bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Exogenous Amino Acids on Yield and Quality of Tartary Buckwheat in Non-saline and Saline-alkali Soil
Authors: Song Jin-Nan , Wang Ya-Qi , Li Fa-Liang , Hu Yan-Jiang , Yang Hong-Bing 
Published: December 2019

Disclaimer StatementThe authors have withdrawn this manuscript (BIORXIV/2019/887778) entitled “Effect of Exogenous Amino Acids on Yield and Quality of Tartary Buckwheat in Non-saline and Saline-alkali Soil” because it requires adding new data and further modifications. Therefore, the authors do not wish this work to be cited (https://www.biorxiv.org/content/10.1101/2019.12.24.887778v5) as reference for the project. If you have any questions, please contact the corresponding author.
Chemical map–based prediction of nucleosome positioning using the Bioconductor package nuCpos
Authors: Kato Hiroaki , Shimizu Mitsuhiro , Urano Takeshi 
Published: December 2019

AbstractBackgroundAssessing the nucleosome-forming potential of specific DNA sequences is important for understanding complex chromatin organization. Methods for predicting nucleosome positioning include bioinformatics and biophysical approaches. An advantage of bioinformatics methods, which are based onin vivonucleosome maps, is the use of natural sequences that may contain previously unknown elements involved in nucleosome positioningin vivo. The accuracy of such prediction attempts reflects the genomic coordinate resolution of the nucleosome maps applied. Nucleosome maps are constructed using micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq). However, as MNase has a strong preference for A/T-rich sequences, MNase-seq may not be appropriate for this purpose. In addition to MNase-seq–based maps, base pair–resolution chemical maps ofin vivonucleosomes from three different species (budding and fission yeasts, and mice) are currently available. However, these chemical maps have yet to be integrated into publicly available computational methods.ResultsWe developed a Bioconductor package (named nuCpos) to demonstrate the superiority of chemical maps in predicting nucleosome positioning. The accuracy of chemical map–based prediction in rotational settings was higher than that of the previously developed MNase-seq–based approach. With our method, predicted nucleosome occupancy reasonably matchedin vivoobservations and was not affected by A/T nucleotide frequency. Effects of genetic alterations on nucleosome positioning that had been observed in living yeast cells could also be predicted. nuCpos calculates individual histone binding affinity (HBA) scores for given 147-bp sequences to examine their suitability for nucleosome formation. We also established local HBA as a new parameter to predict nucleosome formation, which was calculated for 13 overlapping nucleosomal DNA subsequences. HBA and local HBA scores for various sequences agreed well with previousin vitroandin vivostudies. Furthermore, our results suggest that nucleosomal subsegments that are disfavored in different rotational settings contribute to the defined positioning of nucleosomes.ConclusionsOur results demonstrate that chemical map–based statistical models are beneficial for studying nucleosomal DNA features. Studies employing nuCpos software can enhance understanding of chromatin regulation and the interpretation of genetic alterations and facilitate the design of artificial sequences.
DPPH-scavenging and antimicrobial activities of Asteraceae medicinal plants on uropathogenic bacteria
Authors: Phan Trinh Canh , Le Thao Thi Thanh , Hoang Ha Tran Viet , Nguyen TuAnh 
Published: December 2019

