bluuebunny/crossref_metadata_2025 huggingface dataset:
REM Sleep Behavior Disorder in Parkinson’s Disease: Change in Cognitive, Psychiatric, and Functional Outcomes from Baseline to 16–47-Month Follow-Up
Authors: Van Patten Ryan , Mahmood Zanjbeel , Pickell Delaney , Maye Jacqueline E , Roesch Scott , Twamley Elizabeth W , Filoteo J Vincent , Schiehser Dawn M
Published: May 2021

Objective

Rapid Eye Movement Sleep Behavior Disorder (RBD) is common in Parkinson’s Disease (PD) and is associated with cognitive impairment; however, the majority of the evidence on the impact of RBD on multidomain cognitive batteries in PD is cross-sectional. This study evaluated the longitudinal impact of probable RBD (pRBD) on cognitive, psychiatric, and functional outcomes in people with PD.

Method

Case–control study. A total of 65 people with PD completed the study protocol at baseline and 16-to-47-month follow-up. Participants were classified as pRBD+ (n = 25) or pRBD− (n = 40) based on an established cutoff of 6 on the RBD Sleep Questionnaire (RBDSQ). Participants also completed a) comprehensive cognitive testing, b) self-report measures of depression, anxiety, and apathy, and c) performance-based and other-report forms of instrumental activities of daily living.

Results

Baseline mean age was 67.8 (SD = 8.1; range = 45–86) and baseline mean years of education was 16.4 (SD = 2.1; range = 12–20). The two groups did not differ on measured demographic characteristics. Baseline mean T-scores for cognitive tests were in the average range (46–55). Hierarchical linear models tested group differences in cognitive and functional decline from baseline to follow-up, controlling for appropriate demographic and psychiatric variables. Compared to the pRBD− group, pRBD+ participants showed greater decline in attention/working memory (r = −0.31; p = 0.01) and UPSA financial skills (r = −0.31; p = 0.01). No other group differences approached significance.

Conclusions

RBD may differentially affect attention/working memory and financial abilities in PD. Results underscore the importance of regular RBD screening in older adults with PD in order to triage symptomatic patients to appropriate cognitive and medical interventions.
Deformation of Needle Tips During Facial Soft Tissue Filler Injections: An Electron-Microscopic Study
Authors: Pineiro Mildred Lopez , Green Jeremy B , Kaufman Joely , Blackwelder Patricia L , Freytag David L , Frank Konstantin , Alfertshofer Michael , Cotofana Sebastian
Published: May 2021

Background

Injectable soft tissue fillers are used on a global scale for a variety of aesthetic indications. Despite their widespread use, there is a dearth of information regarding needle deformation following injection procedures. Repeated injections with the same needle could lead to progressive needle tip deformation, potentially resulting in decreased precision and increased patient discomfort.

Objectives

The objective of this study was to quantify the magnitude of needle tip deformation utilizing scanning electron microscopy (SEM) image analysis.

Methods

An observational study was performed evaluating 4 differently sized needles following soft tissue filler injections for 5 different aesthetic indications (zygomatic arch, infraorbital, midcheek, nasolabial sulcus, and perioral) in patients aged 36 to 64 years. Following treatment, each needle was visualized and imaged through SEM, and the percentage of deformation in relation to the total amount of needle tip surface was calculated.

Results

The factor most influencing needle tip damage was revealed to be the number of injection passes, ie, dermal transitions. Per injection procedure, an increase in needle tip damage of 4.7% occurred. Touching the bone deformed the needle tip by 9.6% and an increase in needle size resulted in 0.13% more damage.

Conclusions

To the authors’ knowledge, this is the first SEM investigation to provide objective evidence for the deformation of needle tips after repeated facial soft tissue filler injections. These data may help improve patient safety and comfort during these minimally invasive procedures.

Level of Evidence: 3
Nonmalignant CD30+ Cells in Contralateral Peri-Implant Capsule of Patient With BIA-ALCL: A Premalignant Step?
Authors: Kadin Marshall E , Xu Haiying , Hunsicker Lisa M , Guan Yingjie
Published: May 2021

CD30 lymphocyte activation antigen and phosphorylated STAT3 (pSTAT3) are consistent markers of tumor cells in breast implant–associated anaplastic large cell lymphoma (BIA-ALCL). We present a case of BIA-ALCL in a breast implant capsule containing clustered tumor cells expressing CD30, pSTAT3, pSTAT6, interleukin 9, and granzyme B tumor cell biomarkers. Remarkably, the contralateral breast contained many scattered large, atypical CD30+ cells surrounded by inflammatory cells, raising a suspicion of bilateral BIA-ALCL, known to occur in some patients. To clarify the diagnosis, immunohistochemistry and multilabel immunofluorescence were performed. Unlike the tumor cells, the atypical CD30+ cells of the contralateral breast lacked pSTAT3, pSTAT6, interleukin 9, and granzyme B, eliminating a diagnosis of bilateral BIA-ALCL. This case highlights the importance of interpreting CD30 staining in the context of other tumor cell biomarkers and histopathology to avoid an incorrect diagnosis of BIA-ALCL. We believe the findings also suggest the possibility of CD30 expression as an early event in the multistep pathogenesis of BIA-ALCL.

