title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1080
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: A new ophiacanthid brittle star (Echinodermata, Ophiuroidea) from sublittoral crinoid and seagrass communities of late Maastrichtian age in the southeast Netherlands
link: https://peerj.com/articles/9671
last-modified: 2020-08-24
description: A new species of brittle star, Ophiomitrella floorae, is recorded from the lower two meters of the Gronsveld Member (Maastricht Formation), of late Maastrichtian age (c. 66.7 Ma). These relatively fine-grained biocalcarenites reflect shallow-water deposition in a sheltered setting with a relatively firm sea floor and clear waters, under middle sublittoral and subtropical conditions. Associated echinoderm taxa comprise more robust, sturdy-plated ophiomusaid and ophiodermatid brittle stars and numerous bourgueticrinine sea lilies. The new brittle star described herein belongs to a family whose present-day members are predominantly restricted to bathyal depths. Its small size and the exceptional preservation of a single articulated specimen partially wrapped around the stalk of a bourgueticrinine suggest that O. floorae n. sp. was probably epizoic and specifically associated with stalked crinoids.
creator: Ben Thuy
creator: Lea Numberger-Thuy
creator: John W.M. Jagt
uri: https://doi.org/10.7717/peerj.9671
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Thuy et al.

title: Root architecture, rooting profiles and physiological responses of potential slope plants grown on acidic soil
link: https://peerj.com/articles/9595
last-modified: 2020-08-24
description: Globally, there has been an increase in the frequency of landslides which is the result of slope failures. The combination of high intensity rainfall and high temperature resulted in the formation of acidic soil which is detrimental to the healthy growth of plants. Proper plant coverage on slopes is a prerequisite to mitigate and rehabilitate the soil. However, not all plant species are able to grow in marginal land. Thus, this study was undertaken to find a suitable slope plant species. We aimed to evaluate the effect of different soil pH on root profiles and growth of three different potential slope plant species namely, Melastoma malabathricum, Hibiscus rosa-sinensis and Syzygium campanulatum. M. malabathricum showed the highest tolerance to acidic soil as it recorded the highest plant height and photosynthetic rate. The root systems of M. malabathricum, H. rosa-sinensis and S. campanulatum were identified as M, VH- and R-types, respectively. The study proposed M. malabathricum which possessed dense and shallow roots to be planted at the toe or top of the slope while H. rosa-sinensis and S. campanulatum to be planted in the middle of a slope. S. campanulatum consistently recorded high root length and root length density across all three types of soil pH while M. malabathricum showed progressive increase in length as the soil pH increased. The root average diameter and root volume of M. malabathricum outperformed the other two plant species irrespective of soil pH. In terms of biomass, M. malabathricum exhibited the highest root and shoot dry weights followed by S. campanulatum. Thus, we propose M. malabathricum to be planted on slopes as a form of soil rehabilitation. The plant species displayed denser rooting, hence a stronger root anchorage that can hold the soil particles together which will be beneficial for slope stabilization.
creator: Deivaseeno Dorairaj
creator: Muhammad Fahmi Suradi
creator: Nursyamimi Syafiqah Mansor
creator: Normaniza Osman
uri: https://doi.org/10.7717/peerj.9595
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Dorairaj et al.

title: Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment
link: https://peerj.com/articles/9627
last-modified: 2020-08-24
description: PurposeThe aim of this study was to explore the effective immune scoring method and mine the novel and potential immune microenvironment-related diagnostic and prognostic markers for cervical squamous cell carcinoma (CSSC).Materials and MethodsThe Cancer Genome Atlas (TCGA) data was downloaded and multiple data analysis approaches were initially used to search for the immune-related scoring system on the basis of Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data (ESTIMATE) algorithm. Afterwards, the representative genes in the gene modules correlated with immune-related scores based on ESTIMATE algorithm were further screened using Weighted Gene Co-expression Network Analysis (WGCNA) and network topology analysis. Gene functions were mined through enrichment analysis, followed by exploration of the correlation between these genes and immune checkpoint genes. Finally, survival analysis was applied to search for genes with significant association with overall survival and external database was employed for further validation.ResultsThe immune-related scores based on ESTIMATE algorithm was closely associated with other categories of scores, the HPV infection status, prognosis and the mutation levels of multiple CSCC-related genes (HLA and TP53). Eighteen new representative immune microenvironment-related genes were finally screened closely associated with patient prognosis and were further validated by the independent dataset GSE44001.ConclusionOur present study suggested that the immune-related scores based on ESTIMATE algorithm can help to screen out novel immune-related diagnostic indicators, therapeutic targets and prognostic predictors in CSCC.
creator: Jiong Ma
creator: Pu Cheng
creator: Xuejun Chen
creator: Chunxia Zhou
creator: Wei Zheng
uri: https://doi.org/10.7717/peerj.9627
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Ma et al.