AbstractAsteraceae species were widely applied in traditional medicines in Asia countries as sources of natural antioxidants and antimicrobial agents. This study aimed to evaluate DPPH-scavenging capacities and antimicrobial activities of nine Asteraceae species collected from Southern Vietnam. Antioxidant and antimicrobial activities were determined by standard protocols. Essential oils fromAgeratum conyzoides, Helianthus annuus, Artemisia vulgarisindicated significant inhibitory effects onStaphyloccocus aureusandCandidaspp.. Crude extracts and fractions fromTaraxacum officinale, Chrysanthemum morifolium, Ageratum conyzoides, Tagetes erectashowed inhibitory ability on at least one testing bacterial strains includingS. aureus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa. Study on clinical isolates, ethyl acetate fraction fromA. conyzoidesdisplayed the most potent effect on uropathogenicE. coliandK. pneumoniaewith MIC at 1.25-10 mg/ml and 5-12.5 mg/ml, respectively. DPPH scavenging assay indicated thatTagetes erectaextract had the lowest IC50(17.280 μg/ml) and 2.5 times higher than vitamin C (7.321 μg/ml). This study revealed thatA. conyzoideshas good potential against uropathogenicE. coliandK. pneumoniae, and could, therefore, apply to prophylactic urinary tract infection.
Characterization of neural communication dynamics in the Ventral Attention Network across distinct spatial and spatio-temporal scales
Authors: Ghosh Priyanka , Roy Dipanjan , Banerjee Arpan 
Published: December 2019

AbstractThe Ventral Attention Network (VAN) is involved in reorienting attention from an ongoing task when a salient (pop-out) stimulus is detected in the environment. Previous neuroimaging studies have extensively evaluated the structural and functional connectivity of the VAN. However, directed effective connectivity within the network and the neural oscillations driving it still remain elusive. Functional magnetic resonance imaging (fMRI) studies have not been able to address this issue due to lack of appropriate temporal resolution required to capture the process of reorientation. In this study, we recorded scalp electroencephalography (EEG) and behavioural data from healthy human volunteers, obtained saliency-specific spectral changes, localized the sources underlying the spectral power modulations with individual-specific structural MRI scans, reconstructed the waveforms of the sources and investigated the causal relationships between the areas of the VAN using Granger causality (GC). Using a custom-designed experiment involving visual search on static images and a dynamic motion tracking task, we investigated the neural processing of salient distractors operating at very slow and very fast time scales, respectively. Our results revealed how a task-independent but context-specific VAN encompassing the right insula, the right lateral pre-frontal cortex, the anterior and the posterior right temporo-parietal junction communicating in the alpha frequency band (8-12 Hz) supports saliency processing.
Low-dose ethanol produces mixed effects on cortico-hippocampal theta rhythms and modifies hippocampal theta frequency through multiple mechanisms
Authors: Young Calvin K. , McNaughton Neil 
Published: December 2019

AbstractEthanol is one of the most widely used drugs – with many psychoactive effects, including anxiolysis. The deleterious effects on brain function and general health of chronic and high-level ethanol use are well-studied. However, the neurophysiology of acute low dose ethanol has not been systematically investigated. Here, we examined the effects of low dose (0.25 and 0.5 g/kg) ethanol on midline (prefrontal, cingulate and retrosplenial) cortical and hippocampal theta oscillations in freely moving rats. We also tested low dose ethanol on reticular-elicited and running-elicited hippocampal theta frequency and assessed the linear relationship of theta frequency to stimulation intensity and running speed, respectively. Low dose ethanol had mixed effects on cortical theta oscillations. It most reliably reduced theta frequency, produced a weak inverted-U effect on theta power, and had no detectable effect on cortico-hippocampal theta coherence. Ethanol dose-dependently decreased the y-intercept of the speed-theta frequency function without affecting the slope, but decreased the slope of the stimulation intensity-theta frequency function without affecting the y-intercept; thus decreasing theta frequency in both cases but through different mechanisms. We conclude low dose ethanol has weak but detectable effects on cortical and hippocampal theta oscillations. These effects may underlie positive cognitive and behavioural outcomes reported in the literature using low dose ethanol. The double dissociation of slope and y-intercept specific changes relating to different methods of hippocampal theta elicitation suggests that multiple mechanisms contribute to anxiolytic effects on theta and so hippocampal function.
Temperature-dependence of metabolic rate in tropical and temperate aquatic insects: support for the Climate Variability Hypothesis in mayflies but not stoneflies
Authors: Shah Alisha A. , Woods H. Arthur , Havird Justin C. , Encalada Andrea C. , Flecker Alexander S. , Funk W. Chris , Guayasamin Juan M. , Kondratieff Boris C. , Poff N. LeRoy , Thomas Steven A. , Zamudio Kelly R. , Ghalambor Cameron K. 
Published: December 2019

