bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of High-Level Acylsugar-Producing Tomato Lines on the Development of Tomato Psyllids (Hemiptera: Triozidae)
Authors: Li Zhenyu , Kund Gregory , De Jong Darlene M , Feng Xia , Mutschler Martha A , Trumble John T 
Published: March 2019

Abstract
Acylsugars have been shown to provide activity against numerous insect pests of tomatoes. Comparison of acylsugar levels in four tomato plant lines, FA7/AS, FA2/AS, CU071026, and ‘Yellow Pear’, found that the acylsugar contents in the elevated acylsugar lines were significantly higher than the commercial Yellow Pear (control) tomato plant line. Adult choice tests indicated that the tomato psyllid, Bactericera cockerelli, preferred to settle on the Yellow Pear and FA2/AS lines over the line with the highest content of acylsugars, FA7/AS, and the parental line, CU071026. The no-choice test demonstrated that adults laid fewer eggs on the high acylsugar tomato lines than on the control tomato line, Yellow Pear. For all high acylsugar lines, the relative growth index of the psyllid was significantly lower compared with the commercial line, indicating a reduced potential for population growth. Although some tomato psyllids completed their life cycle on the high acylsugar tomato plant lines, the percent survival of psyllids to the adult stage when developing on the high acylsugar lines was significantly less (range = 43.7–57.1%) than on the commercial tomato line (83.8%). All mortality occurred during the early stages of development (egg stage to third instar), which has implications for acquisition and transmission of Candidatus Liberibacter solanacearum, the causal agent of tomato vein greening disease. Therefore, with reduced attractiveness for tomato psyllids and significantly reduced survival, the high-acylsugar tomato plant lines have the potential to be part of an integrated pest management program for this pest.
Mitochondrial ROS promote macrophage pyroptosis by inducing GSDMD oxidation
Authors: Wang Yufang , Shi Peiliang , Chen Qin , Huang Zan , Zou Dayuan , Zhang Jingzi , Gao Xiang , Lin Zhaoyu 
Published: March 2019

Abstract
Disrupted mitochondrial membrane potential (MMP) and reactive oxygen species (ROS) generation are often associated with macrophage pyroptosis. It remains unclear how these forms of mitochondrial dysfunction relate to inflammasome activation and gasdermin-D (Gsdmd) cleavage, two central steps of the pyroptotic process. Here, we also found MMP collapse and ROS generation induced by Nlrp3 inflammasome activation as previous studies reported. The elimination of ROS alleviated the cleavage of Gsdmd, suggesting that Gsdmd cleavage occurs downstream of ROS release. Consistent with this result, hydrogen peroxide treatment augmented the cleavage of Gsdmd by caspase-1. Indeed, four amino acid residues of Gsdmd were oxidized under oxidative stress in macrophages. The efficiency of Gsdmd cleavage by inflammatory caspase-1 was dramatically reduced when oxidative modification was blocked by mutation of these amino acid residues. These results demonstrate that Gsdmd oxidation serves as a de novo mechanism by which mitochondrial ROS promote Nlrp3 inflammasome-dependent pyroptotic cell death.
Optical character recognition of typeset Coptic text with neural networks
Authors: Miyagawa So , Bulert Kirill , Büchler Marco , Behlmer Heike 
Published: March 2019

Abstract
Digital Humanities (DH) within Coptic Studies, an emerging field of development, will be much aided by the digitization of large quantities of typeset Coptic texts. Until recently, the only Optical Character Recognition (OCR) analysis of printed Coptic texts had been executed by Moheb S. Mekhaiel, who used the Tesseract program to create a text model for liturgical books in the Bohairic dialect of Coptic. However, this model is not suitable for the many scholarly editions of texts in the Sahidic dialect of Coptic which use noticeably different fonts. In the current study, DH and Coptological projects based in Göttingen, Germany, collaborated to develop a new Coptic OCR pipeline suitable for use with all Coptic dialects. The objective of the study was to generate a model which can facilitate digital Coptic Studies and produce Coptic corpora from existing printed texts. First, we compared the two available OCR programs that can recognize Coptic: Tesseract and Ocropy. The results indicated that the neural network model, i.e. Ocropy, performed better at recognizing the letters with supralinear strokes that characterize the published Sahidic texts. After training Ocropy for Coptic using artificial neural networks, the team achieved an accuracy rate of &gt;91% for the OCR analysis of Coptic typeset. We subsequently compared the efficiency of Ocropy to that of manual transcribing and concluded that the use of Ocropy to extract Coptic from digital images of printed texts is highly beneficial to Coptic DH.
Quantifying the impact of dirty OCR on historical text analysis: Eighteenth Century Collections Online as a case study
Authors: Hill Mark J , Hengchen Simon 
Published: March 2019

