bluuebunny/crossref_metadata_2025 huggingface dataset:
Linking Terrestrial and Aquatic Biodiversity to Ecosystem Function Across Scales, Trophic Levels, and Realms
Authors: Dahlin Kyla M. , Zarnetske Phoebe L. , Read Quentin D. , Twardochleb Laura A. , Kamoske Aaron G. , Cheruvelil Kendra Spence , Soranno Patricia A.
Published: June 2021

Global declines in biodiversity have the potential to affect ecosystem function, and vice versa, in both terrestrial and aquatic ecological realms. While many studies have considered biodiversity-ecosystem function (BEF) relationships at local scales within single realms, there is a critical need for more studies examining BEF linkages among ecological realms, across scales, and across trophic levels. We present a framework linking abiotic attributes, productivity, and biodiversity across terrestrial and inland aquatic realms. We review examples of the major ways that BEF linkages form across realms–cross-system subsidies, ecosystem engineering, and hydrology. We then formulate testable hypotheses about the relative strength of these connections across spatial scales, realms, and trophic levels. While some studies have addressed these hypotheses individually, to holistically understand and predict the impact of biodiversity loss on ecosystem function, researchers need to move beyond local and simplified systems and explicitly investigate cross-realm and trophic interactions and large-scale patterns and processes. Recent advances in computational power, data synthesis, and geographic information science can facilitate studies spanning multiple ecological realms that will lead to a more comprehensive understanding of BEF connections.
Fire in Semi-Arid Shrublands and Woodlands: Spatial and Temporal Patterns in an Australian Landscape
Authors: van Etten Eddie J. B. , Davis Robert A. , Doherty Tim S.
Published: June 2021

Semi-arid landscapes are of interest to fire ecologists because they are generally located in the climatic transition zone between arid lands (where fires tend to be rare due to lack of fuel, but are enhanced following large rainfall episodes) and more mesic regions (where fire activity tends to be enhanced following severe rainfall deficits). Here we report on the characteristics of the contemporary fire regimes operating in a semi-arid region of inland south-western Australia with rainfall averaging around 300 mm per annum. To characterize fire regimes, we analyzed a geodatabase of fire scars (1960–2018) to derive fire preferences for each major vegetation type and fire episode and used known fire intervals to model fire hazard over time and calculate typical fire frequencies. We also used super epoch analysis and correlations to explore relationships between annual fire extent and rainfall received before the fire. We found fires strongly favored sandplain shrublands, and these tended to experience hot crown fires once every 100 years (median fire interval), with fire hazard increasing linearly over time. In contrast, fires were rare in eucalypt woodland and other vegetation types, with a median interval of 870 years and broadly consistent fire hazard over time. Annual fire extent was most strongly linked with high rainfall in the year prior to fire, and this was particularly so for eucalypt woodlands. Large-scale fires in shrublands tended to favor areas burnt in previous large fires, whereas in woodlands they favored edges. In conclusion, we found divergent fire regimes across the major vegetation types of the region. Sandplain shrublands were similar to Mediterranean shrublands in that they experienced intense stand-replacing wildfires which recovered vigorously although slowly, meaning burnt shrublands did not experience fires again for at least 25 and 100 years on average. In contrast, eucalypt woodlands were fire sensitive (trees readily killed by fire) and experienced fires mostly around the edges, spreading into core areas only after large rainfall events elevated fuel levels. Overall, both vegetation types subscribed to typical arid-zone fire regimes where elevated rainfall, and not drought, promoted fires, although the role of fuel accumulation over time was more important in the shrublands.
Exploring the Ecomorphology of Two Cretaceous Enantiornithines With Unique Pedal Morphology
Authors: Clark Alexander D. , O’Connor Jingmai K.
Published: June 2021

Recently, ∼100 Ma amber from Myanmar has become an important source of information regarding the morphology of Late Cretaceous enantiornithines. Two specimens consisting of partial hindlimbs exhibit unusual morphologies when compared to both extant avian taxa and other Cretaceous enantiornithines. Pedal morphology is extremely ecologically informative in Aves as it represents the interface between body and substrate. These seemingly bizarre pedal morphologies represent adaptations that allowed these birds to utilize certain niches present in their paleoenvironment. Specific ecological niches apply the same general pressures to different species over time, and in doing so, through natural selection, produce morphologies that function much the same, although they may be anatomically dissimilar. As such, extant animals can provide useful information pertaining to the functional morphology of extinct animals, even in the absence of direct analogs, as in the case of these two Hukawng enantiornithines. Comparisons to extant taxa in the same predicted niches of these enantiornithines can be used to either support or contradict previous hypotheses regarding thein vivofunction of these unique pedal morphologies.Elektorornis chenguangiexhibits a hypertrophied third pedal digit, originally interpreted as an appendage used for probing. We support this interpretation, which allows informed speculation as to the cranial anatomy of this taxon since extant animals that probe in woody substrates consistently pair elongate probing structures with a second robust structure that functions as a means to penetrate into this hard substrate. This suggests that the rostrum ofElektororniswould have been robust and most likely edentulous. The second specimen YLSNHM01001 exhibits an unusually mediolaterally robust fourth pedal digit, nearly double the width of digit II. Given that no such morphology is present in any other bird in the Mesozoic or Cenozoic we feel the unusual morphology justifies erection of a new taxon,Fortipesavis prehendensgen. et sp. nov. Although distinct, the morphology inF. prehendensresembles the syndactyl condition in some extant avian groups, and we hypothesize the robust digit similarly functioned to increase the surface area of the foot, facilitating grip on perches through increased friction. The necessity for increased grip and the lateral placement of this digit may suggestF. prehendensutilized mobile perches similar to extant kingfishers.
Citizen Science Data Collection for Integrated Wildlife Population Analyses
Authors: Sun Catherine C. , Hurst Jeremy E. , Fuller Angela K.
Published: June 2021

