bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creating multi‐scale nested MRIO tables for linking localized impacts to global consumption drivers
Authors: Fry Jacob , Geschke Arne , Langdon Sarah , Lenzen Manfred , Li Mengyu , Malik Arunima , Sun Ya‐Yen , Wiedmann Thomas 
Published: June 2021

AbstractIndustrial Ecology Virtual Laboratories (IELabs) enable the construction of national‐to‐local‐scale multi‐regional input–output (MRIO) models. These IELabs have been proven to be especially important for analyzing research questions that warrant sub‐national spatial detail. The field of industrial ecology has clearly progressed from the time of national‐only input–output tables. Here, we present a newly developed tool called NLab—“nested IELab”—that nests sub‐national MRIO tables within global country‐scale MRIOs. This capability allows for the investigation of interactions between sub‐national production and consumption systems, with global systems interlinked via international trade. We provide a technical and mathematical roadmap for construction of nested input–output tables in the NLab, and demonstrate this capability through a real‐world assessment of the Western Australian wine industry. Our results suggest that nested MRIO tables provide an added layer of detail at a regional level, when undertaking consumption‐based footprint assessments, leading to improved assessment of quantification of regional impacts. The NLab presented in this work provides tools for analysis of complex trade linkages between industries at various scales, which has the further potential to open avenues for policy‐makers to analyze the implications of local decisions at a global level, and vice versa.
Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog
Authors: Medina Ricardo , Wogan Guinevere O. U. , Bi Ke , Termignoni‐García Flavia , Bernal Manuel Hernando , Jaramillo‐Correa Juan P. , Wang Ian J. , Vázquez‐Domínguez Ella 
Published: June 2021

AbstractUnderstanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter‐Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome‐wide SNP data together with behavioural and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the banana tree‐dwelling frog, Boana platanera, distributed across an environmental gradient in Central Colombia (northern South America). Here, we analysed the relationships between environmentally (temperature and precipitation) associated genetic and phenotypic differentiation and the potential drivers of isolation by environment along an elevation gradient. We identified candidate SNPs associated with temperature and body size, which follow a clinal pattern of genome‐wide differentiation tightly coupled with phenotypic variation: as elevation increases, B. platanera exhibits larger body size and longer call duration with more pulses but lower pulse rate and frequency. Thus, the environmental landscape has rendered a scenario where isolation by environment and candidate loci show concordance with phenotypic divergence in this tropical frog along an elevation gradient in the Colombian Andes. Our study sets the basis for evaluating the role of temperature in the genetic structure and local adaptation in tropical treefrogs and its putative effect on life cycle (embryos, tadpoles, adults) along elevation gradients.
A sliver of the past: The decimation of the genetic diversity of the Mexican wolf
Authors: Taron Ulrike H. , Salado Isabel , Escobar‐Rodríguez Mariana , Westbury Michael V. , Butschkau Susanne , Paijmans Johanna L. A. , vonHoldt Bridgett M. , Hofreiter Michael , Leonard Jennifer A. 
Published: June 2021

AbstractThe endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long‐term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole‐genome analyses of five historical Mexican wolves (1907–1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole‐genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.
Rhythmic Processes in Schoenberg's Pierrot lunaire
Authors: Muniz John 
Published: June 2021

ABSTRACTAnalysts have given renewed attention to rhythm in Schoenberg's atonal music; simultaneously, scholars of rhythm and metre have given increasing consideration to listeners’ changing perceptions of metrical structure in real time, as well as the cognition of metrical ambiguity. The present article joins these two threads of research, applying analytical techniques developed by Christopher Hasty (1997) to Pierrot lunaire. Hasty's approach suits Pierrot because it allows for evanescence and vagueness in the perception of rhythmic and metric qualities. The article describes several types of processes of rhythmic change in Pierrot: contraction and expansion of projective functions, hypermetrical formation and dispersion and metrical promotion and demotion. The resulting analytical model and typology can serve as a point of departure for analysing works in various corpora in addition to those of the Second Viennese School.
Egg enrichment with vitamin D: The Sunshine Eggs projects
Authors: Clark Adam , Kuznesof Sharron , Davies Sarah , Waller Anthony , Ritchie Avril , Wilson Simon , Harbord Lance , Hill Tom 
Published: June 2021

