%), and were as a result of falls from trampolines (34.3%) and climbing apparatuses (28.2%). Over half the playground falls led to fractures of the elbow and wrist (54.7%). The total hospital cost of playground fall‐related injuries was $18 million.ConclusionRates of hospitalisation of children for playground fall injuries remain high despite implementation of national playground safety standards in Australia. This research highlights where interventions should be targeted to reduce the incidence and burden of injuries following falls from playground equipment.
Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir‐containing regimens
Authors: Bhardwaj N. , Ragonnet‐Cronin M. , Murrell B. , Chodavarapu K. , Martin R. , Chang S. , Miller M. D. , Feld J. J. , Sulkowski M. , Mangia A. , Wertheim J. O. , Osinusi A. , McNally J. , Brainard D. , Mo H. , Svarovskaia E. S. 
Published: November 2017

SummaryTreatment with the direct‐acting antiviral agent (DAA) sofosbuvir (SOF), an NS5B inhibitor, and velpatasvir (VEL), an NS5A inhibitor, demonstrates viral cure rates of ≥95% in hepatitis C virus (HCV) genotypes (GT) 1‐6. Here, we investigated intrapatient HCV diversity in NS5A and NS5B using Shannon entropy to examine the relationship between viral diversity and treatment outcome. At baseline, HCV diversity was lowest in patients infected with HCV GT3 as compared to the other GTs, and viral diversity was greater in NS5A than NS5B (P < .0001). Treatment outcome with SOF/VEL or the comparator regimen of SOF with ribavirin (RBV) was not correlated with baseline diversity. However, among persons treated with SOF/VEL, a decrease in diversity from baseline was observed at relapse in the majority virologic failures, consistent with a viral bottleneck event at relapse. In contrast, an increase in diversity was observed in 27% of SOF+RBV virologic failures. We investigated whether the increase in diversity was due to an increase in the transition rate, one mode of potential RBV‐mediated mutagenesis; however, we found no evidence of this mechanism. Overall, we did not observe that viral diversity at baseline influenced treatment outcome, but the diversity changes observed at relapse can improve our understanding of RBV viral suppression in vivo.
Antifungals discovery: an insight into new strategies to combat antifungal resistance
Authors: Fuentefria A.M. , Pippi B. , Dalla Lana D.F. , Donato K.K. , de Andrade S.F. 
Published: November 2017

Abstract
Undeniably, new antifungal treatments are necessary against pathogenic fungi. Fungal infections have significantly increased in recent decades, being highlighted as important causes of morbidity and mortality, particularly in immunocompromised patients. Five main antifungal classes are used: (i) azoles, (ii) echinocandins, (iii) polyenes, (iv) allylamines and (v) pyrimidine analogues. Moreover, the treatment of mycoses has several limitations, such as undesirable side effects, narrow activity spectrum, a small number of targets and fungal resistance, which are still of major concern in clinical practice. The discovery of new antifungals is mostly achieved by the screening of natural or synthetic/semisynthetic chemical compounds. The most recent discoveries in drug resistance mechanism and their avoidance were explored in a review, focusing on different antifungal targets, as well as new agents or strategies, such as combination therapy, that could improve antifungal therapy.

Significance and Impact of the Study
The failure to respond to antifungal therapy is complex and is associated with microbiological resistance and increased expression of virulence in fungal pathogens. Thus, this review offers an overview of current challenges in the treatment of fungal infections associated with increased antifungal drug resistance and the formation of biofilms in these opportunistic pathogens. Furthermore, the most recent and potential strategies to combat fungal pathogens are explored here, focusing on new agents as well as innovative approaches, such as combination therapy between antifungal drugs or with natural compounds.
Transcriptional profile and differential fitness in a specialist milkweed insect across host plants varying in toxicity
Authors: Birnbaum Stephanie S. L. , Rinker David C. , Gerardo Nicole M. , Abbot Patrick 
Published: November 2017

AbstractInteractions between plants and herbivorous insects have been models for theories of specialization and co‐evolution for over a century. Phytochemicals govern many aspects of these interactions and have fostered the evolution of adaptations by insects to tolerate or even specialize on plant defensive chemistry. While genomic approaches are providing new insights into the genes and mechanisms insect specialists employ to tolerate plant secondary metabolites, open questions remain about the evolution and conservation of insect counterdefences, how insects respond to the diversity defences mounted by their host plants, and the costs and benefits of resistance and tolerance to plant defences in natural ecological communities. Using a milkweed‐specialist aphid (Aphis nerii) model, we test the effects of host plant species with increased toxicity, likely driven primarily by increased secondary metabolites, on aphid life history traits and whole‐body gene expression. We show that more toxic plant species have a negative effect on aphid development and lifetime fecundity. When feeding on more toxic host plants with higher levels of secondary metabolites, aphids regulate a narrow, targeted set of genes, including those involved in canonical detoxification processes (e.g., cytochrome P450s, hydrolases, UDP‐glucuronosyltransferases and ABC transporters). These results indicate that A. nerii marshal a variety of metabolic detoxification mechanisms to circumvent milkweed toxicity and facilitate host plant specialization, yet, despite these detoxification mechanisms, aphids experience reduced fitness when feeding on more toxic host plants. Disentangling how specialist insects respond to challenging host plants is a pivotal step in understanding the evolution of specialized diet breadths.
Temporal variation in brain transcriptome is associated with the expression of female mimicry as a sequential male alternative reproductive tactic in fish
Authors: Cardoso Sara D. , Gonçalves David , Goesmann Alexander , Canário Adelino V. M. , Oliveira Rui F. 
Published: November 2017

