bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of 1:1 orthology maps and updated datasets into Echinobase
Authors: Foley Saoirse , Ku Carolyn , Arshinoff Brad , Lotay Vaneet , Karimi Kamran , Vize Peter D , Hinman Veronica 
Published: May 2021

AbstractEchinobase (https://echinobase.org) is a central online platform that generates, manages and hosts genomic data relevant to echinoderm research. While the resource primarily serves the echinoderm research community, the recent release of an excellent quality genome for the frequently studied purple sea urchin (Strongylocentrotus purpuratus genome, v5.0) has provided an opportunity to adapt to the needs of a broader research community across other model systems. To this end, establishing pipelines to identify orthologous genes between echinoderms and other species has become a priority in many contexts including nomenclature, linking to data in other model organisms, and in internal functionality where data gathered in one hosted species can be associated with genes in other hosted echinoderms. This paper describes the orthology pipelines currently employed by Echinobase and how orthology data are processed to yield 1:1 ortholog mappings between a variety of echinoderms and other model taxa. We also describe functions of interest that have recently been included on the resource, including an updated developmental time course for S.purpuratus, and additional tracks for genome browsing. These data enhancements will increase the accessibility of the resource to non-echinoderm researchers and simultaneously expand the data quality and quantity available to core Echinobase users.Database URL: https://echinobase.org
emiRIT: a text-mining-based resource for microRNA information
Authors: Roychowdhury Debarati , Gupta Samir , Qin Xihan , Arighi Cecilia N , Vijay-Shanker K 
Published: May 2021

Abstract
microRNAs (miRNAs) are essential gene regulators, and their dysregulation often leads to diseases. Easy access to miRNA information is crucial for interpreting generated experimental data, connecting facts across publications and developing new hypotheses built on previous knowledge. Here, we present extracting miRNA Information from Text (emiRIT), a text-miningbased resource, which presents miRNA information mined from the literature through a user-friendly interface. We collected 149 ,233 miRNA –PubMed ID pairs from Medline between January 1997 and May 2020. emiRIT currently contains ‘miRNA –gene regulation’ (69 ,152 relations), ‘miRNA disease (cancer)’ (12 ,300 relations), ‘miRNA –biological process and pathways’ (23, 390 relations) and circulatory ‘miRNAs in extracellular locations’ (3782 relations). Biological entities and their relation to miRNAs were extracted from Medline abstracts using publicly available and in-house developed text-mining tools, and the entities were normalized to facilitate querying and integration. We built a database and an interface to store and access the integrated data, respectively. We provide an up-to-date and user-friendly resource to facilitate access to comprehensive miRNA information from the literature on a large scale, enabling users to navigate through different roles of miRNA and examine them in a context specific to their information needs. To assess our resource’s information coverage, we have conducted two case studies focusing on the target and differential expression information of miRNAs in the context of cancer and a third case study to assess the usage of emiRIT in the curation of miRNA information.
Database URL: https://research.bioinformatics.udel.edu/emirit/
Population-based incidence and outcomes of acute aortic dissection in Japan
Authors: Yamaguchi Tetsuo , Nakai Michikazu , Yano Takao , Matsuyama Masakazu , Yoshino Hideaki , Miyamoto Yoshihiro , Sumita Yoko , Matsuda Hitoshi , Inoue Yousuke , Okita Yutaka , Minatoya Kenji , Ueda Yuichi , Ogino Hitoshi 
Published: May 2021

Abstract

Aims
The population-based incidence and outcomes of acute aortic dissection (AAD) are still unknown because some patients are already dead on arrival, and the accurate diagnosis of AAD is difficult due to the low autopsy rate. We performed a population-based review of all patients with AAD in a well-defined geographical area in Japan between 2016 and 2018.