Citizen science, or community science, has emerged as a cost-efficient method to collect data for wildlife monitoring. To inform research and conservation, citizen science sampling designs should collect data that match the robust statistical analyses needed to quantify species and population patterns. Further increasing the contributions of citizen science, integrating citizen science data with other datasets and datatypes can improve population estimates and expand the spatiotemporal extent of inference. We demonstrate these points with a citizen science program called iSeeMammals developed in New York state in 2017 to supplement costly systematic spatial capture-recapture sampling by collecting opportunistic data from one-off observations, hikes, and camera traps. iSeeMammals has initially focused on the growing population of American black bear (Ursus americanus), with integrated analysis of iSeeMammals camera trap data with systematic data for a region with a growing bear population. The triumvirate of increased spatial and temporal coverage by at least twofold compared to systematic sampling, an 83% reduction in annual sampling costs, and improved density estimates when integrated with systematic data highlight the benefits of collecting presence-absence data in citizen science programs for estimating population patterns. Additional opportunities will come from applying presence-only data, which are oftentimes more prevalent than presence-absence data, to integrated models. Patterns in data submission and filtering also emphasize the importance of iteratively evaluating patterns in engagement, usability, and accessibility, especially focusing on younger adult and teenage demographics, to improve data quality and quantity. We explore how the development and use of integrated models may be paired with citizen science project design in order to facilitate repeated use of datasets in standalone and integrated analyses for supporting wildlife monitoring and informing conservation.
Effects of Simulated Heat Wave on Oxidative Physiology and Immunity in Asian Yellow Pond Turtle (Mauremys mutica)
Authors: Li Shuran , Li Jinhuan , Chen Wei , Xu Zhiwang , Xie Lei , Zhang Yongpu
Published: June 2021

Global warming has led to an increase in the frequency, duration, and intensity of heat waves in the summer, which can cause frequent and acute heat stress on ectotherms. Thus, determining how ectothermic animals respond to heat waves has been attracting growing interest among ecologists. However, the physiological and biochemical responses to heat waves in reptiles, especially aquatic reptiles, are still poorly understood. The current study investigated the oxidant physiology, immunity, and expression levels of heat shock proteins (HSP) mRNA after exposure to a simulated heat wave (1 week, 35 ± 4°C), followed by a recovery period (1 week, 28 ± 4°C) in juvenile Asian yellow pond turtle (Mauremys mutica), a widely farmed aquatic turtle in East Asia. The contents of malondialdehyde (MDA) in the liver and muscle were not significantly affected by the heat wave or recovery. Of all antioxidant enzymes, only the activity of glutathione peroxidase (GSH-Px) in muscles increased after heat wave, while the total superoxide dismutase (T-SOD), catalase activity (CAT), and total antioxidant capacity (T-AOC) did not change during the study. The organo-somatic index for the liver and spleen of M. mutica decreased after the heat wave but increased to the initial level after recovery. In contrast, plasma lysozyme activity and serum complement C4 levels increased after the heat wave, returning to the control level after recovery. In addition, heat waves did not alter the relative expression of HSP60, HSP70, and HSP90 mRNA in the liver. Eventually, heat wave slightly increased the IBR/n index. Therefore, our results suggested that heat waves did not lead to oxidative damage to lipids in M. mutica, but deleteriously affected the turtles’ immune organs. Meanwhile, the constitutive levels of most antioxidative enzyme activities, HSPs and enhanced blood immune functions might protect the turtles from the threat of heat waves under the current climate scenarios.
Associations Between Sleep Quality and Health Span: A Prospective Cohort Study Based on 328,850 UK Biobank Participants
Authors: Sambou Muhammed Lamin , Zhao Xiaoyu , Hong Tongtong , Fan Jingyi , Basnet Til Bahadur , Zhu Meng , Wang Cheng , Hang Dong , Jiang Yue , Dai Juncheng
Published: June 2021

Objective

To examine the associations between sleep quality and health span using a prospective cohort design based on the UK Biobank (UKB).

Materials and Methods

This longitudinal cohort study enrolled 328,850 participants aged between 37 and 73 years from UKB to examine the associations between sleep quality and risk of terminated health span. End of health span was defined by eight events strongly associated with longevity (cancer, death, congestive heart failure, myocardial infarction, chronic obstructive pulmonary disease, stroke, dementia, and diabetes), and a sleep score was generated according to five sleep behavioral factors (sleep duration, chronotype, sleeplessness, daytime sleepiness, and snoring) to characterize sleep quality. The hazard ratio (HR) and 95% confidence intervals (CIs) were calculated by multivariate-adjusted Cox proportional hazards model. Moreover, we calculated population attributable risk percentage (PAR%) to reflect the public health significance of healthy sleep quality.

