bluuebunny/crossref_metadata_2025 huggingface dataset:
Is the distribution of the Acorn Woodpecker (Melanerpes formicivorus flavigula) associated with oaks and granaries? A local study in an urban area in northern South America
Authors: Oikawa Hana Londoño , Pulgarín-R Paulo C.
Published: September 2019

Abiotic and biotic factors are known to be key in limiting the geographical distribution of species. However, our understanding on the influence of habitat heterogeneity on ecological interactions and behavior in tropical animals is limited. We studied groups of Acorn Woodpeckers (Melanerpes formicivorus flavigula) in urban and rural areas in northern South America to understand how habitat and resource requirements (food storage structures) influences patterns of distribution across the Aburrá Valley, in the northern area of the Central Andes of Colombia. Using focal observations of 10 different groups over nearly a two-year period, we estimated territory size, habitat use, and described the use and presence of granaries. We found that territory size, tree diversity, and the use of granaries varied among groups. Accordingly, Acorn Woodpeckers use a wide variety of tree species to make cavities, to feed and to build granaries for social interactions. Our study supports the hypothesis that Acorn Woodpeckers do not rely on the Colombian Oak (Quercus humboldtiiBonpl.) for feeding, nesting or foraging in the Aburrá Valley, and that the construction of granaries to store food is present in urban populations, despite the lack of strong seasonal changes in tropical areas. We suggest that the distribution of the Acorn Woodpecker in our study area is strongly associated with one particular species of tree,Albizia carbonariaBritton, and the behavior of granaries construction might be hardwired in this species for the maintenance and cohesion of family groups.
European maize genomes unveil pan-genomic dynamics of repeats and genes
Authors: Haberer G. , Bauer E. , Kamal N. , Gundlach H. , Fischer I. , Seidel M.A. , Spannagl M. , Marcon C. , Ruban A. , Urbany C. , Nemri A. , Hochholdinger F. , Ouzunova M. , Houben A. , Schön C.-C. , Mayer K.F.X.
Published: September 2019

The exceptional diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report high qualityde novogenome sequences of the four European flint lines EP1, F7, DK105 and PE0075 assembled to pseudomolecules with scaffold N50 ranging between 6.1 to 10.4 Mb. Comparative analyses with the two US Corn Belt genomes B73 and PH207 elucidates the pronounced differences between both germplasm groups. While overall syntenic order and consolidated gene annotations reveal only moderate pan-genomic differences, whole genome alignments delineating the core and dispensable genome, and the analysis of repeat structures, heterochromatic knobs and orthologous long terminal repeat retrotransposons (LTRs) unveil the extreme dynamics of the maize genome. Haplotypes derived from core genome SNPs demonstrate the tessellation of modern maize resulting from a complex breeding history. The high quality genome sequences of the flint pool are a crucial complement to the maize pan-genome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.
Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
Authors: Puig Marta , Lerga-Jaso Jon , Giner-Delgado Carla , Pacheco Sarai , Izquierdo David , Delprat Alejandra , Gayà-Vidal Magdalena , Regan Jack F. , Karlin-Neumann George , Cáceres Mario
Published: September 2019

Despite the interest in characterizing all genomic variation, the presence of large repeats at the breakpoints of many structural variants hinders their analysis. This is especially problematic in the case of inversions, since they are balanced changes without gain or loss of DNA. Here we tested novel linkage-based droplet digital PCR (ddPCR) assays on 20 inversions ranging from 3.1 to 742 kb and flanked by long inverted repeats (IRs) of up to 134 kb. Among these, we validated 13 inversions predicted by different genome-wide techniques. In addition, we have generated new experimental human population information across 95 African, European and East-Asian individuals for 16 of them, including four already known inversions for which there were no high-throughput methods to determine directly the orientation, like the well-characterized 17q21 inversion. Through comparison with previous data, independent replicates and both inversion breakpoints, we have demonstrated that the technique is highly accurate and reproducible. Most of the studied inversions are frequent and widespread across continents, showing a negative correlation with genetic length. Moreover, all except two show clear signs of being recurrent, and the new data allowed us to define more clearly the factors affecting recurrence levels and estimate the inversion rate across the genome. Finally, thanks to the generated genotypes, we have been able to check inversion functional effects in multiple tissues, validating gene expression differences reported before for two inversions and finding new candidate associations. Our work therefore provides a tool to screen these and other complex genomic variants quickly in a large number of samples for the first time, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications.
Ciprofloxacin facilitates the transfer of XDR plasmids from commensalE. coliinto epidemic fluoroquinolone-resistantShigella sonnei
Authors: Duy Pham Thanh , Nguyen To Nguyen Thi , Thuy Duong Vu , The Hao Chung , Alcock Felicity , Boinett Christine , Thanh Ho Ngoc Dan , Tuyen Ha Thanh , Thwaites Guy E. , Rabaa Maia A , Baker Stephen
Published: September 2019