AbstractVitamin D deficiency is a significant public health issue in the UK with almost one in five adults having poor vitamin D status and most people failing to meet the Reference Nutrient Intake of 10 µg/day. There is an urgent need to address poor population vitamin D status through the development of food‐based strategies. Eggs can be enriched with vitamin D through manipulating vitamin D content in hens’ feed. The Sunshine Eggs project was launched in 2015 through Innovate UK funding and brought together Noble Foods Ltd, DSM Nutritional Products Ltd and Newcastle University. The research demonstrated that feeding flocks of commercial hens up to 75 µg of 25‐D/kg (25‐hydroxyvitamin D3 via Rovimix® Hy‐D®) of feed for 6 weeks improved egg total vitamin D content by 40%. These results informed the reformulation of the UK’s leading free‐range egg brand ‘Happy Egg’ in October 2018, offering vitamin D–enriched eggs to the consumer. This article outlines the aims of a second Innovate UK‐funded Sunshine Eggs 2 project, which seeks to maximise the commercial potential of vitamin D–enriched eggs through several objectives. These relate to understanding (1) how storage/cooking methods affect egg vitamin D content; (2) whether enriched egg consumption improves vitamin D status in a human intervention trial; (3) consumer attitudes towards enriched eggs; and (4) market research to identify commercial opportunities for enriched eggs. The project seeks to drive fundamental impact across academic, commercial and public health nutrition sectors, in helping to offer viable vitamin D–enriched foods for UK consumers.
Ne2, a typical CC–NBS–LRR‐type gene, is responsible for hybrid necrosis in wheat
Authors: Si Yaoqi , Zheng Shusong , Niu Jianqing , Tian Shuiquan , Gu Mengjun , Lu Qiao , He Yilin , Zhang Juan , Shi Xiaoli , Li Yiwen , Ling Hong‐Qing 
Published: June 2021

Summary

Hybrid necrosis, caused by complementary genes Ne1 and Ne2, is a serious barrier for combining desirable traits from different genotypes of wheat, affecting the full utilisation of heterosis. To date, both Ne1 and Ne2 are still not isolated although they were documented decades ago.

We report here the map‐based cloning and functional characterisation of Ne2, encoding a coiled coil–nucleotide‐binding site–leucine‐rich repeat (CC–NBS–LRR) protein. Homozygous frameshift mutations generated using the CRISPR/Cas9 approach confirmed the Ne2‐inducing hybrid necrosis in wheat. Upregulated expression of Ne2 induced by Ne1 and excess hydrogen peroxide accumulation are associated with the necrosis formation.

Genetic analyses of a Ne2 allele (Ne2m) and leaf rust resistance gene LrLC10/Lr13 revealed that they might be the same gene. Furthermore, we demonstrated that the frequency of the Ne2 allele was much lower in landraces (2.00%) compared with that in modern cultivars (13.62%), suggesting that Ne2 allele has been partially applied in wheat genetic improvement.

