bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cattle graph genome incorporating global breed diversity
Authors: Talenti A. , Powell J. , Hemmink J.D. , Cook E.A.J. , Wragg D. , Jayaraman S. , Paxton E. , Ezeasor C. , Obishakin E.T. , Agusi E.R. , Tijjani A. , Marshall K. , Fisch A. , Ferreira B. , Qasim A. , Chaudhry U.N. , Wiener P. , P. Toye , Morrison L.J. , Connelley T. , Prendergast J. 
Published: June 2021

AbstractDespite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds. To mitigate this issue, we have generated the first assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into the first graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.
Phylodynamic assessment of control measures for highly pathogenic avian influenza epidemics in France
Authors: Chakraborty Debapriyo , Guinat Claire , Müller Nicola F. , Briand Francois-Xavier , Andraud Mathieu , Scoizec Axelle , Lebouquin Sophie , Niqueux Eric , Schmitz Audrey , Grasland Beatrice , Guerin Jean-Luc , Paul Mathilde C. , Vergne Timothée 
Published: June 2021

AbstractPhylodynamic methods have successfully been used to describe viral spread history but their applications for assessing specific control measures are rare. In 2016-17, France experienced a devastating epidemic of a highly pathogenic avian influenza virus (H5N8 clade 2.3.4.4b). Using 196 viral genomes, we conducted a phylodynamic analysis combined with generalised linear model and showed that the large-scale preventive culling of ducks significantly reduced the viral spread betweendépartements(French administrative division). We also found that the virus likely spread more frequently betweendépartementsthat shared borders, but the spread was not linked to duck transport betweendépartements. Duck transport withindépartementsincreased the within-départementtransmission intensity, although the association was weak. Together, these results indicated that the virus spread in short-distances, either between adjacentdépartementsor withindépartements. Results also suggested that the restrictions on duck transport withindépartementsmight not have stopped the viral spread completely. Overall, by testing specific hypothesis related to different control measures, we demonstrated that phylodynamics methods are capable of investigating the impacts of control measures on viral spread.
Molecular Features Underlying Shp1/Shp2 Discrimination by Immune Checkpoint Receptors
Authors: Xu Xiaozheng , Masubuchi Takeya , Zhao Yunlong , Hui Enfu 
Published: June 2021

AbstractNumerous inhibitory immunoreceptors operate by recruiting phosphatase effectors Shp1 and Shp2 through conserved motifs ITIM and ITSM. Despite the similarity, these receptors exhibit distinct effector binding specificities, as exemplified by PD-1 and BTLA, which preferentially recruit Shp2 and Shp1 respectively. The molecular basis of Shp1/Shp2 discrimination is unclear. Here, we provide evidence that optimal PD-1 and BTLA binding to both Shp1 and Shp2 occurs via a bivalent, parallel mode that involves both SH2 domains of Shp1/Shp2. Moreover, PD-1 mainly uses its ITSM to discriminate Shp2 from Shp1 via their C-terminal SH2 domains. Supportive of this model, swapping the Shp1-cSH2 with Shp2-cSH2 enabled PD-1:Shp1 association in T cells. In contrast, BTLA primarily utilizes its ITIM to discriminate Shp1 from Shp2 via their N-terminal SH2 domains. Substitution of glycine at pY+1 position of the PD-1-ITIM with alanine, a residue conserved in several Shp1-recruiting receptors, was sufficient to induce PD-1:Shp1 interaction in T cells. Finally, mutagenesis screening shows that Shp1 recruitment exhibits a bell-shaped dependence on the side chain volume of the pY+1 residue of ITIM. Collectively, we provide a molecular interpretation of the Shp1/Shp2-binding specificities of PD-1 and BTLA, with general implications for the mechanism of effector discrimination by inhibitory receptors.
The current trends in mosque architecture in the northern cities of the United Arab Emirates (UAE)
Authors: Awad Jihad 
Published: June 2021

