bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing taxonomic metagenome profilers with OPAL
Authors: Meyer Fernando , Bremges Andreas , Belmann Peter , Janssen Stefan , McHardy Alice C. , Koslicki David 
Published: July 2018

AbstractTaxonomic metagenome profilers predict the presence and relative abundance of microorganisms from shotgun sequence samples of DNA isolated directly from a microbial community. Over the past years, there has been an explosive growth of software and algorithms for this task, resulting in a need for more systematic comparisons of these methods based on relevant performance criteria. Here, we present OPAL, a software package implementing commonly used performance metrics, including those of the first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, OPAL implements diversity metrics from microbial ecology, as well as run time and memory efficiency measurements. By allowing users to customize the relative importance of metrics, OPAL facilitates in-depth performance comparisons, as well as the development of new methods and data analysis workflows. To demonstrate the application, we compared seven profilers on benchmark datasets of the first and second CAMI challenges using all metrics and performance measurements available in OPAL. The software is implemented in Python 3 and available under the Apache 2.0 license on GitHub (https://github.com/CAMI-challenge/OPAL).Author summaryThere are many computational approaches for inferring the presence and relative abundance of taxa (i.e. taxonomic profiling) from shotgun metagenome samples of microbial communities, making systematic performance evaluations a very important task. However, there has yet to be introduced a computational framework in which profiler performances can be compared. This delays method development and applied studies, as researchers need to implement their own custom evaluation frameworks. Here, we present OPAL, a software package that facilitates standardized comparisons of taxonomic metagenome profilers. It implements a variety of performance metrics frequently employed in microbiome research, including runtime and memory usage, and generates comparison reports and visualizations. OPAL thus facilitates and accelerates benchmarking of taxonomic profiling techniques on ground truth data. This enables researchers to arrive at informed decisions about which computational techniques to use for specific datasets and research questions.
Compensatory and additive helper effects in the cooperatively breeding Seychelles warbler (Acrocephalus sechellensis)
Authors: van Boheemen Lotte A. , Hammers Martijn , Kingma Sjouke A. , Richardson David S. , Burke Terry , Komdeur Jan , Dugdale Hannah L. 
Published: July 2018

ABSTRACTIn cooperatively breeding species, helper aid may affect dominant breeders’ investment trade-offs between current and future reproduction. By compensating for the care provided by helpers, breeders can reduce the costs of reproduction and improve chances of survival. Also, helper care can be additive to that of dominants, resulting in higher success of the current brood.However, the influence of helpers on offspring care itself may be the by-product of group size and territory quality. Therefore to make conclusive inferences about causation of additive and compensatory care as a result of helpper serequires disentangling the impact of helping from other factors determining parental investment.In this study, we use 20 years of offspring provisioning data to investigate the effect of helping on breeder and overall offspring provisioning rates in the facultative cooperatively breeding Seychelles warbler (Acrocephalus sechellensis). Our extensive dataset allowed us to effectively control for the effects of living in a larger group and in territories with higher food availability.We show compensatory and additive care in response to helper aid. Helpers lightened the provisioning load of the dominant male and female and increased the total provisioning to the nestlings. This was irrespective of group size or territory quality (food availability).Our results illustrate how multiple benefits of helping behaviour can simultaneously be fundamental to the evolutionary maintenance of cooperative behaviour.
Diffusion of exit sites on the endoplasmic reticulum – a random walk on a shivering backbone
Authors: Stadler L. , Speckner K. , Weiss M. 
Published: July 2018

AbstractMajor parts of the endoplasmic reticulum (ER) in eukaryotic cells are organized as a dynamic network of membrane tubules connected by three-way junctions. On this network, self-assembled membrane domains, called ER exit sites (ERES), provide platforms at which nascent cargo proteins are packaged into vesicular carriers for subsequent transport along the secretory pathway. While ERES appear stationary and spatially confined on long time scales, we show here via single-particle tracking that they exhibit a microtubule-dependent anomalous diffusion behavior on short and intermediate time scales. By quantifying key parameters of their random walk, we show that the subdiffusive motion of ERES is distinct from that of ER junctions, i.e. ERES are not tied to junctions but rather are mobile on ER tubules. We complement and corroborate our experimental findings with model simulations that also indicate that ERES are not actively moved by microtubules. Altogether, our study shows that ERES perform a random walk on the shivering ER backbone, indirectly powered by microtubular activity. Similar phenomena can be expected for other domains on subcellular structures, setting a caveat for the interpretation of domain tracking data.
Plant resistance in different cell layers affects aphid probing and feeding behaviour during poor- and non-host interactions
Authors: Escudero-Martinez Carmen , Leybourne Daniel J. , Bos Jorunn I.B. 
Published: July 2018