title: Reliability and validity of the physical activity monitor for assessing energy expenditures in sedentary, regularly exercising, non-endurance athlete, and endurance athlete adults
link: https://peerj.com/articles/9717
last-modified: 2020-08-24
description: BackgroundInertial sensors, such as accelerometers, serve as convenient devices to predict the energy expenditures (EEs) during physical activities by a predictive equation. Although the accuracy of estimate EEs especially matter to athletes receive physical training, most EE predictive equations adopted in accelerometers are based on the general population, not athletes. This study included the heart rate reserve (HRR) as a compensatory parameter for physical intensity and derived new equations customized for sedentary, regularly exercising, non-endurance athlete, and endurance athlete adults.MethodsWith indirect calorimetry as the criterion measure (CM), the EEs of participants on a treadmill were measured, and vector magnitudes (VM), as well as HRR, were simultaneously recorded by a waist-worn accelerometer with a heart rate monitor. Participants comprised a sedentary group (SG), an exercise-habit group (EHG), a non-endurance group (NEG), and an endurance group (EG), with 30 adults in each group.ResultsEE predictive equations were revised using linear regression with cross-validation on VM, HRR, and body mass (BM). The modified model demonstrates valid and reliable predictions across four populations (Pearson correlation coefficient, r: 0.922 to 0.932; intraclass correlation coefficient, ICC: 0.919 to 0.930).ConclusionUsing accelerometers with a heart rate monitorcan accurately predict EEs of athletes and non-athletes with an optimized predictive equation integrating the VM, HRR, and BM parameters.
creator: Chun-Hao Chang
creator: Yi-Ju Hsu
creator: Fang Li
creator: Yu-Tsai Tu
creator: Wei-Lun Jhang
creator: Chih-Wen Hsu
creator: Chi-Chang Huang
creator: Chin-Shan Ho
uri: https://doi.org/10.7717/peerj.9717
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Chang et al.

title: Evaluation of wet and dry event’s trend and instability based on the meteorological drought index
link: https://peerj.com/articles/9729
last-modified: 2020-08-24
description: A temporal imbalance in the water availability, which is consistently below average or more than average rainfall, can lead to extremely dry or wet conditions. This impacts on agricultural yields, water resources and human activities. Weather instabilities and trends of wet/dry events have not yet been explored in Pakistan. In this study, we have two-fold objectives: (1) evaluate the weather instabilities, and (2) the trend of dry/wet events of selected stations of Pakistan. To observe weather instabilities, we used Mean Marginal Hilbert Spectrum (MMHS) and Continuous Wavelet Power Spectrum (CWPS) as meteorological series are mostly non-linear and non-stationary. We used Ensemble Empirical Mode Decomposition (EEMD) for the analysis of temporal characteristics of dry/wet events. We found that all stations are facing severe weather instabilities during the short period of 5 and 10 months using MMHS method and CWPS has shown the weather instabilities during 4 to 32 months of periodicity for all stations. Ultimately, the achieved short-term weather instabilities indicated by MMHS is consistent with CWPS. In summary, these findings might be useful for water resource management and policymakers.
creator: Muhammad Haroon Shaukat
creator: Ahmad Al-Dousari
creator: Ijaz Hussain
creator: Muhammad Faisal
creator: Muhammad Ismail
creator: Alaa Mohamd Shoukry
creator: Elsayed Elsherbini Elashkar
creator: Showkat Gani
uri: https://doi.org/10.7717/peerj.9729
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Shaukat et al.