Results

Compared with poor sleep quality, participants with healthy sleep quality had a 15% (HR: 0.85, 95% CI: 0.81–0.88) reduced risk of terminated health span, and those of less-healthy sleep quality had a 12% (HR: 0.88, 95% CI: 0.85–0.92) reduced risk. Linear trend results indicated that the risk of terminated health span decreased by 4% for every additional sleep score. Nearly 15% health span termination events in this cohort would have been prevented if a healthy sleep behavior pattern was adhered to (PAR%: 15.30, 95% CI: 12.58–17.93).

Conclusion

Healthy sleep quality was associated with a reduced risk of premature end of health span, suggesting healthy sleep behavior may extend health span. However, further studies are suggested for confirmation of causality and potential mechanism.
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme
Authors: Kalya Manasa , Kel Alexander , Wlochowitz Darius , Wingender Edgar , Beißbarth Tim
Published: June 2021

Only 2% of glioblastoma multiforme (GBM) patients respond to standard therapy and survive beyond 36 months (long-term survivors, LTS), while the majority survive less than 12 months (short-term survivors, STS). To understand the mechanism leading to poor survival, we analyzed publicly available datasets of 113 STS and 58 LTS. This analysis revealed 198 differentially expressed genes (DEGs) that characterize aggressive tumor growth and may be responsible for the poor prognosis. These genes belong largely to the Gene Ontology (GO) categories “epithelial-to-mesenchymal transition” and “response to hypoxia.” In this article, we applied an upstream analysis approach that involves state-of-the-art promoter analysis and network analysis of the dysregulated genes potentially responsible for short survival in GBM. Binding sites for transcription factors (TFs) associated with GBM pathology like NANOG, NF-κB, REST, FRA-1, PPARG, and seven others were found enriched in the promoters of the dysregulated genes. We reconstructed the gene regulatory network with several positive feedback loops controlled by five master regulators [insulin-like growth factor binding protein 2 (IGFBP2), vascular endothelial growth factor A (VEGFA), VEGF165, platelet-derived growth factor A (PDGFA), adipocyte enhancer-binding protein (AEBP1), and oncostatin M (OSMR)], which can be proposed as biomarkers and as therapeutic targets for enhancing GBM prognosis. A critical analysis of this gene regulatory network gives insights into the mechanism of gene regulation by IGFBP2 via several TFs including the key molecule of GBM tumor invasiveness and progression, FRA-1. All the observations were validated in independent cohorts, and their impact on overall survival has been investigated.
Ovine FABP4 Variation and Its Association With Flystrike Susceptibility
Authors: Burrows L. E. R. , Zhou H. , Frampton C. M. A. , Forrest R. H. J. , Hickford J. G. H.
Published: June 2021

Flystrike is a major cost and a welfare issue for the New Zealand sheep industry. There are several factors that can predispose sheep to flystrike, such as having fleecerot, a urine-stained breech, and “dags” (an accumulation of fecal matter in the wool of the breech). The FABP4 gene (FABP4) has been associated with variation in ovine fleecerot resistance, with a strong genetic correlation existing between fleecerot and flystrike occurrence. In this study, blood samples were collected from sheep with and without flystrike for DNA typing. PCR-SSCP analyses were used to genotype two regions of ovine FABP4. Sheep with the A1 variant of FABP4 were found to be less likely (odds ratio 0.689, P = 0.014) to have flystrike than those without A1. The likelihood of flystrike occurrence decreased as copy number of A1 increased (odds ratio 0.695, P = 0.006). This suggests that FABP4 might be a candidate gene for flystrike resilience in sheep, although further research is required to verify this association.
Differentially Expressed MiRNAs of Goat Submandibular Glands Among Three Developmental Stages Are Involved in Immune Functions
Authors: Wang Aili , Ji Zhibin , Xuan Rong , Zhao Xiaodong , Hou Lei , Li Qing , Chu Yunpeng , Chao Tianle , Wang Jianmin
Published: June 2021

Submandibular glands (SMGs) are one of the primary components of salivary glands in goats. The proteins and biologically active substances secreted by the SMGs change with growth and development. Our previous studies showed that most of the differentially expressed genes in the SMGs of goats at different developmental stages are involved in immune-related signaling pathways, but the miRNA expression patterns in the same tissues are unknown. The aim of this study was to reveal the expression profile of miRNAs at three different developmental stages, detect differentially expressed miRNAs (DE miRNAs) and predict disease-related DE miRNAs. SMG tissue samples were collected from groups of 1-month-old kids, 12-month-old maiden goats and 24-month-old adult goats (three samples from each group), and high-throughout transcriptome sequencing was conducted. A total of 178, 241 and 7 DE miRNAs were discovered between 1-month-old kids and 12-month-old maiden goats, between 1-month-old kids and 24-month-old adult goats, and between 12-month-old maiden goats and 24-month-old adult goats, respectively. Among these DE miRNAs, 88 DE miRNAs with medium or high expression levels (TPM ≥50) were classified into five expression pattern clusters. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that some of the predicted target genes of the DE miRNAs in the five clusters were enriched in disease-related GO terms and pathways. MiRNA target genes in significant pathways were significantly enriched in Hepatitis B (FDR = 9.03E-10) and Pathways in cancer (FDR = 4.2E-10). Further analysis was performed with a PPI network, and 10 miRNAs were predicted to play an important role in the occurrence and prevention of diseases during the growth and development of goats.
Scalable and Robust Regression Methods for Phenome-Wide Association Analysis on Large-Scale Biobank Data
Authors: Bi Wenjian , Lee Seunggeun
Published: June 2021