AbstractDistinct patterns of gene expression often underlie intra‐ and intersexual differences, and the study of this set of coregulated genes is essential to understand the emergence of complex behavioural phenotypes. Here, we describe the development of a de novo transcriptome and brain gene expression profiles of wild‐caught peacock blenny, Salaria pavo, an intertidal fish with sex‐role reversal in courtship behaviour (i.e., females are the courting sex) and sequential alternative reproductive tactics in males (i.e., larger and older nest‐holder males and smaller and younger sneaker males occur). Sneakers mimic both female's courtship behaviour and nuptial coloration to get access to nests and sneak fertilizations, and later in life transition into nest‐holder males. Thus, this species offers the unique opportunity to study how the regulation of gene expression can contribute to intersex phenotypes and to the sequential expression of male and female behavioural phenotypes by the same individual. We found that at the whole brain level, expression of the sneaker tactic was paralleled by broader and divergent gene expression when compared to either females or nest‐holder males, which were more similar between themselves. When looking at sex‐biased transcripts, sneaker males are intersex rather than being either nest‐holder or female‐like, and their transcriptome is simultaneously demasculinized for nest‐holder‐biased transcripts and feminized for female‐biased transcripts. These results indicate that evolutionary changes in reproductive plasticity can be achieved through regulation of gene expression, and in particular by varying the magnitude of expression of sex‐biased genes, throughout the lifetime of the same individual.
Metatranscriptomic data reveal the effect of different community properties on multifunctional redundancy
Authors: Beier Sara , Shen Dandan , Schott Thomas , Jürgens Klaus 
Published: November 2017

AbstractThe assessment of functional redundancy (FR) is essential to understand community structure‐function relationships because FR buffers the functional performance of communities against changes in community composition. We introduce a novel metatranscriptome‐based approach to quantify FR, which permits multifunctional aspects to be addressed. FR among prokaryotes was ranked in water samples after exposure to changing salinity. FR was higher for functional categories with mostly broad functions shared among many taxa than for functional categories containing many narrow functions. Furthermore, community characteristics had a higher impact on FR than environmental conditions. The metric also allows FR to be estimated between selected groups of taxa, and FR was high between more closely related organisms if communities were grown in similar environmental conditions. Overall, our data revealed a pronounced influence of functional diversity on the one hand but also the characteristics of individual community members on FR, which was specifically high in those communities whose members were more sensitive to salinity changes.
Subfamily‐dependent alternative reproductive strategies in worker honeybees
Authors: Yagound Boris , Duncan Michael , Chapman Nadine C. , Oldroyd Benjamin P. 
Published: November 2017

AbstractFunctional worker sterility is the defining feature of insect societies. Yet, workers are sometimes found reproducing in their own or foreign colonies. The proximate mechanisms underlying these alternative reproductive phenotypes are keys to understanding how reproductive altruism and selfishness are balanced in eusocial insects. In this study, we show that in honeybee (Apis mellifera) colonies, the social environment of a worker, that is, the presence and relatedness of the queens in a worker's natal colony and in surrounding colonies, significantly influences her fertility and drifting behaviour. Furthermore, subfamilies vary in the frequency of worker ovarian activation, propensity to drift and the kind of host colony that is targeted for reproductive parasitism. Our results show that there is an interplay between a worker's subfamily, reproductive state and social environment that substantially affects her reproductive phenotype. Our study further indicates that honeybee populations show substantial genetic variance for worker reproductive strategies, suggesting that no one strategy is optimal under all the circumstances that a typical worker may encounter.
Coronary microvascular Kv1 channels as regulatory sensors of intracellular pyridine nucleotide redox potential
Authors: Dwenger Marc M. , Ohanyan Vahagn , Navedo Manuel F. , Nystoriak Matthew A. 
Published: November 2017

AbstractSmooth muscle voltage‐gated potassium (Kv) channels are important regulators of microvascular tone and tissue perfusion. Recent studies indicate that Kv1 channels represent a key component of the physiological coupling between coronary blood flow and myocardial oxygen demand. While the mechanisms by which metabolic changes in the heart are transduced to alter coronary Kv1 channel gating and promote vasodilation are unclear, a growing body of evidence underscores a pivotal role of Kv1 channels in sensing the cellular redox status. Here, we discuss current knowledge of mechanisms of Kv channel redox regulation with respect to pyridine nucleotide modulation of Kv1 function via ancillary Kvβ proteins as well as direct modulation of channel activity via reactive oxygen and nitrogen species. We identify areas of additional research to address the integration of regulatory processes under altered physiological and pathophysiological conditions that may reveal insights into novel treatment strategies for conditions in which the matching of coronary blood supply and myocardial oxygen demand is compromised.
Peptidase inhibitors in tick physiology
Authors: PARIZI L. F. , ALI A. , TIRLONI L. , OLDIGES D. P. , SABADIN G. A. , COUTINHO M. L. , SEIXAS A. , LOGULLO C. , TERMIGNONI C. , DA SILVA VAZ I. 
Published: November 2017

AbstractPeptidase inhibitors regulate a wide range of physiological processes involved in the interaction between hematophagous parasites and their hosts, including tissue remodeling, the immune response and blood coagulation. In tick physiology, peptidase inhibitors have a crucial role in adaptation to improve parasitism mechanisms, facilitating blood feeding by interfering with defense‐related host peptidases. Recently, a larger number of studies on this topic led to the description of several new tick inhibitors displaying interesting novel features, for example a role in pathogen transmission to the host. A comprehensive review discussing these emerging concepts can therefore shed light on peptidase inhibitor functions, their relevance to tick physiology and their potential applications. Here, we summarize and examine the general characteristics, functional diversity and action of tick peptidase inhibitors with known physiological roles in the tick−host−pathogen interaction.