PurposeThe main aim of this study is to identify the prevailing design trends in contemporary mosques in northern cities of the United Arab Emirates (UAE). It highlights the key elements and features to categorize mosques.Design/methodology/approachBased on the literature review, four major stylistic expressions were identified, which formed the theoretical basis for a survey conducted to study 50 mosques in each of the four northern cities: Sharjah, Ajman, Umm Al Quwain and Ras Al Khaimah. The 200 visited mosques were investigated and analyzed based on the four categories. The comparison between these mosques enabled the author to identify the key elements and features that can be adopted in classifying mosques in relation to the four main trends.FindingsThe study reveals that there is a strong attachment with local historic styles. In total, 86% of the mosques follow traditional and historic styles. While 74% of Sharjah mosques follow historicism, 64–72% in the other cities adopt local traditional. Almost all investigated mosques follow one layout, but with diverse stylistic expressions. Some major elements are common among all mosques, while other minor elements are found in all congregational mosques. The study identified key indicators that can be used to help classifying mosques in other cities and countries.Originality/valueThis is the first study to categorize mosques in the UAE. There are few studies on mosques in Sharjah and Ajman, focusing on typology and sustainability, with less emphasis on styles. The results of this study can be considered by architects as well as by authorities. It can also be used as a reference for other studies.
Prioritising public spaces architectural strategies for autistic users
Authors: Sheykhmaleki Pariya , Yazdanfar Seyed Abbas Agha , Litkouhi Sanaz , Nazarian Masoumeh , Price Andrew David Freeman 
Published: June 2021

PurposeAccording to architectural research, modifying environmental features has the potential to create an appropriate sensory environment for autistic children. Considering the design of public environments, it is difficult to accommodate the diverse requirements of each autistic child. The main objective of this paper is to find out the most prevalent architectural strategies and to prioritise them for the design of the public spaces addressing autistic children's needs.Design/methodology/approachThis research is designed in two stages: (1) descriptive approach in which architectural strategies are extracted from theories on autism design to determine a theoretical test module; and (2) quantitative approach in which the frequency of gained strategies are studied in two groups of references: general references and key references (i.e. most cited and well-reputed researchers in autism architecture) while universal design strategies and the timeline of each strategy is considered for the conclusion.FindingsThe following strategies were highly significant: (1) acoustical control, (2) visual control, (3) legibility, (4) safety and security, (5) predictable spaces. Acoustic was frequently considered in both control and general groups while it was highlighted in timeline study and universal design strategies.Research limitations/implicationsThe main limitation is that these strategies have been prioritised according to their frequency in some limited articles and a control group including the pioneer of autism design researchers while verifying these strategies may not be strong enough. Likewise, the conclusion related to these data cannot be accurate enough. Establishing a case study survey that provides an opportunity to test all these strategies directly on a majority of autistic children and measure their prevalence is advised. Finally, it should be considered that although the five mentioned strategies are all the most prevalent strategies among autistic children, as each autistic child differs from others, generalising the conclusion for all the public area would be impossible, as though we need to study it for each group of them.Originality/valueSeeking to improve the strategies' prioritisation as determined by previous researchers, this article aims to define the most essential strategies categories in this field to eliminate the confusion of researchers and designers.
Does the attention-grabbing mechanism work on Sundays? Influence of social and religious factors on investors' attention
Authors: Ferretti Riccardo , Sciandra Andrea 
Published: June 2021

PurposeThis paper focuses on the influence of social, cultural and religious factors on investors' attention. In particular, the authors examined if the attention-grabbing mechanism works on Sundays, that is, if the Italians' Sunday activities and habits lead to a lower attention to second-hand financial news, compared to Saturdays.Design/methodology/approachThe authors analyzed the market reaction to equivalent stale events published on the Saturday and Sunday editions of an Italian financial newspaper and conducted a standard event study on abnormal returns and abnormal volumes for Saturday and Sunday columns and a multivariate analysis on abnormal returns for columns reporting positive recommendations. As a robustness check, the authors performed a sentiment analysis of the columns and included this variable in the regression analysis, but sentiment proved to be not significant in the final model.FindingsThe study’s results confirmed that the attention-grabbing mechanism directed buying decisions, while had no influence on selling decisions. Furthermore, event study and multivariate analysis showed a significant lower market reaction to Sunday columns, supporting the study hypothesis of a Sunday investors' inattention which can be traced to cultural and/or religious factors since Sunday in Italy is a day devoted to family, entertainment and religious rituals.Practical implicationsThe lower investors' attention on Sundays and the related influence of social, cultural and religious factors have implications for the timing of both corporate communications and financial advertising.Originality/valueThe authors’ paper provides an original contribution, on the empirical ground, to the attention-grabbing theory and to the growing theoretical literature in microeconomics that models attention.
Invasion theory as a management tool for increasing native biodiversity in urban ecosystems
Authors: Cadotte Marc W. , Potgieter Luke J. , Wang Chih Julie , MacIvor J. Scott 
Published: June 2021

Abstract

Human activity has altered ecosystems in some places to a point where traditional restoration, ecosystem management and conservation interventions might not be feasible. This is especially true in densely populated urban areas if ongoing stressors are not ameliorated. As a result, different management options are needed for increasing native biodiversity and ecosystem function in novel urban ecosystems.

