bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cue identification in phenology: A case study of the predictive performance of current statistical tools
Authors: Simmonds Emily G. , Cole Ella F. , Sheldon Ben C. 
Published: June 2019

Abstract

Changes in the timing of life‐history events (phenology) are a widespread consequence of climate change. Predicting population resilience requires knowledge of how phenology is likely to change over time, which can be gained by identifying the specific environmental cues that drive phenological events. Cue identification is often achieved with statistical testing of candidate cues. As the number of methods used to generate predictions increases, assessing the predictive accuracy of different approaches has become necessary.

This study aims to (a) provide an empirical illustration of the predictive ability of five commonly applied statistical methods for cue identification (absolute and relative sliding time window analyses, penalized signal regression, climate sensitivity profiles and a growing degree‐day model) and (b) discuss approaches for implementing cue identification methods in different systems.

Using a dataset of mean clutch initiation timing in wild great tits (Parus major), we explored how the days of the year identified as most important, and the aggregate statistic identified as a cue, differed between statistical methods and with respect to the time span of data used. Each method's predictive capacity was tested using cross‐validation and assessed for robustness to varying sample size.

We show that the identified critical time window of cue sensitivity was consistent across four of the five methods. The accuracy and precision of predictions differed by method with penalized signal regression resulting in the most accurate and most precise predictions in our case. Accuracy was maximal for near‐future predictions and showed a relationship with time. The difference between predictions and observations systematically shifted across the study from preceding observations to lagging.

This temporal trend in prediction error suggests that the current statistical tools either fail to capture a key component of the cue–phenology relationship, or the relationship itself is changing through time in our system. These two influences need to be teased apart if we are to generate realistic predictions of phenological change. We recommend future phenological studies to challenge the idea of a static cue–phenology relationship and should cross‐validate results across multiple time periods.
The contribution of spatial mass effects to plant diversity in arable fields
Authors: Metcalfe Helen , Hassall Kirsty L. , Boinot Sébastien , Storkey Jonathan 
Published: June 2019

Abstract

In arable fields, plant species richness consistently increases at field edges. This potentially makes the field edge an important habitat for the conservation of the ruderal arable flora (or ‘weeds’) and the invertebrates and birds it supports. Increased diversity and abundance of weeds in crop edges could be owing to either a reduction in agricultural inputs towards the field edge and/or spatial mass effects associated with dispersal from the surrounding landscape.

We contend that the diversity of weed species in an arable field is a combination of resident species, that can persist under the intense selection pressure of regular cultivation and agrochemical inputs (typically more ruderal species), and transient species that rely on regular dispersal from neighbouring habitats (characterised by a more ‘competitive’ ecological strategy).

We analysed a large dataset of conventionally managed arable fields in the UK to study the effect of the immediate landscape on in‐field plant diversity and abundance and to quantify the contribution of spatial mass effects to plant diversity in arable fields in the context of the ecological strategy of the resulting community.

We demonstrated that the decline in diversity with distance into an arable field is highly dependent on the immediate landscape, indicating the important role of spatial mass effects in explaining the increased species richness at field edges in conventionally managed fields.

We observed an increase in the proportion of typical arable weeds away from the field edge towards the centre. This increase was dependent on the immediate landscape and was associated with a higher proportion of more competitive species, with a lower fidelity to arable habitats, at the field edge.

Synthesis and applications. Conserving the ruderal arable plant community, and the invertebrates and birds that use it as a resource, in conventionally managed arable fields typically relies on the targeted reduction of fertilisers and herbicides in so‐called ‘conservation headlands’. The success of these options will depend on the neighbouring habitat and boundary. They should be placed along margins where the potential for ingress of competitive species, that may become dominant in the absence of herbicides, is limited. This will enhance ecosystem services delivered by the ruderal flora and reduce the risk of competitive species occurring in the crop.
Large‐scale manipulation of the acoustic environment can alter the abundance of breeding birds: Evidence from a phantom natural gas field
Authors: Cinto Mejia Elizeth , McClure Christopher J. W. , Barber Jesse R. 
Published: June 2019

Abstract

Altered animal distributions are a consequence of human expansion and development. Anthropogenic noise can be an important predictor of abundance declines near human infrastructure, yet more information is needed to understand noise impacts at the spatial and temporal scales necessary to alter populations.