AbstractAphids are phloem-feeding insects that cause economic losses to crops globally. Whilst aphid interactions with susceptible plants and partially resistant genotypes have been well characterised with regards to aphid probing and feeding behaviour, the interactions with non-natural host species are not well understood. Using aphid choice assays with the broad host range pest Myzus persicae and the cereal pest Rhopalosiphum padi we show that about 10% of aphids settle on non-/poor-host species over a 24h time period. We used the Electrical Penetration Graph technique to assess aphid probing and feeding behaviour during the non-/poor-host interactions. In the Arabidopsis non-host interaction with the cereal pest R. padi aphids were unable to reach and feed from the phloem, with resistance likely residing in the mesophyll cell layer. In the barley poor-host interaction with M. persicae, resistance is likely phloem-based as aphids were able to reach the phloem but ingestion was reduced compared with the host interaction. Overall our data suggests that plant resistance to aphids in non-host and poor-host interactions with these aphid species likely resides in different plant cell layers. Future work will take into account specific cell layers where resistances are based to dissect the underlying mechanisms and gain a better understanding of how we may improve crop resistance to aphids.
Drought adaptation in nature by extensive genetic loss-of-function
Authors: Monroe J.G. , Powell T. , Price N. , Mullen J.L. , Howard A. , Evans K. , Lovell J.T. , McKay J.K. 
Published: July 2018

AbstractVisions of a second green revolution empowered by emerging technologies have called for interdisciplinary syntheses to scale up the discovery of functionally definitive gene variants responsible for climate adaptation in plants. We integrated novel approaches using whole genome sequences and satellite remote sensing to identify natural knockout alleles associated with drought histories in wild Arabidopsis thaliana. Genes identified exhibit signatures of parallel molecular evolution, selection for loss-of-function alleles, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses 7 times more often than expected by chance. Artificial knockout lines then confirmed predicted phenotypes experimentally. These findings further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature and inspire new opportunities for engineering climate resilience in crops.One sentence summaryWhole genome sequences and satellite-detected droughts point to gene knockouts as valuable genetic fuel for climate adaptation.
Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice
Authors: Bacon Wendi A. , Hamilton Russell S. , Yu Ziyi , Kieckbusch Jens , Hawkes Delia , Krzak Ada M. , Abell Chris , Colucci Francesco , Charnock-Jones D. Stephen 
Published: July 2018

AbstractFetal growth restriction (FGR) causes a wide variety of defects in the neonate which can lead to increased risk of heart disease, diabetes, anxiety and other disorders later in life. However, the effect of FGR on the immune system, is poorly understood. We used a well-characterized mouse model of FGR in which placental Igf-2 production is lost due to deletion of the placental specificIgf-2P0promotor. The thymi in such animals were reduced in mass with a ∼70% reduction in cellularity. We used single cell RNA sequencing (Drop-Seq) to analyze 7264 thymus cells collected at postnatal day 6.We identified considerable heterogeneity among the Cd8/Cd4 double positive cells with one subcluster showing marked upregulation of transcripts encoding a sub-set of proteins that contribute to the surface of the ribosome. The cells from the FGR animals were underrepresented in this cluster. Furthermore, the distribution of cells from the FGR animals was skewed with a higher proportion of immature double negative cells and fewer mature T-cells. Cell cycle regulator transcripts also varied across clusters. The T-cell deficit in FGR mice persisted into adulthood, even when body and organ weights approached normal levels due to catch-up growth. This finding complements the altered immunity found in growth restricted human infants. This reduction in T-cellularity may have implications for adult immunity, adding to the list of adult conditions in which thein uteroenvironment is a contributory factor.
Demand for pesticide-free, cisgenic food? Exploring differences between consumers of organic and conventional food
Authors: Edenbrandt Anna Kristina 
Published: July 2018

Purpose
The purpose of this paper is to explore the consumer acceptance of foods that are pesticide-free while obtained by cisgenics, a form of genetic modification that only allows gene transfers between sexually compatible species. Potential differences in acceptance between conventional and organic consumer segments are explored.

Design/methodology/approach
Data were collected from a survey, including a choice experiment, which was distributed to a consumer panel in Denmark. Survey responses were combined with actual purchase data among the same respondents and thereby providing information about the respondents’ share of organic consumption.

Findings
No consumer segment differentiated between pesticide-free, cisgenic bread and conventional alternatives. Conventional consumers preferred cisgenics over transgenics, while pesticide-free is not highly valued. Frequent organic consumers were having willingness-to-pay (WTP) a large premium for organic, indicating that they will continue to purchase such products even if cisgenic, pesticide-free products are introduced.

