bluuebunny/crossref_metadata_2025 huggingface dataset:
AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs
Authors: Gorjanc Gregor , Hickey John M.
Published: January 2018

AlphaMate is a flexible program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimisation of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimisation can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimisation objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier.

Availability

Executable versions of AlphaMate for Windows, Mac, and Linux platforms are available at http://www.alpha-genes.roslin.ed.ac.uk/AlphaMate

Contact

gregor.gorjanc@roslin.ed.ack.uk
Low spatial structure and selection against secreted virulence factors attenuates pathogenicity inPseudomonas aeruginosa
Authors: Granato Elisa T. , Ziegenhain Christoph , Marvig Rasmus L. , Kümmerli Rolf
Published: January 2018

Bacterial opportunistic pathogens are feared for their difficult-to-treat nosocomial infections and for causing morbidity in immunocompromised patients. Here, we study how such a versatile opportunist,Pseudomonas aeruginosa, adapts to conditions inside and outside its model hostCaenorhabditis elegans, and use phenotypic and genotypic screens to identify the mechanistic basis of virulence evolution. We found that virulence significantly dropped in unstructured environments both in the presence and absence of the host, but remained unchanged in spatially structured environments. Reduction of virulence was either driven by a substantial decline in the production of siderophores (in treatments without hosts) or toxins and proteases (in treatments with hosts). Whole-genome sequencing of evolved clones revealed positive selection and parallel evolution across replicates, and showed an accumulation of mutations in regulator genes controlling virulence factor expression. Our study identifies the spatial structure of the non-host environment as a key driver of virulence evolution in an opportunistic pathogen.
The genetics of behavioral isolation in an island system
Authors: Blankers Thomas , Oh Kevin P. , Shaw Kerry L.
Published: January 2018

Mating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variation in the cricketsLaupala eukoleaandL. cerasina, which occur on different islands (Maui and Hawai’i). We then compare these results with a similar study of an independently evolving species pair that diverged within the same island. Finally, we annotate theL. cerasinatranscriptome and test whether QTL fall in functionally enriched genomic regions. We document a polygenic architecture behind song rhythm divergence in the inter-island species pair that is remarkably similar to that previously found for an intra-island species pair in the same genus. Importantly, QTL regions were significantly enriched for potential homologs of genes involved in pathways that may be modulating cricket song rhythm. These clusters of loci could constrain the spatial genomic distribution of genetic variation underlying cricket song variation and harbor several candidate genes that merit further study.
RNA polymerase II pausing regulates a quiescence-dependent transcriptional program, priming cells for cell cycle reentry
Authors: Gala Hardik P. , Saha Debarya , Venugopal Nisha , Aloysius Ajoy , Dhawan Jyotsna
Published: January 2018

Adult stem cells persist in mammalian tissues by entering a state of reversible arrest or quiescence associated with low transcription. Using cultured myoblasts and primary muscle stem cells, we show that RNA synthesis is strongly repressed in G0, returning within minutes of activation. We investigate the underlying mechanism and reveal a role for promoter-proximal RNAPol II pausing: by mapping global Pol II occupancy using ChIP-seq, in conjunction with RNA-seq to identify repressed transcriptional networks unique to G0. Strikingly, Pol II pausing is enhanced in G0on genes encoding regulators of RNA biogenesis (Ncl, Rps24, Ctdp1), and release of pausing is critical for cell cycle re-entry. Finally, we uncover a novel, unexpected repressive role of the super-elongation complex component Aff4 in G0-specific stalling. We propose a model wherein Pol II pausing restrains transcription to maintain G0, preconfigures gene networks required for the G0-G1transition, and sets the timing of their transcriptional activation.
HIF-2α is essential for carotid body development and function
Authors: Macías David , Cowburn Andrew S. , Torres-Torrelo Hortensia , Ortega-Sáenz Patricia , López-Barneo José , S. Johnson Randall
Published: January 2018

Mammalian adaptation to oxygen flux occurs at many levels, from shifts in cellular metabolism to physiological adaptations facilitated by the sympathetic nervous system and carotid body (CB). Interactions between differing forms of adaptive response to hypoxia, including transcriptional responses orchestrated by the Hypoxia Inducible transcription Factors (HIFs), are complex and clearly synergistic. We show here that there is an absolute developmental requirement for HIF-2a, one of the HIF isoforms, for growth and survival of oxygen sensitive glomus cells of the carotid body. The loss of these cells renders mice incapable of ventilatory responses to hypoxia, and this has striking effects on processes as diverse as arterial pressure regulation, exercise performance, and glucose homeostasis. We show that the expansion of the glomus cells is correlated with mTORC1 activation, and is functionally inhibited by rapamycin treatment. These findings demonstrate the central role played by HIF-2a in carotid body development, growth and function.
Assessing Combinability of Phylogenomic Data using Bayes Factors
Authors: Neupane Suman , Fučíková Karolina , Lewis Louise A. , Kuo Lynn , Chen Ming-Hui , Lewis Paul O.
Published: January 2018