AbstractA fundamental gap in climate change vulnerability research is an understanding of the relative thermal sensitivity of ectotherms. Aquatic insects are vital to stream ecosystem function and biodiversity but insufficiently studied with respect to their thermal physiology. With global temperatures rising at an unprecedented rate, it is imperative that we know how aquatic insects respond to increasing temperature and whether these responses vary among taxa, latitudes, and elevations. We evaluated the thermal sensitivity of standard metabolic rate in stream-dwelling baetid mayflies and perlid stoneflies across a ~2,000 m elevation gradient in the temperate Rocky Mountains in Colorado, U.S.A., and the tropical Andes in Napo, Ecuador. We used temperature-controlled water baths and microrespirometry to estimate changes in oxygen consumption. Tropical mayflies generally exhibited greater thermal sensitivity in metabolism compared to temperate mayflies; tropical mayfly metabolic rates increased more rapidly with temperature and the insects more frequently exhibited behavioral signs of thermal stress. By contrast, temperate and tropical stoneflies did not clearly differ. Varied responses to temperature among baetid mayflies and perlid stoneflies may reflect differences in evolutionary history or ecological roles as herbivores and predators, respectively. Our results show that there is physiological variation across elevations and species and that low elevation tropical mayflies may be especially imperiled by climate warming. Given such variation among species, broad generalizations about the vulnerability of tropical ectotherms should be made more cautiously.
Coagulation factor XII, XI, and VIII activity levels and secondary events after first ischemic stroke
Authors: Rohmann Jessica L. , Huo Shufan , Sperber Pia S. , Piper Sophie K. , Rosendaal Frits R. , Heuschmann Peter U. , Endres Matthias , Liman Thomas G. , Siegerink Bob 
Published: December 2019

AbstractBackground and PurposeThough risk for recurrent vascular events is high following ischemic stroke, little is known about risk factors for secondary events post-stroke. The coagulation factors XII, XI, and VII (FXII, FXI, and FVIII) have already been implicated in first thrombotic events, and our aim was to estimate their effects on vascular outcomes within 3 years after first stroke.MethodsIn the PROSpective Cohort with Incident Stroke Berlin (PROSCIS-B) study, we followed participants aged 18 and older for three years after first mild to moderate ischemic stroke event or until occurrence of recurrent stroke, myocardial infarction or all-cause mortality (combined endpoint). High coagulation factor activity levels were compared to normal and low levels, and activities were also analyzed as continuous variables. We used Cox proportional hazards models adjusted for age, sex, and cardiovascular risk factors to estimate hazard ratios (HRs) for the combined endpoint.ResultsIn total, 92 events occurred in 570 included participants, resulting in an absolute rate of 6.6 events per 100 person-years. After confounding adjustment, high FVIII activity showed the strongest relationship with the combined endpoint (HR=2.05, 95%CI 1.28-3.29). High FXI activity was also associated with an increased risk (HR=1.80, 95%CI 1.09-2.98). Contrarily, high FXII activity was not associated with the combined endpoint (HR=0.86, 95%CI 0.49-1.51). Continuous analyses per standard deviation of each biomarker yielded similar results.ConclusionsIn our study of mild to moderate ischemic stroke patients, high activity levels of FXI and FVIII but not FXII were associated with worse vascular outcomes in the three-year period after first ischemic stroke. This is of special interest in light of the ongoing trials of antithrombotic treatments targeting FXI.
To resect or not to resect? Unbiased performances of single and combined biomarkers in intra-operative corticography for tailoring during epilepsy surgery
Authors: Demuru Matteo , Kalitzin Stiliyan , Zweiphenning Willemiek , van Blooijs Dorien , van ’t Klooster Maryse , Van Eijsden Pieter , Leijten Frans , Zijlmans Maeike 
Published: December 2019