Energy development and associated anthropogenic noise are globally pervasive, and expanding. For example, 600,000 new natural gas wells have been drilled across central North America in less than 20 years.

We experimentally broadcast energy sector noise (recordings of compressor engines) in Southwest Idaho (USA). We placed arrays of speakers creating a ‘phantom natural gas field' in a large‐scale experiment and tested the effects of noise alone on breeding songbird abundance. To examine variation in human‐caused noise, we broadcast two types of compressor noise, one with a slightly higher sound intensity and greater bandwidth than the other.

Our phantom natural gas field encompassed approximately 100 km2. We broadcast noise over three continuous months, for each of two seasons, and quantified over 20,000 hr of background sound levels.

Brewer's sparrows (Spizella breweri) were affected by our narrowband playback, declining 30%, 50 m from the speaker arrays. During our broadband playback, all species combined and Brewer's sparrows decreased 20% and 33%, respectively, at the scale of our sites (~0.5 km2; up to 400 m from speaker arrays).

Synthesis and applications. Our results show the importance of incorporating the acoustic structure of noise when estimating the cost of noise exposure for populations. We suggest an urgent need for noise mitigation, such as quieting compressor stations, in energy extraction fields and other sources in natural areas broadly.
Practical Empirical Research Using gretl and hansl
Authors: Tarassow Artur 
Published: June 2019

AbstractThis article provides an introduction to the free open‐source statistics and econometrics software gretl. The software is an attempt to bridge the different demands for teaching at different levels. Furthermore, it also provides functionalities required for professional work. We also introduce gretl's powerful and intuitive scripting language ‘hansl’. This article can be seen as an illustrated step‐by‐step guide that uses a real‐life data analysis example. Finally, I estimate a vector autoregressive time‐series model using gretl for structural analyses as well as for forecasting purposes.
Distributing Student Places in Australian Higher Education
Authors: Norton Andrew 
Published: June 2019

AbstractHigher education systems need policies for distributing student places between higher education providers, courses and students. In supply‐driven systems, government and university decisions dominate. In demand‐driven systems, student choices play a larger role. Over the last 35 years Australia has moved from a supply‐driven to a largely demand‐driven university system and then partly back again. When students pay their own costs, both major political parties have supported market distribution of student places for decades. But for subsidised student places there is policy instability, due to fluctuating priorities for containing public expenditure and responding to demographic and labour market changes.
Causative alternations in Siraiki
Authors: Lowe John J. , Birahimani Ali H. 
Published: June 2019

AbstractSiraiki is a major but understudied Indo‐Aryan language spoken mainly in central Pakistan. Its causative system, which has never been described in detail, shows many similarities with causative systems in related modern Indo‐Aryan languages, but also differences which render it unique within this family. We provide a detailed account of causativization in Siraiki, and attempt to explain the synchronic complexity of the Siraiki data, as well as the broader variation within modern Indo‐Aryan, in diachronic terms.
Financialization, Urban Governance and the Planning System: Utilizing ‘Development Viability’ as a Policy Narrative for the Liberalization of Ireland's Post‐Crash Planning System
Authors: Waldron Richard 
Published: June 2019

