title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=912 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Artificial light source selection in seaweed production: growth of seaweed and biosynthesis of photosynthetic pigments and soluble protein link: https://peerj.com/articles/11351 last-modified: 2021-05-11 description: Seaweed growth is often limited by light. Artificial light supply has been well studied in terrestrial agriculture, however, much less is known about its effect in seaweed aquaculture. In this study, the effects of four artificial light sources (white, red, green, and blue LEDs light) on a brown alga Sargassum fusiforme and a green alga Ulva pertusa were investigated. Seaweed growth, accumulation of photosynthetic pigments (chlorophyll a and carotenoid), and soluble protein were evaluated. White LED light was the optimal supplementary light when cultivating Ulva pertusa and Sargassum fusiforme, because it promoted seaweed growth while maintaining protein production. Meanwhile, red LED was unfavored in the cultivation of S. fusiforme, as it affected the seaweed growth and has a lower residual energy ratio underneath the water. LEDs would be a promising supplementary light source for seaweed cultivation. creator: Shitao Huang creator: Ke Li creator: Yaoru Pan creator: Yan Yu creator: Thomas Wernberg creator: Thibaut de Bettignies creator: Jiaping Wu creator: Chaosheng Zhou creator: Zhixing Huang creator: Xi Xiao uri: https://doi.org/10.7717/peerj.11351 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Huang et al. title: Durnonovariaodus maiseyi gen. et sp. nov., a new hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of England link: https://peerj.com/articles/11362 last-modified: 2021-05-11 description: A partial skeleton of a hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of Dorset, England, is described and designated as a new genus and species, Durnonovariaodus maiseyi gen. et sp. nov. The holotype and only known specimen, which is represented by disarticulated splanchnocranial elements with associated teeth, a single dorsal fin spine, the pelvic girdle, as well as unidentifiable cartilage fragments, plus countless dermal denticles, exhibits a puzzling combination of dental and skeletal features, providing important new insights into the morphological and ecological diversity of hybodontiforms. Durnonovariaodus gen. nov. displays a unique set of dental characters, showing close morphological resemblance to Secarodus from the Middle Jurassic of England, which was erected for distinctive, strongly labio-lingually compressed multicuspid cutting teeth originally described as Hybodus polyprion. Skeletally, Durnonovariaodus gen. nov. resembles Hybodus and Egertonodus in having a palatoquadrate with a palatobasal process and an ethmoidal articular surface, combined with the possession of dorsal fin spines ornamented with costae. Therefore, and given the absence of any conclusive phylogenetic framework, Durnonovariaodus maiseyi gen. et sp. nov. is here tentatively referred to Hybodontidae until more complete material becomes available in order to enable a more reliable suprageneric identification. The holotype of Durnonovariaodus maiseyi gen. et sp. nov. contains two separate pelvic half-girdles, a feature previously considered as evolutionarily primitive among hybodontiforms. However, unfused pelvic half-girdles also occur in the supposedly closely related species Hybodus hauffianus and may in fact have been more widely distributed among hybodontiforms than previously thought, thus rendering the phylogenetic utility of separated pelvic half-girdles for inferring hybodontiform interrelationships difficult and unresolved. creator: Sebastian Stumpf creator: Steve Etches creator: Charlie J. Underwood creator: Jürgen Kriwet uri: https://doi.org/10.7717/peerj.11362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Stumpf et al. title: Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations link: https://peerj.com/articles/11372 last-modified: 2021-05-11 description: BackgroundCarex buxbaumii and C. hartmaniorum are sister species of the clade Papilliferae within the monophyletic section Racemosae. An unambiguous identification of these species is relatively difficult due to the interspecific continuum of some morphological characters as well as the intraspecific variability. The study was aimed at determining the range of variability, both morphological and genetic, within and between these two closely related and similar species.MethodsThe sedges were collected during botanical expeditions to Armenia, Estonia, the Netherlands, and Poland. The morphological separation of the two species and their populations was tested using the Discriminant Function Analysis (DFA). The genetic variability of the 19 Carex populations was assessed in the presence of eight Inter Simple Sequence Repeat (ISSR) primers.ResultsResults of the study indicate a considerable genetic affinity between the two sedge species (mean Si = 0.619). However, the populations of C. hartmaniorum are, morphologically and genetically, more homogenous than the populations of C. buxbaumii. Compared to C. hartmaniorum, C. buxbaumii usually has wider