With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes/sites to infer phylogeny of any study system. While sampling large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the addition of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths. We explore using marginal likelihood to assess data subset combinability when data subsets have varying levels of phylogenetic discordance due to deep coalescence events among genes (simulated within a species tree), and compare the results with our recently-described phylogenetic informational dissonance index (D) estimated for each data set. BF effectively detects phylogenetic incongruence, and provides a way to assess the statistical significance of D values. We discuss methods for calibrating BFs, and use calibrated BFs to assess data combinability using an empirical data set comprising 56 plastid genes from green algae order Volvocales.
Gene flow and Andean uplift shape the diversification ofGasteracantha cancriformis(Araneae: Araneidae) in Northern South America
Authors: Salgado-Roa Fabian C. , Pardo-Diaz Carolina , Paulis Eloisa Lasso De , Arias Carlos F. , Solferini Vera Nisaka , Salazar Camilo
Published: January 2018

Aim

The Andean uplift has played a major role shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here we examined the phylogeography of the widespread and color polymorphic spiderGasteracantha cancriformisto: (i) evaluate the effect of the northern Andean uplift on its divergence and, (ii) assess whether its diversification occurred in the presence of gene flow.

Location

Northern Andes and Brazil

Methods

We inferred phylogenetic relationships and divergence times inG. cancriformisusing mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence and population structure were quantified. We also compared multiple demographic scenarios for this species using a model-based approach (PHRAPL) to establish divergence with or without gene flow. Finally, we evaluated the association between genetic variation and color polymorphism.

Results

Both nuclear and mitochondrial data supported two well-differentiated clades, which correspond to populations occurring in opposite sides of the Eastern cordillera of the Colombian Andes. The splitting between these clades occurred in the early Pleistocene, around 2.13 million years ago (95% HPD = 0.98–3.93).

Despite this vicariant event, there is shared genetic variation between the clades, which is better explained by a scenario of historical divergence in the face of gene flow. Color polymorphism was randomly scattered in both clades and is not statistically associated with the genetic variation studied here.

Main Conclusions

The final uplift of Eastern cordillera of the Colombian Andes was identified as the major force that shaped the diversification ofG. cancriformisin Northern South America, resulting in acis- andtrans-Andean phylogeographic structure for the species. The divergence in the face of gene flow betweencis- andtrans-Andean populations found for this spider has been likely facilitated by the presence of low-elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example where the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.
Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass- and dicot-cutter ants
Authors: Khadempour Lily , Fan Huan , Keefover-Ring Ken , Carlos Camila , Nagamoto Nilson S. , Dam Miranda A. , Pupo Monica T. , Currie Cameron R.
Published: January 2018

Leaf-cutter ants in the genusAttaare dominant herbivores in the Neotropics. While most species ofAttacut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12Attafungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. These differences in bacterial community composition and functional capacity show that different substrate inputs matter for fungus garden bacteria, and sheds light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.
Branch angle responses to photosynthesis are partially dependent on TILLER ANGLE CONTROL 1
Authors: Guseman Jessica M. , Dardick Christopher
Published: January 2018

Light serves as an important environmental cue in regulating plant architecture. Previous work had demonstrated that both photoreceptor-mediated signaling and photosynthesis play a role in determining the orientation of plant organs. TILLER ANGLE CONTROL 1 (TAC1) was recently shown to function in setting the orientation of lateral branches in diverse plant species, but the degree to which it plays a role in light-mediated phenotypes is unknown. Here, we demonstrated that TAC1 expression was light dependent, as expression was lost under dark or far-red growth conditions, but did not display any clear diurnal rhythm. Loss of TAC1 in the dark was gradual, and experiments with photoreceptor mutants indicated this was not dependent upon Red/Far-Red or Blue light signaling, but partially required the signaling integrator CONSTITUTIVE PHOTOMORPHGENESIS 1 (COP1). Over-expression of TAC1 partially prevented the narrowing of branch angles in the dark or under Far-Red light. Treatment with the carotenoid biosynthesis inhibitor Norflurazon or the PSII inhibitor DCMU led to loss of TAC1 expression similar to dark or far-red conditions, but surprisingly expression increased in response to the PSI inhibitor Paraquat. Our results indicate that TAC1 plays an important role in modulating plant architecture in response to photosynthetic signals.

