bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring population responses to environmental change when there’s never enough data; a factor analytic approach
Authors: Hindle Bethan J. , Rees Mark , Sheppard Andy W. , Quintana-Ascencio Pedro F. , Menges Eric S. , Childs Dylan Z. 
Published: September 2017

AbstractTemporal variability in the environment drives variation in individuals’ vital rates, with consequences for population dynamics and life history evolution. Integral projection models (IPMs) are data-driven models widely used to study population dynamics and life history evolution of structured populations in temporally variable environments. However, many data sets have insufficient temporal replication for the environmental drivers of vital rates to be identified with confidence, limiting their use for evaluating population level responses to environmental change.Parameter selection, where the kernel is constructed at each time step by randomly selecting the time-varying parameters from their joint probability distribution, is one approach to including stochasticity in IPMs. We consider a factor analytic (FA) approach for modelling the covariance matrix of time-varying parameters, whereby latent variable(s) describe the covariance among vital rate parameters. This decreases the number of parameters to estimate and, where the covariance is positive, the latent variable can be interpreted as a measure of environmental quality. We demonstrate this using simulation studies and two case studies.The simulation studies suggest the FA approach provides similarly accurate estimates of stochastic population growth rate to estimating an unstructured covariance matrix. We demonstrate how the latent parameter can be perturbed to show how selection on reproductive delays in the monocarpCarduus nutanschanges under different environmental conditions. We develop a demographic model of the fire dependent herbEryngium cuneifoliumto show how a causal indicator (i.e. a driver of the changes in the environmental quality) can be incorporated with the addition of a single parameter. Using perturbation analyses we determine optimal management strategies for this species.This approach estimates fewer parameters than previous approaches and allows novel eco-evolutionary insights. Predictions on population dynamics and life history evolution under different environmental conditions can be made without necessarily identifying causal factors. Environmental drivers can be incorporated with relatively few parameters, allowing for predictions on how populations will be affected by changes to these drivers.
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Authors: Yue Jia-Xing , Liti Gianni 
Published: September 2017

AbstractLong-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast,Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here we present LRSDAY, the first one-stop solution to streamline this process. LRSDAY can produce chromosome-level end-to-end genome assembly and comprehensive annotations for various genomic features (including centromeres, protein-coding genes, tRNAs, transposable elements and telomere-associated elements) that are ready for downstream analysis. Although tailored forS. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable for virtually any eukaryotic organisms. Applying LRSDAY to aS. cerevisiaestrain takes ∼43 hrs to generate a complete and well-annotated genome from ∼100X Pacific Biosciences (PacBio) reads using four threads.
Biological influence of extracts of cryopreserved fragments of piglets’ heart and skin
Authors: Rohoza Liliia A. , Bespalova Iryna G. , Chizh Mykola O. , Halchenko Sergiy Ye. , Sandomirsky Boris P. 
Published: September 2017

ABSTRACTOne of the new directions on which the searches used to find the methods to effectively correct the regeneration in case of different pathologies is the application of biologically active peptides and their mixtures. In the work there was investigated the biological influence of extracts of cryopreserved fragments of skin and heart of newborn piglets with the cold wound of skin and myocardial ischemia in rats respectively. For investigations the extracts were obtained from cryopreserved fragments of newborn piglets’ skin and heart. Cold wound of skin was modelled in rats by 10 mm copper applicator cooled in liquid nitrogen down to -196°C; the areas of wounds were determined by planimetric method, the white blood cells’ counts were analysed. In rats with myocardial ischemia there were studied the electrocardiograms, heart rate variability and proliferative activity of heart cells. The injection of extracts of cryopreserved fragments of skin to the animal’s abdominal cavity accelerates the healing of cold wound of skin and normalizes the response of immune system to an injury. After the injection during 2 months to the animals with myocardial ischemia with extracts of cryopreserved fragments of heart the normalization of electrophysiological indices of heart activity was observed that testified about the improved blood supply to a heart muscle. Being injected to healthy animals and those with myocardial ischemia the extracts of cryopreserved fragments of heart resulted in an increase in proliferative activity of heart cells. The studied extracts have a high biological effect and can be applied when designing the drugs for regenerative medicine.Summary statementThe extracts of cryopreserved fragments of piglets’ heart or skin were shown as stimulating reparative regeneration of heart tissues in myocardial ischemia of rats and skin in a cold wound, respectively.
The Moran coalescent in a discrete one-dimensional spatial model
Authors: Shpak Max , Lu Jie , Townsend Jeffrey P. 
Published: September 2017

