bluuebunny/crossref_metadata_2025_split huggingface dataset:
The production of short chain fatty acid and colonic development in weaning piglets
Authors: Zhou Zirui , Zhang Jie , Zhang Xianlian , Mo Shilan , Tan Xian , Wang Lixia , Li Jianzhong , Li Yali , Ding Xueqin , Liu Xianyong , Ma Xingqun , Yang Huansheng , Yin Yulong 
Published: July 2019

AbstractWeaning process widely affects the small intestinal structure and function in piglets, while the responses of large intestine to weaning stress are still obscure. The purpose of this study was to determine the developmental changes (i.e., short chain fatty acids (SCFAs) concentrations, growth parameters, crypt‐related indices and antioxidant capacity) in colon of piglet during weaning. Forty piglets were weaned at day 21 and euthanized to collect colonic tissues and digesta samples on day 0, 1, 3, 7 and 14 post‐weaning (n = 8). Piglet growth performance was improved (p < .001) on day 7 and 14 post‐weaning. The concentrations of acetate, propionate, butyrate, valerate, isobutyrate, isovalerate and total SCFAs were higher (p < .001) during the late post‐weaning period. The mRNA abundances of SCFAs transporters were greater (p < .001) on day 7 and 14. The absolute and relative weights, absolute length and perimeter of colon were greater (p < .001) on day 7 and 14. Similarly, post‐weaning increases (p < .001) in colonic crypt depth and Ki67 positive cells numbers per crypt were observed during the same period. Colonic crypt fission indices decreased (p < .01), while total crypt numbers increased (p < .001) on day 14 after weaning. Moreover, total SCFAs concentration was significantly associated with colonic growth parameters and Ki67 cells/crypt (p < .001). In addition, catalase content was decreased on day 3, 7, and 14, whereas, the concentrations of total superoxide dismutase (T‐SOD) and manganese‐containing superoxide dismutase (MnSOD) were higher (p < .05) on day 1 and 3 post‐weaning. These results showed that weaning process has a significant effect on colonic growth and development, which might be associated with the change of SCFAs concentrations in colon.
Exploring the potential of nuclear and mitochondrial sequencing data generated through genome‐skimming for plant phylogenetics: A case study from a clade of neotropical lianas
Authors: Fonseca Luiz Henrique M. , Lohmann Lúcia G. 
Published: July 2019

AbstractFew botanical studies have explored the potential of nuclear ribosomal DNA (nrDNA) and mitochondrial DNA (mtDNA) data obtained through genome skimming for phylogeny reconstruction. Here, we analyzed the phylogenetic information included in the nrDNA and mtDNA of 44 species of the “Adenocalymma‐Neojobertia” clade (Bignoniaceae). To deal with intraindividual polymorphisms within the nrDNA, different coding schemes were explored through the analyses of four datasets: (i) “nrDNA contig,” with base call following the majority rule; (ii) “nrDNA ambiguous,” with ambiguous base calls; (iii) “nrDNA informative,” with ambiguities converted to multistate characters; and, (iv) “mitochondrial,” with 39 mitochondrial genes. Combined analyses using the nrDNA and mtDNA data and previously published “plastid” datasets were also conducted. Trees were obtained using Maximum Likelihood and Bayesian criteria. The congruence among genomes was assessed. The nrDNA datasets were shown to be highly polymorphic within individuals, while the “mitochondrial” dataset was the least informative, with 0.36% of informative bases within the ingroup. The topologies inferred using the nrDNA and mtDNA datasets were broadly congruent with the tree derived from the analyses of the “plastid” dataset. The topological differences recovered were generally poorly supported. The topology that resulted from the analyses of the “combined” dataset largely resembles the “plastid” tree. These results highlight limitations of nuclear ribosomal DNA and mitochondrial genes for phylogeny reconstruction obtained through genome skimming and the need to include more data from both genomes. The different topologies observed among genomes also highlight the importance of exploring data from various genomes in plant phylogenetics.
Fire severity and changing composition of forest understory plant communities
Authors: Stevens Jens T. , Miller Jesse E. D. , Fornwalt Paula J. 
Published: July 2019