HIGHLIGHT

Branch angles narrow in darkness or under far-red light. This response is partially mediated by TAC1 which responds to photosynthetic signals, providing a key link between photosynthesis and plant architecture.
Quantitative analysis of synaptic pathology and neuroinflammation: an initial study in a female rhesus monkey model of the “synaptic” phase of Alzheimer’s disease
Authors: Beckman Danielle , Donis-Cox Kristine , Ott Sean , Roberts Mary , Novik Lisa , Janssen William G. , Bliss-Moreau Eliza , Rudebeck Peter H. , Baxter Mark G. , Morrison John H.
Published: January 2018

Background

Soluble oligomers of the Aβ peptide (AβOs) are toxins that target and disrupt synapses. Generation of AβOs has been recently recognized as a probable initiating event in Alzheimer’s disease (AD), leading to cognitive impairment. There is a translational gap in AD studies, with promising drugs developed based on work in rodent models failing in AD patients in clinical trials. Additionally, although women have a two-fold greater lifetime risk of developing AD compared to men, females have not been a focus of preclinical studies. Thus, we sought to develop a model of AβO toxicity in female rhesus monkeys, to take advantage of the more highly differentiated cortical structure in this species as well as the similarities in the endocrine system between rhesus monkeys and humans.

Methods

Repeated intracerebroventricular (i.c.v) injections of AβOs were performed in adult female rhesus monkeys. Controls were unoperated aged matched monkeys. High-resolution confocal microscopy and morphometric analysis of Alexa 568 (A568) filled neurons were used to evaluate synaptic, neuronal, and glial markers in the dorsolateral prefrontal cortex (dlPFC) and hippocampus after AβO injections. Cerebrospinal fluid (CSF) and brain tissue were also collected and analyzed for biomarkers of AD pathology, including: phosphorylated Tau protein (pTau), total Tau, Aβ1-42, Aβ1-40 and TNF-α levels.

Results

Here, we report that AβO injection into the lateral ventricle of the brain induces loss of 37% of thin spines in targeted dlPFC neurons, an area highly vulnerable in AD and aging. Further, AβOs associate with the synaptic marker PSD95, inducing loss of more than 60% of local excitatory synapses. AβOs induce a robust neuroinflammatory response in the hippocampus, far from the injection site, with numerous activated ameboid microglia and TNF-α release. Finally, AβOs increased CSF levels of Aβ1-42, pTau Ser396 and pTau Ser199, but not Aβ1-40 or total Tau.

Conclusions

These initial findings from detailed quantitative analysis of effects of AβO administration on synapses in a female nonhuman primate model are a very promising step toward understanding the mechanism of early AD pathogenesis in the primate brain, and may help develop an effective disease-modifying therapy of high relevance to women’s health.
Fall prevention strategy in an emergency department
Authors: Muray Mwali , Bélanger Charles H. , Razmak Jamil
Published: January 2018

Purpose

The purpose of this paper is to document the need for implementing a fall prevention strategy in an emergency department (ED). The paper also spells out the research process that led to approving an assessment tool for use in hospital outpatient services.

Design/methodology/approach

The fall risk assessment tool was based on the Morse Fall Scale. Gender mix and age above 65 and 80 years were assessed on six risk assessment variables using χ2 analyses. A logistic regression analysis and model were used to test predictor strength and relationships among variables.

Findings

In total, 5,371 (56.5 percent) geriatric outpatients were deemed to be at fall risk during the study. Women have a higher falls incidence in young and old age categories. Being on medications for patients above 80 years exposed both genders to equal fall risks. Regression analysis explained 73-98 percent of the variance in the six-variable tool.

Originality/value

Canadian quality and safe healthcare accreditation standards require that hospital staff develop and adhere to fall prevention policies. Anticipated physiological falls can be prevented by healthcare interventions, particularly with older people known to bear higher risk factors. An aging population is increasing healthcare volumes and medical challenges. Precautionary measures for patients with a vulnerable cognitive and physical status are essential for quality care.
Integrating resilience in a supply chain planning model
Authors: Das Kanchan
Published: January 2018

Purpose

The purpose of this paper is to create a resilient supply chain (SC) plan to contain disruptions and risks in the overall operations of a business.

Design/methodology/approach

The study integrates resilience considerations in a business planning model that formulates resilience performance (RP) of SC functions in terms of flexibility, reliability, and similar system factors. It evaluates the RP of SC plans and determines their vulnerability considering required and planned resources. The model estimates the possible effects of disasters on vulnerable functions using a scenario-based analysis and plans containment options. It also includes decision options for deploying resources to achieve the expected levels of resilience by preventing potential vulnerabilities. The model takes optimum decision in a what-if approach by comparing performance of the existing business plan, with options for containing the vulnerabilities inherent in not considering potential risks when planning to fulfill market demand, and the performance of a resilient plan that includes decision options to prevent vulnerabilities where possible and mitigate them otherwise.

