title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=504 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Is coconut coir dust an efficient biofertilizer carrier for promoting coffee seedling growth and nutrient uptake? link: https://peerj.com/articles/15530 last-modified: 2023-06-14 description: BackgroundAs a method for sustainable agriculture, biofertilizers containing plant growth-promoting bacteria (PGPB) have been recommended as an alternative to chemical fertilizers. However, the short shelf-life of inoculants remains a limiting factor in the development of biofertilizer technology. The present study aimed to (i) evaluate the effectiveness of four different carriers (perlite, vermiculite, diatomite and coconut coir dust) on the shelf-life of S2-4a1 and R2-3b1 isolates over 60 days after inoculation and (ii) evaluate isolated bacteria as growth-promoting agents for coffee seedlings.MethodsThe rhizosphere soil-isolated S2-4a1 and plant-tissue-isolated R2-3b1 were chosen based on their P and K-solubilizing capacities and their ability to produce IAA. To evaluate the alternative carriers, two selected isolates were inoculated with the four different carriers and incubated at 25 °C for 60 days. The bacterial survival, pH, and EC in each carrier were investigated. In addition, coconut coir dust inoculated with the selected isolates was applied to the soil in pots planted with coffee (Coffea arabica). At 90 days following application, variables such as biomass and total N, P, K, Ca, and Mg uptakes of coffee seedlings were examined.ResultsThe results showed that after 60 days of inoculation at 25 °C, the population of S2-4a1 and R2-3b1 in coconut coir dust carriers was 1.3 and 2.15 × 108 CFU g−1, respectively. However, there were no significant differences among carriers (P > 0.05). The results of the present study suggested that coconut coir dust can be used as an alternative carrier for S2-4a1 and R2-3b1 isolates. The significant differences in pH and EC were observed by different carriers (P < 0.01) after inoculation with both bacterial isolates. However, pH and EC declined significantly only with coconut coir dust during the incubation period. In addition, coconut coir dust-based bioformulations of both S2-4a1 and R2-3b1 enhanced plant growth and nutrient uptake (P, K, Ca, Mg), providing evidence that isolated bacteria possess additional growth-promoting properties. creator: Yupa Chromkaew creator: Thewin Kaeomuangmoon creator: Nipon Mawan creator: Nilita Mukjang creator: Nuttapon Khongdee uri: https://doi.org/10.7717/peerj.15530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chromkaew et al. title: Three new species of Axinulus (Bivalvia: Thyasiridae) from the Japan and Kuril-Kamchatka trenches and abyssal zone of the northern Pacific Ocean link: https://peerj.com/articles/15543 last-modified: 2023-06-14 description: The Thyasiridae is one of the most species-rich families of bivalves in the deep-sea areas of the northern Pacific Ocean. Many thyasirid species form abundant populations in these regions and play an important role in the functioning of deep-sea benthic communities. However, most of these deep-sea thyasirid species have not been identified and many of them are new to science. Based on the material of bivalves collected by eight deep-sea expeditions in the northern Pacific Ocean during the period from 1954 to 2016, three new species of the genus Axinulus (Axinulus krylovae sp. nov., A. alatus sp. nov., and A. cristatus sp. nov.) are described from the Kuril-Kamchatka and Japan trenches, the Bering Sea, and other deep-water regions of the northern Pacific Ocean (3,200–9,583 m depth). The new species are distinguished due to a unique and complex sculpture of the prodissoconch, including tubercles and numerous thin folds of varying length and shape, as well as due to a thickening of the shell in the adductor scar areas, thus rendering the scars raised above the inner surface of the shell. Comparisons with all species of the genus Axinulus are provided. creator: Gennady M. Kamenev uri: https://doi.org/10.7717/peerj.15543 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kamenev title: Expression, localization, and function of P4HB in the spermatogenesis of Chinese mitten crab (Eriocheir sinensis) link: https://peerj.com/articles/15547 last-modified: 2023-06-14 description: BackgroundThe sperm of Chinese mitten crab (Eriocheir sinensis) have special noncondensed nuclei. The formation and stability of the special nuclei are closely related to the correct folding of proteins during spermatogenesis. P4HB plays a key role in protein folding, but its expression and role in the spermatogenesis of E. sinensis are