AbstractQuestionsGradients of fire severity in dry conifer forests can be associated with variation in understory floristic composition. Recent work in dry conifer forests in California, USA, has suggested that more severely burned stands contain more thermophilic taxa (those associated with warmer and drier conditions), and that forest disturbance may therefore accelerate floristic shifts already underway due to climate change. However, it remains unknown how rapidly thermophilic taxa shifts occur following disturbance, how long such shifts are likely to persist, and how different thermophilic post‐disturbance communities are from pre‐disturbance communities.LocationColorado Front Range, USA.MethodsWe investigated these questions using a unique 15‐year vegetation plot dataset that captures pre‐ and post‐fire understory community composition across a gradient of fire severity in dry conifer forests, classifying taxa using the biogeographic affinity concept.ResultsThermophilization (defined here as a decrease in the ratio of cool‐mesic taxa to warm‐xeric taxa, based on biogeographic affinity of paleobotanical lineages) was observed as early as one year post‐fire for all fire severity classes, but was stronger at sites that burned at higher severity. The ratio of cool‐mesic to warm‐xeric taxa recovered to pre‐fire levels within 10 years in stands that burned at low severity, but not in stands that burned at moderate or high severity. The process of thermophilization after high‐severity fire appears to be driven primarily by the gain of warm‐xeric taxa that were absent before the fire, but losses of cool‐mesic taxa, which did not return during the duration of the study, also played a role.ConclusionsDecreases in canopy cover appear to be a main contributor to understory thermophilization. Fine‐scale heterogeneity in post‐fire forest structure is likely an important driver of floristic diversity, creating the microclimatic variation necessary to maintain floristic refugia for species mal‐adapted to increasingly warm and dry conditions.
Using structural equation modelling to understand the contributors to anaemia among young Burkinabe children
Authors: Bliznashka Lilia , Arsenault Joanne E. , Becquey Elodie , Ruel Marie T. , Olney Deanna K. 
Published: July 2019

AbstractAnaemia is a persistent problem among young Burkinabe children, yet population‐specific information on its determinants is scant. We used baseline data from an evaluation of Helen Keller International's Enhanced Homestead Food Production Program (n=1210 children) to quantify household‐, mother‐, and child‐level factors associated with anaemia in Burkinabe children aged 6‐12 months. We used structural equation modelling to assess a theoretical model, which tested four categories of factors: (a) household food security and dietary diversity, (b) household sanitation and hygiene (latrine and poultry access and bednet ownership), (c) maternal factors (anaemia, stress, cleanliness, and health, hygiene and feeding knowledge and practices), and (d) child nutrition and health (iron deficiency (ID), retinol binding protein (RBP), malaria, and inflammation). The model also included household socio‐economic status, size, and polygamy; maternal age and education; and child age and sex. Results showed that ID, malaria, and inflammation were the primary direct determinants of anaemia, contributing 15%, 10%, and 10%, respectively. Maternal knowledge directly explained improved child feeding practices and household bednet ownership. Household dietary diversity directly explained 18% of child feeding practices. Additionally, RBP, child age and sex, and maternal anaemia directly predicted child haemoglobin. Our findings suggest that program effectiveness could be increased by addressing the multiple, context‐specific contributors of child anaemia. For young Burkinabe children, anaemia control programs that include interventions to reduce ID, malaria, and inflammation should be tested. Other potential intervention entry points suggested by our model include improving maternal knowledge of optimal health, hygiene, and nutrition practices and household dietary diversity.
Insights into the use of an unmanned aerial vehicle (UAV) to investigate the behavior of humpback whales (Megaptera novaeangliae) in Vava'u, Kingdom of Tonga
Authors: Fiori Lorenzo , Martinez Emmanuelle , Bader Martin K.‐F. , Orams Mark B. , Bollard Barbara 
Published: July 2019