title: Giant cell tumor stromal cells: osteoblast lineage-derived cells secrete IL-6 and IL-10 for M2 macrophages polarization
link: https://peerj.com/articles/9748
last-modified: 2020-08-24
description: BackgroundThe giant cell tumor (GCT) is a benign tumor which consists of three types cells: mononuclear histiocytic cells (MNHCs), multinuclear giant cells (MNGCs), and GCT stromal cells (GCTSCs). Numerous studies claim that GCTSCs have mesenchymal stem cells (MSCs) characters and play an important role in osteoclastogenesis; however, there are no research studies concerning macrophage polarization among GCT, which can be regarded as an ingredient for tumor aggression.MethodWe tested the effect of GCTSCs from three GCT samples which were collected from patients on proliferation, apoptosis and polarization of macrophage.ResultIn this article, we verified that GCTSCs expressed MSCs markers and had higher proliferation and relative lower differentiation abilities compared with BMMSCs. What’s more, we found a higher proportion of M2 macrophages among neoplasm. Co-culturing GCTSCs with macrophages resulted in prominent macrophage M2 polarization and increased the release of IL-6 (Interleukin-6) and IL-10 (Interleukin-10)from GCTSCs. In conclusion, GCTSCs, as originating from MSCs, can secret IL-6 and IL-10, which may play a significant role in macrophage M2 polarization.
creator: Kuan Yang
creator: Lihui Bao
creator: Xiaoning He
creator: Wanmin Zhao
creator: Dongdong Fei
creator: Bei Li
creator: Yang Xue
creator: Zhiwei Dong
uri: https://doi.org/10.7717/peerj.9748
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Yang et al.

title: Additional records and stratigraphic distribution of the middle Eocene carettochelyid turtle Anosteira pulchra from the Uinta Formation of Utah, North America
link: https://peerj.com/articles/9775
last-modified: 2020-08-24
description: BackgroundAnosteira pulchra is one of two species of the obligately-aquatic freshwater clade Carettochelyidae (pig-nosed turtles) from the Eocene of North America. Anosteira pulchra is typically rare in collections, and their distribution is poorly documented. The Uinta Formation [Fm.] contains a diverse assemblage of turtles from the Uintan North American Land Mammal Age. Whereas turtles are abundantly preserved in the Uinta Fm., A. pulchra has been reported only from a few specimens in the Uinta C Member.MethodsWe describe new records of Anosteira pulchra from the Uinta Basin and analyze the distribution of 95 specimens from multiple repositories in the previously published stratigraphic framework of the middle and upper Uinta Fm.ResultsHere we report the first records of the species from the Uinta B interval, document it from multiple levels within the stratigraphic section and examine its uncommon appearance in only approximately 5% of localities where turtles have been systematically collected. This study details and extends the range of A. pulchra in the Uinta Fm. and demonstrates the presence of the taxon in significantly lower stratigraphic layers. These newly described fossils include previously unknown elements and associated trace fossils, with new anatomical information presented. This study provides insight into the taxonomy of Anosteira spp. in the middle Eocene, and suggests the presence of a single species, though no synonymy is defined here due to limits in Bridger material.
creator: Brent Adrian
creator: Patricia A. Holroyd
creator: J. Howard Hutchison
creator: KE Beth Townsend
uri: https://doi.org/10.7717/peerj.9775
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Adrian et al.