Level of Evidence: 5
Influence of carbon source on wood decay-associated gene expression in sequential hyphal zones of the brown rot fungusGloeophyllum trabeum
Authors: Umezawa Kiwamu , Itakura Shuji
Published: May 2021

Brown rot fungi show a two-step wood degradation mechanism comprising oxidative radical-based and enzymatic saccharification systems. Recent studies have demonstrated that the brown rot fungus Rhodonia placenta expresses oxidoreductase genes ahead of glycoside hydrolase genes and spatially protects the saccharification enzymes from oxidative damage of the oxidoreductase reactions. This study aimed to assess the generality of the spatial gene regulation of these genes in other brown rot fungi and examine the effects of carbon source on the gene regulation. Gene expression analysis was performed on 14 oxidoreductase and glycoside hydrolase genes in the brown rot fungus Gloeophyllum trabeum, directionally grown on wood, sawdust-agar, and glucose-agar wafers. In G. trabeum, both oxidoreductase and glycoside hydrolase genes were expressed at higher levels in sections behind the wafers. The upregulation of glycoside hydrolase genes was significantly higher in woody substrates than in glucose, whereas the oxidoreductase gene expression was not affected by substrates.
SKSV: ultrafast structural variation detection from circular consensus sequencing reads
Authors: Liu Yadong , Jiang Tao , Su Junhao , Liu Bo , Zang Tianyi , Wang Yadong
Published: May 2021

Circular consensus sequencing reads are promising for the comprehensive detection of structural variants (SVs). However, alignment-based SV calling pipelines are computationally intensive due to the generation of complete read-alignments and its post-processing. Herein, we propose a SKeleton-based analysis toolkit for Structural Variation detection (SKSV). Benchmarks on real and simulated datasets demonstrate that SKSV has an order of magnitude of faster speed than state-of-the-art SV calling approaches; moreover, it achieves higher F1 scores for various types of SVs.

Availability and implementation

SKSV is available from https://github.com/ydLiu-HIT/SKSV.

Supplementary information

Supplementary data are available at Bioinformatics online.
The International Vertebrate Pet Trade Network and Insights from US Imports of Exotic Pets
Authors: Sinclair James S , Stringham Oliver C , Udell Bradley , Mandrak Nicholas E , Leung Brian , Romagosa Christina M , Lockwood Julie L
Published: May 2021

The international trade in exotic vertebrate pets provides key social and economic benefits but also drives associated ecological, ethical, and human health impacts. However, despite its clear importance, we currently lack a full understanding of the structure of the pet trade, hampering efforts to optimize its benefits while mitigating its negative effects. In the present article, we represent and review the structure of the pet trade as a network composed of different market actors (nodes) and trade flows (links). We identify key data gaps in this network that, if filled, would enable network analyses to pinpoint targets for management. As a case study of how data-informed networks can realize this goal, we quantified spatial and temporal patterns in pets imported to the United States. Our framework and case study illustrate how network approaches can help to inform and manage the effects of the growing demand for exotic pets.
Computer-assisted technology for enhanced abdominal surgery
Authors: O’Connell L. , Winter D. C.
Published: May 2021

The application of computer-based technology to surgery has the potential to enhance the accuracy and outcomes of surgical procedures and perioperative care. Such innovative technologies include the integration of artificial intelligence into surgical decision-making, and the use of three-dimensional (3D) visual imaging, other real-time imaging techniques, and 3D printing technology.
On the intersection between systemic infection, brain vascular dysfunction and dementia
Authors: Huuskonen Mikko T , Kisler Kassandra , Sagare Abhay P , Zlokovic Berislav V
Published: May 2021

This scientific commentary refers to ‘Systemic infection exacerbates cerebrovascular dysfunction in Alzheimer’s disease’ by Asby et al. (doi:10.1093/brain/awab094).
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data
Authors: Zanettini Claudio , Omar Mohamed , Dinalankara Wikum , Imada Eddie Luidy , Colantuoni Elizabeth , Parmigiani Giovanni , Marchionni Luigi
Published: May 2021