AbstractVertical take‐off and landing (VTOL) unmanned aerial vehicles (UAVs) are becoming invaluable data collection platforms for cetacean research. In particular, multi‐rotors can be used to measure whales and investigate their behavior. Moreover, VTOL UAVs are increasingly accessible for recreational and commercial pilots, and close encounters with whales are widely documented. Unfortunately, quantitative assessments of potential disturbance for the targeted animals are not yet published and guidelines for responsible use of UAVs around cetaceans are still under development. We conducted VTOL UAV surveys on humpback whales in Vava'u, Kingdom of Tonga. Interestingly, whale behaviors such as socializing and nurturing were not detected by trained observers on board the research vessel, but were evident from the UAV. Nevertheless, no significant differences were detected in diving and swim parameters between absence and presence of UAV flying at 30 m altitude. These results suggest that VTOL UAVs can be a noninvasive tool to gather morphometric and behavioral data on baleen whales. However, further research is necessary to establish whether applications that require flight altitudes lower than 30 m and targeting different species may elicit behavioral responses.
The maggot therapy supply chain: a review of the literature and practice
Authors: Stadler F. 
Published: July 2019

AbstractMaggot therapy (MT) is the clinical application of living fly larvae for the treatment of non‐healing wounds and wounds that require debridement. This systematized and expanded literature review is the first study to investigate MT through the conceptual and disciplinary framework of supply chain management. The review of 491 selected academic papers was expanded to include the grey literature and online information resources to construct a first‐pass theory of the medicinal maggot supply chain. It shows that the literature to date has focused on isolated discussions of echelon‐specific issues such as diet improvement and sterilization protocols in the production echelon, and the relative effectiveness of medicinal maggot application methods in the treatment echelon. There is little knowledge in the public domain regarding the transport and distribution of medicinal maggots, but existing supply chains for vaccines, blood and pathology specimens may provide learning and supply chain integration opportunities. Maggot therapy knowledge across the treatment echelon is generally substantive but there is still insufficient knowledge regarding patients' and health care providers' attitudes toward the therapy, and their experiences of receiving and administering MT. Moreover, there is no research concerned with the humane disposal of medicinal flies during production and after treatment.
Multifocal neuropathy and treatment‐induced neuropathy of diabetes following diabetic ketoacidosis
Authors: Triplett James D , Yiannikas Con 
Published: July 2019

AbstractDiabetes is associated with numerous neuropathies; some accompanies poor glycemic control including diabetic ketoacidosis‐associated (DKA) neuropathies, others occur following improved glycemic control including treatment‐induced neuropathies of diabetes (TIND). A 27‐year‐old poorly controlled type I diabetic female developed multifocal weakness and pains accompanied by widespread autonomic dysfunction following an episode of DKA with rapid and subsequent sustained glycemic control. Injury was thought to have occurred secondary to disruptions of the endoneurial microenvironment following rapid glycemic control.
TaD27‐B gene controls the tiller number in hexaploid wheat
Authors: Zhao Bin , Wu Ting Ting , Ma Shan Shan , Jiang Deng Ji , Bie Xiao Min , Sui Na , Zhang Xian Sheng , Wang Fang 
Published: July 2019

SummaryTillering is a significant agronomic trait in wheat which shapes plant architecture and yield. Strigolactones (SLs) function in inhibiting axillary bud outgrowth. The roles of SLs in the regulation of bud outgrowth have been described in model plant species, including rice and Arabidopsis. However, the role of SLs genes in wheat remains elusive due to the size and complexity of the wheat genomes. In this study, TaD27 genes in wheat, orthologs of rice D27 encoding an enzyme involved in SLs biosynthesis, were identified. TaD27‐RNAi wheat plants had more tillers, and TaD27‐B‐OE wheat plants had fewer tillers. Germination bioassay of Orobanche confirmed the SLs was deficient in TaD27‐RNAi and excessive in TaD27‐B‐OE wheat plants. Moreover, application of exogenous GR24 or TIS108 could mediate the axillary bud outgrowth of TaD27‐RNAi and TaD27‐B‐OE in the hydroponic culture, suggesting that TaD27‐B plays critical roles in regulating wheat tiller number by participating in SLs biosynthesis. Unlike rice D27, plant height was not affected in the transgenic wheat plants. Transcription and gene coexpression network analysis showed that a number of genes are involved in the SLs signalling pathway and axillary bud development. Our results indicate that TaD27‐B is a key factor in the regulation of tiller number in wheat.
Metal ligands in micronutrient acquisition and homeostasis
Authors: Clemens Stephan 
Published: July 2019