title: Identifying mangrove-coral habitats in the Florida Keys
link: https://peerj.com/articles/9776
last-modified: 2020-08-24
description: Coral reefs are degrading due to many synergistic stressors. Recently there have been a number of global reports of corals occupying mangrove habitats that provide a supportive environment or refugium for corals, sheltering them by reducing stressors such as oxidative light stress and low pH. This study used satellite imagery and manual ground-truthing surveys to search for mangrove-coral habitats in the Florida Keys National Marine Sanctuary and then collected basic environmental parameters (temperature, salinity, dissolved oxygen, pHNBS, turbidity) at identified sites using a multi-parameter water quality sonde. Two kinds of mangrove-coral habitats were found in both the Upper and Lower Florida Keys: (1) prop-root corals, where coral colonies were growing directly on (and around) mangrove prop roots, and (2) channel corals, where coral colonies were growing in mangrove channels under the shade of the mangrove canopy, at deeper depths and not in as close proximity to the mangroves. Coral species found growing on and directly adjacent to prop roots included Porites porites (multiple morphs, including P. divaricata and P. furcata), Siderastrea radians, and Favia fragum. Channel coral habitats predominantly hosted S. radians and a few S. siderea, although single colonies of Solenastrea bournoni and Stephanocoenia intersepta were observed. Although clear, low-turbidity water was a consistent feature of these mangrove-coral habitats, the specific combination of environmental factors that determine which mangrove habitats are favorable for coral recruitment remains to be defined. Circumstantial evidence suggests additional coral communities existed on mangrove shorelines of oceanside and backcountry islands until destroyed, likely by Hurricane Irma. These mangrove-coral habitats may be climate refugia for corals and could be included in ecosystem management plans and considered for their applications in coral restoration.
creator: Christina A. Kellogg
creator: Ryan P. Moyer
creator: Mary Jacobsen
creator: Kimberly Yates
uri: https://doi.org/10.7717/peerj.9776
license: https://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Epibiont hydroids on beachcast Sargassum in the Mexican Caribbean
link: https://peerj.com/articles/9795
last-modified: 2020-08-24
description: Massive accumulations of pelagic species of Sargassum have generated recent social, economic and ecological problems along Caribbean shores. In the Mexican Caribbean, these events have prompted the study of diverse biological and ecological aspects of these macroalgae. However, studies on their associated biota, including Hydrozoa, remain scarce. This research provides important species observations in an area where data is lacking. The occurrence and percent cover of hydroids on Sargassum thalli collected on the beach at Puerto Morelos, Quintana Roo, Mexico from April 2018 to March 2019 was studied. Three pelagic species and morphotypes of Sargassum from this area were analyzed: Sargassum fluitans III, S. natans I and S. natans VIII, as well as a benthic species, S. polyceratium var. ovatum. A total of 14 taxa of hydroids, belonging to the superorders “Anthoathecata” and Leptothecata, were identified. In our study, more hydroid taxa were observed on axes of the different species of Sargassum than on leaves or aerocysts. In general, the greatest species richness of hydroids was observed from February to April. Results show that live hydrozoans attached to pelagic Sargassum are transported into the area. This should be considered in future management measures that address the recurring coastal abundance of Sargassum and its associated biota in the Caribbean region.
creator: María A. Mendoza-Becerril
creator: Elisa Serviere-Zaragoza
creator: Alejandra Mazariegos-Villarreal
creator: Crisalejandra Rivera-Perez
creator: Dale R. Calder
creator: Erika F. Vázquez-Delfín
creator: Yolanda Freile-Pelegrín
creator: José Agüero
creator: Daniel Robledo
uri: https://doi.org/10.7717/peerj.9795
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Mendoza-Becerril et al.

title: Valanginian occurrence of Pelomedusoides turtles in northern South America: revision of this hypothesis based on a new fossil remain
link: https://peerj.com/articles/9810
last-modified: 2020-08-24
description: Pelomedusoides constitutes the most diverse group of Mesozoic and Cenozoic side-necked turtles. However, when it originated is still being poorly known and controversial. Fossil remains from the Early Cretaceous (Valanginian) Rosa Blanca Formation of Colombia were described almost a decade ago as potentially belonging to Podocnemidoidea (a large subclade inside Pelomedusoides) and representing one of the earliest records of this group of turtles. Here, I revise this hypothesis based on a new fragmentary specimen from the Rosa Blanca Formation, represented by a right portion of the shell bridge, including the mesoplastron and most of peripherals 5 to 7. The equidimensional shape of the mesoplatron allows me to support its attribution as belonging to Pelomedusoides, a group to which the previously podocnemidoid material is also attributed here. Although the Valanginian pelomesudoid material from Colombia is still too fragmentary as to be considered the earliest indisputable record of the Pelomedusoides clade, their occurrence is at least in agreement with current molecular phylogenetic hypotheses that suggest they split from Chelidae during the Jurassic and should occur in the Late Jurassic and Early Cretaceous fossil record.
creator: Edwin-Alberto Cadena
uri: https://doi.org/10.7717/peerj.9810
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Cadena