bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks
Authors: Wang Tina , Ma Jianzhu , Hogan Andrew N. , Fong Samson , Licon Katherine , Tsui Brian , Kreisberg Jason F. , Adams Peter D. , Carvunis Anne-Ruxandra , Bannasch Danika L. , Ostrander Elaine A. , Ideker Trey 
Published: November 2019

SUMMARYMammals progress through similar physiological stages during life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects conserved molecular events is unclear. Here, we map common epigenetic changes experienced by mammalian genomes as they age, focusing on evolutionary comparisons of humans to dogs, an emerging model of aging. Using targeted sequencing, we characterize the methylomes of 104 Labrador retrievers spanning a 16 year age range, achieving >150X coverage within mammalian syntenic blocks. Comparison with human methylomes reveals a nonlinear relationship which translates dog to human years, aligns the timing of major physiological milestones between the two species, and extends to mice. Conserved changes center on specific developmental gene networks which are sufficient to capture the effects of anti-aging interventions in multiple mammals. These results establish methylation not only as a diagnostic age readout but as a cross-species translator of physiological aging milestones.
DEK influences the trade-off between growth and arrest via H2A.Z-nucleosomes in Arabidopsis
Authors: Brestovitsky Anna , Ezer Daphne , Waidmann Sascha , Maslen Sarah L. , Balcerowicz Martin , Cortijo Sandra , Charoensawan Varodom , Martinho Claudia , Rhodes Daniela , Jonak Claudia , Wigge Philip A 
Published: November 2019

AbstractThe decision of whether to grow and proliferate or to restrict growth and develop resilience to stress is a key biological trade-off. In plants, constitutive growth results in increased sensitivity to environmental stress1,2. The underlying mechanisms controlling this decision are however not well understood. We used temperature as a cue to discover regulators of this process in plants, as it both enhances growth and development rates within a specific range and is also a stress at extremes. We found that the conserved chromatin-associated protein DEK plays a central role in balancing the response between growth and arrest in Arabidopsis, and it does this via H2A.Z-nucleosomes. DEK target genes show two distinct categories of chromatin architecture based on the distribution of H2A.Z in +1 nucleosome and gene body, and these predict induction or repression by DEK. We show that these chromatin signatures of DEK target genes are conserved in human cells, suggesting that DEK may act through an evolutionarily conserved mechanism to control the balance between growth and arrest in plants and animals.
A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study
Authors: Wambua Sammy , Gourlé Hadrien , de Villiers Etienne P. , Ngoi Joyce , Macdonald Angus , Bongcam-Rudloff Erik , de Villiers Santie 
Published: November 2019

AbstractMicrobial communities are essential components of natural ecosystems. Of the global oceans, the Indian Ocean remains the least studied in terms of its microbial diversity, despite it being a highly dynamic tropical water body. Metagenomics methods have significantly advanced studies in marine microbial ecology in recent years. Preliminary metabarcoding assessments are recommended to mitigate against the associated costs, prior to the metagenomics study, to give an impression of the diversity expected and determine the sequencing effort required.We report here the first metabarcoding survey of bacterial diversity of the western Indian Ocean (WIO) using samples used for optimizing environmental DNA (eDNA) isolation as pilot experiment for a metagenomic study investigating the coral-reef microbiome of the region. Sampling of water and sediment samples was done near-shore sublittoral and within the coral reef.About 3,000 microbial ribotypes were inferred, from which 41 phyla were uncovered. Sediments registered higher alpha diversity than seawater samples. The phylum Proteobacteria was dominant with its members constituting over 60% of the ribosomal sequence variants (RSVs). The other abundant bacteria were members of Bacteroidetes and Cyanobacteria phyla. We identified bacterial species with potential broad biotechnological applications, underscoring the WIO’s richness and the usefulness of eDNA metabarcoding approaches in bioprospecting as well as monitoring and/or surveying marine ecosystems.
Ultra-high field imaging of hippocampal neuroanatomy in first episode psychosis demonstrates receptor-specific morphometric patterning
Authors: Park Min Tae M. , Jeon Peter , Khan Ali R. , Dempster Kara , Chakravarty M. Mallar , Lerch Jason P. , Mackinley Michael , Théberge Jean , Palaniyappan Lena 
Published: November 2019