Since the beginning of the coronavirus disease-2019 (COVID-19) pandemic in 2020, there has been a tremendous accumulation of data capturing different statistics including the number of tests, confirmed cases and deaths. This data wealth offers a great opportunity for researchers to model the effect of certain variables on COVID-19 morbidity and mortality and to get a better understanding of the disease at the epidemiological level. However, in order to draw any reliable and unbiased estimate, models also need to take into account other variables and metrics available from a plurality of official and unofficial heterogenous resources. In this study, we introduce covid19census, an R package that extracts from many different repositories and combines together COVID-19 metrics and other demographic, environment- and health-related variables of the USA and Italy at the county and regional levels, respectively. The package is equipped with a number of user-friendly functions that dynamically extract the data over different timepoints and contains a detailed description of the included variables. To demonstrate the utility of this tool, we used it to extract and combine different county-level data from the USA, which we subsequently used to model the effect of diabetes on COVID-19 mortality at the county level, taking into account other variables that may influence such effects. In conclusion, it was observed that the ‘covid19census’ package allows to easily extract area-level data from both the USA and Italy using few functions. These comprehensive data can be used to provide reliable estimates of the effect of certain variables on COVID-19 outcomes.

Database URL: https://github.com/c1au6i0/covid19census
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

Echinobase (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

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

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

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

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 > 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 < 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 < 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

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

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

Synopsis

Intra- 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

Efforts 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

Disease 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.
Antibiotic resistance, antimicrobial residues, and bacterial community diversity in pasture-raised poultry, swine, and beef cattle manures
Authors: Rothrock Michael James , Min Byeng Ryel , Castleberry Lana , Waldrip Heidi , Parker David , Brauer David , Pitta Dipti , Indugu Nagaraju
Published: May 2021

Animal manure can be a source of antibiotic-resistant genes (ARGs) and pharmaceutical residues; however, few studies have evaluated the presence of ARG in pasture-raised animal production systems. The objective of this study was to examine changes in microbiome diversity and the presence of antibiotic residues (ABRs) on three farms that contained a diverse range of animal species: pasture-raised poultry (broiler and layer), swine, and beef cattle. Total bacterial communities were determined using 16S rRNA microbiome analysis, while specific ARGs (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR (real-time PCR). Results indicated that the ARG abundances (Sul1 [P < 0.05] and TetA [P < 0.001]) were higher in layer hen manures (16.5 × 10−4 and 1.4 × 10−4 µg kg−1, respectively) followed by broiler chickens (2.9 × 10−4 and 1.7 × 10−4 µg kg−1, respectively), swine (0.22 × 10−4 and 0.20 × 10−4 µg kg−1, respectively) and beef cattle (0.19 × 10−4 and 0.02 × 10−4 µg kg−1, respectively). Average fecal TetA ABR tended to be greater (P = 0.09) for broiler chickens (11.4 µg kg−1) than for other animal species (1.8 to 0.06 µg kg−1), while chlortetracycline, lincomycin, and oxytetracycline ABRs were similar among animal species. Furthermore, fecal microbial richness and abundances differed significantly (P < 0.01) both among farms and specific species of animal. This study indicated that the microbial diversity, ABR, ARG concentrations, and types in feces varied from farm-to-farm and from animal species-to-animal species. Future studies are necessary to perform detailed investigations of the horizontal transfer mechanism of antibiotic-resistant microorganisms (ARMs) and ARG.
Effects of genetic polymorphisms on the sulfation of doxorubicin by human SULT1C4 allozymes
Authors: Gohal Saud A , Rasool Mohammed I , Bairam Ahsan F , Alatwi Eid S , Alherz Fatemah A , Abunnaja Maryam S , El Daibani Amal A , Kurogi Katsuhisa , Liu Ming-Cheh
Published: May 2021