Methods and results
Data of all patients with AAD at Miyazaki Prefectural Nobeoka Hospital (MPNH), which performs medical care for 120 000 residents, were collected retrospectively. The emergency medical service is dedicated to the transfer of all patients in this area to the MPNH. For all patients who were dead on arrival, the diagnosis of AAD was made by autopsy imaging (AI) using computed tomography. The age-adjusted incidence and mortality per 100 000 population were calculated using the Japanese population distribution model in 2015. The total incidence of AAD was 79 (type A: 64.5%, n = 51). Of those, 60.8% (31/51) of patients with type A and 21.4% (6/28) with type B were dead on arrival and diagnosed by AI. The 30-day mortality rates were 74.5% (38/51) in type A and 25.0% (7/28) in type B. The age-adjusted incidence and mortality of AAD per 100 000 inhabitants were 17.6 (type A: 11.3, type B: 6.2) and 9.9 (type A: 8.4, type B: 1.5), respectively.

Conclusions
The population-based survey of AAD showed that the age-adjusted incidence of AAD was two-fold higher than in previous reports, and the actual mortality rates were markedly higher due to the high incidence of dead-on-arrival.
Coronary artery calcium is associated with increased risk for lung and colorectal cancer in men and women: the Multi-Ethnic Study of Atherosclerosis (MESA)
Authors: Dzaye Omar , Berning Philipp , Dardari Zeina A , Mortensen Martin Bødtker , Marshall Catherine Handy , Nasir Khurram , Budoff Matthew J , Blumenthal Roger S , Whelton Seamus P , Blaha Michael J 
Published: May 2021

Abstract

Aims
This study explored the association of coronary artery calcium (CAC) with incident cancer subtypes in the Multi-Ethnic Study of Atherosclerosis (MESA). CAC is an established predictor of cardiovascular disease (CVD), with emerging data also supporting independent predictive value for cancer. The association of CAC with risk for individual cancer subtypes is unknown.

Methods and results
We included 6271 MESA participants, aged 45–84 and without known CVD or self-reported history of cancer. There were 777 incident cancer cases during mean follow-up of 12.9 ± 3.1 years. Lung and colorectal cancer (186 cases) were grouped based on their strong overlap with CVD risk profile; prostate (men) and ovarian, uterine, and breast cancer (women) were considered as sex-specific cancers (in total 250 cases). Incidence rates and Fine and Gray competing risks models were used to assess relative risk of cancer-specific outcomes stratified by CAC groups or Log(CAC+1). The mean age was 61.7 ± 10.2 years, 52.7% were women, and 36.5% were White. Overall, all-cause cancer incidence increased with CAC scores, with rates per 1000 person-years of 13.1 [95% confidence interval (CI): 11.7–14.7] for CAC = 0 and 35.8 (95% CI: 30.2–42.4) for CAC ≥400. Compared with CAC = 0, hazards for those with CAC ≥400 were increased for lung and colorectal cancer in men [subdistribution hazard ratio (SHR): 2.2 (95% CI: 1.1–4.7)] and women [SHR: 2.2 (95% CI: 1.0–4.6)], but not significantly for sex-specific cancers across sexes.

Conclusion
CAC scores were associated with cancer risk in both sexes; however, this was stronger for lung and colorectal when compared with sex-specific cancers. Our data support potential synergistic use of CAC scores in the identification of both CVD and lung and colorectal cancer risk.
Risk predicting for acute coronary syndrome based on machine learning model with kinetic plaque features from serial coronary computed tomography angiography
Authors: Wang Yabin , Chen Haiwei , Sun Ting , Li Ang , Wang Shengshu , Zhang Jibin , Li Sulei , Zhang Zheng , Zhu Di , Wang Xinjiang , Cao Feng 
Published: May 2021

Abstract

Aims
More patients with suspected coronary artery disease underwent coronary computed tomography angiography (CCTA) as gatekeeper. However, the prospective relation of plaque features to acute coronary syndrome (ACS) events has not been previously explored.

