bluuebunny/crossref_metadata_2025 huggingface dataset:
Availability, access, analysis and dissemination of small-area data
Authors: Hodgson Susan , Fecht Daniela , Gulliver John , Iyathooray Daby Hima , Piel Frédéric B , Yip Fuyuen , Strosnider Heather , Hansell Anna , Elliott Paul
Published: March 2019

In this era of ‘big data’, there is growing recognition of the value of environmental, health, social and demographic data for research. Open government data initiatives are growing in number and in terms of content. Remote sensing data are finding widespread use in environmental research, including in low- and middle-income settings. While our ability to study environment and health associations across countries and continents grows, data protection rules and greater patient control over the use of their data present new challenges to using health data in research. Innovative tools that circumvent the need for the physical sharing of data by supporting non-disclosive sharing of information, or that permit spatial analysis without researchers needing access to underlying patient data can be used to support analyses while protecting data confidentiality. User-friendly visualizations, allowing small-area data to be seen and understood by non-expert audiences, are revolutionizing public and researcher interactions with data. The UK Small Area Health Statistics Unit’s Environment and Health Atlas for England and Wales, and the US National Environmental Public Health Tracking Network offer good examples. Open data facilitates user-generated outputs, and ‘mash-ups’, and user-generated inputs from social media, mobile devices and wearable tech are new data streams that will find utility in future studies, and bring novel dimensions with respect to ethical use of small-area data.
The triglyceride-glucose index as a measure of insulin resistance and risk of obesity-related cancers
Authors: Fritz Josef , Bjørge Tone , Nagel Gabriele , Manjer Jonas , Engeland Anders , Häggström Christel , Concin Hans , Teleka Stanley , Tretli Steinar , Gylling Björn , Lang Alois , Stattin Pär , Stocks Tanja , Ulmer Hanno
Published: March 2019

Background

The role of insulin resistance as a mediator in the association of body mass index (BMI) with site-specific cancer risk has, to our knowledge, never been systematically quantified.

Methods

Altogether 510 471 individuals from six European cohorts, with a mean age of 43.1 years, were included. We used the triglyceride glucose product (TyG index) as a surrogate measure for insulin resistance. We fitted Cox models, adjusted for relevant confounders, to investigate associations of TyG index with 10 common obesity-related cancers, and quantified the proportion of the effect of BMI mediated through TyG index on the log-transformed hazard ratio (HR) scale.

Results

During a median follow-up of 17.2 years, 16 052 individuals developed obesity-related cancers. TyG index was associated with the risk of cancers of the kidney HR per one standard deviation increase 1.13, 95% confidence interval: 1.07 to 1.20], liver (1.13, 1.04 to 1.23), pancreas (1.12, 1.06 to 1.19), colon (1.07, 1.03 to 1.10) and rectum (1.09, 1.04 to 1.14). Substantial proportions of the effect of BMI were mediated by TyG index for cancers of the pancreas (42%), rectum (34%) and colon (20%); smaller proportions for kidney (15%) and liver (11%). Little or no mediation was observed for breast (postmenopausal), endometrial and ovarian cancer. Results were similar for males and females, except for pancreatic cancer where the proportions mediated were 20% and 91%, respectively.

Conclusions

The TyG index was associated with increased risk of cancers of the digestive system and substantially mediated the effect of BMI, suggesting that insulin resistance plays a promoting role in the pathogenesis of gastrointestinal cancers.
Evaluating passing ability in association football
Authors: Håland Else Marie , Wiig Astrid Salte , Stålhane Magnus , Hvattum Lars Magnus
Published: March 2019

In this paper, the passing ability of football players is determined by building three generalized additive mixed models that each explains a different aspect of a pass’ success: difficulty, risk and potential. The models are built on data from the 2014–2016 seasons of the Norwegian top division Eliteserien, and their predictive power is tested on the 2017 season. The results provide insight into the factors affecting the success of a pass in Eliteserien. These include the location of the pass, the relationship to previous passes and to situations such as throw-ins, corners, free kicks or tackles, as well as conditions specific to the Eliteserien, such as the time of season and the ground surface type. Finally, the key pass makers in the league are identified.
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