With the advances in genotyping technologies and electronic health records (EHRs), large biobanks have been great resources to identify novel genetic associations and gene-environment interactions on a genome-wide and even a phenome-wide scale. To date, several phenome-wide association studies (PheWAS) have been performed on biobank data, which provides comprehensive insights into many aspects of human genetics and biology. Although inspiring, PheWAS on large-scale biobank data encounters new challenges including computational burden, unbalanced phenotypic distribution, and genetic relationship. In this paper, we first discuss these new challenges and their potential impact on data analysis. Then, we summarize approaches that are scalable and robust in GWAS and PheWAS. This review can serve as a practical guide for geneticists, epidemiologists, and other medical researchers to identify genetic variations associated with health-related phenotypes in large-scale biobank data analysis. Meanwhile, it can also help statisticians to gain a comprehensive and up-to-date understanding of the current technical tool development.
Dietary Supplementation With Eicosapentaenoic Acid Inhibits Plasma Cell Differentiation and Attenuates Lupus Autoimmunity
Authors: Kobayashi Azusa , Ito Ayaka , Shirakawa Ibuki , Tamura Atsushi , Tomono Susumu , Shindou Hideo , Hedde Per Niklas , Tanaka Miyako , Tsuboi Naotake , Ishimoto Takuji , Akashi-Takamura Sachiko , Maruyama Shoichi , Suganami Takayoshi
Published: June 2021

Accumulating evidence suggests that cholesterol accumulation in leukocytes is causally associated with the development of autoimmune diseases. However, the mechanism by which fatty acid composition influences autoimmune responses remains unclear. To determine whether the fatty acid composition of diet modulates leukocyte function and the development of systemic lupus erythematosus, we examined the effect of eicosapentaenoic acid (EPA) on the pathology of lupus in drug-induced and spontaneous mouse models. We found that dietary EPA supplementation ameliorated representative lupus manifestations, including autoantibody production and immunocomplex deposition in the kidneys. A combination of lipidomic and membrane dynamics analyses revealed that EPA remodels the lipid composition and fluidity of B cell membranes, thereby preventing B cell differentiation into autoantibody-producing plasma cells. These results highlight a previously unrecognized mechanism by which fatty acid composition affects B cell differentiation into autoantibody-producing plasma cells during autoimmunity, and imply that EPA supplementation may be beneficial for therapy of lupus.
Metformin-Inducible Small Heterodimer Partner Interacting Leucine Zipper Protein Ameliorates Intestinal Inflammation
Authors: Yang SeungCheon , Park Jin-Sil , Hwang Sun-Hee , Cho Keun-Hyung , Na Hyun Sik , Choi JeongWon , Jhun Jooyeon , Kim Seung-Jun , Lee Bo-In , Park Sung-Hwan , Cho Mi-La
Published: June 2021

Small heterodimer partner interacting leucine zipper protein (SMILE) is an orphan nuclear receptor and a member of the bZIP family of proteins. We investigated the mechanism by which SMILE suppressed the development of inflammatory bowel disease (IBD) using a DSS-induced colitis mouse model and peripheral blood mononuclear cells (PBMCs) from patients with ulcerative colitis (UC). Metformin, an antidiabetic drug and an inducer of AMPK, upregulated the level of SMILE in human intestinal epithelial cells and the number of SMILE-expressing cells in colon tissues from DSS-induced colitis mice compared to control mice. Overexpression of SMILE using a DNA vector reduced the severity of DSS-induced colitis and colitis-associated intestinal fibrosis compared to mock vector. Furthermore, SMILE transgenic mice showed ameliorated DSS-induced colitis compared with wild-type mice. The mRNA levels of SMILE and Foxp3 were downregulated and SMILE expression was positively correlated with Foxp3 in PBMCs from patients with UC and an inflamed mucosa. Metformin increased the levels of SMILE, AMPK, and Foxp3 but decreased the number of interleukin (IL)-17–producing T cells among PBMCs from patients with UC. These data suggest that SMILE exerts a therapeutic effect on IBD by modulating IL-17 production.
Iron Oxide Nanoparticles in Bioimaging – An Immune Perspective
Authors: Geppert Mark , Himly Martin
Published: June 2021

Iron oxide nanoparticles (IONPs) bear big hopes in nanomedicine due to their (potential) applications in tumor therapy, drug delivery or bioimaging. However, as foreign entities, such particles may be recognized by the immune system and, thus, lead to inflammation, hypersensitivity or anaphylactic shock. In addition, an overload with iron is known to cause oxidative stress. In this short review, we summarize the biological effects of such particles with a major focus on IONP-formulations used for bioimaging purposes and their effects on the human immune system. We conclude that especially the characteristics of the particles (size, shape, surface charge, coating, etc.) as well as the presence of bystander substances, such as bacterial endotoxin are important factors determining the resulting biological and immunological effects of IONPs. Further studies are needed in order to establish clear structure-activity relationships.
Retinoic Acid: A New Old Friend of IL-17A in the Immune Pathogeny of Liver Fibrosis
Authors: Kartasheva-Ebertz Daria M. , Pol Stanislas , Lagaye Sylvie
Published: June 2021