AbstractObjectiveThe hippocampus is considered a putative marker in schizophrenia with early volume deficits of select subfields. Certain subregions are thought to be more vulnerable due to a glutamate-driven mechanism of excitotoxicity, hypermetabolism, and then degeneration. Here, we explored whether hippocampal anomalies in first-episode psychosis (FEP) correlate with glutamate receptor density via a serotonin receptor proxy by leveraging structural neuroimaging, spectroscopy (MRS), and gene expression.MethodsHigh field 7T brain MR images were collected from 27 control, 41 FEP participants, along with 1H-MRS measures of glutamate. Automated methods were used to delineate the hippocampus and atlases of the serotonin receptor system were used to map receptor density across the hippocampus and subfields. We used gene expression data from the Allen Human Brain Atlas to test for correlations between serotonin and glutamate receptor genes.ResultsWe found reduced hippocampal volumes in FEP, replicating previous findings. Amongst the subfields, CA4-dentate gyrus showed greatest reductions. Gene expression analysis indicated 5-HTR1A and 5-HTR4 receptor subtypes as predictors of AMPA and NMDA receptor expression, respectively. Volumetric differences in the subfields correlated most strongly with 5-HT1A (R=0.64, p=4.09E-03) and 5-HT4 (R=0.54, p=0.02) densities as expected, and replicated using previously published data from two FEP studies. Measures of individual structure-receptor alignment were derived through normative modeling of hippocampal shape and correlations to receptor distributions, termed Receptor-Specific Morphometric Signatures (RSMS). Right-sided 5-HT4 RSMS was correlated with glutamate (R=0.357, p=0.048).ConclusionsWe demonstrate glutamate-driven hippocampal remodeling in FEP through a receptor-density gated mechanism, thus providing a mechanistic explanation of how redox dysregulation affects brain structure and symptomatic heterogeneity in schizophrenia.
Separable regulation of POW1 in TAF2-mediated grain development and BR-mediated leaf angle formation in rice
Authors: Zhang Li , Wang Ruci , Wang Yueming , Xu Yufang , Fang Shuang , Chu Jinfang , Yao Shanguo 
Published: November 2019

ABSTRACTLeaf angle is one of the key factors determining rice plant architecture. However, improvement of the leaf angle appears to be unsuccessful in practical breeding because of the simultaneous occurrence of unfavorable traits such as grain size reduction. In this study, we identified the pow1 (put on weight 1) mutant with enlarged grain size and leaf angle, typical brassinosteroid (BR)-related phenotypes caused by excessive cell proliferation and cell expansion. We show that POW1 encodes a novel protein functioning in grain size regulation by repressing the transcription activity of the interacting protein TAF2, a highly conserved member of the transcription initiation complex TFIID. Loss of function of POW1 increases the phosphorylation of OsBZR1 and decreases the inhibitory effect of OsBZR1 on the transcription of BR biosynthesis genes OsDWARF4 (D4) and D11, thus participates in BR-mediated leaf angle regulation. The separable functions of POW1 in grain size and leaf angle control provide a promising strategy to design high-yielding varieties in which both traits would be favorably developed, i.e., compact plant architecture and increased grain size, thus would promote the high-yield breeding a step forward in rice.
Some insights into composition and monoterpene emission rates from selected dominant tropical tree species of Central India: Plant‐specific seasonal variations
Authors: Malik Tanzil G. , Gajbhiye Triratnesh , Pandey Sudhir K. 
Published: November 2019