One strategy for increasing biodiversity in urban ecosystems is to employ invasion biology theory to augment the establishment and proliferation of desirable native species. Invasion hypotheses, including fluctuating resources, enemy release, novel weapons, invasional meltdown (facilitation) and propagule pressure, all provide insights into the mechanisms that increase the establishment and spread of populations. These hypotheses point to specific interventions that can be used in urban restoration and management.

Synthesis and applications. Viewing invasion mechanisms as a way to increase native biodiversity in novel urban ecosystems provides a useful reframing for assessing possible applications and management interventions for the most difficult‐to‐restore landscapes. We argue that conservation managers can use and test invasion hypotheses to inform biodiversity management practices in novel landscapes.
Evidence‐based restoration of freshwater biodiversity after mining: Experience from Central European spoil heaps
Authors: Kolar Vojtech , Tichanek Filip , Tropek Robert 
Published: June 2021

Abstract

Post‐mining freshwater habitats can serve as secondary habitats for threatened species. Being globally plentiful, their efficient restoration should be based on detailed evidence, especially under the current global decline of freshwater biodiversity. Synthetic studies focusing on the effects of restoration on freshwater communities are surprisingly rare, even for the most common restoration approaches. Such a lack of evidence limits the efficiency of habitat restoration in post‐mining landscapes.

We combined a landscape‐scale field study of aquatic beetles and hemipterans in 29 freshwater pools at lignite spoil heaps in Czechia with a comparative synthesis of all 14 available datasets on freshwater communities at habitats created by coal mining in Central Europe. We compared the diversity and conservation value of freshwater habitats created by the main restoration approaches, including technical reclamation, spontaneous succession and their combination. Additionally, we analysed the detailed influence of key habitat descriptors on their conservation potential.

Communities of aquatic beetles and hemipterans had more species in spontaneously and semi‐spontaneously developed pools, which were also preferred by more red‐listed species of both studied groups. The reviewed studies showed the same trend for amphibians, odonates, dipterans and macrozoobenthos, although some technically created pools and drainage ditches harboured some threatened species of aquatic plants, odonates and macrozoobenthos as well.

Relatively independent of the restoration approach, the conservation value of freshwater communities was related to the particular characteristics of the restored habitats. The key beneficial features were as follows: smaller area of restored water bodies, heterogeneous littoral vegetation with suppressed dominants, heterogeneous bottom substrate with low and gradually sloping banks, absence of fish, sun‐exposed water surface and some forests in the surroundings.

Synthesis and applications. Efficient restoration of freshwater habitats at post‐mining landscapes can create important secondary refuges for threatened and common species. Freshwater communities of high conservation value can be supported by all main restoration approaches if heterogeneous habitats are created. A combination of technical reclamation with spontaneous succession seems to be the most efficient approach to maximise biodiversity in freshwater habitats at coal‐mining spoil heaps.
DNA‐stable isotope probing (DNA‐SIP) identifies marine sponge‐associated bacteria actively utilizing dissolved organic matter (DOM)
Authors: Campana Sara , Busch Kathrin , Hentschel Ute , Muyzer Gerard , de Goeij Jasper M. 
Published: June 2021

SummarySponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge‐associated community structure with DOM utilization is essential to understand host–microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA‐stable isotope probing (DNA‐SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled (12C) and labelled (13C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA‐SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge‐associated bacteria to the consumption of DOM.
Family imaginaries in the disclosure of a blood‐borne virus
Authors: Smith Anthony K J , Persson Asha , Drysdale Kerryn , Bryant Joanne , valentine kylie , Wallace Jack , Hamilton Myra , Gray Rebecca M. , Newman Christy E. 
Published: June 2021