Methods and results
One hundred and one out of 452 patients with documented ACS event and received more than once CCTA during the past 12 years were recruited. Other 101 patients without ACS event were matched as case control. Baseline, follow-up, and changes of anatomical, compositional, and haemodynamic parameters [e.g. luminal stenosis, plaque volume, necrotic core, calcification, and CCTA-derived fractional flow reserve (CT-FFR)] were analysed by independent CCTA measurement core laboratories. Baseline anatomical, compositional, and haemodynamic parameters of lesions showed no significant difference between the two cohorts (P &gt; 0.05). While the culprit lesions exhibited significant increase of luminal stenosis (10.18 ± 2.26% vs. 3.62 ± 1.41%, P = 0.018), remodelling index (0.15 ± 0.14 vs. 0.09 ± 0.01, P &lt; 0.01), and necrotic core (4.79 ± 1.84% vs. 0.43 ± 1.09%, P = 0.019) while decrease of CT-FFR (−0.05 ± 0.005 vs. −0.01 ± 0.003, P &lt; 0.01) and calcium ratio (−4.28 ± 2.48% vs. 4.48 ± 1.46%, P = 0.004) between follow-up CCTA and baseline scans in comparison to that of non-culprit lesion. The XGBoost model comprising the top five important plaque features revealed higher predictive ability (area under the curve 0.918, 95% confidence interval 0.861–0.968).

Conclusions
Dynamic changes of plaque features are highly relative with subsequent ACS events. The machine learning model of integrating these lesion characteristics (e.g. CT-FFR, necrotic core, remodelling index, plaque volume, and calcium) can improve the ability for predicting risks of ACS events.
The Elasticity of Taxable Income: A Meta-Regression Analysis
Authors: Neisser Carina 
Published: May 2021

Abstract
The elasticity of taxable income is a key parameter in tax policy analysis. To examine the large variation found in the literature of taxable and broad income elasticities, I conduct a comprehensive meta-regression analysis using information from 61 studies containing 1,720 estimates. My findings reveal that estimated elasticities are not immutable parameters. They are correlated with contextual factors and the choice of the empirical specification influences the estimated elasticities. Finally, selective reporting bias is prevalent, and the direction of bias depends on whether deductions are included in the tax base.
Seismic anisotropy and mantle deformation in NW Iran inferred from splitting measurements of SK(K)S and direct S phases
Authors: Arvin Shiva , Sobouti Farhad , Priestley Keith , Ghods Abdolreza , Motaghi Khalil , Tilmann Frederik , Eken Tuna 
Published: May 2021

SUMMARY
We present the results of a shear wave splitting analysis performed on the teleseismic SK(K)S and direct S wave recordings of 68 temporary broad-band stations to investigate the mantle deformation on the northern side of the Arabia–Eurasia collision zone in NW Iran. We used the Reference Station Technique to overcome potential contamination from the source-side anisotropy on the direct S wave signals. This method enabled us to expand our splitting measurement database beyond the usual SK(K)S phases. The average splitting delay time over the entire region was found to be 1.14 ± 0.42 s for the SK(K)S wave and 1.36 ± 0.26 s for the direct S wave. In most parts of the study area, the fast polarization directions for both shear phases are consistent and show a uniform NE–SW direction with an average of 36° and 37° for SK(K)S and S wave-derived results, respectively. This direction is in close agreement with the direction of the absolute plate motion vector in NW Iran (N39°E). The fast directions are associated with neither the surface geological trends, nor the geodetic strain fields. We propose that the observed anisotropy is mainly controlled by the LPO fabric developed due to the shearing of the asthenospheric layer in response to the motion of the lithosphere relative to the deeper mantle. Only in a narrow region near the tectonic boundaries of central Iran with NW Iran and the Alborz, NW–SE oriented SK(K)S fast directions tend to align with the major geological structures. Fast directions obtained from direct S wave indicate significantly smoother variations in the same regions and mostly continue to be aligned in the NE–SW direction. We attribute these differences to the change in the structure of the lithosphere in the tectonic boundary zone. The western margins of central Iran possess a strong deformational fabric as evidenced by the major active strike-slip zones there. Considering that the depth extent of this fabric expands over a relatively narrow zone in the mantle, it can locally influence the SK(K)S phases. The direct S waves, on the other hand, have a larger footprint and therefore average over a larger region, and relative to the SK(K)S phases, are influenced more strongly by the asthenospheric fabric due to their larger angles of incidence, which results in a larger zone of influence for station average anisotropy parameters.
Reproductive- and Social-State Plasticity of Multiple Sensory Systems in a Cichlid Fish
Authors: Maruska Karen P , Butler Julie M 
Published: May 2021

