title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=861 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum) link: https://peerj.com/articles/11634 last-modified: 2021-07-27 description: Many pollination studies with honey bees have examined the effect of colony density on crop yield and yet overlook the effect of variation in the population size of these colonies. High colony density in northern highbush blueberry has been met with concerns from beekeepers who feel higher densities will intensify outbreaks of European foulbrood (EFB, Melissococcus plutonius, Truper and dé Clari), a honey bee brood disease. The purpose of this study was to confirm the prevalence of EFB in colonies pollinating blueberries and to determine whether field-level variation in the population of adult workers in colonies explained variation in blueberry fruit set and/or yield. We addressed these objectives over the course of two production seasons at 13 commercial blueberry fields in Oregon, USA, stocked with identical densities of 10 colonies/ha. We confirmed that all colonies had negligible symptoms of EFB at the start of blueberry pollination, but 53% of colonies in 2019 and 41% in 2020 had symptoms immediately following the pollination season. We also validated a method for rapidly assessing adult honey bee colony populations, namely by counting the rate of foragers returning to colonies, and it was found to be strongly correlated to true internal adult bee population independent of year and ambient temperature at the time of evaluation. Using returning forager counts, we determined there was considerable variation in the average population of colonies at each field, ranging from an estimated 10,300 to 30,700 adult worker bees per colony. While average colony strength did not predict variation in fruit set, it was related to variation in yield, independent of year. Our linear model of flight count (as a proxy for colony strength) predicts estimated yield increases of up to 25,000 kg/ha of blueberries could be achieved by colonies stronger than the recommended six frame minimum, suggesting that higher pollination benefits could be achieved without increasing hive density if stronger colonies are promoted. creator: Kennedy Judith Grant creator: Lisa DeVetter creator: Andony Melathopoulos uri: https://doi.org/10.7717/peerj.11634 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Grant et al. title: A new HSI denoising method via interpolated block matching 3D and guided filter link: https://peerj.com/articles/11642 last-modified: 2021-07-27 description: A new hyperspectral images (HSIs) denoising method via Interpolated Block-Matching and 3D filtering and Guided Filtering (IBM3DGF) denoising method is proposed. First, inter-spectral correlation analysis is used to obtain inter-spectral correlation coefficients and divide the HSIs into several adjacent groups. Second, high-resolution HSIs are produced by using adjacent three images to interpolate. Third, Block-Matching and 3D filtering (BM3D) is conducted to reduce the noise level of each group; Fourth, the guided image filtering is utilized to denoise HSI of each group. Finally, the inverse interpolation is applied to retrieve HSI. Experimental results of synthetic and real HSIs showed that, comparing with other state-of-the-art denoising methods, the proposed IBM3DGF method shows superior performance according to spatial and spectral domain noise assessment. Therefore, the proposed method has a potential to effectively remove the spatial/spectral noise for HSIs. creator: Ping Xu creator: Bingqiang Chen creator: Jingcheng Zhang creator: Lingyun Xue creator: Lei Zhu uri: https://doi.org/10.7717/peerj.11642 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication link: https://peerj.com/articles/11663 last-modified: 2021-07-27 description: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming. creator: Susana Marcela Simancas-Giraldo creator: Nan Xiang creator: Meghan Moger Kennedy creator: Rassil Nafeh creator: Edoardo Zelli creator: Christian Wild uri: https://doi.org/10.7717/peerj.11663 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Simancas-Giraldo et al. title: MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions link: https://peerj.com/articles/11750 last-modified: 2021-07-27 description: Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use. creator: Xiaoying Wang creator: Eva Cheng creator: Ian S. Burnett uri: https://doi.org/10.7717/peerj.11750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan link: https://peerj.com/articles/11779 last-modified: 2021-07-27 description: BackgroundInternational and national organizations recommend exclusive breastfeeding for the first 6 months of life, but many women stop earlier. Lay and professional persons can support mothers’ efforts to overcome breastfeeding difficulties. Considering breastfeeding support to comprise emotional support, practical help, and information offered to women who desire to breastfeed (by professionals, family members, and others), we developed and tested a scale to measure it in Japan.MethodsA total of 31 items were generated by literature review and from the authors’ clinical experiences. Those items were tested with 243 mothers who visited public health centers in Tokyo for their infant’s health check-up 3 months after birth. Breastfeeding support and infant feeding status were then assessed 5 months after birth. All the data were collected by using self-administered questionnaires.ResultsOn the basis of the results of factor analysis, the number of items was reduced to 11. There were three factors: support from breastfeeding peers and from people in specifically named healthcare professions, practical help, and support from people the mother can rely on to help meet emotional needs and address breastfeeding concerns. Internal-consistency reliability (alpha) of scores on the 11-item scale was 0.83 when measured 3 months postpartum and 0.85 when measured 5 months postpartum. Higher scores on the 11-item scale 3 months postpartum were associated with more breastfeeding exclusivity both at that time (Kruskal–Wallis test, chi-squared = 14.871, df = 3, n = 211, p = 0.002, eta-squared = 0.071) and also 5 months postpartum (Kruskal–Wallis test, chi-squared = 8.556, df = 3, n = 159, p = 0.036, eta-squared = 0.054). Further, the area under the Receiver Operating Characteristic curve was 0.73 (95% CI [0.57–0.88]), which indicates that scores on the 11-item scale 3 months postpartum may be useful to predict which mothers will be less exclusive in breastfeeding 5 months postpartum. In conclusion, scores on this 11-item scale were reasonably reliable and valid for measuring breastfeeding support provided by lay and professional persons to mothers in Japan. Further research is required to evaluate this scale’s applicability in other settings. creator: Keiko Nanishi creator: Joseph Green creator: Hiroko Hongo uri: https://doi.org/10.7717/peerj.11779 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2021 Nanishi