Our findings open opportunities of thoroughly investigating the molecular mechanism of hybrid necrosis, selecting Lr13 and simultaneously avoiding hybrid necrosis in wheat breeding through marker‐assisted selection.
A large‐scale genomic association analysis identifies a fragment in Dt11 chromosome conferring cotton Verticillium wilt resistance
Authors: Zhang Yan , Chen Bin , Sun Zhengwen , Liu Zhengwen , Cui Yanru , Ke Huifeng , Wang Zhicheng , Wu Liqiang , Zhang Guiyin , Wang Guoning , Li Zhikun , Yang Jun , Wu Jinhua , Shi Rongkang , Liu Song , Wang Xingfen , Ma Zhiying 
Published: June 2021

SummaryVerticillium wilt (VW) is a destructive disease that results in great losses in cotton yield and quality. Identifying genetic variation that enhances crop disease resistance is a primary objective in plant breeding. Here we reported a GWAS of cotton VW resistance in a natural‐variation population, challenged by different pathogenicity stains and different environments, and found 382 SNPs significantly associated with VW resistance. The associated signal repeatedly peaked in chromosome Dt11 (68 798 494‐69 212 808) containing 13 core elite alleles undescribed previously. The core SNPs can make the disease reaction type from susceptible to tolerant or resistant in accessions with alternate genotype compared to reference genotype. Of the genes associated with the Dt11 signal, 25 genes differentially expressed upon Verticillium dahliae stress, with 21 genes verified in VW resistance via gene knockdown and/or overexpression experiments. We firstly discovered that a gene cluster of L‐type lectin‐domain containing receptor kinase (GhLecRKs‐V.9) played an important role in VW resistance. These results proved that the associated Dt11 region was a major genetic locus responsible for VW resistance. The frequency of the core elite alleles (FEA) in modern varieties was significantly higher than the early/middle varieties (12.55% vs 4.29%), indicating that the FEA increased during artificial selection breeding. The current developmental resistant cultivars, JND23 and JND24, had fixed these core elite alleles during breeding without yield penalty. These findings unprecedentedly provided genomic variations and promising alleles for promoting cotton VW resistance improvement.
Circadian clock protein BMAL1 regulates melanogenesis through MITF in melanoma cells
Authors: Sarkar Soumyadeep , Porter Kenneth I. , Dakup Panshak P. , Gajula Rajendra P. , Koritala Bala S. C. , Hylton Ryan , Kemp Michael G. , Wakamatsu Kazumasa , Gaddameedhi Shobhan 
Published: June 2021

AbstractSolar ultraviolet B radiation (UVB) is one of the leading causes of various skin conditions, including photoaging, sunburn erythema, and melanoma. As a protective response, the skin has inbuilt defense mechanisms, including DNA repair, cell cycle, apoptosis, and melanin synthesis. Though DNA repair, cell cycle, and apoptosis are clock controlled, the circadian mechanisms associated with melanin synthesis are not well understood. Using human melanocytes and melanoma cells under synchronized clock conditions, we observed that the microphthalmia‐associated transcription factor (MITF), a rate‐limiting protein in melanin synthesis, is expressed rhythmically with 24‐hr periodicity in the presence of circadian clock protein, BMAL1. Furthermore, we demonstrated that BMAL1 binds to the promoter region of MITF and transcriptionally regulates its expression, which positively influences melanin synthesis. Finally, we report that an increase in melanin levels due to BMAL1 overexpression protects human melanoma cells from UVB. In conclusion, our studies provide novel insights into the mechanistic role of the circadian clock in melanin synthesis and protection against UVB‐mediated DNA damage and genomic instability.
Spectroscopic Analysis of Apoferritin Associates with the Water‐Soluble Porphyrins
Authors: Sakae Hiroki 
Published: June 2021