AbstractIn this article, we discuss about the seasonal variations in the monoterpene emission rates and chemical composition of monoterpenes from selected tropical tree species of Central India. The highest normalized total average monoterpene emission rates (normalized at 30°C) from all the plant species were found in summer followed by rainy and winter seasons, respectively. The composition of individual monoterpene compounds emitted from all the tropical plant species showed significant seasonal variations. Nine monoterpene compounds were determined across three seasons from these selected plants: α‐pinene, β‐pinene, and limonene represented up to 72.6% of the total monoterpene emission. Although the main compounds emitted were α‐pinene, β‐pinene, and limonene, the other minor compounds were also found at varying emission rates. α‐Terpinene and carene were not observed in Eucalyptus globulus and Pongamia pinnata during winter and rainy seasons. Sabinene was only recorded from Azadirachta indica. We have thus observed clearly that the seasonal as well as monthly variations in chemical composition of monoterpene emission rate are species specific. Furthermore, the effect of environmental variables such as temperature (TEM), photosynthetically active radiation (PAR), relative humidity, and carbon dioxide from plant species in distinct seasons revealed that the monoterpene emissions were mainly temperature (TEM) and PAR dependent.
Holding on tight – NPM and the New Zealand performance improvement framework
Authors: Allen Barbara , Eppel Elizabeth 
Published: November 2019

AbstractThe New Zealand Government's Performance Improvement Framework (PIF) is aimed at public sector organisational improvement. The PIF exemplifies how the characteristics of new public management (NPM) challenge the evolution of performance systems attempting to go beyond performance management. The paper provides an empirical example of the operation of the PIF, using a theoretical frame derived from the literature. The analysis suggests that the PIF design does not yet mitigate the effects of gaming, synecdoche, and reputation‐protecting behaviour. The common graded ratings continue to hold the attention of those to whom the PIF is important, acting as a proxy for the whole performance of the organisation. This is a case study of how, despite promising adaptations, performance improvement efforts remain hampered by NPM limitations.
Internationalism Under Platform Capitalism: Brexit and the Organisation of UK Fast Food Workers
Authors: Colás Alejandro 
Published: November 2019

AbstractIn October 2018, a coalition of UK trade unions and civil society organisations called a strike across the UK’s fast food sector in support of a living wage, union recognition and the end to zero‐hour contracts in the sector. This paper takes the day of action—labelled the McStrike—as a starting point for an account of the place of the EU and Brexit in the campaign for fast food rights, as well as the contrasting political standpoints adopted by the different trade unions involved in the action. Brexit is used as a prism through which to analyse aspects of Britain’s contemporary food politics, especially those pertaining to freedom of movement, workplace organisation, and the role of EU legislation in protecting workers’ rights. In exploring the international dimensions of union organisation among the UK’s fast food workers, other, more conceptual considerations regarding the changing nature of public and private food consumption and the incorporation of food‐to‐go into the gig economy are also broached.
A tool for assessing the satisfaction of a diet: Development and preliminary validation of the Diet Satisfaction Score
Authors: Jospe Michelle R. , Haszard Jillian J. , Taylor Rachael W. , Freedhoff Yoni 
Published: November 2019

AbstractAimAdherence to dietary change is crucial for long‐term benefit and a key element of adherence is the satisfaction of a given diet. We aimed to develop a brief questionnaire, suitable for use in clinical practice that can assess satisfaction with a diet, and to conduct preliminary evaluation of its reliability and validity.MethodsThe questionnaire was developed and drafts were sent to two expert panels for content review. The final questionnaire was assessed for internal consistency, face and construct validity, and test‐retest reliability. Expert feedback was provided by nine clinicians/researchers. The tool was assessed in three phases in different international populations who were recruited using social media. It included adults who were currently following a diet (total n = 1604), and those who had recently abandoned their diet (phase 3 only).ResultsThe Diet Satisfaction Score consisted of 10 items measuring one dimension (Cronbach's alpha = 0.85), and participants had a mean total Diet Satisfaction Score of 3.7 (SD = 0.50) from a possible range of 1 to 5. Test‐retest reliability was good as indicated by an intraclass correlation coefficient of 0.64 and a mean difference (95% confidence interval, CI) between repeated test scores of 0.03 (−0.02, 0.09). Each 1‐point increase in Diet Satisfaction Score was associated with longer diet duration by 1.7 weeks (95% CI = 1.5, 2.0, P < .001).ConclusionsThe Diet Satisfaction Score showed good reliability and preliminary validity and may be a useful clinical tool for assessing diet satisfaction and has the potential to predict adherence.
Improving comparability between qPCR‐based telomere studies
Authors: Verhulst Simon 
Published: November 2019