The global dissemination of a ciprofloxacin-resistant (cipR)S. sonneiclone outlines the mobility of this important agent of diarrheal disease, and threatens the utility of ciprofloxacin as a first-line antimicrobial for shigellosis. Here, we aimed to track the emergence of cipRS. sonneiin Vietnam to understand how novel antimicrobial resistant (AMR)Shigellaclones become established in new locations. From 2014 to 2016, we isolated and genome sequenced 79S. sonneifrom children hospitalized with dysenteric diarrhea in southern Vietnam. The novel cipRS. sonneiclone displaced the resident ciprofloxacin-susceptible lineage while acquiring resistance against third-generation cephalosporins, macrolides, and aminoglycosides. This process was not the result of a single clonal expansion, as we identified at least thirteen independent acquisitions of ESBL-encoding plasmids. The frequency and diversity of the variable AMR repertoire in an expanding clonal background ofS. sonneiis unprecedented and we speculated that it was facilitated by horizontal gene transfer from commensal organisms in the human gut. Consequently, we characterized non-ShigellaEnterobacteriaceae fromShigella-infected and healthy children by shotgun metagenomics. We identified a wide array of AMR genes and plasmids in the commensal Enterobacteriaceae, including anE. coliisolated from aShigella-infected child with an identical ESBL plasmid to that characterized in the infectingS. sonnei. We confirmed that these AMR plasmids could be exchanged between commensalE. coliandS. sonneiand found that supplementation of ciprofloxacin into the conjugation media significantly increased the conjugation frequency of IncI/blaCTX-M-15, IncB/O/blaCTX-M-27and IncF/blaCTX-M-27plasmids. In a setting with high antimicrobial use and a high prevalence of AMR commensals, cipRS. sonneimay be propelled towards pan-resistance by adherence to outdated international treatment guidelines. Our work highlights the role of the gut microbiota in transferring resistance plasmids into enteric pathogens and provides essential data to restrict the use of ciprofloxacin globally.
Dynamic production and loss of flagellar filaments during the bacterial life cycle
Authors: Zhuang Xiang-Yu , Guo Shihao , Li Zhuoran , Zhao Ziyi , Kojima Seiji , Homma Michio , Wang Pengyuan , Lo Chien-Jung , Bai Fan
Published: September 2019

Bacterial flagella are large extracellular protein organelles that drive bacteria motility and taxis in response to environmental changes. Previous research has focused mostly on describing the flagellar assembly, its rotation speed and power output. However, whether flagella are permanent cell structures and, if not, the circumstances and timing of their production and loss during the bacterial life cycle remain poorly understood. Here we used the single polar flagellum ofVibrio alginolyticusas our model and, usingin vivofluorescence imaging, revealed that the percentage of flagellated bacteria (PFB) in a population varies substantially across different bacterial growth phases. In the early-exponential phase, the PFB increases rapidly in respect to incubation time, mostly through widespread flagella production. In the mid-exponential phase, the PFB peaks at around 76% and the partitioning of flagella between the daughter cells is 1:1 and strictly at the old poles. After entering the stationary phase, the PFB starts to decline, mainly because daughter cells stop making new flagella after cell division. Interestingly, we discovered that bacteria can actively abandon flagella after prolonged stationary culturing, though cell division has long been suspended. Lack of glucose was found to be a major factor promoting flagellar disassembly. We also revealed that the active loss of flagella was initiated by breakage in the rod connecting the extracellular filament to the basal body formed by MS- and C-rings. Our results highlight the dynamic production and loss of flagellar filaments during the bacterial life cycle.
Extinction probabilities, times to extinction, basic reproduction number and growth rates for tsetse (Glossinaspp) populations as a function of temperature
Authors: Are Elisha B. , Hargrove John W.
Published: September 2019

Increases in temperature over recent decades have led to a significant reduction in the populations of tsetse flies (Glossinaspp) in parts of the Zambezi Valley of Zimbabwe. If this is true for other parts of Africa, populations of tsetse may actually be going extinct in some parts of the continent. Extinction probabilities for tsetse populations have not so far been estimated as a function of temperature. We develop a time-homogeneous branching process model for situations where tsetse flies live at different levels of fixed temperatures. We derive a probability distributionpk(T) for the number of female offspring an adult female tsetse is expected to produce in her lifetime, as a function of the fixed temperature at which she is living. We show thatpk(T) can be expressed as a geometric series: its generating function is therefore a fractional linear type. We obtain expressions for the extinction probability, expected number of female offspring per female tsetse, and time to extinction. No tsetse population can escape extinction if subjected, for extended periods, to temperatures outside the range 16 °C - 32°C. Extinction probability increases more rapidly as temperatures approach and exceed the upper and lower limits. If the number of females is large enough, the population can still survive even at high temperatures (28°C - 31°C). Small decreases or increases in constant temperature in the neighbourhoods of 16°C and 31°C, respectively, can drive tsetse populations to extinction. Further study is needed to estimate extinction probabilities for tsetse populations in field situations where temperatures vary continuously.