unclear.ObjectiveTo investigate the expression and distribution characteristics of P4HB in the spermatogenesis of E. sinensis as well as its possible role.MethodsThe testis tissues of adult and juvenile E. sinensis were used as materials. We utilized a variety of techniques, including homology modeling, phylogenetic analysis, RT-qPCR, western blotting, and immunofluorescence staining to predict the protein structure and sequence homology of P4HB, analyze its expression in the testis tissues, and localize and semi-quantitatively assess its expression in different male germ cells.ResultsThe sequence of P4HB protein in E. sinensis shared a high similarity of 58.09% with the human protein disulfide isomerase, and the phylogenetic tree analysis indicated that the protein sequence was highly conserved among crustaceans, arthropods, and other animals species. P4HB was found to be expressed in both juvenile and adult E. sinensis testis tissues, with different localization patterns observed all over the developmental stages of male germ cells. It was higher expressed in the spermatogonia, spermatocytes, and stage I spermatids, followed by the mature sperm than in the stage II and III spermatids. The subcellular localization analysis revealed that P4HB was predominantly expressed in the cytoplasm, cell membrane, and extracellular matrix in the spermatogonia, spermatocytes, stage I and stage II spermatids, with some present in specific regions of the nuclei in the spermatogonia. In contrast, P4HB was mainly localized in the nuclei of stage III spermatids and sperm, with little expression observed in the cytoplasm.ConclusionP4HB was expressed in the testis tissues of both adult and juvenile E. sinensis, but the expression and localization were different in male germ cells at various developmental stages. The observed differences in the expression and localization of P4HB may be an essential factor in maintaining the cell morphology and structure of diverse male germ cells in E. sinensis. Additionally, P4HB expressed in the nuclei of spermatogonia, late spermatids, and sperm may play an indispensable role in maintaining the stability of the noncondensed spermatozoal nuclei in E. sinensis. creator: Yulian Tang creator: Anni Ni creator: Shu Li creator: Lishuang Sun creator: Genliang Li uri: https://doi.org/10.7717/peerj.15547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tang et al. title: Accounting for spatial habitat and management boundaries when estimating forest bird population distribution and density: inferences from a soap film smoother link: https://peerj.com/articles/15558 last-modified: 2023-06-14 description: Birds are often obligate to specific habitats which can result in study areas with complex boundaries due to sudden changes in vegetation or other features. This can result in study areas with concave arcs or that include holes of unsuitable habitat such as lakes or agricultural fields. Spatial models used to produce species’ distribution and density estimates need to respect such boundaries to make informed decisions for species conservation and management. The soap film smoother is one model for complex study regions which controls the boundary behaviour, ensuring realistic values at the edges of the region. We apply the soap film smoother to account for boundary effects and compare it with thin plate regression spline (TPRS) smooth and design-based conventional distance sampling methods to produce abundance estimates from point-transect distance sampling collected data on Hawai‘i ‘Ākepa Loxops coccineus in the Hakalau Forest Unit of the Big Island National Wildlife Refuge Complex, Hawai‘i Island, USA. The soap film smoother predicted zero or near zero densities in the northern part of the domain and two hotspots (in the southern and central parts of the domain). Along the boundary the soap film model predicted relatively high densities where ‘Ākepa occur in the adjacent forest and near zero elsewhere. The design-based and soap film abundance estimates were nearly identical. The width of the soap film confidence interval was 16.5% and 0.8% wider than the width of the TPRS smooth and design-based confidence intervals, respectively. The peaks in predicted densities along the boundary indicates leakage by the TPRS smooth. We provide a discussion of the statistical methods, biological findings and management implications of applying soap film smoothers to estimate forest bird population status. creator: Richard J. Camp creator: David L. Miller creator: Stephen T. Buckland creator: Steve J. Kendall uri: https://doi.org/10.7717/peerj.15558 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: What are the Andean Colombian anurans? Empirical