leaf blades, a shorter inflorescence, a lower number of spikes which are shorter, but wider, and longer bracts and utricles. The AMOVA showed a larger variation between the populations of C. buxbaumii, representing 25.65% of the total variation in the taxon. Two populations of C. buxbaumii (from Poland and Estonia) are separated from the remaining populations, both genetically and morphologically; their individuals show shorter utricles and glumes, compared to the typical specimens of C. buxbaumii, and correspond with the morphology of putative infraspecific taxa described by Cajander (var. brevisquamosa and var. confusa).ConclusionsThe taxonomic status of the putative infraspecific taxa within C. buxbaumii requires further studies throughout the distribution range of C. buxbaumii, addressing habitats, morphology and genetics (including a chromosome count or a combination of different genetic methods), particularly as the variability in C. buxbaumii may be associated with the species’ polyploid origin. creator: Helena Więcław creator: Magdalena Szenejko creator: Thea Kull creator: Zofia Sotek creator: Ewa Rębacz-Maron creator: Jacob Koopman uri: https://doi.org/10.7717/peerj.11372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Więcław et al. title: Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements link: https://peerj.com/articles/11386 last-modified: 2021-05-11 description: Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37–89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72–96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements. creator: Jose Luis Gonzalez-Pimentel creator: Tamara Martin-Pozas creator: Valme Jurado creator: Ana Zelia Miller creator: Ana Teresa Caldeira creator: Octavio Fernandez-Lorenzo creator: Sergio Sanchez-Moral creator: Cesareo Saiz-Jimenez uri: https://doi.org/10.7717/peerj.11386 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gonzalez-Pimentel et al. title: Mapping open knowledge institutions: an exploratory analysis of Australian universities link: https://peerj.com/articles/11391 last-modified: 2021-05-11 description: While the movement for open research has gained momentum in recent years, there remain concerns about the broader commitment to openness in knowledge production and dissemination. Increasingly, universities are under pressure to transform themselves to engage with the wider community and to be more inclusive. Open knowledge institutions (OKIs) provide a framework that encourages universities to act with the principles of openness at their centre; not only should universities embrace digital open access (OA), but also lead actions in cultivating diversity, equity, transparency and positive changes in society. This leads to questions of whether we can evaluate the progress of OKIs and what are potential indicators for OKIs. As an exploratory study, this article reports on the collection and analysis of a list of potential OKI indicators. Data for these indicators are gathered for 43 Australian universities. The indicators provide high-dimensional and complex signals about university performances. They show evidence of large disparities in characteristics such as Indigenous employment and gender equity, and a preference for repository-mediated OA across Australian universities. We demonstrate use of the OKI evaluation framework to categorise these indicators into three platforms of diversity, communication and coordination. The analysis provides new insights into the Australian open knowledge landscape and ways of mapping different paths of OKIs. creator: Chun-Kai (Karl) Huang creator: Katie Wilson creator: Cameron Neylon creator: Alkim Ozaygen creator: Lucy Montgomery creator: Richard Hosking uri: https://doi.org/10.7717/peerj.11391 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huang et al. title: Shiftwork, functional bowel symptoms, and the microbiome link: https://peerj.com/articles/11406 last-modified: 2021-05-11 description: BackgroundThere are about 15 million Americans working full-time on evening, night, or rotating shifts. Between 48% and 81.9% of those working rotating or night shifts report abdominal pain, constipation, diarrhea and other symptoms of functional bowel disorders. The basis for this high prevalence of functional bowel disorders, including irritable bowel syndrome (IBS), among shift workers is unknown. Animal studies, however, suggest that circadian disruption, similar to that in shift workers, may contribute to the development of GI complaints among shift workers by altering the composition and normal diurnal rhythmicity of the resident intestinal microbes. Therefore, the present study was designed to determine if there were differences in (1) composition and diversity of the microbiome of night shift workers compared to day shift workers; and (2) the composition and diversity of the microbiome among shift workers experiencing functional bowel symptoms compared to shift workers who did not experience functional bowel symptoms.MethodsFifty-one full time staff nurses who worked either 12-hour day or night shifts completed demographic information, and the Rome III IBS module. They also collected two samples of gut microbiota before the