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

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

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 >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

This 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.
Fungi Associated with and Influence of Moisture on Development of Kernel Mold of Hazelnut
Authors: Pscheidt J. W. , Heckert S. , Wiseman M. , Jones L.
Published: March 2019

Kernel mold on hazelnuts is defined by the United States Department of Agriculture, U.S.A., as any visible fungal growth either on the outside or inside of the kernel. Only one yeast and one filamentous fungus have been associated with kernel mold of hazelnut in Oregon. In this report, fungi were isolated from kernels with mold and identified using morphological and molecular characters. Penicillium spp. were isolated most often from kernels with mold, but species of Aspergillus and Cladosporium and Diaporthe rudis were also frequently isolated. Additional fungi from three other genera were also isolated. All of the same fungi were also isolated from symptomless kernels. Eremothecium coryli or Ramularia sp. previously associated with kernel defects in Oregon were not found associated with symptoms of kernel mold. Incidence of mold was the highest when nuts were incubated in moist chambers on wet, nonautoclaved orchard soil and was significantly higher than kernel mold found in nuts incubated on either air-dried soil or wet, autoclaved soil. Preventing hazelnuts from coming in contact with wet soil in the field using elevated wire screens resulted in significantly less mold development in two out of three years evaluated. Nuts on screens had a greater chance to dry out between rainstorms as measured by significantly lower nut moisture levels at harvest.
Phylogenetic Analysis and Fungicide Baseline Sensitivities of Monilia mumecola in China
Authors: Yin L. F. , Du S. F. , Chaisiri C. , Cheewangkoon R. , Luo C. X.
Published: March 2019

Monilia mumecola is one of the causal agents of peach brown rot in China. In this study, M. mumecola isolates from different locations and hosts were used to analyze the genetic diversity and to assay the sensitivity to four generally used fungicides: carbendazim, tebuconazole, azoxystrobin, and boscalid. Results showed that isolates from different locations tended to be separated. Interestingly, isolates from different hosts (e.g., peach and apricot) at the same locations generally clustered together, indicating that the M. mumecola isolates may infect different hosts in the same areas. The fungicide sensitivity assay of 93 M. mumecola isolates showed that the average effective concentration for 50% mycelial growth inhibition values for carbendazim, tebuconazole, azoxystrobin, and boscalid were 0.103, 0.034, 0.325, and 0.419 µg/ml, respectively. The sensitivity distributions of the tested isolates to the four fungicides showed continuous unimodal curves, indicating no qualitative shift of resistance. No significant difference of sensitivity to tested fungicides was observed among isolates from either different locations or different hosts.
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

Zinc 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

R-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

Climate 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

It 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

Rodents’ 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

Natural 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

Background

Cerebral 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.

Methods

We 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.

Results

In 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.

Conclusions

Contemporaneous 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

Plant 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

Nanoscale 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.

Highlights

Localization 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.
An experimental manipulation of species’ phenologies overturns competitive hierarchies
Authors: Blackford Christopher , Germain Rachel M. , Gilbert Benjamin
Published: March 2019

Ecological theory produces opposing predictions about whether differences in the timing of life history transitions, or ‘phenology’, promote or limit coexistence. Phenological separation is predicted to create temporal niche differences, increasing coexistence, yet phenological separation may competitively favour one species, increasing fitness differences and hindering coexistence. We experimentally manipulated relative germination timing, a critical phenological event, of two annual grass species,Vulpia microstachysandV. octoflora, to test these contrasting predictions. We parameterized a competition model to estimate within-season niche differences, fitness differences, and coexistence, and to estimate coexistence when among-year fluctuations of germination timing occur. Increasing germination separation caused parallel changes in niche and fitness differences, with the net effect of weakening within-year coexistence. Both species experienced a competitive advantage by germinating earlier, strongly enough to allow the generally inferior competitor to exclude the other with at least a four day head start. The overall consequence of germination separation was to limit coexistence within a given year, although among-year variation in relative timing of germination was sufficient to support long-term coexistence. Our results clarify how phenological differences structure competitive interactions, and highlight the need to quantify among-year variation in these differences to better understand species coexistence.
Evolutionary patterns of the chimerical retrogenes in Oryza
Authors: Zhou Yanli , Song Huazhi , Xiao Jinghua , Zhang Qifa , Long Manyuan , Zhang Chengjun
Published: March 2019