Doxorubicin is a chemotherapeutic drug widely utilized in cancer treatment. An enzyme critical to doxorubicin metabolism is the cytosolic sulfotransferase (SULT) SULT1C4. This study investigated the functional impact of SULT1C4 single nucleotide polymorphisms (SNPs) on the sulfation of doxorubicin by SULT1C4 allozymes. A comprehensive database search was performed to identify various SULT1C4 SNPs. Ten nonsynonymous SULT1C4 SNPs were selected, and the corresponding cDNAs, packaged in pGEX-2TK expression vector, were generated via site-directed mutagenesis. Respective SULT1C4 allozymes were bacterially expressed and purified by affinity chromatography. Purified SULT1C4 allozymes, in comparison with the wild-type enzyme, were analysed for sulphating activities towards doxorubicin and 4-nitrophenol, a prototype substrate. Results obtained showed clearly differential doxorubicin-sulphating activity of SULT1C4 allozymes, implying differential metabolism of doxorubicin through sulfation in individuals with distinct SULT1C4 genotypes.
Development and validation of a novel mRNA signature for predicting early relapse in non-small cell lung cancer
Authors: Lin Jingping , Weng Jinsen , Lin Shaofeng , Lin Cuibo , Huang Jieping , Zhang Chunxia , Zhang Shen , Dong Chuanpeng , Ji Haizhou , Ke Xi
Published: May 2021

Background

Recurrence after initial primary resection is still a major and ultimate cause of death for non-small cell lung cancer patients. We attempted to build an early recurrence associated gene signature to improve prognostic prediction of non-small cell lung cancer.

Methods

Propensity score matching was conducted between patients in early relapse group and long-term survival group from The Cancer Genome Atlas training series (N = 579) and patients were matched 1:1. Global transcriptome analysis was then performed between the paired groups to identify tumour-specific mRNAs. Finally, using LASSO Cox regression model, we built a multi-gene early relapse classifier incorporating 40 mRNAs. The prognostic and predictive accuracy of the signature was internally validated in The Cancer Genome Atlas patients.

Results

A total of 40 mRNAs were finally identified to build an early relapse classifier. With specific risk score formula, patients were classified into a high-risk group and a low-risk group. Relapse-free survival was significantly different between the two groups in both discovery (HR: 3.244, 95% CI: 2.338-4.500, P < 0.001) and internal validation series (HR 1.970, 95% CI 1.181-3.289, P = 0.009). Further analysis revealed that the prognostic value of this signature was independent of tumour stage, histotype and epidermal growth factor receptor mutation (P < 0.05). Time-dependent receiver operating characteristic analysis showed that the area under receiver operating characteristic curve of this signature was higher than TNM stage alone (0.771 vs 0.686, P < 0.05). Further, decision curve analysis curves analysis at 1 year revealed the considerable clinical utility of this signature in predicting early relapse.

Conclusions

We successfully established a reliable signature for predicting early relapse in stage I–III non-small cell lung cancer.
An Absolute Test of Racial Prejudice
Authors: Marx Philip
Published: May 2021

Disparities along racial and ethnic lines persist across domains. Distinguishing among the possible sources of such disparities matters. This article introduces an absolute test for identifying prejudice in the presence of statistical discrimination. In the context of police officers deciding whether to conduct vehicle searches, the key intuition of the test is that each officer’s search decisions and search outcomes generate a point on a concave “return possibility frontier,” (RPF) whose slope equals the officer’s search cost, or personal standard of evidence for conducting a search. Variation along a RPF provides information about search costs, and a discrepancy in these costs across drivers of different races constitutes prejudice. The model and test generalize and unify the existing literature, and the test can be partially extended to the setting where officers vary in the quality of their information, or discernment. Higher discernment generates an expansion of the frontier, and a version of the test remains valid for more discerning officers. Empirically, the test finds suggestive evidence of prejudice against Hispanic drivers and of varying discernment among officers of different races and ethnicities. These results are robust to (and not well explained by) officer experience. (JEL C26, K42, J15)
Demand for and Economic Value of Nonmotorized Boating Access in Rivers at US National Forests
Authors: Chapagain Binod P , Poudyal Neelam C , Bowker J M , Askew Ashley E , English Donald B K , Hodges Donald G
Published: May 2021

Nonmotorized boating (NMB) is a popular recreation activity in the US National Forest System. Previous studies on NMB were from an individual river or site, which limited aggregating benefit across the system or generalizing to rivers across the country. Further, whether and how site and river characteristics affect the use of rivers for NMB activities are unknown. This study combined trip data collected from visitor surveys across the system with spatially explicit data on river characteristics in a travel cost model, and in the analysis step, characterized the economic benefit of NMB access and evaluated the effect of site and river characteristics. Net economic benefit of NMB access was estimated to be in the range of $56 to $73 per trip, depending on the modeling assumptions used. When aggregated across visits over the country, the total annual economic value of NMB access in National Forest System ranged from $92 million to $120 million. Results further suggest that site and river characteristics including water velocity, ramp availability, and rapid level were significantly related to NMB demand. Results may be useful in highlighting the use and public value of NMB access in rivers and in understanding the importance of site and river characteristics.
Presentation, management and outcome of aorto-esophageal fistula in young patients: two case-reports and literature review
Authors: Al-Thani Hassan , Wahlen Bianca M , El-Menyar Ayman , Hussein Ahmed , Sadek Ahmed , Fares Amr , Saih Mohamed Musbah , Almulla Abdulwahid
Published: May 2021