regionalization proposals vs. observed patterns of compositional dissimilarity link: https://peerj.com/articles/15217 last-modified: 2023-06-13 description: BackgroundDefining Andean anurans through their altitudinal limits has been a common practice in species lists, studies of responses to climate change among others, especially in the northern Andes. At least three proposals to differentiate Andean anurans from lowland anurans through elevation and at least one to differentiate Andean anurans from high mountain anurans have been formulated. However, the most frequently used altitudinal limits are not based on theoretical or numerical support, but on observations or practical definitions. Additionally, these proposals have been applied equally to different portions of the Andes, ignoring the fact that even between slopes of the same mountain, environmental conditions (and therefore the distribution of species) may differ. The objective of this work was to evaluate the concordance between the altitudinal distribution of anurans in the Colombian Andes and four different altitudinal delimitation proposals.MethodsWe constructed our study area in a manner that allowed us to include species from the Andean region (as traditionally defined) and adjacent lowlands, because if the boundaries criteria were applied they would separate the species of the latter by themselves. We divided the study area into eight entities according to the watershed and the course of the most important rivers. We conducted a bibliographic search for all anurans in the cordilleras and inter-Andean valleys of Colombia and complemented the search with information on anurans for the region available in the GBIF. After curing the species distribution points, we generated elevation bands of 200 m amplitude for both the study area and for each Andean entity. Subsequently, we performed a cluster analysis to evaluate the grouping of the elevation bands according to their species composition.ResultsIn none of the cases (neither for the entire study area nor for any of the entities) we found a correspondence of any of the traditionally used boundaries and the altitudinal distribution of Anurans in the Andean region of Colombia. Instead, on average, the altitudinal delimitation proposals arbitrarily spanned the altitudinal distribution of about one third of the species distributed in the study area.ConclusionsWe suggest that, although, based on our results, some Andean entities can be divided according to the altitudinal composition of the species that occur in them, we did not find any results that support the idea of a generalizable altitudinal limit for the Colombian Andes. Thus, to avoid biases in studies that may later be used by decision makers, the selection of anuran species in studies in the Colombian Andes should be based on biogeographic, phylogenetic or natural history criteria and not on altitudinal limits as they have been used. creator: Jorge Mario Herrera-Lopera creator: Viviana Andrea Ramírez Castaño creator: Carlos A. Cultid-Medina uri: https://doi.org/10.7717/peerj.15217 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Herrera-Lopera et al. title: A review of visual sustained attention: neural mechanisms and computational models link: https://peerj.com/articles/15351 last-modified: 2023-06-13 description: Sustained attention is one of the basic abilities of humans to maintain concentration on relevant information while ignoring irrelevant information over extended periods. The purpose of the review is to provide insight into how to integrate neural mechanisms of sustained attention with computational models to facilitate research and application. Although many studies have assessed attention, the evaluation of humans’ sustained attention is not sufficiently comprehensive. Hence, this study provides a current review on both neural mechanisms and computational models of visual sustained attention. We first review models, measurements, and neural mechanisms of sustained attention and propose plausible neural pathways for visual sustained attention. Next, we analyze and compare the different computational models of sustained attention that the previous reviews have not systematically summarized. We then provide computational models for automatically detecting vigilance states and evaluation of sustained attention. Finally, we outline possible future trends in the research field of sustained attention. creator: Huimin Huang creator: Rui Li creator: Junsong Zhang uri: https://doi.org/10.7717/peerj.15351 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Comparing quantile regression spline analyses and supervised machine learning for environmental quality assessment