AbstractThis article aims to quantify the impact optical character recognition (OCR) has on the quantitative analysis of historical documents. Using Eighteenth Century Collections Online as a case study, we first explore and explain the differences between the OCR corpus and its keyed-in counterpart, created by the Text Creation Partnership. We then conduct a series of specific analyses common to the digital humanities: topic modelling, authorship attribution, collocation analysis, and vector space modelling. The article concludes by offering some preliminary thoughts on how these conclusions can be applied to other datasets, by reflecting on the potential for predicting the quality of OCR where no ground-truth exists.
Aversion to playing God and moral condemnation of technology and science
Authors: Waytz Adam , Young Liane 
Published: March 2019

This research provides, to our knowledge, the first systematic empirical investigation of people's aversion toplaying God. Seven studies validate this construct and show its association with negative moral judgements of science and technology. Motivated by three nationally representative archival datasets that demonstrate this relationship, studies 1 and 2 demonstrate that people condemn scientific procedures they perceive to involve playing God. Studies 3–5 demonstrate that dispositional aversion to playing God corresponds to decreased willingness to fund the National Science Foundation and lower donations to organizations that support novel scientific procedures. Studies 6a and 6b demonstrate that people judge a novel (versus established) scientific practice to involve more playing God and to be more morally unacceptable. Finally, study 7 demonstrates that reminding people of an existing incident of playing God reduces concerns towards scientific practices. Together, these findings provide novel evidence for the impact of people's aversion to playing God on science and policy-related decision-making.This article is part of the theme issue ‘From social brains to social robots: applying neurocognitive insights to human–robot interaction’.
Mediator subunit MDT-15/MED15 and Nuclear Receptor HIZR-1/HNF4 cooperate to regulate toxic metal stress responses in Caenorhabditis elegans
Authors: Shomer Naomi , Kadhim Alexandre Zacharie , Grants Jennifer Margaret , Cheng Xuanjin , Poon Amy Fong-Yuk , Lee Michelle Ying Ya , Bhanshali Forum , Muhuri Anik , Park Jung In , Lee Dongyeop , Lee Seung-Jae V. , Lynn Francis Christopher , Taubert Stefan 
Published: March 2019

AbstractZinc is essential for cellular functions as it is a catalytic and structural component of many proteins. In contrast, cadmium is not required in biological systems and is toxic. Zinc and cadmium levels are closely monitored and regulated as their excess causes cell stress. To maintain homeostasis, organisms induce metal detoxification gene programs through stress responsive transcriptional regulatory complexes. In Caenorhabditis elegans, the MDT-15 subunit of the evolutionarily conserved Mediator transcriptional coregulator is required to induce genes upon exposure to excess zinc and cadmium. However, the regulatory partners of MDT-15 in this response, its role in cellular and physiological stress adaptation, and the putative role mammalian for MED15 in the metal stress responses remain unknown. Here, we show that MDT-15 interacts physically and functionally with the Nuclear Hormone Receptor HIZR-1 to promote molecular, cellular, and organismal adaptation to excess metals. Using gain- and loss-of-function mutants and qPCR and reporter analysis, we find that mdt-15 and hizr-1 cooperate to induce zinc and cadmium responsive genes. Moreover, the two proteins interact physically in yeast-two-hybrid assays and this interaction is enhanced by the addition of zinc or cadmium, the former a known ligand of HIZR-1. Functionally, mdt-15 and hizr-1 mutants show defective storage of excess zinc in the gut, and at the organismal level, mdt-15 mutants are hypersensitive to zinc- and cadmium-induced reductions in egg-laying. Lastly, mammalian MDT-15 orthologs bind genomic regulatory regions of metallothionein and zinc transporter genes in a metal-stimulated fashion, and human MED15 is required to induce a metallothionein gene in lung adenocarcinoma cells exposed to cadmium. Collectively, our data show that mdt-15 and hizr-1 cooperate to regulate metal detoxification and zinc storage and that this mechanism appears to be at least partially conserved in mammals.
Sen1 is required for RNA Polymerase III transcription termination in an R-loop independent manner
Authors: Rivosecchi Julieta , Larochelle Marc , Teste Camille , Grenier Frédéric , Malapert Amélie , Ricci Emiliano P. , Bernard Pascal , Bachand François , Vanoosthuyse Vincent 
Published: March 2019