Originality/value
This paper provides insights on the potential reception of cisgenic food, and if there is a positive willingness to pay for a pesticide-free label if this is cisgenics. Moreover, the possibility to allow new breeding techniques in the organic requirements has been discussed, and this paper contributes with insights on the organic consumers’ preferences on this matter.
Australian food retail supply chain analysis
Authors: Jie Ferry , Gengatharen Denise 
Published: July 2018

PurposeThe Australian retail food sector, comprising mostly small enterprises, is undergoing change as a result of the innovative supply chain approach adopted. This change has implications across the entire food value chain in Australia. The purpose of this paper is to empirically investigate the adoption of supply chain management practices on small and medium enterprises (SMEs) in the Australian food retail industry.Design/methodology/approachThe study surveys 120 SME retailers in the food sector. A stepwise multiple regression using SPSS version 14.0 was performed on the data.FindingsStatistical results suggest that lean thinking and the quality of information shared can lead to greater efficient supply chain performance.Research limitations/implicationsThe small sample is the main limitation. The findings bear important implications for further research as understanding these dimensions can help to position key changes and industry improvement that will increase revenue and reduce cost to the SMEs in the food retail supply chain.Practical implicationsAdopting lean thinking and improving information sharing in the supply chain can reduce the cost for SMEs.Social implicationsThis study has unique implications for social sustainability, especially the smaller food enterprises, which are hard pressed to combat the challenges within the food sector.Originality/valueInnovative supply chain management helps SMEs to see beyond the silo mentality and helps them to focus on greater value addition in the supply chain.
Business process orientation in the Slovenian power supply
Authors: Novak Rajko , Janeš Aleksander 
Published: July 2018

PurposeThe purpose of this paper is to empirically evaluate business process orientation (BPO) of the Slovenian power supply business.Design/methodology/approachWithin the empirical investigation, the level of BPO maturity was measured in the 19 organizations of the power supply business. The survey was focused on the top, middle and lower managers. As a measuring instrument, a questionnaire for the extended concept of process orientation with nine elements was used.FindingsThe results of the BPO measurement show that, despite this long-standing preoccupation with processes, certified management system and the computerization of operations, process maturity is not high. Particularly the lowest score for information technology represents a surprise.Practical implicationsThis research makes significant contributions to the literature and above all to scholars and practitioners who work professionally in this field and will find useful guidance for a better understanding of applying BPO and maturity models.Social implicationsOne important reason for performing the maturity measurement in the power supply business is the importance of its activities for the operation and development and environmental impact of the whole of Slovenian society.Originality/valuePresented research is the first one which considers the BPO maturity in the Slovenian power supply business and therefore contributes to understanding of the “intangible factors” which have impact on the introduction of business process management and BPO.
Performance pay and enterprise productivity: the details matter
Authors: Kato Takao , Kauhanen Antti 
Published: July 2018

PurposeThe purpose of this paper is to provide novel and rigorous evidence on the productivity effect of varying attributes of performance-related pay (PRP) and shows that the details of PRP indeed matter.Design/methodology/approachIn doing so, the authors exploit the panel nature of the Finnish Linked Employer–Employee Data on the details of PRP.FindingsThe authors first establish that the omitted variable bias is serious, which makes the cross-sectional estimates on the productivity effect of the details of PRP biased upward substantially. Relying on the fixed effect estimates that account for such bias, the authors find: (first, group incentive PRP is more potent in boosting enterprise productivity than individual incentive PRP; second, group incentive PRP with profitability as a performance measure is especially powerful in raising firm productivity; third, when a narrow measure (such as cost reduction) is already used, adding another narrow measure (such as quality improvement) yields no additional productivity gain; and fourth, PRP with greater power of incentives (the share of PRP in total compensation) results in greater productivity gains, and returns to power of incentives diminishes very slowly.Originality/valueMuch of the empirical literature on PRP focuses on a question of whether the firm can increase firm performance in general and enterprise productivity in particular by introducing PRP and if so, how much. However, not all PRP programs are created equal and PRP programs vary significantly in a variety of attributes. This paper provides novel and rigorous evidence on the productivity effect of varying attributes of PRP and shows that the details of PRP indeed matter.
Survey of disease awareness, treatment behavior and treatment satisfaction in patients with atopic dermatitis in Korea: A multicenter study
Authors: Jung Hye Jung , Bae Joo Youn , Kim Jung Eun , Na Chan Ho , Park Gyeong Hun , Bae You In , Shin Min Kyung , Lee Young Bok , Lee Un Ha , Jang Yong Hyun , Han Tae Young , Ahn Ji Young 
Published: July 2018

