bluuebunny/crossref_metadata_2025_split huggingface dataset:
Which Combinations of Environmental Conditions and Microphysical Parameter Values Produce a Given Orographic Precipitation Distribution?
Authors: Morales Annareli , Posselt Derek J. , Morrison Hugh 
Published: December 2020

AbstractThis study applies an idealized modeling framework, alongside a Bayesian Markov chain Monte Carlo (MCMC) algorithm, to explore which combinations of upstream environmental conditions and cloud microphysical parameter values can produce a particular precipitation distribution over an idealized two-dimensional, bell-shaped mountain. Simulations focus on orographic precipitation produced when an atmospheric river interacts with topography. MCMC-based analysis reveals that different combinations of parameter values produce a similar precipitation distribution, with the most influential parameters being relative humidity (RH), horizontal wind speed (U), surface potential temperature (θsfc), and the snow fall speed coefficient (As). RH, U, and As exhibit interdependence: changes in one or more of these factors can be mitigated by compensating changes in the other(s) to produce similar orographic precipitation rates. The results also indicate that the parameter sensitivities and relationships can vary for spatial subregions and given different environmental conditions. In particular, high θsfc values are more likely to produce the target precipitation rate and spatial distribution, and thus the ensemble of simulations shows a preference for liquid precipitation at the surface. The results presented here highlight the complexity of orographic precipitation controls, and have implications for flood and water management, observational efforts, and climate change.
Turbulence Driven by Reflected Internal Tides in a Supercritical Submarine Canyon
Authors: Hamann Madeleine M. , Alford Matthew H. , Lucas Andrew J. , Waterhouse Amy F. , Voet Gunnar 
Published: December 2020

AbstractThe La Jolla Canyon System (LJCS) is a small, steep, shelf-incising canyon offshore of San Diego, California. Observations conducted in the fall of 2016 capture the dynamics of internal tides and turbulence patterns. Semidiurnal (D2) energy flux was oriented up-canyon; 62% ± 20% of the signal was contained in mode 1 at the offshore mooring. The observed mode-1 D2 tide was partly standing based on the ratio of group speed times energy cgE and energy flux F. Enhanced dissipation occurred near the canyon head at middepths associated with elevated strain arising from the standing wave pattern. Modes 2–5 were progressive, and energy fluxes associated with these modes were oriented down-canyon, suggesting that incident mode-1 waves were back-reflected and scattered. Flux integrated over all modes across a given canyon cross section was always onshore and generally decreased moving shoreward (from 240 ± 15 to 5 ± 0.3 kW), with a 50-kW increase in flux occurring on a section inshore of the canyon’s major bend, possibly due to reflection of incident waves from the supercritical sidewalls of the bend. Flux convergence from canyon mouth to head was balanced by the volume-integrated dissipation observed. By comparing energy budgets from a global compendium of canyons with sufficient observations (six in total), a similar balance was found. One exception was Juan de Fuca Canyon, where such a balance was not found, likely due to its nontidal flows. These results suggest that internal tides incident at the mouth of a canyon system are dissipated therein rather than leaking over the sidewalls or siphoning energy to other wave frequencies.
The evolution of the Sesia Zone (Western Alps) from Carboniferous to Cretaceous: insights from zircon and allanite geochronology
Authors: Vho Alice , Rubatto Daniela , Lanari Pierre , Regis Daniele 
Published: December 2020