ABSTRACTR-loop disassembly by the human helicase Senataxin contributes to genome stability and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin-mediated R-loop disassembly also contributes to transcription termination at other classes of genes has remained unclear. Here we show in fission yeast that SenataxinSen1promotes efficient termination of RNA Polymerase III (RNAP3) transcriptionin vivo. In the absence of SenataxinSen1, RNAP3 accumulates downstream of the primary terminator at RNAP3-transcribed genes and produces long exosome-sensitive 3’-extended transcripts. Importantly, neither of these defects was affected by the removal of R-loops. The finding that SenataxinSen1acts as an ancillary factor for RNAP3 transcription terminationin vivochallenges the pre-existing view that RNAP3 terminates transcription autonomously. We propose that Senataxin is a cofactor for transcription termination that has been co-opted by different RNA polymerases in the course of evolution.
Positive genetic associations among fitness traits support evolvability of a reef-building coral under multiple stressors
Authors: Wright Rachel M. , Mera Hanaka , Kenkel Carly D. , Nayfa Maria , Bay Line K. , Matz Mikhail V. 
Published: March 2019

AbstractClimate change threatens organisms in a variety of interactive ways that requires simultaneous adaptation of multiple traits. Predicting evolutionary responses requires an understanding of the potential for synergistic interactions among stressors and the genetic variance and covariance among fitness-related traits that may reinforce or constrain an adaptive response. Here we investigate the capacity ofAcropora millepora, a reef-building coral, to adapt to multiple environmental stressors: rising sea surface temperature, ocean acidification, and increased prevalence of infectious diseases. We measured growth rates (weight gain), coral color (a proxy for Symbiodiniaceae density), and survival, in addition to nine physiological indicators of coral and algal health in 40 coral genets exposed to each of these three stressors singly and combined. Individual stressors resulted in predicted responses (e.g., corals developed lesions after bacterial challenge and bleached under thermal stress). However, corals did not suffer substantially more when all three stressors were combined. Nor were tradeoffs observed between tolerances to different stressors; instead, individuals performing well under one stressor also tended to perform well under every other stressor. An analysis of genetic correlations between traits revealed positive co-variances, suggesting that selection to multiple stressors will reinforce rather than constrain the simultaneous evolution of traits related to holobiont health (e.g.,weight gain and algal density). These findings support the potential for rapid coral adaptation under climate change and emphasize the importance of accounting for corals’ adaptive capacity when predicting the future of coral reefs.
Weed regulation by crop and grassland competition: critical biomass level and persistence rate
Authors: Schuster Mauricio Z. , Gastal François , Doisy Diana , Charrier Xavier , Moraes Anibal de , Médiène Safia , Barbu Corentin M. 
Published: March 2019

AbstractIt is widely agreed that competition regulates plant populations and shapes communities. Many studies have suggested that crop and grassland competition can be used for cost-effective sustainable weed control. However, effective weed management requires a precise knowledge of the effects of agronomic practices and there is a lack of quantitative indicators to compare and predict the success of weed biocontrol by competition.We studied weed abundance dynamics over a 12-year period in crop-grassland rotations (rotation treatments consisted of maize, wheat and barley crops, alternating with temporary grassland maintained for three or six years in the rotation and fertilised with two different levels of nitrogen). In addition to classical statistical analysis of the different aforementioned rotation treatments, we also modelled weed abundance as a function of the crop and grassland competition, expressed here by biomasses harvested in the preceding years.We show that weed abundance decreases over the years in grassland and subsequent crops only if the grassland receives sufficient nitrogen fertiliser. Our model had a much greater explanatory power than the rotation treatments. This model estimates a critical biomass level above which weeds are suppressed in subsequent years, and below which they tend to thrive. This critical biomass level was 24.3 and 4.7 tonnes ha−1 of dry matter for crops and grassland, respectively, highlighting the greater competitiveness of grasslands than of crops. Several clear differences between weed functional groups emerged.Synthesis and applications - This new modelling approach directly links the interannual dynamics of weed populations to current and previous biomass production levels. This approach facilitates the development of environment-friendly weed management strategies and paves the way for comparisons of the competitiveness against weeds of crops and grassland under various pedoclimatic conditions and agronomic practices.
USVSEG: A robust segmentation of rodents’ ultrasonic vocalization
Authors: Tachibana Ryosuke O. , Kanno Kouta , Okabe Shota , Kobayasi Kohta I. , Okanoya Kazuo 
Published: March 2019