SynopsisIntra- and inter-sexual communications are vital to the survival and reproductive success of animals. In species that cycle in and out of breeding or other physiological condition, sensory function can be modulated to optimize communication at crucial times. Little is known, however, about how widespread this sensory plasticity is across taxa, whether it occurs in multiple senses or both sexes within a species, and what potential modulatory substances and substrates are involved. Thus, studying modulation of sensory communication in a single species can provide valuable insights for understanding how sensory abilities can be altered to optimize detection of salient signals in different sensory channels and social contexts. The African cichlid fish Astatotilapia burtoni uses multimodal communication in social contexts such as courtship, territoriality, and parental care and shows plasticity in sensory abilities. In this review, we synthesize what is known about how visual, acoustic, and chemosensory communication is used in A. burtoni in inter- and intra-specific social contexts, how sensory funtion is modulated by an individual’s reproductive, metabolic, and social state, and discuss evidence for plasticity in potential modulators that may contribute to changes in sensory abilities and behaviors. Sensory plasticity in females is primarily associated with the natural reproductive cycle and functions to improve detection of courtship signals (visual, auditory, chemosensory, and likely mechanosensory) from high-quality males for reproduction. Plasticity in male sensory abilities seems to function in altering their ability to detect the status of other males in the service of territory ownership and future reproductive opportunities. Changes in different classes of potential modulators or their receptors (steroids, neuropeptides, and biogenic amines) occur at both peripheral sensory organs (eye, inner ear, and olfactory epithelium) and central visual, olfactory, and auditory processing regions, suggesting complex mechanisms contributing to plasticity of sensory function. This type of sensory plasticity revealed in males and females of A. burtoni is likely more widespread among diverse animals than currently realized, and future studies should take an integrative and comparative approach to better understand the proximate and ultimate mechanisms modulating communication abilities across taxa.
Discovering and Applying the Urban Rules of Life to Design Sustainable and Healthy Cities
Authors: Langen Tom A , Cannon Charles H , Blackburn David C , Morgan Eric L , Mera Paola E 
Published: May 2021

Synopsis
The city and its urban biome provides an extreme laboratory for studying fundamental biological questions and developing best practices for sustaining biodiverse and well-functioning ecological communities within anthropogenic built environments. We propose by studying urban organisms, urban biotic communities, the urban biome, and the interactions between the urban biome and peri-urban built and natural environments, we can (1) discover new “rules of life” for the structure, function, interaction, and evolution of organisms; (2) use these discoveries to understand how novel emerging biotic communities affect and are affected by anthropogenic environmental changes in climate and other environmental factors; and (3) apply what we have learned to engage residents of the urban biome, and design cities that are more biologically diverse, are provided with more and better ecosystem services, and are more equitable and healthier places to live. The built environment of the urban biome is a place that reflects history, economics, technology, governance, culture, and values of the human residents; research on and applications of the rules of life in the urban biome can be used by all residents in making choices about the design of the cities where they live. Because inhabitants are directly invested in the environmental quality of their neighborhoods, research conducted in and about the urban environment provides a great opportunity to engage wide and diverse communities of people. Given the opportunity to engage a broad constituency—from basic researchers to teachers, civil engineers, landscape planners, and concerned citizens—studying the translation of the rules of life onto the urban environment will result in an integrative and cross-cutting set of questions and hypotheses, and will foster a dialog among citizens about the focus of urban biome research and its application toward making more equitable, healthy, livable, sustainable, and biodiverse cities.
Next-generation regional ocean projections for living marine resource management in a changing climate
Authors: Drenkard Elizabeth J , Stock Charles , Ross Andrew C , Dixon Keith W , Adcroft Alistair , Alexander Michael , Balaji Venkatramani , Bograd Steven J , Butenschön Momme , Cheng Wei , Curchitser Enrique , Lorenzo Emanuele Di , Dussin Raphael , Haynie Alan C , Harrison Matthew , Hermann Albert , Hollowed Anne , Holsman Kirstin , Holt Jason , Jacox Michael G , Jang Chan Joo , Kearney Kelly A , Muhling Barbara A , Buil Mercedes Pozo , Saba Vincent , Sandø Anne Britt , Tommasi Désirée , Wang Muyin 
Published: May 2021

