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
Body composition and bone mineral density in athletes with a physical impairment
Background The impact of the type and the severity of disability on whole-body and regional body composition (BC), and bone mineral density (BMD) must be considered for dietary advice in athletes with a physical impairment (PI). This study aimed to investigate the impact of the type and the severity of disability on BC, the pattern of distribution of fat mass at the regional level, and BMD in athletes with a PI. Methods Forty-two male athletes with spinal cord injury (SCI, n = 24; age = 40.04 ± 9.95 years, Body Mass Index [BMI] = 23.07 ± 4.01 kg/m2) or unilateral lower limb amputation (AMP, n = 18; age = 34.39 ± 9.19 years, BMI = 22.81 ± 2.63 kg/m2) underwent a Dual-Energy X-Ray Absorptiometry scan. Each athlete with a PI was matched by age with an able-bodied athlete (AB, n = 42; age = 37.81 ± 10.31 years, BMI = 23.94 ± 1.8 kg/m2). Results One-Way Analysis of Variance showed significant differences between the SCI, AMP and AB groups for percentage fat mass (%FM) (P < 0.001, eta squared = 0.440). Post-hoc analysis with Bonferroni’s correction showed that athletes with SCI had significantly higher %FM vs. the AMP and AB groups (25.45 ± 5.99%, 21.45 ± 4.21% and 16.69 ± 2.56%, respectively; P = 0.008 vs. AMP and P < 0.001 vs. AB). The %FM was also significantly higher in the AMP vs. the AB group (P < 0.001). Whole-body BMD was negatively affected in SCI athletes, with about half of them showing osteopenia or osteoporosis. In fact, the mean BMD and T-score values in the SCI group (1.07 ± 0.09 g/cm2 and −1.25 ± 0.85, respectively) were significantly lower in comparison with the AB group (P = 0.001 for both) as well as the AMP group (P = 0.008 for both). The type of disability affected BC and BMD in the trunk, android, gynoid and leg regions in SCI athletes and the impaired leg only in AMP athletes. Conclusions In conclusion, the type of disability and, partly, the severity of PI impact on BC and BMD in athletes with a PI. Nutritionists, sports medicine doctors, clinicians, coaches and physical conditioners should consider athletes with SCI or AMP separately. Athletes with a PI would benefit from specific nutrition and training programs taking into account the type of their disability.
Cavedon et al. (2021) Body composition and bone mineral density in athletes with a physical impairment. PeerJ 9:e11296 https://doi.org/10.7717/peerj.11296
A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research
The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community.
Calvert et al. (2021) A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research. PeerJ 9:e11389 https://doi.org/10.7717/peerj.11389
Media exposure predicts acute stress and probable acute stress disorder during the early COVID-19 outbreak in China
Background The COVID-19 has led to unprecedented psychological stress on the general public. However, the associations between media exposure to COVID-19 and acute stress responses have not been explored during the early COVID-19 outbreak in China. Methods An online survey was conducted to investigate the relationships between media exposure to COVID-19 and acute stress responses, and to recognize associated predictors of acute stress responses on a sample of 1,450 Chinese citizens from February 3 to February 10, 2020. Media exposure questionnaire related to COVID-19 was developed to assess media exposure time, media exposure forms and media exposure content. The Stanford Acute Stress Reaction Questionnaire (SASRQ) was used to measure acute stress responses, including continuous acute stress symptom scores and the risk of probable acute stress disorder (ASD). A series of regression analyses were conducted. Results Longer media exposure time and social media use were associated with higher acute stress and probable ASD. Viewing the situation of infected patients was associated with higher acute stress, whereas viewing the latest news about pandemic data was associated with lower odds of probable ASD. Being females, living in Hubei Province, someone close to them diagnosed with COVID-19, history of mental illness, recent adverse life events and previous collective trauma exposure were risk factors for acute stress responses. Conclusions These findings confirmed the associations between indirect media exposure to pandemic events and acute stress responses. The governments should be aware of the negative impacts of disaster-related media exposure and implement appropriate interventions to promote psychological well-being following pandemic events.
Luo et al. (2021) Media exposure predicts acute stress and probable acute stress disorder during the early COVID-19 outbreak in China. PeerJ 9:e11407 https://doi.org/10.7717/peerj.11407
Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa
Spatial distribution of zooplankton communities depends on numerous factors, especially temperature and salinity conditions (hydrological factor), sampled depth, chlorophyll concentration, and diel cycle. We analyzed and compared the impact of these factors on mesoplankton abundance, biodiversity, quantitative structure based on proportion of taxa and qualitative structure based on presence/absence of taxa in the Southern Ocean. Samples (43 stations, three vertical strata sampled at each station, 163 taxa identified) were collected with a Juday net along the SR02 transect in December 2009. Mesoplankton abundance in discrete vertical layers ranged from 0.2 to 13,743.6 ind. m−3, i.e., five orders of magnitude, maximal and minimal values were recorded in the upper mixed and in the deepest layer, respectively. Within the combined 300-m layer, abundances ranged from 16.0 to 1,455.0 ind. m−3, i.e., two orders of magnitude suggesting that integral samples provide little information about actual variations of mesoplankton abundances. A set of analyses showed that depth was the major driver of mesoplankton distribution (abundance, biodiversity, quantitative structure), hydrological factors influenced two of them (quantitative and qualitative structure), chlorophyll concentration strongly affected only quantitative structure, and diel cycle had an insignificant effect on mesoplankton distribution. Using our current knowledge of the fine structure of the Antarctic Circumpolar Current, we compared effects of four hydrological fronts, i.e., boundaries between different water-masses with distinct environmental characteristics, and eight dynamic jets (narrow yet very intense currents) on mesoplankton distribution. Subtropical, Polar, and Subantarctic Fronts drove quantitative and qualitative structure of mesoplankton assemblages (decreasing in order of influence), while the Southern Boundary affected only qualitative structure. Effects of dynamic jets were insignificant. We suggest that mesoplankton composition is driven by hydrological parameters and further maintained through compartmentalization by fronts. Impact of local eddies and meanders on biodiversity, abundance, qualitative and quantitative structure of mesoplankton is comparable to that of hydrological fronts. Qualitative structure of mesoplankton assemblages mirrors hydrological structure of the Southern Ocean better than quantitative structure and may be recommended for biogeographic analyses of the Southern Ocean. Comparisons with previous reports from the same area retrieved no significant changes in mesoplankton distribution during the period 1992–2009.
Vereshchaka et al. (2021) Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa. PeerJ 9:e11411 https://doi.org/10.7717/peerj.11411