AbstractObjectiveSignal analysis biomarkers, in an intra-operative setting, may be complementary tools to guide and tailor the resection in drug-resistant epilepsy patients. Unbiased assessment of biomarker performances are needed to evaluate their clinical usefulness and translation. We defined a realistic ground-truth scenario and compared the effectiveness of different biomarkers alone and combined to localize epileptogenic tissue.MethodsWe investigated the performances of univariate, bivariate and multivariate signal biomarkers applied to 1 minute inter-ictal intra-operative electrocorticography to discriminate between electrodes covering normal or pathologic activity in 47 drug-resistant people with epilepsy (temporal and extra-temporal) who had been seizure-free one year after the operation.ResultsThe best result using a single biomarker was obtained using the phase-amplitude coupling measure for which the epileptogenic tissue was localized in 16 out of 47 patients. Combining the whole set of biomarkers provided an improvement of the performances: 20 out of 47 patients. Repeating the analysis only on the temporal-lobe resections we reached a sensitivity of 93% (28 out of 30) combining all the biomarkers.ConclusionWe suggest that the assessment of biomarker performances on a ground-truth scenario is required to have a proper estimate on how biomarkers translate into clinical use. Phase-amplitude coupling seems the best performing single biomarker and combining biomarkers improves localization of epileptogenic tissue. However, sensitivity achieved is not adequate for the usage as a tool in the operation theater, but it can improve the understanding of pathophysiological process.
Neuronal ON/OFF Motion Detection Circuits Underlying Looming-Evoked Escape Behavior inDrosophila
Authors: Kyung Yeosun , Dewell Richard B. , Dierick Herman A. , Gabbiani Fabrizio 
Published: December 2019

AbstractInDrosophila, early visual processing of motion information segregates in separate ON and OFF pathways. These pathways have been studied in the context of local directional motion detection leading to the encoding of optic flow that provides visual information for flight stabilization. Less is known about their role in detecting impending collision and generating escape behaviors. ‘Looming’, the simulated approach of an object at constant speed towards an animal, provides a powerful stimulus eliciting jump escape behaviors in stationary flies. We presented looming stimuli mimicking the approach of either a dark object on a bright background or a light object on a dark background, while inactivating neurons belonging either to the ON- or the OFF-motion detection pathways by expressing the dominantDrosophilatemperature-sensitive mutantshibiretsin different cells of the ON/OFF pathway. Inactivation of ON, respectively OFF, neurons led to selective decreases in escape behavior to light, resp. dark, looming stimuli. Quantitative analysis showed a nearly perfect splitting of these effects according to the ON/OFF type of the targeted neural populations. Our results suggest thatDrosophilaON/OFF motion detection pathways play an important role in controlling jump escape responses according to looming stimulus polarity. They further imply that the biophysical circuits triggeringDrosophilajump escape behaviors likely differ substantially from those characterized in other arthropods.SummaryInactivating fly neurons of the ON or OFF directional motion detection pathways during escape behavior selectively reduced jump responses to light and dark looming stimuli, respectively.
Viral fitness determines the magnitude of transcriptomic and epigenomic reprogramming of defense responses in plants
Authors: Corrêa Régis L. , Sanz-Carbonell Alejandro , Kogej Zala , Müller Sebastian Y. , López-Gomollón Sara , Gómez Gustavo , Baulcombe David C. , Elena Santiago F. 
Published: December 2019

SUMMARYAlthough epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus (TuMV) with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses were larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Several transposable elements (TEs) located in different chromatin contexts and epigenetic-related genes were also affected. Correspondingly, mutant plants having loss or gain of repressive marks were, respectively, more tolerant and susceptible to TuMV, with a more efficient response against the ancestral isolate. In wild-type plants both isolates induced similar levels of cytosine methylation changes, including in and around TEs and stress-related genes. Results collectively suggested that apart from RNA silencing and basal immunity systems, DNA methylation and histone modification pathways may also be required for mounting proper antiviral defenses in plants and that the effectiveness of this type of regulation strongly depends on the degree of viral adaptation to the host.
Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation inPhaeodactylum tricornutum
Authors: Zhao Xue , Rastogi Achal , Cabanillas Anne Flore Deton , Mohamed Ouardia Ait , Cantrel Catherine , Lombard Berangère , Murik Omer , Genovesio Auguste , Bowler Chris , Bouyer Daniel , Loew Damarys , Lin Xin , Veluchamy Alaguraj , Vieira Fabio Rocha Jimenez , Tirichine Leila 
Published: December 2019