at coastal marine aquaculture installations link: https://peerj.com/articles/15425 last-modified: 2023-06-13 description: Organic enrichment associated with marine finfish aquaculture is a local stressor of marine coastal ecosystems. To maintain ecosystem services, the implementation of biomonitoring programs focusing on benthic diversity is required. Traditionally, impact-indices are determined by extracting and identifying benthic macroinvertebrates from samples. However, this is a time-consuming and expensive method with low upscaling potential. A more rapid, inexpensive, and robust method to infer the environmental quality of marine environments is eDNA metabarcoding of bacterial communities. To infer the environmental quality of coastal habitats from metabarcoding data, two taxonomy-free approaches have been successfully applied for different geographical regions and monitoring goals, namely quantile regression splines (QRS) and supervised machine learning (SML). However, their comparative performance remains untested for monitoring the impact of organic enrichment introduced by aquaculture on marine coastal environments. We compared the performance of QRS and SML using bacterial metabarcoding data to infer the environmental quality of 230 aquaculture samples collected from seven farms in Norway and seven farms in Scotland along an organic enrichment gradient. As a measure of environmental quality, we used the Infaunal Quality Index (IQI) calculated from benthic macrofauna data (reference index). The QRS analysis plotted the abundance of amplicon sequence variants (ASVs) as a function to the IQI from which the ASVs with a defined abundance peak were assigned to eco-groups and a molecular IQI was subsequently calculated. In contrast, the SML approach built a random forest model to directly predict the macrofauna-based IQI. Our results show that both QRS and SML perform well in inferring the environmental quality with 89% and 90% accuracy, respectively. For both geographic regions, there was high correspondence between the reference IQI and both the inferred molecular IQIs (p < 0.001), with the SML model showing a higher coefficient of determination compared to QRS. Among the 20 most important ASVs identified by the SML approach, 15 were congruent with the good quality spline ASV indicators identified via QRS for both Norwegian and Scottish salmon farms. More research on the response of the ASVs to organic enrichment and the co-influence of other environmental parameters is necessary to eventually select the most powerful stressor-specific indicators. Even though both approaches are promising to infer environmental quality based on metabarcoding data, SML showed to be more powerful in handling the natural variability. For the improvement of the SML model, addition of new samples is still required, as background noise introduced by high spatio-temporal variability can be reduced. Overall, we recommend the development of a powerful SML approach that will be onwards applied for monitoring the impact of aquaculture on marine ecosystems based on eDNA metabarcoding data. creator: Kleopatra Leontidou creator: Verena Rubel creator: Thorsten Stoeck uri: https://doi.org/10.7717/peerj.15425 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Leontidou et al. title: Collateral damage: has the COVID-19 pandemic more strongly impacted medical research than other scientific areas? link: https://peerj.com/articles/15436 last-modified: 2023-06-13 description: The principle of resource allocation states that diversion of resources to attend a function may compromise others. The COVID-19 pandemic required a rapid response with a justifiable relocation of equipment, funds and human resources. Based on the ecological principle of allocation, we tested whether the relocation of resources to support COVID-19 research was more detrimental to medical research than to research in other scientific areas. We compared the yearly number of published articles from 2015 to 2021 using disease-related keywords and non-medical scientific keywords. Contrary to the expectation, we found an abrupt reduction in the publication rates in all research areas from 2019 to 2020 or 2021, compared to the pre-pandemic period (2015–2019). The allocation effect on medical research may be overshadowed by stronger effects of the pandemic, or it may become evident in the coming years. The drastic reduction in published papers could have negative consequences for scientific advancements, including understanding and curing diseases other than COVID-19 that strongly affect humanity. creator: Alejandro Farji-Brener creator: Sabrina Amador-Vargas uri: https://doi.org/10.7717/peerj.15436 