Findings

It is possible, for example, to evaluate RP of SC plans, identify vulnerable functions, and decide optimum option to create resilient business system.

Research limitations/implications

The present study takes a generic approach and creates bases to explore its application in any industry-based case.

Originality/value

The research introduces formulations for RPs and vulnerability indices that can be included in a planning model to create a resilient SC.
Multiplayer online role-playing as information retrieval and system use: an ethnographic study
Authors: Harviainen J. Tuomas , Rapp Amon
Published: January 2018

Purpose

The purpose of this paper is to expand the research of games as information systems. It illustrates how significant parts of massively multiplayer online role-playing function like information retrieval from a library database system.

Design/methodology/approach

By combining ideas from earlier contributions on the topics of game environments as information systems, the paper explores how gameplay connects to information retrieval, restricted content access, and information system structure. The paper then proceeds to examine this idea through an ethnographic study conducted inWorld of Warcraftduring 2012-2016.

Findings

By discussing how multiplayer digital game play is a form of information retrieval, the paper shows that players enjoy the well-restricted access to information that is a constitutive element of gameplay. Examining controlled access, procedural literacies and emphatic keywords, the paper finds that content relevances and system use may be influenced by hedonic concerns rather than task efficiency.

Originality/value

The study of retrieval issues related to gaming enriches our knowledge on inferences in retrieval. It shows that people may prefer that their access to information be limited, in order to make system use more interesting.
A task completion framework to support single-interaction IR research
Authors: van der Vegt Anton , Zuccon Guido , Koopman Bevan , Bruza Peter
Published: January 2018

Purpose

A conceptual model describes important factors within a system and how they relate to one another. They are important because they help to identify system changes that can yield the greatest improvement. Within information retrieval (IR), most research is directed towards multi-document retrieval and a multi-interaction IR user scenario. There are few, if any, IR conceptual models supporting minimal or single-interaction IR (siIR) user scenarios, however the need for siIR systems is growing rapidly. The purpose of this paper is to take the first step towards constructing a task-oriented conceptual model and experimental framework to support siIR research.

Design/methodology/approach

A first principles approach is employed to develop a task-oriented conceptual model, called bridging information retrieval (BIR). This model is contrasted with the concept of relevance, a central factor within IR research.

Findings

BIR introduces the central concept of bridging information (BI) as the objective of IR systems. BI is the additional information a user requires to complete a task, beyond their innate knowledge. The relationship between BI and relevance is determined.

Research limitations/implications

The theoretical basis of BIR is derived axiomatically; however the resulting system evaluation model is speculative.

Practical implications

The proposed operational framework offers researchers a systematic approach to designing and evaluating siIR systems.

Originality/value

This work contributes a novel task-oriented IR conceptual model and evaluation framework, both centred around the concept of BI for siIR. It also contributes a novel search task classification method.
Oral lichenoid reaction showing multiple ulcers associated with anti‐programmed death cell receptor‐1 treatment: A report of two cases and published work review
Authors: Obara Koya , Masuzawa Mamiko , Amoh Yasuyuki
Published: January 2018

Anti‐programmed cell death receptor‐1 (PD‐1) antibodies represent an effective treatment opinion for advanced melanoma and non‐small‐cell lung cancer, as well as other cancerous entities. Immune checkpoint inhibitors such as anti‐PD‐1 antibody result in a unique side‐effect profile, commonly described as immune‐related adverse events (irAE). These irAE affect the skin, gastrointestinal tract, liver, endocrine system and other organ systems. We report two cases of oral lichenoid reaction showing multiple ulcers associated with nivolumab treatment. Both patients presented with multiple ulcers covered with fibrinous plaque over the entire oral mucosa, lips and tongue. Histopathological examination of ulceration showed epithelial necrosis and subepidermal clefts with dense band‐like layers of lymphohistiocytic infiltrate within the upper dermis. Nivolumab was interrupted in both cases. Case 1 responded well to topical corticosteroids. Case 2 required oral corticosteroids, however, nivolumab could be restarted without recurrence of oral ulcers. We provide a comprehensive review of reported cases of lichenoid reaction showing multiple oral ulcers associated with anti‐PD‐1 therapy to date. Early recognition and management may improve treatment, avoid discontinuation of life‐saving therapy and maintain quality of life in these patients.
Epidermal aspects of type VII collagen: Implications for dystrophic epidermolysis bullosa and epidermolysis bullosa acquisita
Authors: Watanabe Mika , Natsuga Ken , Shinkuma Satoru , Shimizu Hiroshi
Published: January 2018