Despite all the medical advances mortality due to cirrhosis and hepatocellular carcinoma, the end stages of fibrosis, continuously increases. Recent data suggest that liver fibrosis is guided by type 3 inflammation with IL-17A at the top of the line. The storage of vitamin A and its active metabolites, as well as genetics, can influence the development and progression of liver fibrosis and inflammation. Retinoic acid (active metabolite of vitamin A) is able to regulate the differentiation of IL-17A+/IL-22–producing cells as well as the expression of profibrotic markers. IL-17A and its pro-fibrotic role in the liver is the most studied, while the interaction and communication between IL-17A, IL-22, and vitamin A–active metabolites has not been investigated. We aim to update what is known about IL-17A, IL-22, and retinoic acid in the pathobiology of liver diseases.
Mechanism of the Immunomodulatory Effect of the Combination of Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus on Immunocompromised Rats
Authors: Lv Longxian , Mu Deguang , Du Yiling , Yan Ren , Jiang Huiyong
Published: June 2021

Immunodeficiency is a very common condition in suboptimal health status and during the development or treatment of many diseases. Recently, probiotics have become an important means for immune regulation. The present study aimed to investigate the mechanism of the immunomodulatory effect of a combination of live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus (CBLEB), which is a drug used by approximately 10 million patients every year, on cyclophosphamide-immunosuppressed rats. Cyclophosphamide (40 mg/kg) was intraperitoneally injected to induce immunosuppression in a rat model on days 1, 2, 3, and 10. Starting from day 4, the rats were continuously gavaged with CBLEB solution for 15 days. The samples were collected to determine routine blood test parameters, liver and kidney functions, serum cytokine levels, gut microbiota, fecal and serum metabolomes, transcriptomes, and histopathological features. The results indicated that CBLEB treatment reduced cyclophosphamide-induced death, weight loss, and damage to the gut, liver, spleen, and lungs and eliminated a cyclophosphamide-induced increase in the mean hemoglobin content and GGT, M-CSF, and MIP-3α levels and a decrease in the red blood cell distribution width and total protein and creatinine levels in the blood. Additionally, CBLEB corrected cyclophosphamide-induced dysbiosis of the gut microbiota and eliminated all cyclophosphamide-induced alterations at the phylum level in rat feces, including the enrichment in Proteobacteria, Fusobacteriota, and Actinobacteriota and depletion of Spirochaetota and Cyanobacteria. Furthermore, CBLEB treatment alleviated cyclophosphamide-induced alterations in the whole fecal metabolome profile, including enrichment in 1-heptadecanol, succinic acid, hexadecane-1,2-diol, nonadecanoic acid, and pentadecanoic acid and depletion of benzenepropanoic acid and hexane. CBLEB treatment also alleviated cyclophosphamide-induced enrichment in serum D-lyxose and depletion of serum succinic acid, D-galactose, L-5-oxoproline, L-alanine, and malic acid. The results of transcriptome analysis indicated that the mechanism of the effect of CBLEB was related to the induction of recovery of cyclophosphamide-altered carbohydrate metabolism and signal transduction. In conclusion, the present study provides an experimental basis and comprehensive analysis of application of CBLEB for the treatment of immunodeficiency.
Body Composition of Common Bottlenose Dolphins in Sarasota Bay, Florida
Authors: Adamczak Stephanie K. , Holser Rachel R. , Costa Daniel P. , Berens McCabe Elizabeth J. , Wells Randall S.
Published: June 2021

Marine mammal body composition has been an important tool that is used as a proxy for the health and condition of individuals within a population. Common bottlenose dolphin (Tursiops truncatus) body composition is influenced by variations in blubber thickness resulting from changes in temperature, prey availability, health, and life-history traits. We examined how environmental, ontogenetic, and reproductive variables influenced the body composition of common bottlenose dolphins in Sarasota Bay using data collected from a long-term monitoring project by the Sarasota Dolphin Research Program (SDRP). We found that both sea surface temperature (SST) and catch per unit effort (CPUE), used as a proxy for prey availability, influenced body composition. There was a high degree of seasonality in body composition, with higher values occurring in winter when SST and CPUE were both low. Ontogeny also greatly influenced body composition, as younger dolphins typically had thicker blubber than mature individuals. Interestingly, young females allocated more energy to allometric growth than deposition of blubber for body composition when compared to young males. However, as females matured and their growth slowed, they invested more in body composition. We found no significant difference in body composition of females of varying reproductive states, providing further evidence of their status as true income breeders. Our work highlights that changes in body composition result from fluctuations in environmental variables and that energy allocation to body composition changes with ontogeny.
Application of Three Deep Learning Schemes Into Oceanic Eddy Detection
Authors: Xu Guangjun , Xie Wenhong , Dong Changming , Gao Xiaoqian
Published: June 2021

Recent years have witnessed the increase in applications of artificial intelligence (AI) into the detection of oceanic features. Oceanic eddies, ubiquitous in the global ocean, are important in the transport of materials and energy. A series of eddy detection schemes based on oceanic dynamics have been developed while the AI-based eddy identification scheme starts to be reported in literature. In the present study, to find out applicable AI-based schemes in eddy detection, three AI-based algorithms are employed in eddy detection, including the pyramid scene parsing network (PSPNet) algorithm, the DeepLabV3+ algorithm and the bilateral segmentation network (BiSeNet) algorithm. To justify the AI-based eddy detection schemes, the results are compared with one dynamic-based eddy detection method. It is found that more eddies are identified using the three AI-based methods. The three methods’ results are compared in terms of the numbers, sizes and lifetimes of detected eddies. In terms of eddy numbers, the PSPNet algorithm identifies the largest number of ocean eddies among the three AI-based methods. In terms of eddy sizes, the BiSeNet can find more large-scale eddies than the two other methods, because the Spatial Path is introduced into the algorithm to avoid destroying the eddy edge information. Regarding eddy lifetimes, the DeepLabV3+ cannot track longer lifetimes of ocean eddies.
Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016
Authors: Hu Yujie , Nguyen Scott V. , Wang Wei , Gan Xin , Dong Yinping , Liu Chang , Cui Xinnan , Xu Jin , Li Fengqin , Fanning Séamus
Published: June 2021