AbstractEfforts to manage living marine resources (LMRs) under climate change need projections of future ocean conditions, yet most global climate models (GCMs) poorly represent critical coastal habitats. GCM utility for LMR applications will increase with higher spatial resolution but obstacles including computational and data storage costs, obstinate regional biases, and formulations prioritizing global robustness over regional skill will persist. Downscaling can help address GCM limitations, but significant improvements are needed to robustly support LMR science and management. We synthesize past ocean downscaling efforts to suggest a protocol to achieve this goal. The protocol emphasizes LMR-driven design to ensure delivery of decision-relevant information. It prioritizes ensembles of downscaled projections spanning the range of ocean futures with durations long enough to capture climate change signals. This demands judicious resolution refinement, with pragmatic consideration for LMR-essential ocean features superseding theoretical investigation. Statistical downscaling can complement dynamical approaches in building these ensembles. Inconsistent use of bias correction indicates a need for objective best practices. Application of the suggested protocol should yield regional ocean projections that, with effective dissemination and translation to decision-relevant analytics, can robustly support LMR science and management under climate change.
Proliferation of peripheral blood mononuclear cells from healthy piglets after mitogen stimulation as indicators of disease resilience
Authors: Jeon Ryan L , Gilbert Caroline , Cheng Jian , Putz Austin M , Dyck Mike K , Plastow Graham S , Fortin Frederic ,   PigGen Canada, Dekkers Jack C M , Harding John C S 
Published: May 2021

AbstractDisease resilience refers to the productivity of an animal under disease. Given the high biosecurity of pig nucleus herds, traits that can be measured on healthy pigs and that are genetically correlated with disease resilience, that is, genetic indicator traits, offer a strategy to select for disease resilience. Our objective was to evaluate mitogen stimulation assays (MSAs) on peripheral blood mononuclear cells (PBMCs) from young healthy pigs as genetic indicators for disease resilience. Data were from a natural disease challenge in which batches of 60 or 75 naïve Yorkshire × Landrace piglets were introduced every 3 wk into a continuous flow barn that was seeded with multiple diseases. In this environment, disease resilience traits, including growth, treatment, and mortality rates, were recorded on 3,136 pigs that were genotyped with a high-density marker panel. PBMCs from 882 of these pigs from 19 batches were isolated from whole blood collected prior to the disease challenge and stimulated with five mitogens: concanavalin A (ConA), phytohemagglutinin (PHA), pokeweed mitogen (PWM), lipopolysaccharide (LPS), and phorbol myristate acetate (PMA). The proliferation of cells was evaluated at 48, 72, and 96 h and compared with unstimulated samples (rest count). Heritabilities of cell proliferation were estimated using a model with batch as a fixed effect and covariates of entry age; rest count; complete blood count proportions of lymphocytes, monocytes, eosinophils, and basophils; and pen, litter, and animal genetics as random effects. Heritability estimates were highest for response to ConA (0.30 ± 0.09, 0.28 ± 0.10, 0.17 ± 0.10, and 0.25 ±0.10 at 48, 72, and 96 h after stimulation and for area under the curve across the three time points, respectively). Estimates were in a similar range for response to PHA and PMA but low for PWM and LPS. Responses to ConA, PHA, and PMA were moderately genetically correlated with several disease resilience traits and in the expected direction, but individual estimates were not significantly different from zero due to large SEs. In conclusion, although validation is needed, MSAss, in particular based on ConA, show promise as genetic indicator traits for disease resilience.