AbstractAmong many organisms, offspring are constrained to occur at sites adjacent to their parents. This applies to plants and animals with limited dispersal ability, to colonies of microbes in biofilms, and to other genetically heterogeneous aggregates of cells, such as cancerous tumors. The spatial structure of such populations leads to greater relatedness among proximate individuals while increasing the genetic divergence between distant individuals. In this study, we analyze a Moran coa-lescent in a one-dimensional spatial model where a randomly selected individual dies and is replaced by the progeny of an adjacent neighbor in every generation. We derive a recursive system of equations using the spatial distance among haplotypes as a state variable to compute coalescent probabilities and coalescent times. The coalescent probabilities near the branch termini are smaller than in the unstructured Moran model (except fort= 1, where they are equal), corresponding to longer branch lengths and greater expected pairwise coalescent times. The lower terminal coalescent probabilities result from a spatial separation of lineages, i.e. a coalescent event between a haplotype and its neighbor in one spatial direction at timetcannot co-occur with a coalescent event with a haplotype in the opposite direction att+ 1. The concomitant increased pairwise genetic distance among randomly sampled haplotypes in spatially constrained populations could lead to incorrect inferences of recent diversifying selection or of population bottlenecks when analyzed using an unconstrained coalescent model as a null hypothesis.
The reality of “food porn”: Larger brain responses to food-related cues than to erotic images predict cue-induced eating
Authors: Versace Francesco , Frank David W. , Stevens Elise M. , Deweese Menton M. , Guindani Michele , Schembre Susan M. 
Published: September 2017

AbstractWhile some individuals can defy the lure of temptation, many others find appetizing food irresistible. Using event-related potentials, we showed that individuals who find food-related images more motivationally relevant than erotic ones (“sign-trackers”) are more susceptible to cue-induced eating and, in the presence of a palatable food option, eat twice as much as individuals with the opposite brain reactivity profile (“goal-trackers”). These findings contribute to the understanding of the neurobiological basis of vulnerability to cue-induced behaviors.
Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution
Authors: Ma Wenxiu , Ay Ferhat , Lee Choli , Gulsoy Gunhan , Deng Xinxian , Cook Savannah , Hesson Jennifer , Cavanaugh Christopher , Ware Carol B. , Krumm Anton , Shendure Jay , Blau C. Anthony , Disteche Christine M. , Noble William S. , Duan ZhiJun 
Published: September 2017

AbstractThe folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes ofcis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods.HighlightsDNase Hi-C, a method for comprehensive mapping of chromatin contacts on a whole-genome scale, is based on random chromatin fragmentation by DNase I digestion instead of sequence-specific restriction enzyme (RE) digestion.Targeted DNase Hi-C, which combines DNase Hi-C with DNA capture technology, is a high-throughput method for mapping fine-scale chromatin architecture of genomic loci of interest at a resolution comparable to that of genomic annotations of functional elements.DNase Hi-C and targeted DNase Hi-C provide the first high-throughput way to overcome the RE-digestion-associated resolution limit of 3C-based methods.Step-by-step whole-genome and targeted DNase Hi-C protocols for mapping global and local 3D genome architecture, respectively, are described.
Climbing Legumes: An Underutilized Resource With Significant Potential to Intensify Farming on Terrace Walls (FTW) for Smallholder Farmers
Authors: Clark Jaclyn C. , Raizada Manish N. 
Published: September 2017

AbstractMillions of subsistence farmers cultivate crops on terraces. These farmers face unique challenges including severe shortages of arable land and remoteness leading to poor access to inputs including nitrogen fertilizer. These challenges contribute to human and livestock malnutrition. Terrace walls (risers) as a vertical surface to grow climbing or trailing legumes represents an opportunity to help overcome these challenges. These crops are rich in minerals and protein, and their associated microbes produce nitrogen fertilizer. Rice bean is already grown on terrace risers in South Asia. This paper reviews the literature concerning crops that are currently farmed on terrace walls (FTW), then surveys climbing legume species that have potential for FTW, focusing on crops that are nutritious and tolerate shade (caused by the terrace wall) and resist drought (many terrace farms experience an extended dry season). A total of 29 legume species are discussed including climbing varieties of jack bean, common bean, cowpea, winged bean, horse gram and velvet bean. The review concludes by discussing the practical challenges of farmer adoption of FTW and makes concrete recommendations. Terrace wall cultivation of legumes represents an opportunity to intensify agriculture and increase resiliency in remote mountainous areas.
Corporate anti-corruption disclosure
Authors: Blanc Renata , Islam Muhammad Azizul , Patten Dennis M. , Branco Manuel Castelo 
Published: September 2017