AbstractThe association behavior of apoferritin species with the anionic porphyrins, 5,10,15,20‐tetrakis(4‐sulfonatophenyl)porphyrin (H2TPPS4−) and its zinc(II) complex (ZnTPPS4−), which are water‐soluble even in acidic solutions, was investigated for the first time through UV–Vis absorption and fluorescence spectroscopy in order to evaluate a potential ability of apoferritin as a stimuli‐responsive molecular capsule. The absorption maximum wavelengths of both porphyrins were redshifted and the fluorescence intensity decreased, indicating the effective association between apoferritin species and the porphyrins, although it depended on the pH adjustment procedure. At pH 2, the ZnTPPS4− associated with apoferritin subunits without demetallating and protonating, while the free base porphyrin formed the J‐aggregate of the diprotonated species (H4TPPS2−)n, with extremely low fluorescence. As the concentration of apoferritin subunits increased, the H2TPPS4−‐subunits associates were formed accompanied by recovering the fluorescence. The association stoichiometries of 1 or 2 subunits/porphyrin obtained under neutral and acidic conditions. The significantly large association constant of ZnTPPS4− as compared with that of H2TPPS4− indicated that the coordination to the zinc(II) center strongly contributes to the association in addition to the electrostatic interaction between apoferritin subunits and the porphyrin under acidic conditions.
Submerged cage aquaculture of marine fish: A review of the biological challenges and opportunities
Authors: Sievers Michael , Korsøen Øyvind , Warren‐Myers Fletcher , Oppedal Frode , Macaulay Georgia , Folkedal Ole , Dempster Tim 
Published: June 2021

AbstractSurface‐based cages are the dominant production technology for the marine finfish aquaculture industry. However, issues such as extreme weather events, poor environmental conditions, interactions with parasites, and conflicts with other coastal users are problematic for surface‐based aquaculture. Submerged cages may reduce many of these problems and commercial interest in their use has increased. However, a broad synthesis of research into the effects of submerged culture on fish is lacking. Here, we review the current status of submerged fish farming worldwide, outline the biological challenges that fish with fundamentally different buoyancy control physiologies face in submerged culture, and discuss production benefits and problems that might arise from submerged fish farming. Our findings suggest that fish with closed swim bladders, and fish without swim bladders, may be well‐suited to submerged culture. However, for fish with open swim bladders, such as salmonids, submergence is more complex as they require access to surface air to refill their swim bladders and maintain buoyancy. Growth and welfare of open swim bladder fish can be compromised by submergence for long periods due to complications with buoyancy regulation, but the recent addition of underwater air domes to submerged cages can alleviate this issue. Despite this advance, a greater understanding of how to couple advantageous environmental conditions with submerged culture to improve fish growth and welfare over the commercial production cycle is required if submerged cages are to become a viable alternative to surface‐based cage aquaculture.
Reconstruction of an extreme flood hydrograph and morphodynamics of a meander bend in a high‐peak discharge variability river (Powder River, USA)
Authors: Ghinassi Massimiliano , Moody John 
Published: June 2021

AbstractUnderstanding of morphodynamic processes associated with large‐scale floods has recently improved following significant advances of modern technologies. Nevertheless, a clear link between flood discharge and in‐channel sedimentation processes remains to be resolved. The hydrological and geomorphological data available for the meandering Powder River (Montana, USA) since 1977 makes it a perfect laboratory to investigate connections between flood discharge and point‐bar sedimentation processes. This study focuses on a point‐bar that accreted laterally ca 70 m during a 50‐year recurrence flood, which lasted about 14 days in May 1978. In September 2018, a trench ca 2 m deep and 70 m long was excavated through the axial point‐bar deposits, and the 1978 flood deposits were delineated based on georeferenced pre‐flood and post‐flood cross‐section surveys. Sedimentological data show that point‐bar deposits accumulated at the early and late flood stages, when the flow was confined to the channel, and have similarities with classical facies models in terms of palaeocurrent patterns and vertical grain‐size trend. However, during high‐stage flood conditions, when the flow overtopped the bar, cross‐cutting of the bar and armouring were typical processes. Integration of sedimentological and palaeo‐hydrological data highlight that the relation between channel cross‐sectional area and flood discharge play a key role in preserving bar deposits. The integrated approach adopted here provides a basis for advancing palaeoflood hydrology beyond the stage of estimating peak discharges to the next stage of estimating palaeoflood hydrographs.
Characteristics and outcomes among lung transplant patients with respiratory syncytial virus infection
Authors: Mahan Luke D. , Points April , Mohanka Manish R. , Bollineni Srinivas , Joerns John , Kaza Vaidehi , La Hoz Ricardo M. , Gao Ang , Zhang Song , Torres Fernando , Banga Amit 
Published: June 2021