AbstractMicroscale dating of distinct domains in minerals that contain relics of multiple metamorphic events is a key tool to characterize the polyphase evolution of complex metamorphic terranes. Zircon and allanite from five metasediments and five metaintrusive high-pressure (HP) rocks from the Eclogite Micaschist Complex of the Sesia Zone were dated by SIMS and LA-ICP-MS. In the metasediments, zircon systematically preserves detrital cores and one or two metamorphic overgrowths. An early Permian age is obtained for the first zircon rim in metasediments from the localities of Malone Valley, Chiusella Valley and Monte Mucrone (292 ± 11, 278.8 ± 3.6 and 285.9 ± 2.9 Ma, respectively). In the Malone Valley and Monte Mucrone samples, the early Permian ages are attributed to high-temperature metamorphism and coincide with the crystallization ages of associated mafic and felsic intrusions. This implies that magmatism and metamorphism were coeval and associated to the same tectono-metamorphic extensional event. In the Malone Valley, allanite from a metasediment is dated at 241.1 ± 6.1 Ma and this age is tentatively attributed to a metasomatic/metamorphic event during Permo-Triassic extension. Outer zircon rims with a late Cretaceous age (67.4 ± 1.9 Ma) are found only in the micaschist from Monte Mucrone. In metagabbro of the Ivozio Complex, zircon cores yield an intrusive age for the protolith of 340.7 ± 6.8 Ma, whereas Alpine allanite are dated at 62.9 ± 4.2 and 55.3 ± 7.3 Ma. The Cretaceous ages constrain the timing of the HP metamorphic stage. The presence of zircon overgrowth only in the central area of the Eclogite Micaschist Complex is attributed to local factors such as (1) multiple fluid pulses at HP that locally enhanced zircon dissolution and recrystallization, and (2) slightly higher temperatures reached in this area during HP metamorphism.
Force–displacement relations of bolted timber joints with slotted-in steel plates parallel to the grain
Authors: Liu Yingyang , Wang Yixuan , Zhang Yiming , Chen Minghui , Nie Xizhe 
Published: December 2020

AbstractTo study the force–displacement relations of bolted timber joints with slotted-in steel plates, we performed a monotonic loading test parallel to the grain on 24 specimens. The influences of the bolt diameter, timber thickness, and their ratio were considered. As shown by the test results, the joints had a high deformation capacity and experienced a linear stage, a stiffness degradation stage, a yield plateau stage, and a failure stage during loading. Based on the curve fitting and parameter identification, the force–displacement relations of the joints were summarized in a mechanical model with two parameters, i.e., the bearing capacity and the elastic stiffness. Based on theoretical analysis, we proposed a theoretical calculation formula for the bearing capacity and elastic stiffness of the joints. Finally, we calculated the force–displacement relation curves of bolted timber joints with slotted-in steel plates using the mechanical model and the theoretical formula. The calculated curves fitted well with the experimental curves.
Concurrent brain structural and functional alterations in patients with migraine without aura: an fMRI study
Authors: Li Zhengjie , Zhou Jun , Lan Lei , Cheng Shirui , Sun Ruirui , Gong Qiyong , Wintermark Max , Zeng Fang , Liang Fanrong 
Published: December 2020

Abstract
Objectives
To explore the possible concurrent brain functional and structural alterations in patients with migraine without aura (MwoA) patients compared to healthy subjects (HS).

Methods
Seventy-two MwoA patients and forty-six HS were recruited. 3D-T1 and resting state fMRI data were collected during the interictal period for MwoA and HS. Voxel-based morphometry (VBM) for structure analysis and regional homogeneity (Reho) for fMRI analysis were applied. The VBM and Reho maps were overlapped to determine a possible brain region with concurrent functional and structural alteration in MwoA patients. Further analysis of resting state functional connectivity (FC) alteration was applied with this brain region as the seed.

Results
Compared with HS, MwoA patients showed decreased volume in the bilateral superior and inferior colliculus, periaqueductal gray matter (PAG), locus ceruleus, median raphe nuclei (MRN) and dorsal pons medulla junction. MwoA patients showed decreased Reho values in the middle occipital gyrus and inferior occipital gyrus, and increased Reho values in the MRN. Only a region in the MRN showed both structural and functional alteration in MwoA patients. Pearson correlation analysis showed that there was no association between volume or Reho values of the MRN and headache frequency, headache intensity, disease duration, self-rating anxiety scale or self-rating depression scale in MwoA patients. Resting state functional connectivity (FC) with the MRN as the seed showed that MwoA patients had increased FC between the MRN and PAG.

Conclusions
MRN are involved in the pathophysiology of migraine during the interictal period. This study may help to better understand the migraine symptoms.