et al. title: Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study link: https://peerj.com/articles/11801 last-modified: 2021-07-27 description: BackgroundThe relationship between impulsivity and suicide is inconsistent in different populations. Hence, the relationship between impulsivity and suicide still needs to be studied among the elderly population. The present study intends to explore the relationship between impulsivity and suicide among the rural Chinese elderly.MethodsA case-control psychological autopsy study was conducted from February 1, 2014 to December 18, 2015 among rural residents over the age of 60 who died by suicide. The sample consisted of 242 suicides as the case group and 242 living individuals as the control group. Data on demographic characteristics, impulsivity, previous history of suicide attempts, social support, negative life events, and suicidal behavior were collected.ResultsOur study found that impulsivity increased the risk of suicide. The case group showed a higher Barratt Impulsiveness Scale score compared with the control group (p < 0.001), which indicates that impulsivity was higher among the elderly suicides. In addition, regression analyses show that impulsivity (odds ratio: 1.03, 95% confidence interval: 1.01–1.06) is an independent risk factor of suicide, after controlling for the effects of marital status, education, family annual income, being left behind, social support, and negative life events. Finally, compared with elderly who do not have a history of attempted suicide, elderly with a history of attempted suicide showed higher impulsivity (p = 0.001). creator: Yunfang Zhou creator: Zhenyu Ma creator: Cun-Xian Jia creator: Liang Zhou uri: https://doi.org/10.7717/peerj.11801 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhou et al. title: ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review link: https://peerj.com/articles/11809 last-modified: 2021-07-27 description: Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker genes. creator: Richard Dormatey creator: Chao Sun creator: Kazim Ali creator: Sajid Fiaz creator: Derong Xu creator: Alejandro Calderón-Urrea creator: Zhenzhen Bi creator: Junlian Zhang creator: Jiangping Bai uri: https://doi.org/10.7717/peerj.11809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dormatey et al. title: The importance of spawning behavior in understanding the vulnerability of exploited marine fishes in the U.S. Gulf of Mexico link: https://peerj.com/articles/11814 last-modified: 2021-07-27 description: The vulnerability of a fish stock to becoming overfished is dependent upon biological traits that influence productivity and external factors that determine susceptibility or exposure to fishing effort. While a suite of life history traits are traditionally incorporated into management efforts due to their direct association with vulnerability to overfishing, spawning behavioral traits are seldom considered. We synthesized the existing biological and fisheries information of 28 fish stocks in the U.S. Gulf of Mexico to investigate relationships between life history traits, spawning behavioral traits, management regulations, and vulnerability to fishing during the spawning season. Our results showed that spawning behavioral traits were not correlated with life history traits but improved identification of species that have been historically overfished. Species varied widely in their intrinsic vulnerability to fishing during spawning in association with a broad range of behavioral strategies. Extrinsic vulnerability was high for nearly all species due to exposure to fishing during the spawning season and few management measures in place to protect spawning fish. Similarly, several species with the highest vulnerability scores were historically overfished in association with spawning aggregations. The most vulnerable species included several stocks that have not been assessed and should be prioritized for further research and monitoring. Collectively, the results of this study illustrate that spawning behavior is a distinct aspect of fish ecology that is important to consider for predictions of vulnerability and resilience to fisheries exploitation. creator: Christopher R. Biggs creator: William D. Heyman creator: Nicholas A. Farmer creator: Shin’ichi Kobara creator: Derek G. Bolser creator: Jan Robinson creator: Susan K. Lowerre-Barbieri creator: Brad E. Erisman uri: https://doi.org/10.7717/peerj.11814 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Effect of modified pomace on copper migration via riverbank soil in southwest China link: https://peerj.com/articles/11844 last-modified: 2021-07-27 description: To explore the effects of modified pomace on copper migration via the soil on the banks of the rivers in northern Sichuan and Chongqing, fruit pomace (P) and ethylene diamine tetra-acetic acid (EDTA) modified P (EP) were evenly added (1% mass ratio) to the soil samples of Guanyuan, Nanbu, Jialing, and Hechuan from the Jialing River; Mianyang and Suining from the Fu River; and Guangan and Dazhou from the Qu River. The geochemical characteristics and migration rules of copper in different amended soils were simulated by column experiment. Results showed that the permeation time of copper in each soil column was categorized as EP-amended > P-amended > original soil, and the permeation time of amended soil samples at different locations was Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guanyuan > Hechuan. Meanwhile, the average flow rate of copper in each soil column showed a reverse trend with the permeation time. Copper in exchangeable, carbonate, and iron–manganese oxide forms decreased with the increase of vertical depth in the soil column, among which the most evident decreases appeared in the carbonate-bonding form. The copper accumulation in different locations presented a trend of Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guangyuan > Hechuan, and the copper content under the same soil showed EP-amended > P-amended > original soil. The copper proportion of the carbonate form was the highest in each soil sample, followed by the exchangeable form. The proportions of iron-manganese oxide and organic matter forms were relatively small. A significant correlation was observed between the cation exchange capacity and the copper content in exchangeable and carbonate forms. Moreover, total organic carbon and copper contents were negatively correlated. creator: Lingyuan Chen creator: Touqeer Abbas creator: Lin Yang creator: Yao Xu creator: Hongyan Deng creator: Lei Hou creator: Wenbin Li uri: https://doi.org/10.7717/peerj.11844 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly link: https://peerj.com/articles/11845 last-modified: 2021-07-27 description: DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets. creator: Maxime Borry creator: Alexander Hübner creator: Adam B. Rohrlach creator: Christina Warinner uri: https://doi.org/10.7717/peerj.11845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Borry et al.