Chimerical retroposition delineate a process by which RNA reverse transcribed integration into genome accompanied with recruiting flanking sequence, which is asserted to play essential roles and drive genome evolution. Although chimerical retrogenes hold high origination rate in plant genome, the evolutionary pattern of retrogenes and their parental genes are not well understood in rice genome. In this study, using maximum likelihood method, we evaluated the substitution ratio along lineages of 24 retrogenes and parental gene pairs to retrospect the evolutionary patterns. The results indicate that some specific lineages in 7 pairs underwent positive selection. Besides the rapid evolution in the initial stage of new chimerical retrogene evolution, an unexpected pattern was revealed: soon or some uncertain period after the origination of new chimerical retrogenes, their parental genes evolved rapidly under positive selection, rather than the rapid evolution of the new chimerical retrogenes themselves. This result lend support to the hypothesis that the new copy assistant the function evolution among parental gene and retrogene. Transcriptionally, we also found that one retrogene (RCG3) have a high expression at the period of calli infection which supported by chip data while its parental gene doesn’t have. Finally, by calibration to Ka/Ks analysis results in other species including Apis mellifera, we concluded that chimerical retrogenes are higher proportionally positive selected than the regular genes in the rice genome.
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features
Authors: Li Yuanyue , Kuhn Michael , Gavin Anne-Claude , Bork Peer
Published: March 2019

Untargeted mass spectrometry is a powerful method for detecting metabolites in biological samples. However, fast and accurate identification of the metabolites’ structures from MS/MS spectra is still a great challenge. We present a new analysis method, called SF-Matching, that is based on the hypothesis that molecules with similar structural features will exhibit similar fragmentation patterns. We combine information on fragmentation patterns of molecules with shared substructures and then use random forest models to predict whether a given structure can yield a certain fragmentation pattern. These models can then be used to score candidate molecules for a given mass spectrum. For rapid identification, we pre-compute such scores for common biological molecular structure databases. Using benchmarking datasets, we find that our method has similar performance to CSI:FingerID and that very high accuracies can be achieved by combining our method with CSI:FingerID. Rarefaction analysis of the training dataset shows that the performance of our method will increase as more experimental data become available.
Molecular and anatomical organization of the dorsal raphe nucleus
Authors: Huang Kee Wui , Ochandarena Nicole E. , Philson Adrienne C. , Hyun Minsuk , Birnbaum Jaclyn E. , Cicconet Marcelo , Sabatini Bernardo L.
Published: March 2019

The dorsal raphe nucleus (DRN) is an important source of neuromodulators in the brain and has been implicated in a wide variety of behavioral and neurological disorders. Although mostly studied as a source of serotonin, the DRN is comprised of multiple cell types that are subdivided into distinct anatomical subregions. However, the complex and incompletely characterized cellular organization of the DRN has impeded efforts to investigate the distinct circuit and behavioral functions of its subdomains. Here we used high-throughput single-cell RNA sequencing within situhybridization and viral tracing to develop a map of transcriptional and spatial profiles of cells in and around the mouse DRN. Our studies reveal the molecular and spatial organization of multiple neuron subtypes that are the cellular bases of functionally and anatomically distinct serotonergic subsystems, and provide a resource for the design of strategies for further dissection of these subsystems and their diverse functions.
Cingulate Cortex Atrophy is Associated with Hearing Loss in Presbycusis with Cochlear Amplifier Dysfunction
Authors: Belkhiria Chama , Vergara Rodrigo C. , Martín Simón San , Leiva Alexis , Marcenaro Bruno , Martínez Melissa , Delgado Carolina , Delano Paul H.
Published: March 2019

