Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations
Background Carex 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. Methods The 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. Results Results 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). Conclusions The 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.
Więcław et al. (2021) Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations. PeerJ 9:e11372 https://doi.org/10.7717/peerj.11372
Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements
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.
Gonzalez-Pimentel et al. (2021) Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements. PeerJ 9:e11386 https://doi.org/10.7717/peerj.11386
Mapping open knowledge institutions: an exploratory analysis of Australian universities
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.
Huang et al. (2021) Mapping open knowledge institutions: an exploratory analysis of Australian universities. PeerJ 9:e11391 https://doi.org/10.7717/peerj.11391
Shiftwork, functional bowel symptoms, and the microbiome
Background There 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. Methods Fifty-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. Results There 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.
Rogers et al. (2021) Shiftwork, functional bowel symptoms, and the microbiome. PeerJ 9:e11406 https://doi.org/10.7717/peerj.11406
GBP2 as a potential prognostic biomarker in pancreatic adenocarcinoma
Background Pancreatic 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. Method We 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. Result GBP2 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. Conclusion GBP2 acted as a potential prognostic biomarker and was associated with immune infiltration and the expression of immune checkpoints in PAAD.
Liu et al. (2021) GBP2 as a potential prognostic biomarker in pancreatic adenocarcinoma. PeerJ 9:e11423 https://doi.org/10.7717/peerj.11423
Eating habits, lifestyle behaviors and stress during the COVID-19 pandemic quarantine among Peruvian adults
Background and aims The 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. Methods We 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. Results A 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. Conclusion Almost four out of ten participants gained weight during the quarantine. This was associated with unhealthy eating habits, physical inactivity, and stressful scenarios.
Agurto et al. (2021) Eating habits, lifestyle behaviors and stress during the COVID-19 pandemic quarantine among Peruvian adults. PeerJ 9:e11431 https://doi.org/10.7717/peerj.11431
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
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.
Etherington (2021) 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. PeerJ 9:e11436 https://doi.org/10.7717/peerj.11436
Alterations in mechanical muscle characteristics and postural control induced by tennis match-play in young players
Background Central 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. Objective This study aimed to investigate alterations induced by a simulated tennis match on postural control and muscle characteristics in young tennis players. Method Seventeen 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. Results No 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). Conclusion An 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.
Colomar et al. (2021) Alterations in mechanical muscle characteristics and postural control induced by tennis match-play in young players. PeerJ 9:e11445 https://doi.org/10.7717/peerj.11445
Patient characteristics and cardiac surgical outcomes at a tertiary care hospital in Kenya, 2008–2017: a retrospective study
Background Cardiac surgeries are high risk procedures that require specialized care and access to these procedures is often limited in resource-poor countries. Although fatalities for surgical patients across Africa are twice that of the global rate, cardiac surgical mortality continent-wide is only slightly higher than all-surgical mortality. Understanding demographic and health characteristics of patients and the associations of these characteristics with morbidity and mortality events is important in guiding care decisions. Therefore, the objectives of this study were to: (a) describe the characteristics of cardiac surgical patients; (b) identify the associations between these characteristics and morbidity and mortality events following cardiac surgery. Methods Patient characteristics and post-surgical complications were abstracted for all cardiac surgical patients treated at a tertiary care hospital in Kenya from 2008 to 2017. Descriptive analyses of demographic factors, co-morbidities, peri-operative conditions, and post-surgical complications were conducted for adult and pediatric patients. Cochran-Armitage trend test was used to assess temporal trends in risk of death. Multivariable ordinary logistic and Firth logistic models were used to investigate predictors of surgical outcomes. Results The study included a total of 181 patients (150 adult and 31 pediatric patients). Most (91.3%) adult patients had acquired conditions while 45.2% of the pediatric patients had congenital defects. Adult patients tended to have co-morbid conditions including hypertension (16.7%), diabetes mellitus (7.3%), and nephropathy (6.7%). Most patients (76.0% adults and 96.8% pediatric patients) underwent ≤ 2 surgical procedures during their hospital stay. Seventy percent of adult and 54.8% of the pediatric patients experienced at least one post-surgical complication including mediastinal hemorrhage, acute kidney injury and death. Patient characteristics played the greatest roles in predicting post-surgical complications. For adult patients, significant predictors of acute kidney injury included atrial fibrillation (OR = 18.25; p = .001), mitral valve replacement (OR = 0.14; p = .019), and use of cardiopulmonary bypass (OR = 0.06; p = .002). Significant predictors of 30-day mortality were age (OR = 1.05; p = .015) and atrial fibrillation (OR = 4.12, p = .018). Although the number of surgeries increased over the decade-long study period, there were no significant (p = .467) temporal trends in the risk of death. Conclusions Awareness of demographic and peri-surgical factors that are predictors of complications is useful in guiding clinical decisions to reduce morbidity and mortality. Identification of co-morbidities as the most useful predictors of post-surgical complications suggests that patient characteristics may be a larger contributor to the incidence of complications than surgical practices.
Chavez-Lindell et al. (2021) Patient characteristics and cardiac surgical outcomes at a tertiary care hospital in Kenya, 2008–2017: a retrospective study. PeerJ 9:e11191 https://doi.org/10.7717/peerj.11191
The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids
Dyrosauridae is a clade of neosuchian crocodyliforms that diversified in terrestrial and aquatic environments across the Cretaceous-Paleogene transition. The postcranial anatomy of dyrosaurids has long been overlooked, obscuring both their disparity and their locomotive adaptations. Here we thoroughly describe of the postcranial remains of an unusually small dyrosaurid, Cerrejonisuchus improcerus, from the middle-late Paleocene Cerrejón Formation of Colombia, and we provide a wealth of new data concerning the postcranial anatomy of the key dyrosaurids: Congosaurus bequaerti and Hyposaurus rogersii. We identify a series of postcranial autapomorphies in Cerrejonisuchus improcerus (an elliptic-shaped odontoid laterally wide, a ulna possessing a double concavity, a fibula bearing a widely flattened proximal end, a pubis showing a large non-triangular distal surface) as well as functionally-important traits such as a relatively long ulna (85% of the humerus’ length), short forelimb (83% of hindlimb’s length), or thoracic vertebra bearing comparatively large lateral process (with widened parapophysis and diapophysis) along with strongly arched thoracic ribs allowing a more sturdy and cylindrical rib cage. These indicate a more terrestrial lifestyle for Cerrejonisuchus compared to the derived members of the clade. We also built a dataset of 187 traits on 27 taxa, that extensively samples the cranial and postcranial architectures of exemplar crocodyliforms. We analyze these data in via Principal Coordinate Analysis (PCoA) to visualize the postcranial morphospace occupation of Dyrosauridae, Thalattosuchia, and Crocodylia. Our data reveal the existence of a distinctive postcranial anatomy for Dyrosauridae that is markedly distinct from that of crocodylians. As a result, modern crocodylians are probably not good functional analog for extinct crocodyliformes. Postcranial data should also be more widely used in phylogenetic and disparity analyses of Crocodyliformes.
Scavezzoni et al. (2021) The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids. PeerJ 9:e11222 https://doi.org/10.7717/peerj.11222