Author summary

Tsetse flies (Glossinaspp) are the vectors of the African sleeping sickness. We derived an expression for the extinction probability, and mean time to extinction, of closed populations of the flies experiencing different levels of fixed temperatures. Temperatures play a key role in tsetse population dynamics: no tsetse populations can escape extinction at constant temperatures < 16°C > 32°C. The effect of temperature is more severe if tsetse populations are already depleted. Increasingly high temperatures due to climate change may alter the distribution of tsetse populations in Africa. The continent may witness local extinctions of tsetse populations in some places, and appearances in places hitherto too cold for them.
Strategies to improve scFvs as crystallization chaperones suggested by analysis of a complex with the human PHD-bromodomain SP140
Authors: Fairhead Michael , Preger Charlotta , Wigren Edvard , Strain-Damerell Claire , Ossipova Elena , Ye Mingda , Makola Mpho , Burgess-Brown Nicola A. , Persson Helena , von Delft Frank , Gräslund Susanne
Published: September 2019

Antibody fragments have great potential as crystallization chaperones for structural biology due to their ability to either stabilise targets, trap certain conformations and/or promote crystal packing. Here we present an example of using a single-chain variable fragment (scFv) to determine the previously unsolved structure of the multidomain protein SP140. This nuclear leukocyte-specific protein contains domains related to chromatin-mediated gene expression and has been implicated in various disease states. The structure of two of the domains (PHD-bromodomain) was solved by crystallizing them as a complex with a scFv generated by phage display technology. SP140 maintains a similar overall fold to previous PHD-bromodomains and the scFv CDR loops predominately interact with the PHD, while the framework regions of the scFv makes numerous interactions with the bromodomain. Analysis of our and other complex structures suggest various protein engineering strategies that might be employed to improve the usefulness of scFvs as crystallization chaperones.
Repurposing cell growth-regulating compounds identifies kenpaullone which ameliorates pathologic pain via normalization of inhibitory neurotransmission
Authors: Yeo Michele , Chen Yong , Jiang Changyu , Chen Gang , Wang Kaiyuan , Bortsov Andrey , Lioudyno Maria , Zeng Qian , Wang Zilong , Busciglio Jorge , Ji Ru-Rong , Liedtke Wolfgang
Published: September 2019

Inhibitory GABA-ergic neurotransmission is fundamental for the adult vertebrate central nervous system and requires low chloride ion concentration in neurons. This basic ionic-homeostatic mechanism relies on expression and function of KCC2, a neuroprotective ionic transporter that extrudes neuronal chloride. Importantly, no other transporter can rescue KCC2 deficit, and attenuated expression of KCC2 is strongly associated with circuit malfunction in chronic pain, epilepsy, neuro-degeneration, neuro-trauma, and other neuro-psychiatric illnesses. To isolate Kcc2 gene expression-enhancing compounds, we screened 1057 cell growth-regulating compounds in cultured primary cortical neurons. We identified kenpaullone (KP), which enhanced Kcc2/KCC2 expression and function in cultured rodent and human neurons by inhibiting GSK3ß. KP effectively reduced pathologic pain in preclinical mouse models of nerve constriction injury and bone cancer. In nerve-injury pain, KP restored Kcc2 expression and GABA-evoked chloride reversal potential in the spinal cord dorsal horn. Delta-catenin, a phosphorylation-target of GSK3ß in neurons, activated the Kcc2 promoter via Kaiso transcription factor. Validating this new pathway in-vivo, transient spinal over-expression of delta-catenin mimicked KP analgesia. With relevance for pathologic pain, our discoveries of a newly repurposed compound and a novel genetically-encoded mechanism that each enhance Kcc2 gene expression enable us to re-normalize disrupted inhibitory neurotransmission through genetic re-programming.
The RAF oncogenes of vertebrates are ohnologs that derive from the two rounds of whole genome duplications early in vertebrate evolution
Authors: Black Amanda Coward , Bailey Mary Clay , Ruane-Foster Marisa , Opazo Juan C. , Hoffmann Federico G.
Published: September 2019