The mcr-1 gene mediating mobile colistin resistance in Escherichia coli was first reported in China in 2016 followed by reports among different species worldwide, especially in E. coli and Klebsiella. However, data on its transmission in Salmonella are still lacking. This study analyzed the antimicrobial resistance (AMR) profiles and the mcr-1 gene presence in 755 foodborne Salmonella from 26 provinces of mainland, China in 2016. Genomic features of two mcr-1-carrying isolates, genome sequencing, serotypes and further resistance profiles were studied. Among the 755 Salmonella tested, 72.6% were found to be resistant to at least one antimicrobial agent and 10% were defined as multi-drug resistant (MDR). Salmonella Derby CFSA231 and Salmonella Typhimurium CFSA629 were mcr-1-harboring isolates. Both expressed an MDR phenotype and included a single circular chromosome and one plasmid. Among the 22 AMR genes identified in S. Derby CFSA231, only the mcr-1 gene was localized on the IncX4 type plasmid pCFSA231 while 20 chromosomal AMR genes, including four plasmid-mediated quinolone resistance (PMQR) genes, were mapped within a 64 kb Salmonella genomic island (SGI) like region. S. Typhimurium CFSA629 possessed 11 resistance genes including an mcr-1.19 variant and two ESBL genes. Two IS26-flanked composite-like transposons were identified. Additionally, 153 and 152 virulence factors were separately identified in these two isolates with secretion system and fimbrial adherence determinants as the dominant virulence classes. Our study extends our concern on mcr-1-carrying Salmonella in regards to antimicrobial resistance and virulence factors, and highlight the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella.
Debaryomyces hansenii Strains Isolated From Danish Cheese Brines Act as Biocontrol Agents to Inhibit Germination and Growth of Contaminating Molds
Authors: Huang Chuchu , Zhang Ling , Johansen Pernille Greve , Petersen Mikael Agerlin , Arneborg Nils , Jespersen Lene
Published: June 2021

The antagonistic activities of native Debaryomyces hansenii strains isolated from Danish cheese brines were evaluated against contaminating molds in the dairy industry. Determination of chromosome polymorphism by use of pulsed-field gel electrophoresis (PFGE) revealed a huge genetic heterogeneity among the D. hansenii strains, which was reflected in intra-species variation at the phenotypic level. 11 D. hansenii strains were tested for their ability to inhibit germination and growth of contaminating molds, frequently occurring at Danish dairies, i.e., Cladosporium inversicolor, Cladosporium sinuosum, Fusarium avenaceum, Mucor racemosus, and Penicillium roqueforti. Especially the germination of C. inversicolor and P. roqueforti was significantly inhibited by cell-free supernatants of all D. hansenii strains. The underlying factors behind the inhibitory effects of the D. hansenii cell-free supernatants were investigated. Based on dynamic headspace sampling followed by gas chromatography-mass spectrometry (DHS-GC-MS), 71 volatile compounds (VOCs) produced by the D. hansenii strains were identified, including 6 acids, 22 alcohols, 15 aldehydes, 3 benzene derivatives, 8 esters, 3 heterocyclic compounds, 12 ketones, and 2 phenols. Among the 71 identified VOCs, inhibition of germination of C. inversicolor correlated strongly with three VOCs, i.e., 3-methylbutanoic acid, 2-pentanone as well as acetic acid. For P. roqueforti, two VOCs correlated with inhibition of germination, i.e., acetone and 2-phenylethanol, of which the latter also correlated strongly with inhibition of mycelium growth. Low half-maximal inhibitory concentrations (IC50) were especially observed for 3-methylbutanoic acid, i.e., 6.32–9.53 × 10–5 and 2.00–2.67 × 10–4 mol/L for C. inversicolor and P. roqueforti, respectively. For 2-phenylethanol, a well-known quorum sensing molecule, the IC50 was 1.99–7.49 × 10–3 and 1.73–3.45 × 10–3 mol/L for C. inversicolor and P. roqueforti, respectively. For acetic acid, the IC50 was 1.35–2.47 × 10–3 and 1.19–2.80 × 10–3 mol/L for C. inversicolor and P. roqueforti, respectively. Finally, relative weak inhibition was observed for 2-pentanone and acetone. The current study shows that native strains of D. hansenii isolated from Danish brines have antagonistic effects against specific contaminating molds and points to the development of D. hansenii strains as bioprotective cultures, targeting cheese brines and cheese surfaces.
Bacterial Inoculants Mitigating Water Scarcity in Tomato: The Importance of Long-Term in vivo Experiments
Authors: Riva Valentina , Mapelli Francesca , Dragonetti Giovanna , Elfahl Mustafa , Vergani Lorenzo , Crepaldi Paola , La Maddalena Nicola , Borin Sara
Published: June 2021