AbstractIn Korea, there is a high dependency on oriental medicine and folk remedies (Korean J Asthma Allergy Clin Immunol, 25, 2005, 110). In addition, inaccurate information available through the Internet is increasing (Korean J Dermatol, 44, 2006, 137). So, there is always a possibility that patients may have difficulty obtaining accurate information about atopic dermatitis (AD). The aim was to determine the awareness, treatment behavior and treatment satisfaction of patients with AD and their caregivers. In October 2017, patients diagnosed with AD at nine hospitals were enrolled in this study. A questionnaire was completed by each patient. A total of 371 subjects were surveyed. In response to the question asking about knowledge of AD, the correct answer rate was 55.4%. Bathing using soap, body scrub and moisturizer showed favorable outcomes. A total of 54.9% patients responded that they were reluctant to use steroid ointment. When asked about their previous treatment, 39.6% reported using oriental medicine and 26.5% had tried folk remedies. The hospital treatment satisfaction score was 6.6. Patients usually applied their knowledge in their daily lives. However, there was a lot of inaccurate knowledge. Therefore, it is important for patients to understand the characteristics of this disease and obtain correct information.
Rare frost events reinforce tropical savanna–forest boundaries
Authors: Hoffmann William A. , Flake Samuel W. , Abreu Rodolfo C. R. , Pilon Natashi A. L. , Rossatto Davi R. , Durigan Giselda 
Published: July 2018

Abstract

The ability of vegetation to ameliorate or exacerbate environmental extremes can generate feedbacks that mediate the distribution of biomes. It has been suggested that feedbacks between vegetation and frost damage may be important for maintaining savanna, particularly at the edge of the tropics.

We quantified frost damage and air temperature across a network of 30 permanent plots distributed across tropical savanna–forest boundaries in Brazil during an uncommonly hard frost.

Tree cover strongly buffered temperatures during frost events, such that forest sites were up to 5°C warmer than nearby sites occupied by open shrub savanna. Consequently, in forest, woody plants were not damaged, but in savanna, there was extensive dieback of trees and shrubs. Within savanna, frost had disproportionately large effects on small individuals, likely due to colder temperatures near the ground and the lower thermal mass of thin stems. Across species, frost tolerance was strongly correlated with latitudinal range limit, revealing the importance of minimum temperature as a species filter at the regional scale. Counterintuitively, savanna species, which are adapted to open habitats where frost is more likely, were more vulnerable to cold than were forest species and experienced more than twice the amount of leaf damage as co‐occurring forest species.

Synthesis. Frost reinforces the effects of fire on vegetation structure by preferentially damaging trees in open environments and generating high loads of dead, flammable fuels. However, frost does not currently occur with sufficient frequency in the region to maintain open savanna by itself. Nevertheless, it occurs with sufficient frequency and severity that it likely acts as an environmental filter and evolutionary selective factor for some of the most frost‐sensitive species.
Biotic and abiotic plant–soil feedback depends on nitrogen‐acquisition strategy and shifts during long‐term ecosystem development
Authors: Png Guochen Kenny , Lambers Hans , Kardol Paul , Turner Benjamin L. , Wardle David A. , Laliberté Etienne 
Published: July 2018

Abstract

Feedback between plants and soil is an important driver of plant community structure, but it remains unclear whether plant–soil feedback (PSF): (i) reflects changes in biotic or abiotic properties, (ii) depends on environmental context in terms of soil nutrient availability, and (iii) varies among plant functional groups. As soil nutrient availability strongly affects plant distribution and performance, soil chemical properties and plant nutrient‐acquisition strategies might serve as important drivers of PSF.

We used soils from young and old stages of a long‐term soil chronosequence to represent sites where productivity is limited by nitrogen (N) and phosphorus (P) availability, respectively. We grew three N‐fixing and three non‐N‐fixing plant species in soils conditioned by co‐occurring conspecific or heterospecific species from each of these two stages. In addition, three soil treatments were used to distinguish biotic and abiotic effects on plant performance, allowing measurements of overall, biotic, and abiotic PSF.

In young, N‐poor soils, non‐N‐fixing plants grew better in soils from N‐fixing plants than in their own soils (i.e., negative PSF). However, this difference was not only associated with improved abiotic conditions in soils from N‐fixing plants but also with changes in soil biota.

By contrast, no significant PSF was observed for N‐fixing plants grown in young soils. Moreover, we did not observe any significant PSF for either N‐fixing or non‐N‐fixing plants growing in old, P‐impoverished soils.

Synthesis. The direction and strength of plant‐soil feedback (PSF) varied among N‐acquisition strategies and soils differing in nutrient availability, with stronger plant‐soil feedback in younger, N‐poor soils compared to older, P‐impoverished soils. Our results highlight the importance of considering soil nutrient availability, plant‐mediated abiotic and biotic soil properties, and plant nutrient‐acquisition strategies when studying plant‐soil feedback, thereby advancing our mechanistic understanding of plant‐soil feedback during long‐term ecosystem development.