AbstractAcquisition and homeostasis of micronutrients such as iron (Fe) and zinc (Zn) pose specific challenges. Poor solubility and high reactivity require controlled synthesis and supply of ligands to complex these metals extracellularly and intracellularly. Cytosolic labile pools represent only a minute fraction of the total cellular content. Several low‐molecular‐weight ligands are known in plants, including sulfur ligands (cysteine and peptides), nitrogen/oxygen ligands (S‐adenosyl‐l‐methionine‐derived molecules and histidine), and oxygen ligands (phenolics and organic acids). Some ligands are secreted into the extracellular space and influence the phytoavailability of metal ions. A second principal function is the intracellular buffering of micronutrients as well as the facilitation of long‐distance transport in xylem and phloem. Furthermore, low‐molecular‐weight ligands are involved in the storage of metals, predominantly in vacuoles. A detailed molecular understanding is hampered by technical limitations, in particular the difficulty to detect and quantify cellular metal–ligand complexes. More, but still too little, is known about ligand synthesis and the transport across membranes, either with or without a complexed metal. Metal ligands have an immediate impact on human well‐being. Engineering metal ligand synthesis and distribution in crops has tremendous potential to improve the nutritional quality of food and to tackle major human health risks.
FAR‐RED ELONGATED HYPOCOTYLS3 negatively regulates shade avoidance responses in Arabidopsis
Authors: Ma Lin , Li Yang , Li Xiuxiu , Xu Di , Lin Xueqiao , Liu Mingmei , Li Gang , Qin Xiaochun 
Published: July 2019

AbstractLight is a key limiting factor of plant growth and development under the canopy. Specific light signals, such as a low ratio of red : far‐red (R:FR) light, trigger the shade avoidance response, which affects hypocotyl, stem, and leaf growth. Although multiple components mediating shade avoidance responses have been identified in the past few decades, the underlying regulatory mechanism remains unclear. In this study, we found that the far‐red elongated hypocotyls 3 (fhy3) mutant exhibited longer hypocotyls and increased expression levels of core shade avoidance response genes under low R:FR shade conditions compared with the wild type No‐0, suggesting that FHY3 negatively regulates shade avoidance responses. Yeast one‐hybrid, chromatin immunoprecipitation, and RT‐qPCR assays revealed that FHY3 directly binds to the promoters and gene body of PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and PAR2 and activates their expression to inhibit shade responses. Furthermore, the overexpression of PAR1 or PAR2 rescued the enhanced shade avoidance responses of fhy3, indicating that both genes are direct downstream targets of FHY3 that mediate shade avoidance responses. Our findings demonstrate that the light‐signalling protein FHY3 positively regulates the transcription of PAR1 and PAR2, which encode two key negative regulators of shade avoidance responses, thus repressing plant responses to shade signals.
Multi‐targeting of viral RNAs with synthetic trans‐acting small interfering RNAs enhances plant antiviral resistance
Authors: Carbonell Alberto , Lisón Purificación , Daròs José‐Antonio 
Published: July 2019

SummaryRNA interference (RNAi)‐based tools are used in multiple organisms to induce antiviral resistance through the sequence‐specific degradation of target RNAs by complementary small RNAs. In plants, highly specific antiviral RNAi‐based tools include artificial microRNAs (amiRNAs) and synthetic trans‐acting small interfering RNAs (syn‐tasiRNAs). syn‐tasiRNAs have emerged as a promising antiviral tool allowing for the multi‐targeting of viral RNAs through the simultaneous expression of several syn‐tasiRNAs from a single precursor. Here, we compared in tomato plants the effects of an amiRNA construct expressing a single amiRNA and a syn‐tasiRNA construct expressing four different syn‐tasiRNAs against Tomato spotted wilt virus (TSWV), an economically important pathogen affecting tomato crops worldwide. Most of the syn‐tasiRNA lines were resistant to TSWV, whereas the majority of the amiRNA lines were susceptible and accumulated viral progenies with mutations in the amiRNA target site. Only the two amiRNA lines with higher amiRNA accumulation were resistant, whereas resistance in syn‐tasiRNA lines was not exclusive of lines with high syn‐tasiRNA accumulation. Collectively, these results suggest that syn‐tasiRNAs induce enhanced antiviral resistance because of the combined silencing effect of each individual syn‐tasiRNA, which minimizes the possibility that the virus simultaneously mutates all different target sites to fully escape each syn‐tasiRNA.
Multiple steps of leaf thickening during sun‐leaf formation in Arabidopsis
Authors: Hoshino Rina , Yoshida Yuki , Tsukaya Hirokazu 
Published: July 2019