SummaryIn multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit H3K27me3 to establish and maintain gene silencing, critical for developmentally regulated processes. PRC2 complex is absent in both widely studied model yeasts which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes.Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di and tri-methylation of lysine 27 of histone H3.H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity.These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species and highlight their ancestral function in a broader evolutionary context than is currently appreciated.
A chromosome-level genome assembly for the beet armyworm (Spodoptera exigua) using PacBio and Hi-C sequencing
Authors: Zhang Feng , Zhang Jianpeng , Yang Yihua , Wu Yidong 
Published: December 2019

AbstractBackgroundThe beet armyworm,Spodoptera exigua(Hübner), is a worldwide, polyphagous agricultural pest feeding on vegetable, field, and flower crops. However, the lack of genome information on this insect severely limits our understanding of its rapid adaptation and hampers the development of efficient pest management strategies.FindingsWe report a chromosome-level genome assembly using single-molecule real-time PacBio sequencing and Hi-C data. The final genome assembly was 446.80 Mb with a scaffold N50 of 14.36 Mb, and captured 97.9% complete arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO, n=1,658). A total of 367 contigs were anchored to 32 pseudo-chromosomes, covering 96.18% (429.74 Mb) of the total genome length. We predicted 17,727 protein-coding genes, of which 81.60% were supported by transcriptome evidence and 96.47% matched UniProt protein records. We also identified 867,102 (147.97 Mb/33.12%) repetitive elements and 1,609 noncoding RNAs. Synteny inference indicated a conserved collinearity between three lepidopteran species. Gene family evolution and function enrichment analyses showed the significant expansions in families related to development, dietary, detoxification and chemosensory system, indicating these families may play a role in host plant specialization and niche adaptation.ConclusionsWe have generated a high-quality chromosomal-level genome that could provide a valuable resource for a better understanding and management of the beet armyworm.
Longitudinal epi-transcriptome profiling reveals the crucial role of m6A in prenatal skeletal muscle development of pigs
Authors: Zhang Xinxin , Yao Yilong , Han Jinghua , Yang Yalan , Chen Yun , Tang Zhonglin , Gao Fei 
Published: December 2019

AbstractBackgroundN6-methyladenosine (m6A) is the most abundant RNA modification and essentially participates in the regulation of skeletal muscle development. However, the status and function of m6A methylation in prenatal myogenesis remains unclear now.ResultsIn our present study, we first demonstrate that chemical suppression of m6A and knockdown METTL14 significantly inhibit the differentiation and promote the proliferation of C2C12 myoblast cells. The mRNA expression of m6A reader protein IGF2BP1, which functions to promote the stability of target mRNA, continually decreases during the prenatal skeletal muscle development. Thereafter, profiling transcriptome-wide m6A for six developmental stage of prenatal skeletal muscle, which spanning two important waves of pig myogenesis, were performed using a refined MeRIP sequencing technology that is optimal for small-amount of RNA samples. Highly dynamic m6A methylomes across different development stages were then revealed, with majority of the affected genes enriched in pathways of skeletal muscle development. In association with the transcriptome-wide alterations, transcriptional regulatory factors (MyoD) and differentiated markers (MyHC, MYH1) of muscle development are simultaneously regulated with m6A and IGF2BP1. Knockdown of IGF2BP1 also suppresses myotube formation and promotes cell proliferation.ConclusionsThe present study clarifies the dynamics of RNA m6A methylation in the regulation of prenatal skeletal muscle development, providing a data baseline for future developmental as well as biomedical studies of m6A functions in muscle development and disease.