The Rapidly Accelerated Fibrosarcoma (RAF) kinases are part of large group of serine/threonine-specific protein kinases that play important roles in cell differentiation and organism development. Animal RAF kinases are key connectors in the signaling cascade that links the small G protein RAS and the Mitogen-activated protein kinase phosphorylation pathway. Mutations in the RAF genes have been linked to a number of cancers including melanoma, lung cancer, colorectal cancer, thyroid cancer, and ovarian cancer. Most animals possess a single RAF gene, but vertebrates have three RAF genes in their genomes, named as A-, B-, and C-RAF, the latter also known as RAF-1. The emergence of the multiple copies of vertebrate RAFs is not well resolved, on the one hand, because of sequence and functional similarities, some authors speculate that vertebrate B-Raf is most closely related to the RAF genes of the fruit fly and Caenorhabditis elegans, whereas a competing hypothesis is that the A-, B- and C-RAF paralogs emerged from the two rounds of whole genome duplications that occurred early in the evolution of vertebrates. We applied a comparative approach grounded in synteny and phylogenetic analyses to evaluate these two scenarios. Our results are consistent with the hypothesis that the RAF genes of vertebrates are paralogs generated by whole genome duplications. Thus, the functional similarities between vertebrate B-RAF and invertebrate RAF probably reflect the retention of ancestral characters. Interestingly, data from the literature indicate that B-RAF is the paralog that associated with cancer more strongly, and also yields the most severe phenotypes when knocked out.
Trajectories from Snapshots: Integrated proteomic and metabolic single-cell assays reveal multiple independent adaptive responses to drug tolerance in a BRAF-mutant melanoma cell line
Authors: Su Yapeng , Li Guideng , Ko Melissa E. , Cheng Hanjun , Zhu Ronghui , Xue Min , Wang Jessica , Lee Jihoon W. , Frankiw Luke , Xu Alexander , Wong Stephanie , Robert Lidia , Takata Kaitlyn , Huang Sui , Ribas Antoni , Levine Raphael , Nolan Garry P. , Wei Wei , Plevritis Sylvia K. , Baltimore David , Heath James R.
Published: September 2019

The determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge, with relevance towards understanding biological changes ranging from cellular differentiation to epigenetic (adaptive) responses of diseased cells to drugging. We report on a combined experimental and theoretic method for determining the trajectories that specific highly plastic BRAFV600E mutant patient-derived melanoma cancer cells take between drug-naïve and drug-tolerant states. Recent studies have implicated non-genetic, fast-acting resistance mechanisms are activated in these cells following BRAF inhibition. While single-cell highly multiplex omics tools can yield snapshots of the cell state space landscape sampled at any given time point, individual cell trajectories must be inferred from a kinetic series of snapshots, and that inference can be confounded by stochastic cell state switching. Using a microfludic-based single-cell integrated proteomic and metabolic assay, we assayed for a panel of signaling, phenotypic, and metabolic regulators at four time points during the first five days of drug treatment. Dimensional reduction of the resultant data set, coupled with information theoretic analysis, uncovered a complex cell state landscape and identified two distinct paths connecting drug-naïve and drug-tolerant states. Cells are shown to exclusively traverse one of the two pathways depending on the level of the lineage restricted transcription factor MITF in the drug-naïve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities, and are independently druggable. Our results update the paradigm of adaptive resistance development in an isogenic cell population and offer insight into the design of more effective combination therapies.
Signaling to TRP53 and TAp63 from CHK1/CHK2 is responsible for elimination of most oocytes defective for either chromosome synapsis or recombination
Authors: Rinaldi Vera D. , Bloom Jordana C. , Schimenti John C.
Published: September 2019

Eukaryotic organisms have evolved mechanisms to prevent the accumulation of cells bearing genetic aberrations. This is especially crucial for the germline, because fecundity, and fitness of progeny would be adversely affected by an excessively high mutational incidence. The process of meiosis poses unique problems for mutation avoidance, due to the requirement for SPO11-induced programmed double strand breaks (DSBs) in recombination-driven pairing and segregation of homologous chromosomes. Mouse meiocytes bearing unrepaired meiotic DSBs or unsynapsed chromosomes are eliminated before completing meiotic prophase I. In previous work, we showed that checkpoint kinase 2 (CHK2; CHEK2), a canonical DNA damage response protein, is crucial for eliminating not only oocytes defective in meiotic DSB repair (e.g.Trip13Gtmutants), but also asynapticSpo11−/−oocytes that accumulate a threshold level of spontaneous DSBs. However, rescue of such oocytes byChk2deficiency was incomplete, raising the possibility that a parallel checkpoint pathway(s) exists. Here, we show that mouse oocytes lacking both TAp63 and TRP53 protects nearly allSpo11−/−andTrip13Gt/Gtoocytes from elimination. We present evidence that checkpoint kinase I (CHK1; CHEK1), which is known to signal to TRP53, also becomes activated by persistent DSBs in oocytes, and to an increased degree when CHK2 is absent. The combined data indicate that nearly all oocytes reaching a threshold level of unrepaired DSBs are eliminated by a semi-redundant pathway of CHK1/CHK2 signaling to TRP53/TAp63.
A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
Authors: Mai Te-Lun , Chuang Trees-Juen
Published: September 2019

Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual can carry dozens of missense variants predicted to be severely deleterious. Why strongly detrimental variants are preserved in a population and not eliminated by negative natural selection remains mostly unclear. Here, we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating genome and transcriptome sequencing data from 447 human lymphoblastoid cell lines, we show that nonsynonymous editing activities (prevalence/level) are negatively correlated with the deleteriousness of A-to-G genomic changes and positively correlated with that of G-to-A genomic changes within the population. We find a significantly negative correlation between nonsynonymous editing activities and allele frequency of A within the population. This negative editing-allele frequency correlation is particularly strong when editing sites are located in highly important genes/loci. Examinations of deleterious missense variants from the 1000 Genomes Project further show a significantly higher proportion of rare missense mutations for G-to-A changes than for other types of changes. The proportion for G-to-A changes increases with increasing deleterious effects of the changes. Moreover, the deleteriousness of G-to-A changes is significantly positively correlated with the percentage of editing enzyme binding motifs at the variants. Overall, we show that nonsynonymous editing is associated with the increased burden of G-to-A missense mutations in healthy individuals, expanding RNA editing in pathogenomics studies.
An approach for fault prediction in SOA-based systems using machine learning techniques
Authors: Bhandari Guru Prasad , Gupta Ratneshwer , Upadhyay Satyanshu Kumar
Published: September 2019

Purpose

Software fault prediction is an important concept that can be applied at an early stage of the software life cycle. Effective prediction of faults may improve the reliability and testability of software systems. As service-oriented architecture (SOA)-based systems become more and more complex, the interaction between participating services increases frequently. The component services may generate enormous reports and fault information. Although considerable research has stressed on developing fault-proneness prediction models in service-oriented systems (SOS) using machine learning (ML) techniques, there has been little work on assessing how effective the source code metrics are for fault prediction. The paper aims to discuss this issue.

Design/methodology/approach

In this paper, the authors have proposed a fault prediction framework to investigate fault prediction in SOS using metrics of web services. The effectiveness of the model has been explored by applying six ML techniques, namely, Naïve Bayes, Artificial Networks (ANN), Adaptive Boosting (AdaBoost), decision tree, Random Forests and Support Vector Machine (SVM), along with five feature selection techniques to extract the essential metrics. The authors have explored accuracy, precision, recall, f-measure and receiver operating characteristic curves of the area under curve values as performance measures.

Findings

The experimental results show that the proposed system can classify the fault-proneness of web services, whether the service is faulty or non-faulty, as a binary-valued output automatically and effectively.

Research limitations/implications

One possible threat to internal validity in the study is the unknown effects of undiscovered faults. Specifically, the authors have injected possible faults into the classes using Java C3.0 tool and only fixed faults are injected into the classes. However, considering the Java C3.0 community of development, testing and use, the authors can generalize that the undiscovered faults should be few and have less impact on the results presented in this study, and that the results may be limited to the investigated complexity metrics and the used ML techniques.

Originality/value

In the literature, only few studies have been observed to directly concentrate on metrics-based fault-proneness prediction of SOS using ML techniques. However, most of the contributions are regarding the fault prediction of the general systems rather than SOS. A majority of them have considered reliability, changeability, maintainability using a logging/history-based approach and mathematical modeling rather than fault prediction in SOS using metrics. Thus, the authors have extended the above contributions further by applying supervised ML techniques over web services metrics and measured their capability by employing fault injection methods.
Employers’ preferences for IT-retrainees: evidence from a discrete choice experiment
Authors: Vooren Melvin , Haelermans Carla , Groot Wim , Maassen van den Brink Henriette
Published: September 2019

Purpose

The purpose of this paper is to present the results of a discrete choice experiment (DCE) on the competencies of potential information technology (IT)-retrainees. The results give insights in the monetary value and relative returns to both soft and hard skills.

Design/methodology/approach

The authors apply a DCE in which the authors propose seven pairs of hypothetical candidates to employers based in the municipality of Amsterdam, the Netherlands. These hypothetical candidates differ on six observable skill attributes and have different starting wages. The authors use the inference from the DCE to calculate the marginal rates of substitution (MRS). The MRS gives an indication of the monetary value of each skill attribute.

Findings

Employers prefer a candidate who possesses a degree in an exact field over a similar candidate from another discipline. Programming experience from previous jobs is the most highly valued characteristic for an IT-retrainee. Employers would pay a candidate with basic programming experience a 53 percent higher starting wage. The most high-valued soft skill is listening skills, for which employers are willing to pay a 46 percent higher wage. The results of this paper show that both hard and soft skills are important, but not all soft skills are equally important.