AbstractComparability of findings from qPCR‐based telomere studies is hampered by such measurement results being assay‐specific, precluding a direct quantitative comparisons of observed differences and/or slopes of associations between studies. It is proposed that this can be partially alleviated by expressing qPCR‐based telomere data as Z‐scores.
Error variance bias in neighbour balance and evenness of distribution designs
Authors: Williams E. R. , Piepho H. P. 
Published: November 2019

SummaryNeighbour balance and evenness of distribution designs help to address user concerns in the two‐dimensional layout of agricultural field trials. This is done by minimising the occurrence of pairwise treatment plot neighbours and ensuring that the replications of treatments are spread out across rows and columns of a trial. Such considerations result in a restriction on the normal randomisation process for a row‐column design which can lead to error variance bias. In this paper, uniformity trial data is used to assess the degree of this bias for both resolvable and non‐resolvable designs. Comparisons are made with a similar investigation using Linear Variance spatial designs.
Using spatial tracking with magnetic resonance imaging/ultrasound‐guided biopsy to identify unilateral prostate cancer
Authors: Zhou Steve R. , Priester Alan M. , Jayadevan Rajiv , Johnson David C. , Yang Jason J. , Ballon Jorge , Natarajan Shyam , Marks Leonard S. 
Published: November 2019

ObjectivesTo create reliable predictive metrics of unilateral disease using spatial tracking from a fusion device, thereby improving patient selection for hemi‐gland ablation of prostate cancer.Patients and MethodsWe identified patients who received magnetic resonance imaging (MRI)/ultrasound‐guided biopsy and radical prostatectomy at a single institution between 2011 and 2018. In addition to standard clinical features, we extracted quantitative features related to biopsy core and MRI target locations predictive of tumour unilaterality. Classification and Regression Tree (CART) analysis was used to create a decision tree (DT) for identifying cancer laterality. We evaluated concordance of model‐determined laterality with final surgical pathology.ResultsA total of 173 patients were identified with biopsy coordinates and surgical pathology available. Based on CART analysis, in addition to biopsy‐ and MRI‐confirmed disease unilaterality, patients should be further screened for cancer detected within 7 mm of midline in a 40 mL prostate, which equates to the central third of any‐sized prostate by radius. The area under the curve for this DT was 0.82. Standard diagnostics and the DT correctly identified disease laterality in 73% and 80% of patients, respectively (P = 0.13). Of the patients identified as unilateral by standard diagnostics, 47% had undetected contralateral disease or were otherwise incorrectly identified. This error rate was reduced to 17% (P = 0.01) with the DT.ConclusionUsing spatial tracking from fusion devices, a DT was more reliable for identifying laterality of prostate cancer compared to standard diagnostics. Patients with cancer detected within the central third of the prostate by radius are poor hemi‐gland ablation candidates due to the risk of midline extension of tumour.
Bird assemblages on Amazonian river islands: Patterns of species diversity and composition
Authors: Borges Sérgio Henrique , Baccaro Fabricio , Moreira Marcelo , Choueri Erik Lacerda 
Published: November 2019

AbstractThe principles of island biogeography are rarely applied to the animal assemblages of Amazonian river islands. Here, we compare bird assemblages of Amazonian river islands with a variety of mainland habitats. We also examine how bird species diversity and composition are related to island physical attributes. Birds were sampled with mist nets and qualitative censuses on 11 river islands and 24 mainland sites on the lower reaches of the Rio Negro in the Brazilian Amazon. Island bird assemblages were characterized by lower species richness and a higher abundance of a few dominant species. Additionally, the species composition of the islands was distinct from that of the mainland, including the nearby floodplain habitats. The number of bird species increased with island size and habitat diversity, and decreased with degree of isolation. In addition, small islands tended to harbor an impoverished subset of the species present on larger ones. Bird species diversity and composition on Amazonian river islands are likely influenced by the ecological succession and historical events affecting island formation. Considering their small total area across the Amazon basin, these insular fluvial communities could be disproportionately threatened by river channel disturbances related to climate change or hydroelectric dam development.Abstract in Portughese is available with online material.
The functional patterns of adolescent mothers leaving foster care: Results from a cluster analysis
Authors: Shpiegel Svetlana , Aparicio Elizabeth M. , King Bryn , Prince Dana , Lynch Jason , Grinnell‐Davis Claudette L. 
Published: November 2019