Age-related hearing loss is associated with cognitive decline and has been proposed as a risk factor for dementia. However, the mechanisms that relate hearing loss to cognitive decline remain elusive. Here, we propose that the impairment of the cochlear amplifier mechanism is associated with structural brain changes and cognitive impairment. Ninety-six subjects aged over 65 years old (63 female and 33 male) were evaluated using brain magnetic resonance imaging, neuropsychological and audiological assessments, including distortion product otoacoustic emissions as a measure of the cochlear amplifier function. All the analyses were adjusted by age, gender and education. The group with cochlear amplifier dysfunction showed greater brain atrophy in the cingulate cortex and in the parahippocampus. In addition, the atrophy of the cingulate cortex was associated with cognitive impairment in episodic and working memories and in language and visuoconstructive abilities. We conclude that the neural abnormalities observed in presbycusis subjects with cochlear amplifier dysfunction extend beyond core auditory network and are associated with cognitive decline in multiple domains. These results suggest that a cochlear amplifier dysfunction in presbycusis is an important mechanism relating hearing impairments to brain atrophy in the extended network of effortful hearing.
Crystal structure of bis[bis(1,4,7-triazacyclononane-κ3N,N′,N′′)chromium(III)] tris(tetrachloridozincate) monohydrate from synchrotron X-ray data
Authors: Moon Dohyun , Choi Jong-Ha
Published: March 2019

The structure of the title compound, [Cr(tacn)2]2[ZnCl4]3·H2O (tacn is 1,4,7-triazacyclononane; C6H15N3), has been determined from synchrotron X-ray data. Each CrIIIcation is coordinated by the six N atoms from the two tacn ligands, displaying a distorted octahedral geometry. Three distorted tetrahedral [ZnCl4]2−anions and one lattice water molecule lie outside this coordination sphere. The Cr—N bond lengths are in the range 2.0621 (11) to 2.0851 (12) Å, while the mean inner N—Cr—N bond angle is 82.51 (5)°. The crystal packing is stabilized by hydrogen-bonding interactions with the N—H groups of the tacn ligands and the water O—H groups acting as donors, and the O atoms of the water molecules and Cl atoms of the [ZnCl4]2−anions as acceptors. Overall these contacts lead to the formation of a three-dimensional network.
Explaining the link between qualitative job insecurity and attitudes
Authors: Lazauskaite-Zabielske Jurgita , Urbanaviciute Ieva , Vander Elst Tinne , De Witte Hans
Published: March 2019

Purpose

Using the framework of fairness heuristic theory and social exchange theory, the purpose of this paper is to explore the mediating role of perceived overall justice in the relationship between qualitative job insecurity and attitudinal outcomes. In line with both theories, job insecurity is hypothesized to negatively relate to perceived overall organization-focused justice that subsequently relates to employees’ attitudes toward the organization.

Design/methodology/approach

A total of 291 white-collar employees were surveyed. Structural equation modeling was used to analyze the data.

Findings

Overall justice was found to mediate the association between qualitative job insecurity and affective commitment, turnover intention and satisfaction with the organization.

Originality/value

The study is the first study to highlight the explanatory role of overall organization-focused justice (in contrast to the justice types) in the qualitative job insecurity–outcomes relationship.
Secularism, race, religion and the Public Instruction Act of 1880 in NSW
Authors: Low Remy
Published: March 2019

Purpose

Through a political genealogy, the purpose of this paper is to demonstrate how the institutionalisation of the so-called “secular principle” in NSW state schools in the late-nineteenth century, which is commonly assumed to be a historical moment when religious neutrality was enshrined in public education, was overdetermined by the politics of racialisation and ethno-nationalism.

Design/methodology/approach

The historiographical method used here is labelled “political genealogy”. This approach foregrounds how every social order and norm is contingent on political struggles that have shaped its form over time. This includes foregrounding the acts of exclusion that constitute any social order and norm.

Findings

The secular principle institutionalised in the NSW Public Instruction Act of 1880, far from being the “neutral” solution to sectarian conflict, was in fact a product of anti-Catholic sentiment fuelled by the racialisation of Irish Catholicism and ethno-nationalist anxieties about its presence in the colony.