PurposeThe purpose of this paper is to investigate whether differences in media exposure regarding corporate corruption appear to influence companies’ anti-corruption disclosures. The authors also examine whether the level of press freedom in firms’ home countries affects disclosure and the impact of media exposure in different ways.Design/methodology/approachThe authors use Transparency International’s 2012 ratings of anti-corruption disclosure by the 105 largest multinational firms in the world, press freedom assessments from the non-governmental organization Reporters Without Borders, and media exposure measures based on a search using the Dow Jones Factiva database. The authors assess relations using regression analysis controlling for other firm-specific factors potentially impacting disclosure choices. Finally, the authors consider the potential effect of other country-level factors.FindingsThe results indicate that media exposure, using either an existence or an extensiveness measure, is positively related to differences in sample companies’ anti-corruption disclosures. The authors also find that disclosure is more (less) extensive where home country press freedom is less (more) restricted and that reduced press freedom appears to reduce the impact of media exposure on the disclosure. The authors further document that press freedom levels explain more difference in anti-corruption disclosures than other country-level factors potentially influencing the practice.Research limitations/implicationsBecause the investigation is limited to very large international firms for a single year, the degree to which the findings apply to other companies and time periods cannot be assessed. Further, the authors cannot determine how the findings would hold using an alternative disclosure rating scheme. Finally, the authors do not assess whether differences in the source of media exposure impact the findings.Social implicationsThe findings suggest that, to the extent that improved anti-corruption disclosure reflects greater corporate attention to corruption issues, the media may be a powerful player in addressing this social ill. Unfortunately, the results also indicate that media efforts may not be sufficient to bring about change in locations where the freedom of the press is limited. Further, the results suggest that disclosure appears to be a function of exposure to social and political exposures, and the authors therefore question whether it will actually lead to improved corruption performance.Originality/valueThe study is the first to consider the impacts of media exposure and press freedom on corporate social disclosures.
United Nations Decade on Biodiversity
Authors: Adler Ralph , Mansi Mansi , Pandey Rakesh , Stringer Carolyn 
Published: September 2017

PurposeThe purpose of this paper is to explore the biodiversity reporting practices and trends of the top 50 Australian mining companies before and after the United Nations (UN) declared the period 2011-2020 as the “Decade on Biodiversity”.Design/methodology/approachUsing content analysis and interviews, this study compares the extent and type of biodiversity disclosures made by the Australian Stock Exchange’s top 50 metals and mining companies both before and after the UN’s “Decade on Biodiversity” declaration in 2010.FindingsA significant increase in the amount of biodiversity reporting is observed between the 2010 fiscal year preceding the UN’s declaration and the 2012 and 2013 fiscal years following the declaration. The findings reveal, however, that the extent of biodiversity reporting is quite variable, with some companies showing substantial increases in their biodiversity reporting and others showing modest or no increases. In particular, the larger companies in the sample showed a statistically significant increase in their disclosures on biodiversity in 2013 compared with 2010, while the increase in biodiversity disclosures by smaller companies was not significant. While interviewees spoke about their companies being more open and transparent, the biodiversity information that is being reported would not enable external parties to assess the company’s biodiversity performance.Research limitations/implicationsTo minimise an organisation’s use of biodiversity reporting as an impression management tool, it is suggested that biodiversity reporting should be more impact based and organisations should provide a report of their activities and their direct and tangible impacts on short-term and long-term biodiversity in and around their operating sites. A possible limitation of the present study pertains to its focus on companies’ voluntary disclosures made in their annual reports and sustainability reports, as opposed to other possible formal or even informal disclosure mediums.Social implicationsAustralia is one of 17 mega-diverse wildlife countries in the world. Finding ways to support the country’s biodiversity framework and strategy are crucial to this continued status. Due to the mining industry’s significant impact on Australia’s biodiversity, a strong need exists for biodiversity reporting by this industry. Furthermore, this reporting should be provided on a site-by-site basis. At present, the reporting aggregation typically conducted by mining companies produces obscure information that is neither useful for stakeholders who are impacted by the mining companies’ activities nor for policymakers who are vested with responsibility for protecting and sustaining the world’s biodiversity.Originality/valueThis study examines the biodiversity reporting and discourse practices of mining companies in Australia and develops a 50-item biodiversity reporting index to measure the biodiversity reporting practices.
Active disturbance rejection control for small unmanned helicopters via Levy flight-based pigeon-inspired optimization
Authors: Zhang Daifeng , Duan Haibin , Yang Yijun 
Published: September 2017

Purpose
The purpose of this paper is to propose a control approach for small unmanned helicopters, and a novel swarm intelligence algorithm is used to optimize the parameters of the proposed controller.