AbstractDrawing upon the Irish case, this article explores the interaction between the financialized economy and the urban planning system. While considerable scholarship has examined the financialization of real estate, it remains unclear how planning systems are being repurposed to facilitate a finance‐led regime of urban growth or how the ‘real estate–financial complex’ seeks to enact planning policy transformations that support its interests. This article explores how such actors have advanced the concept of ‘financial viability of development’ as a means of influencing the post‐crisis re‐regulation of Irish planning policy. This group has argued that housing construction in post‐crash Ireland is unviable given the high development finance costs, onerous planning gain contributions and the lack of development certainty in the planning process. As such, housing construction has been at an all‐time‐low, leading to a new crisis in affordable housing provision. In response, a complicit state has further liberalized the planning system, introducing an array of policies that are evermore facilitative of development interests. Empirical findings, based on interviews with developers, lobbyists and planners, emphasize the importance of informal access to policymakers, the wielding of ‘expert knowledge’ and media management to co‐opt the state into adopting financial viability within planning policymaking.
Are minorities free riders? Applying the social resistance framework to public goods production in Central‐Eastern Europe
Authors: LETKI NATALIA , KUKOŁOWICZ PAULA 
Published: June 2019

AbstractOne of the key reasons for the scholarly and policy concern about the rising levels of ethnic diversity is its apparently detrimental effect on the production of public goods. Although numerous studies have tackled that issue, there is still much ambiguity as to the precise micro‐level mechanisms underpinning this relationship. In this article, a novel theoretical explanation for this relationship is proposed, building on the social resistance framework. This proposition is tested using a new cross‐sectional public opinion survey covering 14,536 respondents in 817 neighbourhoods across 11 Central Eastern European countries. Analysing national minorities defined by postwar border changes means one can overcome the endogeneity problem faced by research based on immigrant groups. The findings show that it is the combination of a minority group's discrimination and its spatial clustering that makes minorities reluctant to contribute to public goods. The article constitutes a novel theoretical and methodological contribution to the research on the effects of diversity on public goods provision.
Multi‐Site Bundling of Drought Tolerant Maize Varieties and Index Insurance
Authors: Awondo Sebastain N. , Kostandini Genti , Setimela Peter , Erenstein Olaf 
Published: June 2019

AbstractDrought Tolerant Maize Varieties (DTMV) and Rainfall Index Insurance (RII) are potential complements, though with limited empirical basis. We employ a multivariate spatial framework to investigate the potential for bundling DTMV with a simulated multi‐site and multi‐environment RII, designed to insure against mild, moderate and severe drought risk. We use yield data from on‐farm trials conducted by the International Maize and Wheat Improvement Center (CIMMYT) and partners over 49 locations in Eastern and Southern Africa spanning 8 countries and 5 mega‐environments (dry lowland, dry mid altitude, wet lower mid altitude, low wetland and wet upper mid altitude) in which 19 different improved maize varieties including DTMV were tested at each location. Spatially correlated daily rainfall data are generated from a first‐order two‐state Markov chain process and used to calibrate the index and predict yields with a hierarchical Bayes multivariate spatial model. Results show high variation in the performance and benefits of different bundles which depend on the maize variety, the risk layer insured, and the type of environment, with high chances of selecting a sub‐optimal and unattractive contract. We find that complementing RII with a specific DTMV produces contracts with lower premiums and higher guaranteed returns especially in dry lowland increasing the chances of scaling up RII within this environment.
Rethinking the Mechanism of the Health Benefits of Proanthocyanidins: Absorption, Metabolism, and Interaction with Gut Microbiota
Authors: Tao Wenyang , Zhang Yu , Shen Xuemin , Cao Yanping , Shi John , Ye Xingqian , Chen Shiguo 
Published: June 2019