Originality/value

This paper makes clear that “the secular” in secular schooling is neither a product of historical and moral “progress” from a more “primitive” state to a more progressive one, nor a principle of neutrality that stands outside of particular historical and political relations of power. Thus, it encourages a more pragmatic and supple understanding of “the secular” in education. It also invites both advocates and critics of secular education to adapt their arguments based on changing historical circumstances, and to justify the exclusions that such arguments imply without recourse to transcendent principles.
Design of an embracing-type climbing robot for variation diameter rod
Authors: Chen Guoda , Yang Huafeng , Cao Huiqiang , Ji Shiming , Zeng Xi , Wang Qian
Published: March 2019

Purpose

For the climbing rod object with large diameter variation and the need of obstacle crossing, this paper aims to propose a new embracing-type climbing robot named as EVOC-I robot.

Design/methodology/approach

The design philosophy and structural scheme are introduced. The kinematic analysis of embracing and telescoping mechanisms is carried out to provide the theoretical foundation for the effective climbing of the robot. Based on the prototype robot, three preliminary experiments are carried out to verify the effectiveness of the designed robot.

Findings

The theoretical and experimental analyses have verified the reasonability and effectiveness of the proposed robot design.

Research limitations/implications

As the preliminary study, the prototype still need a lot of improvement. The experimental verification is also limited. Future work will focus on improving the design and increasing the theoretical analysis, especially increasing experimental study and designing the next generation of the rod climbing robot.

Practical implications

The designed climbing robot can be used for climbing the rod with variation diameter and flange obstacle, especially the lightening rod in the transformer substation.

Originality/value

The paper designs a new climbing robot that integrates the ability of large variation diameter adaptation and obstacle crossing.
Family firm innovation strategy: contradictions and tradition
Authors: Lattuch Frank
Published: March 2019

Purpose

When studying innovation in family firms, several contradictions appear, as the family and the firm represent different social systems that follow different rules and expectations. This paper aims to argue that a deeper understanding and effective management of those paradoxes is crucial for the family firm’s innovation performance.

Design/methodology/approach

Using theory-building principles, this paper has an abductive character; new research propositions are offered to provide insights into the apparently paradoxical aspects of successfully managing a family firm’s innovation strategy.

Findings

Three contradictions are presented and discussed: first, the family can be a hazard and source for the firm; second, family members acting as shareholder and investor; and third, established practice and innovation issues may compete against each other in the quest to sustainably rejuvenate the organization. Inferences are drawn from these apparent contradictions concerning family firm management, providing a basis to form propositions that effectively support innovation.

Originality/value

This paper provides a paradoxical perspective on the innovation phenomenon in family firms and offers practical implications to help leaders better shape their organization’s innovation strategy.
Investigating retail property market dynamics through spatial accessibility measures
Authors: Adebayo Adejimi Alli , Greenhalgh Paul , Muldoon-Smith Kevin
Published: March 2019

Purpose

The retail property market is constantly adopting to the continuous demand of retailers and their consumers. This paper aims to investigate retail property market dynamics through spatial accessibility measures of the City of York street network. It explores how spatial accessibility metrics (SAM) explain retail market dynamics (RMD) through changes in the city’s retail rental values and stock.

Design/methodology/approach

Valuation office agency (VOA) data sets (aspatial) and ordnance survey map (spatial) data form the empirical foundation for this investigation. Changes in rental value and retail stock between 2010 and 2017 VOA data sets represent the RMD variables. While, the configured street network measures of Space Syntax, namely, global integration, local integration, global choice and normalised angular choice form the SAM variables. The relationship between these variables is analysed through geo-visualisation and statistical testing using GIS and SPSS tools.

Findings

The study reveals that there has been an overall negative changes of 15 and 22% in rental value and retail stock, respectively, even though some locations within the sampled city (York, North Yorkshire, England) indicated positive changes. The study further indicated that changes in retail rental value and stock have occurred within locations with good accessibility index. It also verifies that there are spatial and statistical relationship between variables and 22% of RMD variability was jointly accounted for by SAM.

Originality/value

This research is first to investigates changes in retail property market variables through spatial accessibility measures of space syntax. It contributes to the burgeoning research field of real estate and Space Syntax.