Type VII collagen (COL7), a major component of anchoring fibrils in the epidermal basement membrane zone, has been characterized as a defective protein in dystrophic epidermolysis bullosa and as an autoantigen in epidermolysis bullosa acquisita. Although COL7 is produced and secreted by both epidermal keratinocytes and dermal fibroblasts, the role of COL7 with regard to the epidermis is rarely discussed. This review focuses on COL7 physiology and pathology as it pertains to epidermal keratinocytes. We summarize the current knowledge of COL7 production and trafficking, its involvement in keratinocyte dynamics, and epidermal carcinogenesis in COL7 deficiency and propose possible solutions to unsolved issues in this field.
Characterization of skin blister fluids from children with Epstein–Barr virus‐associated lymphoproliferative disease
Authors: Wada Taizo , Toma Tomoko , Miyazawa Hanae , Koizumi Eiko , Shirahashi Tetsujiro , Matsuda Yusuke , Yachie Akihiro
Published: January 2018

Epstein–Barr virus (EBV)‐associated T‐ or natural killer (NK)‐cell lymphoproliferative disease (LPD) is a heterogeneous group of disorders characterized by chronic proliferation of EBV‐infected lymphocytes. Patients may present with severe skin manifestations, including hypersensitivity to mosquito bites (HMB) and hydroa vacciniforme (HV)‐like eruption, which are characterized by blister formation and necrotic ulceration. Skin biopsy specimens show inflammatory reactions comprising EBV‐infected lymphocytes. However, blister fluids have not been fully assessed in patients with this disease. Blister fluids were collected from three patients with EBV‐associated LPD: two with HMB and one with HV. Immunophenotyping of blister lymphocytes and measurement of tumor necrosis factor (TNF)‐α in blister fluids were performed. The patients with HMB and HV exhibited markedly increased percentages of NK and γδ T cells, respectively, in both peripheral blood and blister fluids. These NK and γδ T cells strongly expressed the activation marker human leukocyte antigen‐DR and were considered to be cellular targets of EBV infections. TNF‐α was highly elevated in all blister fluids. Severe local skin reactions of EBV‐associated LPD may be associated with infiltrating EBV‐infected lymphocytes and a high TNF‐α concentration in blister fluids.
Geo‐climatic factors drive diatom community distribution in tropical South American freshwaters
Authors: Benito Xavier , Fritz Sherilyn C. , Steinitz‐Kannan Miriam , Tapia Pedro M. , Kelly Meredith A. , Lowell Thomas V.
Published: January 2018

Patterns that maintain and generate biodiversity of macro‐organisms in the Neotropics are widely discussed in the scientific literature, yet the spatial ecology of micro‐organisms is largely unknown. The unique character of the tropical Andes and adjacent Amazon lowlands generates a wide gradient of environmental conditions to advance our understanding of what drives community assembly and diversity processes.

We analysed the distribution patterns of benthic diatoms (unicellular siliceous algae) as a model group of microbial passive dispersers, including predictors that describe limnological and geo‐climatic gradients for a total of 113 waterbodies (0–28°S and 58–80°W), including lakes and streams. Complementary multivariate statistical analyses were performed to correlate (1) community composition and (2) diatom species richness with environmental and spatial factors to infer niche‐based and dispersal‐based assembly processes, respectively.

Results showed that two gradients structured both diatom assemblages and waterbodies, namely climate and landscape configuration. Variance partitioning revealed that broadscale spatial variables (distance‐based Moran's Eigenvectors) outperformed the two environmental components (limnological and geo‐climatic), suggesting dispersal‐assembled communities. However, diatom assemblages were structured by geo‐climatic (regional) factors in certain lakes in the northern and central Andes, although their effects were partially manifested via local variables after the geographical distances were factored out. In a similar way, climatic and topographic structuring homogenized lake and stream communities within ecoregions, as indicated by the strong overlap between the two community types and the weak correlation between biota and limnological variables. Notably, a significant increase in diatom species richness was related to increased water connectivity, interpreted to indicate that a decrease in the remoteness of the system increase species number.

Synthesis. We emphasize the strength of macroecological gradients (landscape configuration and climatic factors) in affecting both diatom diversity and community composition in the South American tropics. In this context, our results and the commonalities of ecoregion patterning with groups of macro‐organisms (vegetation) suggest the need to integrate microbial ecology into a macroecology framework to unravel mechanisms behind diversity gradients.
The structure of plant spatial association networks is linked to plant diversity in global drylands
Authors: Saiz Hugo , Gómez‐Gardeñes Jesús , Borda Juan Pablo , Maestre Fernando T.
Published: January 2018

Despite commonly used to unveil the complex structure of interactions within ecological communities and their value to assess their resilience against external disturbances, network analyses have seldom been applied in plant communities. We evaluated how plant–plant spatial association networks vary in global drylands and assessed whether network structure was related to plant diversity in these ecosystems.