AbstractProanthocyanidins, as the oligomers or polymers of flavan‐3‐ol, are widely discovered in plants such as fruits, vegetables, cereals, nuts, and leaves, presenting a major part of dietary polyphenols. Although proanthocyanidins exert several types of bioactivities, such as antioxidant, antimicrobial, cardioprotective, and neuroprotective activity, their exact mechanisms remain unclear. Due to the complexity of the structure of proanthocyanidins, such as their various monomers, different linkages and isomers, investigation of their bioavailability and metabolism is limited, which further hinders the explanation of their bioactivities. Since the large molecular weight and degree of polymerization limit the bioavailability of proanthocyanidins, the major effective site of proanthocyanidins is proposed to be in the gut. Many studies have revealed the effects of proanthocyanidins from different sources on changing the composition of gut microbiota based on in vitro and in vivo models and the bioactivities of their metabolites. However, the metabolic routes of proanthocyanidins by gut microbiota and their mutual interactions are still sparse. Thus, this review summarizes the chemistry, absorption, and metabolic pathways of proanthocyanidins ranging from monomers to polymers, as well as the mutual interactions between proanthocyanidins and gut microbiota, in order to better understand how proanthocyanidins exert their health‐promoting functions.
Brown Rice Versus White Rice: Nutritional Quality, Potential Health Benefits, Development of Food Products, and Preservation Technologies
Authors: Saleh Ahmed S. M. , Wang Peng , Wang Na , Yang Liu , Xiao Zhigang 
Published: June 2019

AbstractObesity and chronic diet‐related diseases such as type 2 diabetes, hypertension, cardiovascular disease, cancers, and celiac are increasing worldwide. The increasing prevalence of these diseases has led nutritionists and food scientists to pay more attention to the relationship between diet and different disease risks. Among different foods, rice has received increasing attention because it is a major component of billions of peoples’ diets throughout the world. Rice is commonly consumed after polishing or whitening and the polished grain is known a high glycemic food because of its high starch content. In addition, the removal of the outer bran layer during rice milling results in a loss of nutrients, dietary fiber, and bioactive components. Therefore, many studies were performed to investigate the potential health benefits for the consumption of whole brown rice (BR) grain in comparison to the milled or white rice (WR). The objective of this work was to review the recent advances in research performed for purposes of evaluation of nutritional value and potential health benefits of the whole BR grain. Studies carried out for purposes of developing BR‐based food products are reviewed. BR safety and preservation treatments are also explored. In addition, economic and environmental benefits for the consumption of whole BR instead of the polished or WR are presented. Furthermore, challenges facing the commercialization of BR and future perspectives to promote its utilization as food are discussed.
Decontamination of Microorganisms and Pesticides from Fresh Fruits and Vegetables: A Comprehensive Review from Common Household Processes to Modern Techniques
Authors: Bhilwadikar Tanmayee , Pounraj Saranya , Manivannan S. , Rastogi N. K. , Negi P. S. 
Published: June 2019

AbstractFresh fruits and vegetables are a rich source of micronutrients. However, many foodborne illnesses have been linked to the consumption of fresh fruits and vegetables as they are reported to harbor contaminants such as microorganisms and pesticides. Recently reported foodborne outbreaks have been linked to a diverse group of fruits and vegetables due to the presence of various pathogens including Salmonella, Escherichia coli, and Listeria monocytogenes. Also, the increased use of pesticides has resulted in the deposition of chemical residues on the surface of fruits and vegetables, which has led to the adverse health conditions such as cancer, birth defects, and neurodevelopmental disorders. Fresh commodities are subjected to various treatments to prevent or minimize these outbreaks, and the main targets of such treatments have been the elimination of pathogens and degradation of toxic chemical residues. Here, we have discussed various decontamination methods including simple household washing, chemical treatments, and modern technologies with their mode of action for microbial and pesticide removal. The simple household processes are not very effective in the removal of pathogenic organisms and pesticides. The use of modern techniques like cold plasma, ozone, high hydrostatic pressure, and so on, showed better efficacy in the removal of microorganisms and pesticides. However, their industrial use is limited considering high installation and maintenance cost. In this review, we suggest combined methods based on their mode of decontamination and suitability for a selected fruit or vegetable for effective decontamination of microbes and pesticide together to reduce the treatment cost and enhance food safety.
Unprocessed red meat intakes are associated with increased inflammation, triglycerides and HDL cholesterol in past smokers
Authors: Wu Tianying , Sonoda Samantha , Liu Hongxia 
Published: June 2019