Aorto-esophageal fistula (AEF) is a rare serious surgical event. The first case developed hematemesis 2 weeks post-sleeve gastrectomy. A covered esophageal stent was placed endoscopically. The esophageal stent implantation was followed by massive bleeding due to an AEF. A thoracic endovascular aortic repair (TEVAR) was performed. Aggravated by infection of the aortic stent, another massive bleed occurred after 1 year. The final procedure was resection of the descending aorta with reconstruction using a bovine pericardial patch. The second case presented with hematemesis post-motor vehicle accident. AEF was confirmed by aortogram and treated by TEVAR followed by fully covered esophageal stent. The patient declined definite surgery. In conclusion, initial endovascular approach is useful as a bridge procedure. Once the patient hemodynamics are stabilized, a definitive surgical repair is required. The post-repair infection and life-long antibiotics could be overcome by using bovine pericardial grafts.
Potential use of dermoscopy in atypical tungiasis
Authors: Flajoliet Nolwen , Bertolotti Antoine
Published: May 2021

Tungiasis is an ectoparasitic skin disease, endemic in the Caribbeans, South America and sub-Saharan Africa. Usually, the dark central pore is the most significant sign to confirm the diagnosis. We described an original presentation of a lateral genital opening tungiasis, highlighting the importance of dermoscopic examination when a patient returns from an endemic zone of this parasite.
Translating Public Health Recommendations Using the Army Design Methodology
Authors: Watkins Eren Y , Beymer Matthew R , Johnson Latoya , Ball Jacob D , Benedict Timothy , Ross Michael C , Bibio Desmond , Maule Alexis , Engen Christopher
Published: May 2021

The U.S. Army employs over 470,000 active duty soldiers throughout the world. Although the Army also employs hundreds of public health professionals, public health recommendations are often not framed in ways that are readily actionable to senior Army leaders. This case study shows how public health findings were translated into actionable recommendations using the Army Design Methodology (ADM) and subsequently implemented by installation leadership. Following a perceived increase in suicides at Fort Wainwright, Alaska, in 2019, installation leadership requested that the U.S. Army Public Health Center conduct an epidemiological consultation. A mixed-methods approach was used to gather qualitative and quantitative data. The ADM was used to translate the findings and provide actionable recommendations for senior Army leaders. Many recommendations were implemented within a year of the report’s release and included modifications to gym facilities, dining halls, and sleeping areas. Key improvements included the installation of $900,000 worth of new gym equipment in existing physical fitness facilities, increasing the basic daily food allowance by 44% to facilitate the purchase of healthy options, and the installation of blackout blinds in all barracks to ensure more restful sleep during times of peak sunlight. The ADM is well understood by senior Army leaders. Use of the ADM in future military-specific public health studies could ensure a more effective uptake and implementation of public health recommendations.
V680 Mon – a young mercury–manganese star in an eclipsing heartbeat system
Authors: Paunzen Ernst , Hümmerich Stefan , Fedurco Miroslav , Bernhard Klaus , Komžík Richard , Vaňko Martin
Published: May 2021

Chemically peculiar stars in eclipsing binary systems are rare objects that allow the derivation of fundamental stellar parameters and important information on evolutionary status and the origin of the observed chemical peculiarities. Here we present an investigation of the known eclipsing binary system BD+09 1467 = V680 Mon. Using spectra from the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) and own observations, we identify the primary component of the system as a mercury–manganese (HgMn/CP3) star (spectral type kB9 hB8 HeB9 V HgMn). Furthermore, photometric time series data from the Transiting Exoplanet Survey Satellite (TESS) indicate that the system is a ‘heartbeat star’, a rare class of eccentric binary stars with short-period orbits that exhibit a characteristic signature near the time of periastron in their light curves due to the tidal distortion of the components. Using all available photometric observations, we present an updated ephemeris and binary system parameters as derived from a modelling of the system with the elisa code, which indicate that the secondary star has an effective temperature of Teff = $8300_{-200}^{+200}$ (spectral type ∼A4). V680 Mon is only the fifth known eclipsing CP3 star, and the first one in a heartbeat binary. Furthermore, our results indicate that the star is located on the zero-age main sequence and a possible member of the open cluster NGC 2264. As such, it lends itself perfectly for detailed studies and may turn out to be a keystone in the understanding of the development of CP3 star peculiarities.