We surveyed 185 dryland ecosystems from all continents except Antarctica and built networks using the local spatial association between all the perennial plants species present in the communities studied. Then, for each network, we calculated four descriptors of network structure (link density, link weight mean and heterogeneity, and structural balance) and evaluated their significance with null models. Finally, we used structural equation models to evaluate how abiotic factors (including geography, topography, climate and soil conditions) and network descriptors influenced plant species richness and evenness.

Plant networks were highly variable world‐wide, but at most study sites (72%) presented common structures such as a higher link density than expected. We also find evidence of the presence of high structural balance in the networks studied. Moreover, all network descriptors considered had a positive and significant effect on plant diversity and on species richness in particular.

Synthesis. Our results constitute the first empirical evidence showing the existence of common network architectures structuring dryland plant communities at the global scale and suggest a relationship between the structure of spatial networks and plant diversity. They also highlight the importance of system‐level approaches to explain the diversity and structure of interactions in plant communities, two major drivers of terrestrial ecosystem functioning.
Interpretive walks: advancing the use of mobile methods in the study of entrepreneurial farm tourism settings
Authors: Mackay Michael , Nelson Tracy , Perkins Harvey C.
Published: January 2018

This article draws on the application of interpretive walks in a socio‐geographical study of tourism‐oriented entrepreneurial activity on multi‐generational family farms in New Zealand. We highlight the great potential this method holds for tourism researchers interested in the ways tourist spaces are produced in processes of place‐making. Mobile methods have been a feature of qualitative field research in several disciplines for some time, particularly in cultural geography with its emphasis on human interactions in and with landscapes. The interpretive walk, known also as the walking interview, has been applied mainly in urban neighbourhood, health, transport, and housing research, where it has proven very useful for revealing human connections to place that have been difficult to elicit using stationary face‐to‐face interviews. This article is one of the few that reports on the use of the method in a farm tourism setting. It is also one of few applied studies seeking to understand the local geographies of farm tourism and their connections to the farm site as both family home and place of primary production. The method is characterised as an effective tool for navigating and interpreting the socio‐spatial settings in which new rural tourism ventures emerge, evolve, and are embedded. The approach allows for unexpected encounters with spatial practices and strategies, projects, and objects, behind which lie stories of changing human relationships with the land, economy, and community, and of the exigencies of everyday life that are less readily unearthed using conventional interviews.
Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)
Authors: Gschloessl B. , Dorkeld F. , Berges H. , Beydon G. , Bouchez O. , Branco M. , Bretaudeau A. , Burban C. , Dubois E. , Gauthier P. , Lhuillier E. , Nichols J. , Nidelet S. , Rocha S. , Sauné L. , Streiff R. , Gautier M. , Kerdelhué C.
Published: January 2018

The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well‐studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine‐scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome‐predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high‐quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/).
Serotonin receptor 1A promoter polymorphism, rs6295, modulates human anxiety levels via altering parasympathetic nervous activity
Authors: Huang J.‐H. , Chang H.‐A. , Fang W.‐H. , Ho P.‐S. , Liu Y.‐P. , Wan F.‐J. , Tzeng N.‐S. , Shyu J.‐F. , Chang C.‐C.
Published: January 2018

Objective

The G‐allele of the ‐1019C/G (rs6295) promoter polymorphism of the serotonin receptor 1A (HTR1A) gene has been implicated in anxiety; however, the underlying neurophysiological processes are still not fully understood. Recent evidence indicates that low parasympathetic (vagal) tone is predictive of anxiety. We thus conducted a structural equation model (SEM) to examine whether the HTR1A rs6295 variant can affect anxiety by altering parasympathetic nervous activity.

Method

A sample of 1141 drug‐free healthy Han Chinese was recruited for HTR1A genotyping. Autonomic nervous function was assessed by short‐term spectral analysis of heart rate variability (HRV). Anxiety and stress levels were evaluated by the Beck Anxiety Inventory (BAI) and the Perceived Stress Scale (PSS) respectively.

Results

The number of the HTR1A G allele was inversely correlated with high‐frequency power (HF), a parasympathetic index of HRV. The HF index was negatively associated with BAI scores. Furthermore, the good‐fitting SEM, adjusting for confounding variables (e.g., age and PSS levels), revealed a significant pathway linking rs6295 variant to BAI scores via HF index modulation.