Originality/value

The results on the returns to skills provide guidelines to tailor IT training and retraining programs to the needs of the business environment. A key strength of this paper is that the authors have information on the preference orderings for different skills and kinds of experience.
Airport noise compensation: real estate perspective
Authors: Batóg Jacek , Foryś Iwona , Konowalczuk Jan
Published: September 2019

Purpose

This study aims to present a problem of noise compensation related to the localization of single-family houses in the restricted use areas (RUA) created around airports. The authors presented different methodological approaches to the valuation of such amends and characterized distinct solutions applied in that area in chosen countries and cities.

Design/methodology/approach

To estimate the level of those indemnities, linear models including spatial and generalized linear models, were applied. The set of explanatory variables contains quantitative and qualitative attributes of real estates. The influence of outliers indicated by means of cluster analysis on the received results were also considered.

Findings

The results show that after accounting for noise level and house characteristics, houses in noisier areas were sold for less than houses subjected to less noise. Unit prices of houses located outside the RUA were on average 17.05 per cent higher than the prices observed in zone with noise level for the daytime of 60 dB and 8.95 per cent in zone characterized by noise level for the daytime of 55 dB.

Practical implications

Received results can be compared with results obtained by other authors, but its most important application is possibility of use the proposed methodology by judicial appraisers to assess the proper level of noise compensation for home owners or tenants.

Originality/value

An identification of real estate market heterogeneity and its considering in estimation of compensation related to airport noise evidence some novelty of the research.
Field measurements of comfort, seasonal performance and cold stress in cross-laminated timber (CLT) school buildings
Authors: Adekunle Timothy Oluseun
Published: September 2019

Purpose

The purpose of this paper is to examine the seasonal performance, occupants’ comfort and cold stress in cross-laminated timber school buildings located in the USA (Northeast region).

Design/methodology/approach

The Fall survey was done from October–November 2017. In the Winter, it was considered from December 2017–February 2018. The study measured environmental parameters in the chosen spaces. The research applied the wet-bulb globe temperature (WBGT) model to determine the indexes in various seasons.

Findings

In the Fall, the average inside temperature was 21.2°C, the average RH was 50.7 per cent, and the mean dew-point was 9.3°C. The mean inside temperature was 20.5°C in the Winter while the mean RH was 23.9 per cent and the average dew-point was −1.9°C. The overall mean inside temperatures in both seasons were within the ASHRAE comfort temperature limits for cold seasons. During the surveys, higher average values of temperature, RH and dew-point were measured in the offices than the other spaces.

Practical implications

The research showed people might be subject to lower temperatures in the hall than the other spaces. Some design parameters and occupation hours may contribute to the lower temperatures reported in the hall than the different spaces.

Originality/value

The study proposes the WBGT of 16.0°C and 13.7°C as the stress indexes in the Fall and Winter seasons correspondingly. Last, the research suggests a WBGT of 14.9°C as the overall mean stress index within the spaces considered in this study.
Fire history and plant community composition outweigh decadal multi‐factor global change as drivers of microbial composition in an annual grassland
Authors: Qin Clara , Zhu Kai , Chiariello Nona R. , Field Christopher B. , Peay Kabir G.
Published: September 2019

Soil microbial communities regulate and respond to key biogeochemical cycles and influence plant community patterns. However, microbial communities also respond to disturbance events, motivating an assessment of the relative roles of decadal multi‐factor global change, disturbance and plant community structure on microbial community responses.

We used high‐throughput amplicon sequencing to characterize the diversity and composition of bacterial and fungal communities in bulk soil (0–7 cm) collected in 2014 from the Jasper Ridge Global Change Experiment, a full‐factorial field experiment in which ambient and elevated levels of nitrogen deposition (+7 g N m−2 yr−1 calcium nitrate), CO2 concentration (+275 ppm), temperature (+1–2°C) and precipitation (+50% volume with +3 weeks duration) were applied to a California annual grassland from 1998 to 2014. We used linear mixed‐effects modelling to test for the effects of global change on microbial diversity (observed richness, Shannon index). We also used generalized dissimilarity modelling (GDM) to study controls on compositional dissimilarity in fungal and bacterial communities.

Bacterial community composition was best explained by exposure to fires in 2003 and 2011, whereas fungal community composition was best explained by plant community composition. The richness of fungi increased under elevated nitrogen deposition; bacterial diversity metrics decreased under warmer temperatures. Interactions between global change factors were statistically insignificant or weak.