AimTo determine the associations of unprocessed red meat with serum C‐reactive protein and traditional lipid biomarkers among adults with different smoking status.MethodsUsing a cross‐sectional design, we analysed data collected from 5011 adults (men and women) who had provided information on dietary intakes and the proposed biomarkers for the 2005–2006 National Health and Nutrition Examination Survey (NHANES).ResultsWe found positive associations between unprocessed red meat and serum C‐reactive protein and triglycerides and an inverse association between unprocessed red meat and high‐density lipoprotein (HDL) cholesterol in past smokers, but no associations in never smokers and current smokers. Among past smokers, the percent difference of biomarkers between participants with the highest and the lowest quintiles for the intakes of unprocessed red meat was 42% (P = 0.03) for CRP, 32% for triglycerides and −11% (P = 0.02) for HDL cholesterol. No association was found between unprocessed red meat and other lipid biomarkers.ConclusionsProviding individualised nutritional guidelines according to smoking status is important. Our study provided evidence for developing specific guidelines on red meat for past smokers.
Protocols for yTREX/Tn5‐based gene cluster expression in Pseudomonas putida
Authors: Weihmann Robin , Domröse Andreas , Drepper Thomas , Jaeger Karl‐Erich , Loeschcke Anita 
Published: June 2019

SummaryBacterial gene clusters, which represent a genetic treasure trove for secondary metabolite pathways, often need to be activated in a heterologous host to access the valuable biosynthetic products. We provide here a detailed protocol for the application of the yTREX ‘gene cluster transplantation tool’: Via yeast recombinational cloning, a gene cluster of interest can be cloned in the yTREX vector, which enables the robust conjugational transfer of the gene cluster to bacteria like Pseudomonas putida, and their subsequent transposon Tn5‐based insertion into the host chromosome. Depending on the gene cluster architecture and chromosomal insertion site, the respective pathway genes can be transcribed effectively from a chromosomal promoter, thereby enabling the biosynthesis of a natural product. We describe workflows for the design of a gene cluster expression cassette, cloning of the cassette in the yTREX vector by yeast recombineering, and subsequent transfer and expression in P. putida. As an example for yTREX‐based transplantation of a natural product biosynthesis, we provide details on the cloning and activation of the phenazine‐1‐carboxylic acid biosynthetic genes from Pseudomonas aeruginosa in P. putidaKT2440 as well as the use of β‐galactosidase‐encoding lacZ as a reporter of production levels.
Non‐invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator
Authors: Arce‐Rodríguez Alejandro , Volke Daniel C. , Bense Sarina , Häussler Susanne , Nikel Pablo I. 
Published: June 2019

SummaryThe ability of Pseudomonas species to thrive in all major natural environments (i.e. terrestrial, freshwater and marine) is based on its exceptional capability to adapt to physicochemical changes. Thus, environmental bacteria have to tightly control the maintenance of numerous physiological traits across different conditions. The intracellular pH (pHi) homoeostasis is a particularly important feature, since the pHi influences a large portion of the biochemical processes in the cell. Despite its importance, relatively few reliable, easy‐to‐implement tools have been designed for quantifying in vivo pHi changes in Gram‐negative bacteria with minimal manipulations. Here we describe a convenient, non‐invasive protocol for the quantification of the pHi in bacteria, which is based on the ratiometric fluorescent indicator protein PHP (pH indicator for Pseudomonas). The DNA sequence encoding PHP was thoroughly adapted to guarantee optimal transcription and translation of the indicator in Pseudomonas species. Our PHP‐based quantification method demonstrated that pHi is tightly regulated over a narrow range of pH values not only in Pseudomonas, but also in other Gram‐negative bacterial species such as Escherichia coli. The maintenance of the cytoplasmic pH homoeostasis in vivo could also be observed upon internal (e.g. redirection of glucose consumption pathways in P. putida) and external (e.g. antibiotic exposure in P. aeruginosa) perturbations, and the PHP indicator was also used to follow dynamic changes in the pHi upon external pH shifts. In summary, our work describes a reliable method for measuring pHi in Pseudomonas, allowing for the detailed investigation of bacterial pHi homoeostasis and its regulation.