Global population growth and climate change raise a challenge to agriculture, which, combined with the issues concerning the use of chemical fertilizers, have generated increasing attention in the use of plant-associated bacteria as a sustainable strategy in agri-food systems. The objective of this study is to evaluate the ability of five bacterial strains, previously isolated from the rhizosphere or endosphere of plants adapted to harsh environmental conditions, to act as potential plant biofertilizers in different conditions of water availability. The strain biosafety for a deliberate environmental release was investigated through a literature survey and antibiotic resistance testing. The selected strains were first characterized for their plant growth–promoting (PGP) and rhizocompetence-related traits through in vitro assays and then on short-term in vivo experiments on tomato plants. A long-term greenhouse experiment was further conducted to monitor the PGP effect of the bacteria during the entire life cycle of tomato plants subjected to full irrigation or to severe water deficit conditions, aiming to assess their actual effect on plant productivity, which is the ultimate target of the agricultural sector. Some of the strains showed a potential in improving water use efficiency and mitigating plant water stress. Under severe irrigation deficit, four of the tested strains, Micrococcus yunnanensis M1, Bacillus simplex RP-26, Pseudomonas stutzeri SR7-77, and Paenarthrobacter nitroguajacolicus 2–50, significantly increased the number of productive plants in comparison to non-bacterized control ones. Two of them, Bacillus simplex RP-26 and Paenarthrobacter nitroguajacolicus 2–50, demonstrated also, under full irrigation, to significantly improve the water productivity in comparison with non-bacterized plants. Despite all the strains showed promising PGP potential in short-term assays, the positive effect of the bacterial inoculants on plant physiology and fruit yield was observed in some cases but never corroborated by statistical significance. These results highlight the importance of performing long-term in vivo experiments to define the real PGP ability of a bacterial inoculant to positively impact plant production.
Potential Utilization of APOBEC3-Mediated Mutagenesis for an HIV-1 Functional Cure
Authors: Ikeda Terumasa , Yue Yuan , Shimizu Ryo , Nasser Hesham
Published: June 2021

The introduction of combination antiretroviral therapy (cART) has managed to control the replication of human immunodeficiency virus type 1 (HIV-1) in infected patients. However, a complete HIV-1 cure, including a functional cure for or eradication of HIV-1, has yet to be achieved because of the persistence of latent HIV-1 reservoirs in adherent patients. The primary source of these viral reservoirs is integrated proviral DNA in CD4+ T cells and other non-T cells. Although a small fraction of this proviral DNA is replication-competent and contributes to viral rebound after the cessation of cART, >90% of latent viral reservoirs are replication-defective and some contain high rates of G-to-A mutations in proviral DNA. At least in part, these high rates of G-to-A mutations arise from the APOBEC3 (A3) family proteins of cytosine deaminases. A general model has shown that the HIV-1 virus infectivity factor (Vif) degrades A3 family proteins by proteasome-mediated pathways and inactivates their antiviral activities. However, Vif does not fully counteract the HIV-1 restriction activity of A3 family proteins in vivo, as indicated by observations of A3-mediated G-to-A hypermutation in the proviral DNA of HIV-1-infected patients. The frequency of A3-mediated hypermutation potentially contributes to slower HIV-1/AIDS disease progression and virus evolution including the emergence of cytotoxic T lymphocyte escape mutants. Therefore, combined with other strategies, the manipulation of A3-mediated mutagenesis may contribute to an HIV-1 functional cure aimed at cART-free remission. In this mini-review, we discuss the possibility of an HIV-1 functional cure arising from manipulation of A3 mutagenic activity.
Role of Calpain-1 in Neurogenesis
Authors: Baudry Michel , Su Wenyue , Seinfeld Jeffrey , Sun Jiandong , Bi Xiaoning
Published: June 2021

While calpains have been implicated in neurogenesis for a long time, there is still little information regarding the specific contributions of various isoforms in this process. We took advantage of the availability of mutant mice with complete deletion of calpain-1 to analyze its contribution to neurogenesis. We first used the incorporation of BrdU in newly-generated cells in the subgranular zone of the dentate gyrus to determine the role of calpain-1 deletion in neuronal proliferation. Our results showed that the lack of calpain-1 decreased the rate of cell proliferation in adult hippocampus. As previously shown, it also decreased the long-term survival of newly-generated neurons. We also used data from previously reported RNA and miRNA sequencing analyses to identify differentially expressed genes in brain of calpain-1 knock-out mice related to cell division, cell migration, cell proliferation and cell survival. A number of differentially expressed genes were identified, which could play a significant role in the changes in neurogenesis in calpain-1 knock out mice. The results provide new information regarding the role of calpain-1 in neurogenesis and have implications for better understanding the pathologies associated with calpain-1 mutations in humans.
Age-Related Alterations in DTI Metrics in the Human Brain—Consequences for Age Correction
Authors: Behler Anna , Kassubek Jan , Müller Hans-Peter
Published: June 2021

Background: Over the life span, the diffusion metrics in brain MRI show different, partly nonlinear changes. These age-dependent changes also seem to exhibit regional differences with respect to the brain anatomy. The age correction of a study cohort's diffusion metrics might thus require consideration of age-related factors.

Methods: Diffusion tensor imaging data sets were acquired from 219 healthy participants at ages between 19 and 81 years. Fractional anisotropy (FA), mean diffusivity (MD), and axial and radial diffusivity (AD and RD, respectively) maps were analyzed by a tract of interest-based fiber tracking approach. To describe diffusion metrics as a function of the participant age, linear splines were used to perform curve fitting in 21 specific tract systems covering different functional areas and diffusion directions.