Synthesis. Our results indicate that even on decadal time‐scales, the effects of fire history and plant community composition on bacterial and fungal community composition, respectively, outweigh the effects of multi‐factor global change. Furthermore, global change factors have mostly additive effects on microbial diversity patterns. Our results show that highly variable mediators such as fire history and plant community composition limit the generalizability of soil microbial responses to long‐term global change.
Plant physical and chemical traits associated with herbivory in situ and under a warming treatment
Authors: Descombes Patrice , Kergunteuil Alan , Glauser Gaëtan , Rasmann Sergio , Pellissier Loïc
Published: September 2019

Plants protect themselves against herbivore attacks with physical traits and toxic secondary metabolites. Levels of plant defences and herbivore performance might shift under climate warming, particularly in alpine habitats, where herbivore pressure is currently low. Plant responses to warming should be driven by species‐specific shifts in physical and chemical defence traits.

We investigated the association between plant leaf physical and chemical traits and herbivory under current and warmer climates in three grasslands along a subalpine to alpine gradient. Specifically, we measured the rate of in situ natural herbivory, and performed bioassays to measure overall plant species‐level resistance using the extreme generalist non‐native caterpillarSpodoptera littoralis. We simulated warmer conditions by using open‐top chambers and assessed the effect of warming on leaf physical and chemical traits, and how trait changes affect caterpillar performance.

Natural herbivory and caterpillar performance were associated with plant physical traits, including specific leaf area, and with ordination axes representing dimensions of the plant chemical profile. We found that the warming treatment independently decreased the number of distinct chemical compounds per species, and marginally increased specific leaf area. Changes in leaf functional traits were not systematically associated with changes in caterpillar performance.

Synthesis. Plant physical traits and chemical profiles are both related to natural herbivory and plant resistance againstSpodoptera littoralis. While leaf physical and chemical traits of high elevation plants were modified by the warming treatment, these changes did not result in predictable effects on plant resistance against herbivores.
Getting the Sergeants on your side: the importance of interpersonal relationships and cultural interoperability for generating interagency collaboration between nurses and the police in custody suites
Authors: Rees Gethin
Published: September 2019

In this article, I contribute to the literature around interagency collaboration, especially between law enforcement and health care, by reconciling the previous work of Sarah Charman (2014) with the interprofessional teamwork literature. Drawing upon a semi‐structured interview‐based study with 20 custody nurses working in English police custody suites (analysed using Framework Analysis), I explore the ways they are able to achieve interagency collaboration with a particular police officer, the Desk Sergeant. I argue that nurses accomplish interagency interoperability by interacting regularly with the Desk Sergeant, anticipating their needs and limiting their own goals to those that are commensurate with the Desk Sergeant's, notably providing information and avoiding deaths in custody. Such practices are similar to the strategies of ‘Cultural Interoperability’ noted by Charman (2014); however, this study also identifies that such strategies are only available once a successful working relationship has formed between Desk Sergeant and nurse, and as a result, similarly to the findings of interprofessional teamwork studies, the success or failure of attempts to collaborate across agencies is underpinned by interpersonal relations. The paper concludes by commenting on the importance of analysing both the interpersonal and organisation levels when studying collaboration.
Algorithmic management and app‐work in the gig economy: A research agenda for employment relations and HRM
Authors: Duggan James , Sherman Ultan , Carbery Ronan , McDonnell Anthony
Published: September 2019

Current understanding of what constitutes work in the growing gig economy is heavily conflated, ranging from conceptualisations of independent contracting to other forms of contingent labour. This article calls for a move away from problematic aggregations by proposing a classification of gig work into three variants, all based strongly upon key technological features: app‐work, crowdwork, and capital platform work. Focusing specifically on the app‐work variant, this article's more delineated focus on the textured dimensions of this work proposes new lines of enquiry into employment relationships and human resource management. Examining the crucial role of algorithmic management, we critically discuss the impact of this novel mediation tool used by gig organisations for the nature of employment relations within app‐work, work assignment processes, and performance management. In so doing, we propose a series of research questions that can serve as a guide for future research in this increasingly important field.
Individualized mating system estimation using genomic data
Authors: Colicchio Jack , Monnahan Patrick J. , Wessinger Carolyn A. , Brown Keely , Kern James Russell , Kelly John K.
Published: September 2019

The estimation of outcrossing rates in hermaphroditic species has been a major focus in the evolutionary study of reproductive strategies, and is also essential for plant breeding and conservation. Surprisingly, genomics has thus far minimally influenced outcrossing rate studies. In this article, we generalize a Bayesian inference method (BORICE) to accommodate genomic data from multiple subpopulations of a species. As an empirical demonstration, BORICE is applied to 115 maternal families of Mimulus guttatus. The analysis shows that low‐level whole genome sequencing of parents and offspring is sufficient for individualized mating system estimation: 208 offspring (88.5%) were definitively called as outcrossed, 23 (9.8%) as selfed. After mating system parameters are established (each offspring as outcrossed or selfed and the inbreeding level of maternal plants), BORICE outputs posterior genotype probabilities for each SNP genomewide. Individual SNP calls are often burdened with considerable uncertainty and distilling information from closely linked sites (within genomic windows) can be a useful strategy. For the Mimulus data, principal components based on window statistics were sufficient to diagnose inversion polymorphisms and estimate their effects on spatial structure, phenotypic and fitness measures. More generally, mating system estimation with BORICE can set the stage for population and quantitative genomic analyses, particularly researchers collect phenotypic or fitness data from maternal individuals.
Assessment of genetic diversity and population structure in cultured Australian Pacific oysters
Authors: Kijas J. W. , Gutierrez A. P. , Houston R. D. , McWilliam S. , Bean T. P. , Soyano K. , Symonds J. E. , King N. , Lind C. , Kube P.
Published: September 2019