Design/methodology/approach
Small unmanned helicopters have many advantages over other unmanned aerial vehicles. However, the manual operation process is difficult because the model is always instable and coupling. In this paper, a novel optimized active disturbance rejection control (ADRC) approach is presented for small unmanned helicopters. First, a linear attitude model is built in hovering condition according to small perturbation linearization. To realize decoupling, this model is divided into two parts, and each part is equipped with an ADRC controller. Finally, a novel Levy flight-based pigeon-inspired optimization (LFPIO) algorithm is developed to find the optimal ADRC parameters and enhance the performance of controller.

Findings
This paper applies ADRC method to the attitude control of small unmanned helicopters so that it can be implemented in practical flight under complex environments. Besides, a novel LFPIO algorithm is proposed to optimize the parameters of ADRC and is proved to be more efficient than other homogenous methods.

Research limitations/implications
The model of proposed controller is built in the hovering action, whereas it cannot be used in other flight modes.

Practical implications
The optimized ADRC method can be implemented in actual flight, and the proposed LFPIO algorithm can be developed in other practical optimization problems.

Originality/value
ADRC method can enhance the response and robustness of unmanned helicopters which make it valuable in actual environments. The proposed LFPIO algorithm is proved to be an effective swarm intelligence optimizer, and it is convenient and valuable to apply it in other optimized systems.
Towards structural health monitoring of space vehicles
Authors: Ursu Ioan , Enciu Daniela , Toader Adrian 
Published: September 2017

Purpose
The purpose of this paper is to report the results of a recent project of complex tests on the survival of structural health monitoring (SHM) technology with piezo wafer active sensors (PWAS) and electromechanical impedance spectroscopy (EMIS) at simulating the concomitant action of harsh conditions of outer space: extreme temperatures, radiations, vacuum.

Design/methodology/approach
The tests were conducted on PWAS, consists in adhesive and aluminium discs as structural specimens, with PWAS bonded on them. The substantiating of PWAS-EMIS-based SHM technique consists the fact that real part of the PWAS electromechanical impedance spectrum follows with fidelity the resonance behaviour of the structure vibrating under the PWAS excitation. This EMIS signature is very sensitive to any structural changes and, on this basis, can be monitored the onset and progress of structural damages such as fatigue, cracks, corrosion, etc.

Findings
The conclusion of the tests is that the cumulative impact of severe conditions of temperature, radiation and vacuum has not generated decommissioning of sensors or adhesive, which would have meant the compromise of the methodology. A second important outcome is linked to the capability of this methodology to distinguish between the damages of mechanical origin and the false ones, caused by environmental conditions, which are, basically, harmless.

Originality/value
The question of transfer of PWAS-EMIS-based SHM technology to space vehicles and applications received, as a novelty, a first and encouraging response.
Design of MPCs for a fixed wing UAV
Authors: Ülker Hakan , Baykara Cemal , Özsoy Can 
Published: September 2017

Purpose
The purpose of the paper is to examine a fixed wing unmanned aerial vehicle (UAV) as it undergoes five flight scenarios under straight and level, level climb, level turn, climbing turn and level steady heading sideslip conditions in a desired and controlled manner using constrained multi input multi output (MIMO) model predictive controllers (MPCs).

Design/methodology/approach
An MPC strategy based on the lateral and longitudinal linear models is proposed for the flight control design. Simulations are carried out for the nonlinear closed-loop aircraft Simulink model available from the University of Minnesota UAV research group with the implemented MIMO MPCs designed in this paper.

Findings
The results of the simulations show that the MIMO MPCs can achieve satisfactory performance and flying qualities under three different test conditions in terms of existing unmeasured outputs and unmeasured output disturbances.

Practical Implications
The MPCs designed in this paper can be implemented to UAVs. Therefore, the implementation is considered as an advanced research.

Originality/value
The proposed MPC design in this paper provides more flexibility in terms of tracking complex trajectories comparing with the classical controllers in the literature. Besides they provide to change more than one reference of the states at any time.