beginning and at the end of their last work shift on day 14, using validated field-tested methods consistent with the Human Microbiome Project. After DNA extraction, 16S rRNA sequencing and assignment to the genus level was completed, samples were then compared to determine if there were (1) differences in the diversity and profile of the microbiome by shift type; (2) if there were differences in the microbiome by time of day for collection; and (3) whether there were differences in the diversity and profile of the microbiome of nurses with IBS and those without IBS.ResultsThere were no differences in alpha or beta diversity of gut microbiota when specimens from day and night shift nurses were compared. There were however marginal differences in beta diversity when specimens collected at the beginning and end of the shifts were compared, with seven OTUs being differentially abundant when collected from day shift workers in the evening. There were also three OTUs to be differentially abundant in participants reporting IBS symptoms. creator: Ann E. Rogers creator: Yi-Juan Hu creator: Ye Yue creator: Emily F. Wissel creator: Robert A. Petit III creator: Simone Jarrett creator: Jennifer Christie creator: Timothy D. Read uri: https://doi.org/10.7717/peerj.11406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rogers et al. title: GBP2 as a potential prognostic biomarker in pancreatic adenocarcinoma link: https://peerj.com/articles/11423 last-modified: 2021-05-11 description: BackgroundPancreatic adenocarcinoma (PAAD) is a disease with atypical symptoms, an unfavorable response to therapy, and a poor outcome. Abnormal guanylate-binding proteins (GBPs) play an important role in the host’s defense against viral infection and may be related to carcinogenesis. In this study, we sought to determine the relationship between GBP2 expression and phenotype in patients with PAAD and explored the possible underlying biological mechanism.MethodWe analyzed the expression of GBP2 in PAAD tissues using a multiple gene expression database and a cohort of 42 PAAD patients. We evaluated GBP2’s prognostic value using Kaplan–Meier analysis and the Cox regression model. GO and KEGG enrichment analysis, co-expression analysis, and GSEA were performed to illustrate the possible underlying biological mechanism. CIBERSORT and the relative expression of immune checkpoints were used to estimate the relationship between GBP2 expression and tumor immunology.ResultGBP2 was remarkably overexpressed in PAAD tissue. The overexpression of GBP2 was correlated with an advanced T stage and poor overall survival (OS) and GBP2 expression was an independent risk factor for OS in PAAD patients. Functional analysis demonstrated that positively co-expressed genes of GBP2 were closely associated with pathways in cancer and the NOD-like receptor signaling pathway. Most of the characteristic immune checkpoints, including PDCD1, PDCDL1, CTLA4, CD80, TIGIT, LAG3, IDO2, and VISTA, were significantly expressed in the high-GBP2 expression group compared with the low-GBP2 expression group.ConclusionGBP2 acted as a potential prognostic biomarker and was associated with immune infiltration and the expression of immune checkpoints in PAAD. creator: Bo Liu creator: Rongfei Huang creator: Tingting Fu creator: Ping He creator: Chengyou Du creator: Wei Zhou creator: Ke Xu creator: Tao Ren uri: https://doi.org/10.7717/peerj.11423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Eating habits, lifestyle behaviors and stress during the COVID-19 pandemic quarantine among Peruvian adults link: https://peerj.com/articles/11431 last-modified: 2021-05-11 description: Background and aimsThe coronavirus disease 2019 (COVID‐19) outbreak has led to an unprecedented public health crisis. In Peru, although the quarantine is no longer mandatory, it was during the first months of 2020. To date, no studies have assessed the impact of the COVID-19 on the eating patterns and lifestyle context in the country. We aimed to describe the eating habits, lifestyle behaviors and stress during the COVID-19 pandemic quarantine among Peruvian adults.MethodsWe conducted a cross-sectional study. We used an online survey to collect information regarding eating habits, self-perceived stress and sedentary lifestyle among adults over 18 years of age residing in Lima-Peru and who complied with strict home quarantine. We presented our data according to the weight variation of the participants.ResultsA total of 686 were finally included in the study. The 82.9% were female, the median BMI was 25.97 kg/m2 (IQR: 23.37–29.41) and 68.2% reported a significant variation in their weight (38.9% increased and 29.3% lost weight). All bad habits were significantly associated with weight gain, except for prolonged fasting. Additionally, a sitting time longer than usual (p = 0.001), being in front of a screen for more than five hours in the last week (p = 0.002), and most of the stressful scenarios were significantly associated with weight gain.ConclusionAlmost four out of ten participants gained weight during the quarantine. This was associated with unhealthy eating habits, physical inactivity, and stressful scenarios. creator: Hellen S. Agurto