The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (HE) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low‐density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.
LVAD speed increase during exercise, which patients would benefit the most? A simulation study
Authors: Gross Christoph , Moscato Francesco , Schlöglhofer Thomas , Maw Martin , Meyns Bart , Marko Christiane , Wiedemann Dominik , Zimpfer Daniel , Schima Heinrich , Fresiello Libera
Published: September 2019

Patients supported with a left ventricular assist device (LVAD) have impaired cardiovascular adaptations during exercise, resulting in reduced total cardiac output and exercise intolerance. The aim of this study is to report associations among these impaired cardiovascular parameters and exercise hemodynamics, and to identify in which conditions an LVAD speed increase can provide substantial benefits to exercise. A cardiorespiratory simulator was used to reproduce the average hemodynamics of LVAD patients at exercise. Then, a sensitivity study was conducted where cardiovascular parameters were changed individually ±20% of their baseline value at exercise (heart rate, left/right ventricular contractility, total peripheral resistance, and valve pathologies). Simulations were performed at a baseline LVAD speed of 2700 rpm and repeated at 3500 rpm to evaluate the benefits of a higher LVAD support on hemodynamics. Total cardiac output (TCO) was mostly impaired by a poor left ventricular contractility or vasodilation at exercise (−0.6 L/min), followed by a poor chronotropic response (−0.3 L/min) and by a poor right ventricular contractility (−0.2 L/min). LVAD speed increase better unloads the left ventricle and improves total cardiac output in all the simulated conditions. The most substantial benefits from LVAD speed increase were observed in case of poor left ventricular contractility (TCO + 1.6 L/min) and vascular dysfunction (TCO + 1.4 L/min) followed by lower heart rate (TCO + 1.3 L/min) and impaired right ventricular contractility (TCO + 1.1 L/min). Despite the presence of the LVAD, exercise hemodynamic is strongly depending on the ability of the cardiovascular system to adapt to exercise. A poor left ventricular inotropic response and a poor vascular function can strongly impair cardiac output at exercise. In these conditions, LVAD speed increase can be an effective strategy to augment total cardiac output and unload the left ventricle. These results evidence the need to design a physiological LVAD speed controller, tailored on specific patient’s needs.
Bone, subcutaneous tissue and plasma pharmacokinetics of cefuroxime in total knee replacement patients – a randomized controlled trial comparing continuous and short‐term infusion
Authors: Tøttrup Mikkel , Søballe Kjeld , Bibby Bo M. , Hardlei Tore F. , Hansen Peter , Fuursted Kurt , Birke‐Sørensen Hanne , Bue Mats
Published: September 2019

Cefuroxime is widely used as antibiotic prophylaxis for orthopaedic procedures. We evaluated bone, subcutaneous tissue (SCT) and plasma pharmacokinetics of cefuroxime in male patients undergoing total knee replacement (TKR) after both traditional short‐term infusion (STI) and continuous infusion (CI). Eighteen male patients undergoingTKRwere randomly assigned toSTIorCIof 1.5 g of cefuroxime. Measurements were obtained in plasma,SCT, cancellous and cortical bone every 30 min for 8 h following surgery. For sampling in solid tissues, microdialysis was applied. Population pharmacokinetic modelling was performed in order to estimate pharmacokinetic parameters, and to assess the probability of attaining cefuroxime concentrations above clinically relevant minimal inhibitory concentrations (MICs) for 65% and 90% of the 8 h dosing interval. LowSCTand cortical bone penetration were found in both theSTIand theCIgroup, but the findings were only significant in theSTIgroup. Irrespective ofMIC, tissue and target,CIleads to improved probability of attaining relevant pharmacokinetic targets compared withSTI. For theStaphylococcus aureusMICbreakpoint (4 μg/mL),STIleads to inadequate probability of target attainment.CIof 1.5 g of cefuroxime leads to improved probability of attaining relevant pharmacokinetic targets in maleTKRpatients compared with traditionalSTI. These findings suggest that application ofCImay improve antibiotic prophylaxis for maleTKRpatients.