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: © 2023 Farji-Brener and Amador-Vargas title: Impact of selected risk factors on motor performance in the third month of life and motor development in the ninth month link: https://peerj.com/articles/15460 last-modified: 2023-06-13 description: BackgroundProper motor development can be influenced by a range of risk factors. The resulting motor performance can be assessed through quantitative and qualitative analysis of posture and movement patterns.MethodsThis study was designed as the cohort follow-up of the motor assessment and aimed to demonstrate, in a mathematical way, the impact of particular risk factors on elements of motor performance in the 3rd month and the final motor performance in the 9th month of life. Four hundred nineteen children were assessed (236 male and 183 female), including 129 born preterm. Each child aged 3 month underwent a physiotherapeutic assessment of the quantitative and qualitative development, in the prone and supine positions. The neurologist examined each child aged 9 month, referring to the Denver Development Screening Test II and assessing reflexes, muscle tone and symmetry. The following risk factors were analyzed after the neurological consultation: condition at birth (5th min Apgar score), week of gestation at birth, intraventricular hemorrhage, respiratory distress syndrome, and the incidence of intrauterine hypotrophy and hyperbilirubinemia determined based on medical records.ResultsA combination of several risk factors affected motor development stronger than any one of them solely, with Apgar score, hyperbilirubinemia, and intraventricular hemorrhage exhibiting the most significant impact.ConclusionsPremature birth on its own did not cause a substantial delay in motor development. Nonetheless, its co-occurrence with other risk factors, namely intraventricular hemorrhage, respiratory distress syndrome, and hyperbilirubinemia, notably worsened motor development prognosis. Moreover, improper position of the vertebral column, scapulae, shoulders, and pelvis in the third month of life may predict disturbances in further motor development. creator: Ewa Gajewska creator: Jerzy Moczko creator: Mariusz Naczk creator: Alicja Naczk creator: Magdalena Sobieska uri: https://doi.org/10.7717/peerj.15460 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gajewska et al. title: The link between lymphocyte subpopulations in peripheral blood and metabolic variables in patients with severe obesity link: https://peerj.com/articles/15465 last-modified: 2023-06-13 description: BackgroundObesity, a public health problem, is a state of metainflammation that influences the development of chronic degenerative diseases, particularly in patients with severe obesity.ObjectiveThe objective of this study was to evidence immunometabolic differences in patients with different degrees of obesity, including severe obesity, by determining correlations between lymphocyte subpopulations and metabolic, body composition, and clinical variables.MethodsPeripheral blood immune cells (CD4+, CD8+ memory and effector T lymphocytes) were analyzed, and measures of body composition, blood pressure, and biochemical composition (glucose, glycated hemoglobin (HbA1c), insulin, C-reactive protein (CRP), and the lipid profile) were carried out in patients with different degrees of obesity.ResultsThe patients were classified according to total body fat (TBF) percentage as normal body fat, class 1 and 2 obesity, class 3 obesity, and class 4 obesity. The greater the TBF percentage, the more pronounced the differences in body composition (such as a decrease in the fat-free mass (FFM) that is defined as sarcopenic obesity) and the immunometabolic profile. There was an increase of CD3+ T lymphocytes (mainly CD4+, CD4+CD62-, and CD8+CD45RO+ T lymphocytes) and an increase in the TBF percentage (severity of obesity).ConclusionsThe correlations between lymphocyte subpopulations and metabolic, body composition, and clinical variables demonstrated the existence of a chronic, low-intensity inflammatory process in obesity. Therefore, measuring the immunometabolic profile by means of lymphocyte subpopulations in patients with severe obesity could be useful to determine the severity of the disease and the increased risk of presenting obesity-associated chronic degenerative diseases. creator: Tania Rivera-Carranza creator: Oralia Nájera-Medina creator: Rafael Bojalil-Parra creator: Carmen Paulina Rodríguez-López creator: Eduardo Zúñiga-León creator: Angélica León-Téllez Girón creator: Alejandro Azaola-Espinosa uri: https://doi.org/10.7717/peerj.15465 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rivera-Carranza et al.