AbstractBackgroundTo describe characteristics and outcomes among lung transplantation (LT) patients with respiratory syncytial virus (RSV) infection and elucidate the predictors of 1‐year survival after RSV infection.MethodsThis was a retrospective chart review study among LT patients with RSV infection between 2013 and 2018 (90 episodes among 87 patients; mean age 56.3 ± 13.1 years, M:F 52:35). A contemporaneous control group consisting of LT patients without RSV infection (n = 183) was included. One‐year survival after the RSV infection was the primary endpoint.ResultsMedian time from LT to RSV infection was 30 (1‐155) months. Before RSV infection, the median decline in forced vital capacity (FVC) was 9.7 cc (−17.8 to 83 cc) or 0.29% (−1.4% to 4.6%) per month, while the forced expiratory volume (FEV1) decline was 7.5 cc (−8.8 to 58 cc) or 0.3% (−0.57% to 4.3%) per month with no statistically significant change after RSV infection. One‐year survival among patients with RSV infection was 86.2% (75/87). Pre‐infection diagnosis of chronic lung allograft dysfunction (CLAD; adjusted HR: 4.29, 1.08‐17.0; P = .038) and FVC or FEV1 decline >10% during 6 months post infection (adjusted HR: 35.1, 3.26‐377.1; P = .003) were independently associated with worse survival. On propensity score matched analysis, RSV infection was not associated with worse post‐transplant survival (HR with 95% CI: 0.79, 0.47‐1.34; P = .38).ConclusionsA majority of LT patients in the current cohort did not experience an alteration in the trajectory of FVC or FEV1 decline after developing RSV infection, and their post‐transplant survival was not adversely impacted. Established CLAD at the time of RSV infection and post infection >10% decline in FVC or FEV1 are independently associated with worse survival after RSV infection.
Non‐functional GoFLA19s are responsible for the male sterility caused by hybrid breakdown in cotton (Gossypium spp.)
Authors: Zhang Meng , Wei Hengling , Liu Ji , Bian Yingjie , Ma Qiang , Mao Guangzhi , Wang Hantao , Wu Aimin , Zhang Jingjing , Chen Pengyun , Ma Liang , Fu Xiaokang , Yu Shuxun 
Published: June 2021

SUMMARYHybrid breakdown (HB) functions as a common reproductive barrier and reduces hybrid fitness in many species, including cotton. However, the related genes and the underlying genetic mechanisms of HB in cotton remain unknown. Here, we found that the photosensitive genetic male sterile line CCRI9106 was a hybrid progeny of Gossypium hirsutum and Gossypium barbadense and probably a product of HB. Fine mapping with F2s (CCRI9106 × G. hirsutum/G. barbadense lines) identified a pair of male sterility genes GoFLA19s (encoding fasciclin‐like arabinogalactan family protein) located on chromosomes A12 and D12. Crucial variations occurring in the fasciclin‐like domain and the arabinogalactan protein domain were predicted to cause the non‐functionalization of GbFLA19‐D and GhFLA19‐A. CRISPR/Cas9‐mediated knockout assay confirmed the effects of GhFLA19s on male sterility. Sequence alignment analyses showed that variations in GbFLA19‐D and GhFLA19‐A likely occurred after the formation of allotetraploid cotton species. GoFLA19s are specifically expressed in anthers and contribute to tapetal development, exine assembly, intine formation, and pollen grain maturation. RNA‐sequencing and quantitative reverse transcriptase–polymerase chain reaction analyses illustrated that genes related to these biological processes were significantly downregulated in the mutant. Our research on male sterility genes, GoFLA19s, improves the understanding of the molecular characteristics and evolutionary significance of HB in interspecific hybrid breeding.