creator: Ana L. Alcantara-Diaz creator: Eduardo Espinet-Coll creator: Carlos J. Toro-Huamanchumo uri: https://doi.org/10.7717/peerj.11431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Agurto et al. title: Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method link: https://peerj.com/articles/11436 last-modified: 2021-05-11 description: The Mahalanobis distance is a statistical technique that has been used in statistics and data science for data classification and outlier detection, and in ecology to quantify species-environment relationships in habitat and ecological niche models. Mahalanobis distances are based on the location and scatter of a multivariate normal distribution, and can measure how distant any point in space is from the centre of this kind of distribution. Three different methods for calculating the multivariate location and scatter are commonly used: the sample mean and variance-covariance, the minimum covariance determinant, and the minimum volume ellipsoid. The minimum covariance determinant and minimum volume ellipsoid were developed to be robust to outliers by minimising the multivariate location and scatter for a subset of the full sample, with the proportion of the full sample forming the subset being controlled by a user-defined parameter. This outlier robustness means the minimum covariance determinant and the minimum volume ellipsoid are highly relevant for ecological niche analyses, which are usually based on natural history observations that are likely to contain errors. However, natural history observations will also contain extreme bias, to which the minimum covariance determinant and the minimum volume ellipsoid will also be sensitive. To provide guidance for selecting and parameterising a multivariate location and scatter method, a series of virtual ecological niche modelling experiments were conducted to demonstrate the performance of each multivariate location and scatter method under different levels of sample size, errors, and bias. The results show that there is no optimal modelling approach, and that choices need to be made based on the individual data and question. The sample mean and variance-covariance method will perform best on very small sample sizes if the data are free of error and bias. At larger sample sizes the minimum covariance determinant and minimum volume ellipsoid methods perform as well or better, but only if they are appropriately parameterised. Modellers who are more concerned about the prevalence of errors should retain a smaller proportion of the full data set, while modellers more concerned about the prevalence of bias should retain a larger proportion of the full data set. I conclude that Mahalanobis distances are a useful niche modelling technique, but only for questions relating to the fundamental niche of a species where the assumption of multivariate normality is reasonable. Users of the minimum covariance determinant and minimum volume ellipsoid methods must also clearly report their parameterisations so that the results can be interpreted correctly. creator: Thomas R. Etherington uri: https://doi.org/10.7717/peerj.11436 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Etherington title: Alterations in mechanical muscle characteristics and postural control induced by tennis match-play in young players link: https://peerj.com/articles/11445 last-modified: 2021-05-11 description: BackgroundCentral and peripheric fatigue indicators are among the main reasons for performance decline following competition. Because of the impact of these factors on performance, how these variables are affected by match-play could be of interest, especially in young tennis players.ObjectiveThis study aimed to investigate alterations induced by a simulated tennis match on postural control and muscle characteristics in young tennis players.MethodSeventeen male junior players took part in pre- and post-competition testing sessions performing postural control (displacement, speed and surface area of center of pressures) and muscle characteristics measurements (tone, stiffness, time to relaxation and elasticity). Between trials, participants played an 80-min simulated tennis match.ResultsNo significant differences were observed in any of the tested variables. Moderate-to-large effect sizes (ES) for decreased stiffness and tone and greater time to relaxation were found between pre- and post-conditions in the right rectus abdominis (−9.8%, −4.4% and 7.8%; ES = 0.8, 0.54 and −0.85). Also, a decrease in tone was found in the right vastus medialis (−7.1%; ES = 0.56), while surface area of the center of pressures with eyes open showed trends towards increasing in post-match measurements (55.9%; ES = 0.56).ConclusionAn 80-min simulated tennis match seems insufficient to elicit significant changes in postural control and mechanical muscle characteristics. Results suggest that physiological responses triggered by match-play were closer to those seen after a moderate activity than those present following a strenuous task. creator: Joshua Colomar creator: Francisco Corbi creator: Ernest Baiget uri: https://doi.org/10.7717/peerj.11445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Colomar et al.