Trial registration
NCT01152632. Registered 27 June 2010.
Roles of ROS and cell cycle arrest in the genotoxicity induced by gold nanorod core/silver shell nanostructure
Authors: Wang Dan , Dan Mo , Ji Yinglu , Wu Xiaochun , Wang Xue , Wen Hairuo 
Published: December 2020

AbstractTo understand the genotoxicity induced in the liver by silver nanoparticles (AgNPs) and silver ions, an engineered gold nanorod core/silver shell nanostructure (Au@Ag NR) and humanized hepatocyte HepaRG cells were used in this study. The involvement of oxidative stress and cell cycle arrest in the DNA and chromosome damage induced by 0.4–20 µg mL−1 Au@Ag NR were investigated by comet assay, γ-H2AX assay and micronucleus test. Further, the distribution of Au@Ag NR was analyzed. Our results demonstrated that both Ag+ and Au@Ag NR led to DNA cleavage and chromosome damage (clastogenicity) in HepaRG cells and that the Au@Ag NR retained in the nucleus may further release Ag+, aggravating the damages, which are mainly caused by cell cycle arrest and ROS formation. The results reveal the correlation between the intracellular accumulation, Ag+ ion release and the potential genotoxicity of AgNPs.
Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining
Authors: Zhou Ying , Lei Fang , Wang Qiong , He Weicong , Yuan Bin , Yuan Wenya 
Published: December 2020

Abstract
Background
As rice (Oryza sativa) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by most the single blast-resistance genes is broken after a few years of intensive agricultural use. Therefore, effective resistance breeding in rice requires continual enrichment of the reservoir of resistance genes, alleles, or QTLs. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles.

Results
We carried out a large-scale screen for novel blast-resistance alleles in 1883 rice varieties from major rice-producing areas across China. Of these, 361 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. We used sequence-based allele mining to amplify and sequence the allelic variants of the major rice blast-resistance genes at the Pi2/Pi9 locus of chromosome 6 from the 361 blast-resistant varieties, and the full-length coding region of this gene could be amplified from 107 varieties. Thirteen novel Pi9 alleles (named Pi9-Type1 to Pi9-Type13) were identified in these 107 varieties based on comparison to the Pi9 referenced sequence. Based on the sequencing results, the Pi2/Pi9 locus of the 107 varieties was divided into 15 genotypes (including three different genotypes of Pi9-Type5). Fifteen varieties, each representing one genotype, were evaluated for resistance to 34 M. oryzae isolates. The alleles from seven varieties with the highest resistance and widest resistance spectra were selected for transformation into the susceptible variety J23B to construct near-isogenic lines (NILs). These NILs showed resistance in a field test in Enshi and Yichang, indicating that the seven novel rice blast-resistance tandem-repeat regions at the Pi2/Pi9 locus of chromosome 6 could potentially serve as a genetic resource for molecular breeding of resistance to rice blast.

Conclusions
The thirteen novel Pi9 alleles identified in this study expand the list of available of blast-resistance alleles. Seven tandem-repeat regions of the Pi2/Pi9 locus from different donors were characterized as broad-spectrum rice blast-resistance fragments; these donors enrich the genetic resources available for rice blast-resistance breeding programs.
Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica
Authors: Cao Zhonghong , Rosenkranz David , Wu Suge , Liu Hongjin , Pang Qiuxiang , Zhang Xiufang , Liu Baohua , Zhao Bosheng 
Published: December 2020

Abstract
Background
Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RNAs during the process of head regeneration are not well understood. Furthermore, little is known about the evolutionary conservation of the relevant small RNAs pathways, rendering it difficult to assess whether insights from planarians will apply to other taxa.

Results
In this study, we applied high throughput sequencing to identify miRNAs, tRNA fragments and piRNAs that are dynamically expressed during head regeneration in Dugesia japonica. We further show that knockdown of selected small RNAs, including three novel Dugesia-specific miRNAs, during head regeneration induces severe defects including abnormally small-sized eyes, cyclopia and complete absence of eyes.

Conclusions
Our findings suggest that a complex pool of small RNAs takes part in the process of head regeneration in Dugesia japonica and provide novel insights into global small RNA expression profiles and expression changes in response to head amputation. Our study reveals the evolutionary conserved role of miR-124 and brings further promising candidate small RNAs into play that might unveil new avenues for inducing restorative programs in non-regenerative organisms via small RNA mimics based therapies.
Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia
Authors: Issaka Salia Ousseini , Mitchell Diana M. 
Published: December 2020

Abstract
Background
Unlike mammals, zebrafish have a remarkable capacity to regenerate a variety of tissues, including central nervous system tissue. The function of macrophages in tissue regeneration is of great interest, as macrophages respond and participate in the landscape of events that occur following tissue injury in all vertebrate species examined. Understanding macrophage populations in regenerating tissue (such as in zebrafish) may inform strategies that aim to regenerate tissue in humans. We recently published an RNA-seq experiment that identified genes enriched in microglia/macrophages in regenerating zebrafish retinas. Interestingly, a small number of transcripts differentially expressed by retinal microglia/macrophages during retinal regeneration did not have predicted orthologs in human or mouse. We reasoned that at least some of these genes could be functionally important for tissue regeneration, but most of these genes have not been studied experimentally and their functions are largely unknown. To reveal their possible functions, we performed a variety of bioinformatic analyses aimed at identifying the presence of functional protein domains as well as orthologous relationships to other species.