SummaryPlant morphological and physiological traits exhibit plasticity in response to light intensity. Leaf thickness is enhanced under high light (HL) conditions compared with low light (LL) conditions through increases in both cell number and size in the dorsoventral direction; however, the regulation of such phenotypic plasticity in leaf thickness (namely, sun‐ or shade‐leaf formation) during the developmental process remains largely unclear. By modifying observation techniques for tiny leaf primordia in Arabidopsis thaliana, we analysed sun‐ and shade‐leaf development in a time‐course manner and found that the process of leaf thickening can be divided into early and late phases. In the early phase, anisotropic cell elongation and periclinal cell division on the adaxial side of mesophyll tissue occurred under the HL conditions used, which resulted in the dorsoventral growth of sun leaves. Anisotropic cell elongation in the palisade tissue is triggered by blue‐light irradiation. We discovered that anisotropic cell elongation processes before or after periclinal cell division were differentially regulated independent of or dependent upon signalling through blue‐light receptors. In contrast, during the late phase, isotropic cell expansion associated with the endocycle, which determined the final leaf thickness, occurred irrespective of the light conditions. Sucrose production was high under HL conditions, and we found that sucrose promoted isotropic cell expansion and the endocycle even under LL conditions. Our analyses based on this method of time‐course observation addressed the developmental framework of sun‐ and shade‐leaf formation.
An ‘eFP‐Seq Browser’ for visualizing and exploring RNA sequencing data
Authors: Sullivan Alexander , Purohit Priyank K. , Freese Nowlan H. , Pasha Asher , Esteban Eddi , Waese Jamie , Wu Alison , Chen Michelle , Chin Chih Y. , Song Richard , Watharkar Sneha R. , Chan Agnes P. , Krishnakumar Vivek , Vaughn Matthew W. , Town Chris , Loraine Ann E. , Provart Nicholas J. 
Published: July 2019

SummaryImprovements in next‐generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of ‘‐seq’‐based methods, of which RNA sequencing (RNA‐seq) for generating transcriptomic data is the most popular. By analysing global patterns of gene expression in organs/tissues/cells of interest or in response to chemical or environmental perturbations, researchers can better understand an organism's biology. Tools designed to work with large RNA‐seq data sets enable analyses and visualizations to help generate hypotheses about a gene's function. We present here a user‐friendly RNA‐seq data exploration tool, called the ‘eFP‐Seq Browser’, that shows the read map coverage of a gene of interest in each of the samples along with ‘electronic fluorescent pictographic’ (eFP) images that serve as visual representations of expression levels. The tool also summarizes the details of each RNA‐seq experiment, providing links to archival databases and publications. It automatically computes the reads per kilobase per million reads mapped expression‐level summaries and point biserial correlation scores to sort the samples based on a gene's expression level or by how dissimilar the read map profile is from a gene splice variant, to quickly identify samples with the strongest expression level or where alternative splicing might be occurring. Links to the Integrated Genome Browser desktop visualization tool allow researchers to visualize and explore the details of RNA‐seq alignments summarized in eFP‐Seq Browser as coverage graphs. We present four cases of use of the eFP‐Seq Browser for ABI3, SR34, SR45a and U2AF65B, where we examine expression levels and identify alternative splicing. The URL for the browser is https://bar.utoronto.ca/eFP-Seq_Browser/.Open research badgesThis article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. Tool is at https://bar.utoronto.ca/eFP-Seq_Browser/; RNA‐seq data at https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/ and https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/Klepikova/. Code is available at https://github.com/BioAnalyticResource/eFP-Seq-Browser