Conclusion

These results are the first to show that HTR1A ‐1019C/G polymorphism influences anxiety levels by modulating parasympathetic tone, providing a neurophysiological insight into the role of HTR1A in human anxiety.
Hidradenitis suppurativa, a review of pathogenesis, associations and management. Part 2
Authors: Vekic Dunja Ana , Cains Geoffrey David
Published: January 2018

Hidradenitis suppurativa is a chronic, painful, autoinflammatory condition resulting in nodules, abscesses and sinus tracts. We present an evidence‐based review providing new understanding of the pathogenesis of hidradenitis suppurativa and associated comorbidities. By the nature of their speciality, dermatologists are uniquely positioned to investigate and treat patients.
Liver resection for hepatocellular carcinoma: personal experiences in a series of 1330 consecutive cases in China
Authors: Li Jing , Huang Liang , Yan Jianjun , Qiu Maixuan , Yan Yiqun
Published: January 2018

Background

Liver resection to treat early stage hepatocellular carcinoma (HCC) is widely practised but surgery for intermediate and advanced stages of HCC is not included in the treatment algorithm of the Barcelona Clinic Liver Cancer, which has been adopted in official guidelines; nevertheless, resection beyond early stages is frequently undertaken and documented.

Methods

Between January 2001 and December 2014, all the HCC patients who underwent liver resection for the first time by Dr Yiqun Yan and his surgical team were enrolled. Clinical data were prospectively collected as well as the follow‐up results.

Results

A total of 1330 consecutive patients were included in the study, of which 452 (34.0%) suffered complications after liver resection with a mortality of 0.7%. The overall survival rates at 1‐, 3‐ and 5‐year were 91.2, 63.3 and 36.9%, respectively, while the disease‐free survival rates at 1‐, 3‐ and 5‐year were 67.7, 33.7 and 13.8%, respectively. Cases were classified into Barcelona Clinic Liver Cancer stage A (548 patients, 41.2%), stage B (613 patients, 46.1%) and stage C (169 patients, 12.7%). The overall survival time at 5‐year were 49.8, 32.8 and 10.6%, respectively, in patients with stage A, B and C tumours.

Conclusion

Liver resection to treat HCC is safe in patients with preserved liver function and good functional status. Liver resection should be the first line therapy in patients with single (regardless of tumour size) and resectable 2–3 tumours as well as vascular tumour thrombus if the tumour thrombus does not invade the major trunks.
Systematic misclassification of gestational age by ultrasound biometry: implications for clinical practice and research methodology in the Nordic countries
Authors: Skalkidou Alkistis , Kullinger Merit , Georgakis Marios K. , Kieler Helle , Kesmodel Ulrik S.
Published: January 2018

Historically, pregnancy dating has been based on self‐reported information on the first day of the last menstrual period. In the 1970s, ultrasound biometry was introduced as an alternative for pregnancy dating and is now the leading method in Nordic countries. The use of ultrasound led to a reduction of post‐term births and fewer inductions, and is considered more precise than last menstrual period‐based methods for pregnancy dating. Nevertheless, differences in early growth and specific situations, such as maternal obesity, can render its estimates less precise, leading to gestational age misclassification. Clinical implications of ultrasound dating include effect on timely induction in case of post‐term pregnancies, treatment with corticosteroids in cases of anticipated preterm delivery and decision on viability in cases of extreme prematurity. Furthermore, gestational age misclassification may influence the numbers and the magnitude of some adverse perinatal outcomes, closely related to gestational age, which are recorded in the Nordic birth registers.
Pelvic floor muscle function and quality of life in postmenopausal women with and without pelvic floor dysfunction
Authors: Frota Isabella Parente Ribeiro , Rocha Adriana Bombonato Oliveira , Neto José Ananias Vasconcelos , Vasconcelos Camila Teixeira Moreira , De Magalhaes Thais Fontes , Karbage Sara Arcanjo Lino , Augusto Kathiane Lustosa , Nascimento Simony Lira Do , Haddad Jorge Millem , Bezerra Leonardo Robson Pinheiro Sobreira
Published: January 2018

Introduction

This study aims to compare pelvic floor muscle (PFM) function in postmenopausal women with and without pelvic floor dysfunction (PFD) and the relation between PFM function and quality of life.

Material and methods

A case–control study with 216 postmenopausal women with (n = 126) and without (n = 90) PFD. PFM function was assessed by digital vaginal palpation using the PERFECT scale. Specific quality of life was evaluated using the King's Health Questionnaire for women with urinary incontinence and the Prolapse Quality‐of‐Life Questionnaire for women with pelvic organ prolapse. We analyzed women with PFD into two categories: Oxford's grade ≤2 or ≥3 using a chi‐squared test.