AbstractRodents’ ultrasonic vocalization (USV) provides useful information to assess their social behaviors. Despite of previous efforts for classifying subcategories of time-frequency patterns of USV syllables to associate with their functional relevances, detection of vocal elements from continuously recorded data have remained to be not well-optimized. We here propose a novel procedure for detecting USV segments in continuous sound data with background noises which were inevitably contaminated during observation of the social behavior. The proposed procedure utilizes a stable version of spectrogram and additional signal processing for better separation of vocal signals by reducing variation of the background noise. Our procedure also provides a precise time tracking of spectral peaks within each syllable. We showed that this procedure can be applied to a variety of USVs obtained from several rodent species. A performance test with an appropriate parameter set showed performance for detecting USV syllables than conventional methods.
Landscape and dynamics of the transcriptional regulatory network during natural killer cell differentiation
Authors: Li Kun , Wu Yang , Li Young , Yu Qiaoni , Tian Zhigang , Wei Haiming , Qu Kun 
Published: March 2019

AbstractNatural killer (NK) cells are essential in controlling cancer and infection. However, little is known about the dynamics of the transcriptional regulatory machinery during NK cell differentiation. In this study, we applied assay of transposase accessible chromatin with sequencing (ATAC-seq) technique in a self-developedin vitroNK cell differentiation system. Analysis of ATAC-seq data illustrated two distinct transcription factor (TF) clusters that dynamically regulate NK cell differentiation. Moreover, two TFs from the second cluster, FOSL2 and EGR2, were identified as novel essential TFs that control NK cell maturation and function. Knocking down either of these two TFs significantly impacted NK cell transformation. Finally, we constructed a genome-wide transcriptional regulatory network that provides an understanding of the regulatory dynamics during NK cell differentiation.
Intracranial functional haemodynamic relationships in patients with cerebral small vessel disease
Authors: Blair Gordon W , Thrippleton Michael J , Shi Yulu , Hamilton Iona , Stringer Michael , Chappell Francesca , Dickie David Alexander , Andrews Peter , Marshall Ian , Doubal Fergus N , Wardlaw Joanna M 
Published: March 2019

AbstractBackgroundCerebral small vessel disease (SVD) is a major cause of stroke and dementia. The underlying cerebrovascular dysfunction is poorly understood. We investigated cerebrovascular reactivity, blood flow, vascular and cerebrospinal fluid (CSF) pulsatility, and their independent relationship to SVD features, in patients with minor ischaemic stroke and MRI evidence of SVD.MethodsWe recruited patients with minor ischaemic stroke and assessed CVR using Blood Oxygen Level Dependent (BOLD) MRI during a hypercapnic challenge, cerebral blood flow, vascular and CSF pulsatility using phase contrast MRI, and structural MR brain imaging to quantify white matter hyperintensities (WMH) and perivascular spaces (PVS). We quantified CVR in seven white matter and six subcortical grey matter regions, measured blood flow in carotid and vertebral arteries, intracranial venous sinuses, internal jugular veins and CSF flow at the aqueduct and foramen magnum. We used multiple regression to identify SVD features, blood flow and pulsatility parameters associated with CVR, controlling for patient characteristics.ResultsIn 53 of 60 patients with complete data (age 68.0±8.8, 74% male, 75% hypertensive), CVR in grey and white matter decreased with increasing blood pressure (BP, respectively −0.001%/mmHg, p=0.01 and −0.006%/mmHg, p=0.01, per mmHg increase in BP). After controlling for age, gender and systolic BP, white matter CVR decreased with increasing WMF volume (−0.01%/mmHg per log10 increase in WMH volume, p=0.02) and basal ganglia PVS (−0.01%/mmHg per point increase in PVS score, p=0.02). White matter CVR decreased with increasing venous pulsatility (superior sagittal sinus −0.03%/mmHg, p=0.02, per unit increase in pulsatility index) but not with cerebral blood flow (p=0.58). Lower foramen magnum CSF stroke volume was associated with worse white matter CVR (0.04%/mmHg per ml increase in stroke volume, p=0.04) and increased basal ganglia PVS.ConclusionsContemporaneous assessment of CVR, intracranial vascular and CSF pulsatility demonstrates important interrelationships of these vascular functions in humans. Decreased CVR, increased venous pulsatility and reduced foramen magnum CSF stroke volume suggests that dynamic vascular dysfunctions underpin PVS dysfunction and WMH development. Improved understanding of microvascular dysfunction and CSF dynamics offers new intervention targets to reduce SVD lesion development and their impact on cognitive dysfunction and stroke.
A coevolved EDS1-SAG101-NRG1 module mediates cell death signaling by TIR-domain immune receptors
Authors: Lapin Dmitry , Kovacova Viera , Sun Xinhua , Dongus Joram , Bhandari Deepak D. , Born Patrick von , Bautor Jaqueline , Guarneri Nina , Stuttmann Johannes , Beyer Andreas , Parker Jane E. 
Published: March 2019