Results
Our analyses identified putative functional domains in predicted proteins for a number of selected genes. For example, we confidently predict kinase function for one gene, cytokine/chemokine function for another, and carbohydrate enzymatic function for a third. Predicted orthologs were identified for some, but not all, genes in species with described regenerative capacity, and functional domains were consistent with identified orthologs. Comparison to other published gene expression datasets suggest that at least some of these genes could be important in regenerative responses in zebrafish and not necessarily in response to microbial infection.

Conclusions
This work reveals previously undescribed putative function of several genes implicated in regulating tissue regeneration. This will inform future work to experimentally determine the function of these genes in vivo, and how these genes may be involved in microglia/macrophage roles in tissue regeneration.
New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves
Authors: Urantówka Adam Dawid , Kroczak Aleksandra , Mackiewicz Paweł 
Published: December 2020

AbstractBackgroundBird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first inGallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that ofEudromia elegans.ResultsTherefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes inCrypturellus, RheaandStruthioas well asND6pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication.ConclusionsThe duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus
Authors: Scheben Armin , Severn-Ellis Anita A. , Patel Dhwani , Pradhan Aneeta , Rae Stephen J. , Batley Jacqueline , Edwards David 
Published: December 2020

AbstractBackgroundBrassica napusis an important oilseed crop cultivated worldwide. During domestication and breeding ofB. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering inB. napus. An F2mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type.ResultsFlowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes includingFLC.ConclusionsThese findings demonstrate the effectiveness of the ddRAD approach to sample theB. napusgenome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
Prior exposure of Arabidopsis seedlings to mechanical stress heightens jasmonic acid-mediated defense against necrotrophic pathogens
Authors: Brenya Eric , Chen Zhong-Hua , Tissue David , Papanicolaou Alexie , Cazzonelli Christopher Ian 
Published: December 2020

AbstractBackgroundProlonged mechanical stress (MS) causes thigmomorphogenesis, a stress acclimation response associated with increased disease resistance. What remains unclear is if; 1) plants pre-exposed to a short period of repetitive MS can prime defence responses upon subsequent challenge with necrotrophic pathogens, 2) MS mediates plant immunity via jasmonic acid (JA) signalling, and 3) a short period of repetitive MS can cause long-term changes in gene expression resembling a stress-induced memory. To address these points, 10-days old juvenileArabidopsisseedlings were mechanically stressed for 7-days using a soft brush and subsequently challenged with the necrotrophic pathogens,Alternaria brassicicola,andBotrytis cinerea. Here we assessed how MS impacted structural cell wall appositions, disease symptoms and altered gene expression in response to infection.ResultsThe MS-treated plants exhibited enhanced cell wall appositions and jasmonic acid (JA) accumulation that correlated with a reduction in disease progression compared to unstressed plants. The expression of genes involved in JA signalling, callose deposition, peroxidase and phytoalexin biosynthesis and reactive oxygen species detoxification were hyper-induced 4-days post-infection in MS-treated plants. The loss-of-function in JA signalling mediated by the JA-insensitivecoronatine-insensitive 1(coi1) mutant impaired the hyper-induction of defense gene expression and promoted pathogen proliferation in MS-treated plants subject to infection. The basal expression level ofPATHOGENESIS-RELATED GENE 1andPLANT DEFENSIN 1.2defense marker genes were constitutively upregulated in rosette leaves for 5-days post-MS, as well as in naïve cauline leaves that differentiated from the inflorescence meristem well after ceasing MS.ConclusionThis study reveals that exposure of juvenileArabidopsisplants to a short repetitive period of MS can alter gene expression and prime plant resistance upon subsequent challenge with necrotrophic pathogens via the JA-mediatedCOI1signalling pathway. MS may facilitate a stress-induced memory to modulate the plant’s response to future stress encounters. These data advance our understanding of how MS primes plant immunity against necrotrophic pathogens and how that could be utilised in sustainable agricultural practices.