Results: In the majority of tracts, an interpolation with a change of alteration rate during adult life described the diffusion properties more accurately than a linear model. Consequently, the diffusion properties remained relatively stable until a decrease (of FA) or increase (of MD, AD, and RD) started at a region-specific time point, whereas a uniform change of diffusion properties was observed only in a few tracts. Single tracts, e.g., located in the cerebellum, remained nearly unaltered throughout the ages between 19 and 81 years.

Conclusions: Age corrections of diffusion properties should not be applied to all white matter regions and all age spans in the same way. Therefore, we propose three different approaches for age correction based on fiber tracking techniques, i.e., no correction for areas that do not experience age-related changes and two variants of an age correction depending on the age range of the cohort and the tracts considered.
Investigation of a Model-Based Working Memory Training With and Without Distractor Inhibition and Its Comparative Efficacy: A Randomized Controlled Trial on Healthy Old Adults
Authors: Zuber Priska , Geiter Emanuel , de Quervain Dominique J.-F. , Magon Stefano
Published: June 2021

Background: Various working memory (WM) trainings have been tested, but differences in experimental designs, the lack of theoretical background, and the need of identifying task-related processes such as filtering efficiency limit conclusions about their comparative efficacy.

Objectives: In this study, we compared the efficacy of a model-based WM training with (MB+) and without (MB) distractor inhibition on improving WM capacity to a dual n-back and active control condition.

Methods: This randomized clinical trial included 123 healthy elderly adults (78 women, 45 men; aged 64.1 ± 8.3 years). All groups underwent 12 40-min training sessions over 3 weeks and four cognitive testing sessions. The first two sessions served as double baseline to account for practice effects. Primary outcome was WM capacity post-training measured by complex span tasks. Near and far transfer was assessed by simple span, n-back, visuospatial and verbal learning, processing speed, and reasoning tasks.

Results: Due to preliminary termination (COVID-19), 93 subjects completed the post-training and 60 subjects the follow-up session. On a whole group level, practice effects occurred from prebaseline to baseline in WM capacity (b = 4.85, t(103) = 4.01, p < 0.001, r = 0.37). Linear mixed-effects models revealed a difference in WM capacity post-training between MB+ and MB (b = −9.62, t(82) = −2.52, p = 0.014, r = 0.27) and a trend difference between MB+ and dual n-back (b = −7.59, t(82) = −1.87, p = 0.065, r = 0.20) and control training (b = −7.08, t(82) = −1.86, p = 0.067, r = 0.20). Univariate analyses showed an increase between pre- and post-training for WM capacity within MB+ (t(22) = −3.34, p < 0.05) only. There was no difference between groups pre- and post-training regarding near and far transfer. Univariate analyses showed improved visuospatial learning within MB+ (t(21) = −3.8, p < 0.05), improved processing speed (t(23) = 2.19, p< 0.05) and n-back performance (t(23) = 2.12, p < 0.05) in MB, and improved n-back performance (t(25) = 3.83, p < 0.001) in the dual n-back training.

Interpretation: A model-based WM training including filtering efficacy may be a promising approach to increase WM capacity and needs further investigation in randomized controlled studies.
Green Synthesis: An Eco-friendly Route for the Synthesis of Iron Oxide Nanoparticles
Authors: Priya  , Naveen  , Kaur Kamaljit , Sidhu Amanpreet K.
Published: June 2021

Green approach has received major attention for the synthesis of metal oxide nanoparticles. One such metal oxide nanoparticles are iron oxide nanoparticles (IONPs). IONPs have fetched a great deal of interest in recent era because of their magnetic nature, as they can be easily recovered from the reaction mixture by applying an external magnetic field. Although, a variety of chemical and physical methods of synthesis are known, green synthesis is safer, sustainable and biologically acceptable. Plants and microbes are the main biological materials used for the green synthesis. In present review, the synthesis of IONPs by using plants, bacteria, fungi and algae have been highlighted. IONPs produced by plants, fungi, bacteria and algae usually falls in 1–100 nm range and are of distinct shapes like cubic, tetragonal crystalline, spherical, cylindrical, elliptical, octahedral, orthorhombic, hexagonal rods, nanosphere and quasi spherical. Furthermore, these biomaterials play role of reducing, capping, stabilizing and fabricating agents in green synthesis of nanoparticles. The review put forward a comprehensive report of various routes used for synthesizing IONP, biologically. Intuition into the procedures for synthesis of nanoparticles will help to nourish our learning in the area of nanotechnology.
A Genetic-Algorithm-Based Optimization Routing for FANETs
Authors: Wei Xing , Yang Hua , Huang Wentao
Published: June 2021

In view of the characteristics of high mobility of FANETs nodes, combined with the features of Topology-based class routing protocol on-demand search, a Genetic-algorithm-based routing (GAR) protocol is proposed for FANETs which based on improved genetic algorithm for FANETs route search, and it taking into account the link stability, link bandwidth, node energy, and other factors. GAR improves the selection, crossover, and variation operators of the genetic algorithm so that GAR can finally plan an optimized route from the communication initiating node to the destination node quickly using a smaller cost. The experimental results show that GAR can largely improve the throughput, reduce the delay and improve the stability of the network, which is more suitable for FANETs.