Results

Out of 126 womem with PFD 44 (34.9%) presented stress urinary incontinence, 21 (16.6%) had pelvic organ prolapse and 61 (48.4%) had urinary incontinence + pelvic organ prolapse. Strength had a median value 2 (0–5) in all women studied and most of them had insufficient strength, reduced endurance and repetition without statistical difference between groups. Incontinent women with strength ≤2 had worse perception of general health domain of King's Health Questionnaire (p = 0.007). No association was found between PFM function and Prolapse Quality‐of‐Life Questionnaire.

Conclusions

PFM function assessed by bidigital palpation in postmenopausal women was not sufficiently sensitive to differentiate between women with vs. women without PFM dysfunction and was not related with specific quality of life in women with urinary incontinence and pelvic organ prolapse, respectively. These data should be used to reinforce the widespread recommendation that PFM training is essencial in PFD treatment.
Prospective questionnaire study showed that higher self‐efficacy predicted longer exclusive breastfeeding by the mothers of late preterm infants
Authors: Gerhardsson Emma , Hildingsson Ingegerd , Mattsson Elisabet , Funkquist Eva‐Lotta
Published: January 2018

Aim

An important variable that influences breastfeeding outcomes is how confident a woman feels about her ability to breastfeed successfully at an early stage. We investigated breastfeeding self‐efficacy in the mothers of late preterm infants.

Methods

This was a prospective, comparative study that focused on mothers who had delivered babies at 34 + 0 to 36 + 6 weeks and were recruited in 2012–2015 from a neonatal intensive care unit and a postnatal ward at a Swedish university hospital. The Breastfeeding Self‐Efficacy Scale‐Short Form (BSES‐SF) was used to psychometrically assess the mothers at 40 weeks of postmenstrual age (n = 148) and at three months of corrected age (n = 114).

Results

The BSES‐SF scores were higher in the 87% of mothers that exclusively breastfed when their babies reached 40 weeks (57.1 out of 70) than those who did not (41.4, p < 0.001), indicating better self‐efficacy. The figures remained higher in the 68% of exclusive breastfeeding mothers at three months of corrected age (60.9 versus 51.7).

Conclusion

Self‐efficacy was an important predictor of the length of breastfeeding in mothers of late preterm infants, and the BSES‐SF can be used to detect low self‐efficacy that could lead to early breastfeeding cessation.
TRPV1 antagonists that cause hypothermia, instead of hyperthermia, in rodents: Compounds’ pharmacological profiles, in vivo targets, thermoeffectors recruited and implications for drug development
Authors: Garami A. , Pakai E. , McDonald H. A. , Reilly R. M. , Gomtsyan A. , Corrigan J. J. , Pinter E. , Zhu D. X. D. , Lehto S. G. , Gavva N. R. , Kym P. R. , Romanovsky A. A.
Published: January 2018

Aim

Thermoregulatory side effects hinder the development of transient receptor potential vanilloid‐1 (TRPV1) antagonists as new painkillers. While many antagonists cause hyperthermia, a well‐studied effect, some cause hypothermia. The mechanisms of this hypothermia are unknown and were studied herein.

Methods

Two hypothermia‐inducing TRPV1 antagonists, the newly synthesized A‐1165901 and the known AMG7905, were used in physiological experiments in rats and mice. Their pharmacological profiles against rat TRPV1 were studied in vitro.

Results

Administered peripherally, A‐1165901 caused hypothermia in rats by either triggering tail‐skin vasodilation (at thermoneutrality) or inhibiting thermogenesis (in the cold). A‐1165901‐induced hypothermia did not occur in rats with desensitized (by an intraperitoneal dose of the TRPV1 agonist resiniferatoxin) sensory abdominal nerves. The hypothermic responses to A‐1165901 and AMG7905 (administered intragastrically or intraperitoneally) were absent in Trpv1−/− mice, even though both compounds evoked pronounced hypothermia in Trpv1+/+ mice. In vitro, both A‐1165901 and AMG7905 potently potentiated TRPV1 activation by protons, while potently blocking channel activation by capsaicin.

Conclusion

TRPV1 antagonists cause hypothermia by an on‐target action: on TRPV1 channels on abdominal sensory nerves. These channels are tonically activated by protons and drive the reflectory inhibition of thermogenesis and tail‐skin vasoconstriction. Those TRPV1 antagonists that cause hypothermia further inhibit these cold defences, thus decreasing body temperature.

Significance

TRPV1 antagonists (of capsaicin activation) are highly unusual in that they can cause both hyper‐ and hypothermia by modulating the same mechanism. For drug development, this means that both side effects can be dealt with simultaneously, by minimizing these compounds’ interference with TRPV1 activation by protons.