AbstractContemporary sociological work has emphasised that family is not static, but actively shaped by ideas of who and what makes family. Disclosure of an illness, including diagnosis of stigmatised infections such as HIV, hepatitis B virus and hepatitis C virus, can change the dynamics of family relationships. This paper draws on 61 qualitative semi‐structured interviews conducted between 2017 and 2019 with people in Australia with one or more of these blood‐borne viruses (BBVs) and their family members, to understand the experiences of serodiscordant (mixed viral status) families. Through a thematic analysis, we explore the family imaginaries that participants evoked when describing their disclosure practices in relation to (self‐defined) family members, revealing how some participants disclosed in ways that enabled them to shape their family, to maintain boundaries between self and family or to protect family from distress. Participants' accounts of disclosure to family revealed imaginaries of family as a precious web of connections to be nurtured or protected, but also as sites of ambivalent belonging and complex history. We conclude that BBV disclosure practices within families reveal important ideas about families that are imagined in response to the threat of loss, change and stigma.
Descriptive aroma profiles of fresh sweet basil cultivars (Ocimum spp.): Relationship to volatile chemical composition
Authors: Patel Meera , Lee Rachel , Merchant Emily V. , Juliani H. Rodolfo , Simon Jame E. , Tepper Beverly J. 
Published: June 2021

AbstractFew studies have linked sensory descriptions of the aroma profiles of fresh, sweet basil varieties with their volatile chemistry. Using a recently developed lexicon for fresh basil, a descriptive panel characterized the aroma profiles of seven basil varieties. Chemical analysis of fresh basil leaves was performed using GC‐MS headspace analysis. Analysis of variance probed for differences in the sensory attributes among varieties and principal component analysis (PCA) related the sensory profiles to volatile chemical composition. Three commercial specialty basils, “Queenette Thai” (QT), “Sweet‐Dani” (SD) lemon basil, and MC‐9 (cinnamon basil) had strong anise, lemon, and cinnamon‐like aromas, respectively. These basils were distinguished from breeding lines of traditional Italian sweet basils where SB‐22, CB‐1, and CB‐39 exhibited strong anise‐like aroma and SB‐17 had strong “general spice” aromas, characteristic of a warm spice blend. The PCA accounted for 58.7% of the variation in the data and characterized the samples in two dimensions: general spice—citrus and cinnamon‐like—anise. There was a strong correspondence between the sensory attributes and volatile chemical composition. SD associated with lemon aroma and citral content; QT, CB‐1, and CB‐39 associated with anise aroma and methyl chavicol; and MC‐9 associated with the cinnamon‐like aroma, methyl cinnamate. SB‐17 and SB‐22 associated with general spice aroma and were in close proximity to the spice‐like volatiles, 1,8 cineole, and eugenol, associated with clove aroma. We constructed precise sensory/chemical profiles for fresh basil aroma that can be used to guide breeding programs for variety improvement to meet consumer expectations or market demand.Practical ApplicationSweet basil aroma is due to a complex array of several aromatic volatile compounds. The presence, concentration, and the particular ratios in which these aroma compounds accumulate significantly impact the sensory attributes. Understanding aroma profiles for fresh basil have practical applications in product development, procurement, food preparation, ethnic cuisine, and processing. Plant genetics and breeding of aroma profiles can be used and incorporated in plant improvement programs.
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod
Authors: Mayne Benjamin , Espinoza Thomas , Roberts David , Butler Gavin L. , Brooks Steven , Korbie Darren , Jarman Simon 
Published: June 2021

AbstractAge‐based demography is fundamental to management of wild fish populations. Age estimates for individuals can determine rates of change in key life‐history parameters such as length, maturity, mortality and fecundity. These age‐based characteristics are critical for population viability analysis in endangered species and for developing sustainable harvest strategies. For teleost fish, age has traditionally been determined by counting increments formed in calcified structures such as otoliths. However, the collection of otoliths is lethal and therefore undesirable for threatened species. At a molecular level, age can be predicted by measuring DNA methylation. Here, we use previously identified age‐associated sites of DNA methylation in zebrafish (Danio rerio) to develop two epigenetic clocks for three threatened freshwater fish species. One epigenetic clock was developed for the Australian lungfish (Neoceratodus forsteri) and the second for the Murray cod (Maccullochella peelii) and Mary River cod (Maccullochella mariensis). Age estimation models were calibrated using either known‐age individuals, ages derived from otoliths or bomb radiocarbon dating of scales. We demonstrate a high Pearson's correlation between the chronological and predicted age in both the Lungfish clock (cor = .98) and Maccullochella clock (cor = .92). The median absolute error rate for both epigenetic clocks was also low (Lungfish = 0.86 years; Maccullochella = 0.34 years). This study demonstrates the transferability of DNA methylation sites for age prediction between highly phylogenetically divergent fish species. Given the method is nonlethal and suited to automation, age prediction by DNA methylation has the potential to improve fisheries and other wildlife management settings.