AbstractFew studies have explored the outcomes of adolescent mothers leaving foster care, especially using person‐oriented methods. The current study employed a cluster analysis to identify unique patterns of functioning among adolescent mothers aged 19 (n = 777). Data from the National Youth in Transition Database and the Adoption and Foster Care Analysis and Reporting System were utilized. Findings revealed five subpopulations characterized by distinct constellations of outcomes at age 19. The largest group (43%) exhibited competent functioning across all the domains studied—its members were connected to school and/or employment and did not experience homelessness, substance abuse referrals, or incarceration during the past 2 years (i.e., “resilient”). A relatively small group (12%) exhibited challenges across all the above‐referenced domains, whereas the remaining groups presented challenges in some domains, but not in others. Follow‐up analyses revealed that adolescent mothers classified as resilient at age 19 had the lowest rates of congregate care placements and the highest rates of nonrelative foster care placements at age 17. Moreover, they had lower placement instability and higher rates of extended foster care as compared with members of the other clusters. Implications for practice, policy, and research are discussed.
Historical and contemporary indigenous marine conservation strategies in the North Pacific
Authors: Ban Natalie C. , Wilson Emma , Neasloss Doug 
Published: November 2019

AbstractStrategies to reduce, halt, and reverse global declines in marine biodiversity are needed urgently. We reviewed, coded, and synthesized historical and contemporary marine conservation strategies of the Kitasoo/Xai'xais First Nation in British Columbia, Canada to show how their approaches work. We assessed whether the conservation actions classification system by the Conservation Measures Partnership was able to encompass this nation's conservation approaches. All first‐order conservation actions aligned with the Kitasoo/Xai'xais First Nation's historical and contemporary marine conservation actions; hereditary chief management responsibility played a key role. A conservation ethic permeates Kitasoo/Xai'xais culture, and indigenous resource management and conservation existed historically and remains strong despite extreme efforts by colonizers to suppress all indigenous practices. The Kitasoo/Xai'xais's embodiment of conservation actions as part of their worldview, rather than as requiring actions separate from everyday life (the norm in nonindigenous cultures), was missing from the conservation action classification system. The Kitasoo/Xai'xais are one of many indigenous peoples working to revitalize their governance and management authorities. With the Canadian government's declared willingness to work toward reconciliation, there is an opportunity to enable First Nations to lead on marine and other conservation efforts. Global conservation efforts would also benefit from enhanced support for indigenous conservation approaches, including expanding the conservation actions classification to encompass a new category of conservation or sacredness ethic.
Credit score classification using spiking extreme learning machine
Authors: Kuppili Venkatanareshbabu , Tripathi Diwakar , Reddy Edla Damodar 
Published: November 2019

AbstractCredit score classification is a prominent research problem in the banking or financial industry, and its predictive performance is responsible for the profitability of financial industry. This paper addresses how Spiking Extreme Learning Machine (SELM) can be effectively used for credit score classification. A novel spike‐generating function is proposed in Leaky Nonlinear Integrate and Fire Model (LNIF). Its interspike period is computed and utilized in the extreme learning machine (ELM) for credit score classification. The proposed model is named as SELM and is validated on five real‐world credit scoring datasets namely: Australian, German‐categorical, German‐numerical, Japanese, and Bankruptcy. Further, results obtained by SELM are compared with back propagation, probabilistic neural network, ELM, voting‐based Q‐generalized extreme learning machine, Radial basis neural network and ELM with some existing spiking neuron models in terms of classification accuracy, Area under curve (AUC), H‐measure and computational time. From the experimental results, it has been noticed that improvement in accuracy and execution time for the proposed SELM is highly statistically important for all aforementioned credit scoring datasets. Thus, integrating a biological spiking function with ELM makes it more efficient for categorization.