AbstractPlant intracellular nucleotide-binding/leucine-rich repeat (NLR) immune receptors are activated by pathogen effectors to trigger host defenses and cell death. Toll-Interleukin1-receptor (TIR)-domain NLRs (TNLs) converge on the Enhanced Disease Susceptibility1 (EDS1) family of lipase-like proteins for all resistance outputs. In Arabidopsis TNL immunity,AtEDS1 heterodimers with Phytoalexin Deficient4 (AtPAD4) transcriptionally boost basal defense pathways.AtEDS1 uses the same surface to interact with PAD4-related Senescence-Associated Gene101 (AtSAG101), but the role ofAtEDS1-AtSAG101 heterodimers was unclear. We show thatAtEDS1-AtSAG101 function together withAtNRG1 coiled-coil domain helper NLRs as a coevolved TNL cell death signaling module.AtEDS1-AtSAG101-AtNRG1 cell death activity is transferable to the solanaceous species,Nicotiana benthamiana, and cannot be substituted byAtEDS1-AtPAD4 withAtNRG1 orAtEDS1-AtSAG101 with endogenousNbNRG1. Analysis of EDS1-family evolutionary rate variation and heterodimer structure-guided phenotyping ofAtEDS1 variants orAtPAD4-AtSAG101 chimeras identify closely aligned α-helical coil surfaces in theAtEDS1-AtSAG101 partner C-terminal domains that are necessary for TNL cell death signaling. Our data suggest that TNL-triggered cell death and pathogen growth restriction are determined by distinctive features of EDS1-SAG101 and EDS1-PAD4 complexes and that these signaling machineries coevolved with further components within plant species or clades to regulate downstream pathways in TNL immunity.
Quantitative Analysis of Trans-synaptic Protein Alignment
Authors: Chen Jia-Hui , Blanpied Thomas A , Tang Ai-Hui 
Published: March 2019

AbstractNanoscale distribution of proteins and their relative positioning within a defined subcellular region are key to their physiological functions. Thanks to the super-resolution imaging methods, especially the single-molecule localization microscopy (SMLM), mapping the three-dimensional distribution of multiple proteins has been easier and more efficient than ever. In spite of the many tools available for efficient localization detection and image rendering, it has been a challenge to quantitatively analyze the 3D distribution and relative positioning of proteins in these SMLM data. Here, using the heterogeneously distributed synaptic proteins as examples, we describe in detail a series of analytical methods including detection of nanoscale density clusters, quantification of the trans-synaptic alignment between these protein densities, and automatic enface projection and averaging. These analyses were performed within customized Matlab routines and we make the full scripts available. The concepts behind these analytical methods and the scripts can be adapted for quantitative analysis of spatial organization of other macromolecular complexes.HighlightsLocalization microscopy provides sufficient data for precise quantitative analysis.An algorithm to identify local density peaks within a 3D localization cluster.New methods for quantitative analysis of trans-synaptic proteins alignment and enrichment.These algorithms can be easily adapted to analysis of other subcellular organizations.