Exploring environmental coverages of species: a new variable contribution estimation methodology for rulesets from the genetic algorithm for rule-set prediction
Variable contribution estimation for, and determination of variable importance within, ecological niche models (ENMs) remain an important area of research with continuing challenges. Most ENM algorithms provide normally exhaustive searches through variable space; however, selecting variables to include in models is a first challenge. The estimation of the explanatory power of variables and the selection of the most appropriate variable set within models can be a second challenge. Although some ENMs incorporate the variable selection rubric inside the algorithms, there is no integrated rubric to evaluate the variable importance in the Genetic Algorithm for Ruleset Production (GARP). Here, we designed a novel variable selection methodology based on the rulesets generated from a GARP experiment. The importance of the variables in a GARP experiment can be estimated based on the consideration of the prevalence of each environmental variable in the dominant presence rules of the best subset of models and its coverage. We tested the performance of this variable selection method based on simulated species with both weak and strong responses to simulated environmental covariates. The variable selection method generally performed well during the simulations with over 2/3 of the trials correctly identifying most covariates. We then predict the distribution of Toxostoma rufum (a bird with a cosmopolitan distribution) in the continental United States (US) and apply our variable selection procedure as a real-world example. We found that the distribution of T. rufum could be accurately modeled with 13 or 10 of 21 variables, using an UI cutoff of 0.5 or 0.25, respectively, arriving at parsimonious environmental coverages with good model accuracy. We also provide tools to simulate species distributions for testing ENM approaches using R.
Spatial and Geographic Information Science
Yang et al. (2020) Exploring environmental coverages of species: a new variable contribution estimation methodology for rulesets from the genetic algorithm for rule-set prediction. PeerJ 8:e8968 https://doi.org/10.7717/peerj.8968
EZH2/H3K27Me3 and phosphorylated EZH2 predict chemotherapy response and prognosis in ovarian cancer
Background EZH2 acts as an oncogene through canonical pathway EZH2/H3K27Me3 and uncanonical pathway pAkt1/pS21EZH2 in many solid tumors including ovarian cancer. However, the clinical value of EZH2/H3K27Me3 and pAkt1/pS21EZH2 remain unclear. In the current study, we aim to investigate the correlation between these two pathways to clinical-pathological parameters and prognosis. Methods EZH2, H3K27Me3, pAkt1 and pS21EZH2 expression were evaluated by tissue micro-array and immunohistochemistry in a cohort of ovarian cancer patients. The results were analyzed based on clinical characteristics and survival outcomes. Results EZH2, H3K27Me3, pAkt1 and pS21EZH2 were universally expressed in ovarian cancer specimens with a positive expression rate of 81.54% (53/65), 88.89% (48/54), 63.07% (41/65) and 75.38% (49/65). EZH2-pS21EZH2 (Spearman r = 0.580, P < 0.0001) and pS21EZH2-pAkt1 (Spearman r = 0.546, P < 0.0001) were closely correlated while EZH2- H3K27Me3 were less closely correlated (Spearman r = 0.307, P = 0.002). Low pS21EZH2 associated with better chemotherapy response (OR = 0.184; 95% CI [0.052–0.647], P = 0.008) according to logistic regression with an area under the curve of 0.789 (specificity 89.36%, sensitivity 68.42%) by ROC analysis and predicted improved progression-free survival (HR = 0.453; 95% CI [0.229–0.895], P = 0.023) as indicated by multivariate cox regression. A combination of EZH2low/H3K27Me3low status predicted better chemotherapy response (OR = 0.110; 95% CI [0.013–0.906], P = 0.040) and better progression-free survival (HR = 0.388; 95% CI [0.164–0.917], P = 0.031). The results suggested that EZH2/H3K27Me3 and pEZH2 predicted chemotherapy response and progression-free survival in ovarian cancer.
Sun et al. (2020) EZH2/H3K27Me3 and phosphorylated EZH2 predict chemotherapy response and prognosis in ovarian cancer. PeerJ 8:e9052 https://doi.org/10.7717/peerj.9052
Direct aortic route versus transaxillary route for transcatheter aortic valve replacement: a systematic review and meta-analysis
Background The transfemoral route is contraindicated in nearly 10% of transcatheter aortic valve replacement (TAVR) candidates because of unsuitable iliofemoral vessels. Transaxillary (TAx) and direct aortic (DAo) routes are the principal nonfemoral TAVR routes; however, few studies have compared their outcomes. Methods We performed a systematic review and meta-analysis to compare the rates of mortality, stroke, and other adverse events of TAx and DAo TAVR. The study was prospectively registered with PROSPERO (registration number: CRD42017069788). We searched Medline, PubMed, Embase, and Cochrane databases for studies reporting the outcomes of DAo or TAx TAVR in at least 10 patients. Studies that did not use the Valve Academic Research Consortium definitions were excluded. We included studies that did not directly compare the two approaches and then pooled rates of events from the included studies for comparison. Results In total, 31 studies were included in the quantitative meta-analysis, with 2,883 and 2,172 patients in the DAo and TAx TAVR groups, respectively. Compared with TAx TAVR, DAo TAVR had a lower Society of Thoracic Surgery (STS) score, shorter fluoroscopic time, and less contrast volume use. The 30-day mortality rates were significantly higher in the DAo TAVR group (9.6%, 95% confidence interval (CI) = [8.4–10.9]) than in the TAx TAVR group (5.7%, 95% CI = [4.8–6.8]; P for heterogeneity <0.001). DAo TAVR was associated with a significantly lower risk of stroke in the overall study population (2.6% vs. 5.8%, P for heterogeneity <0.001) and in the subgroup of studies with a mean STS score of ≥8 (1.6% vs. 6.2%, P for heterogeneity = 0.005). DAo TAVR was also associated with lower risks of permanent pacemaker implantation (12.3% vs. 20.1%, P for heterogeneity = 0.009) and valve malposition (2.0% vs. 10.2%, P for heterogeneity = 0.023) than was TAx TAVR. Conclusions DAo TAVR increased 30-day mortality rate compared with TAx TAVR; by contrast, TAx TAVR increased postoperative stroke, permanent pacemaker implantation, and valve malposition risks compared with DAo TAVR.
Lee et al. (2020) Direct aortic route versus transaxillary route for transcatheter aortic valve replacement: a systematic review and meta-analysis. PeerJ 8:e9102 https://doi.org/10.7717/peerj.9102
Early language competence, but not general cognitive ability, predicts children’s recognition of emotion from facial and vocal cues
The ability to accurately identify and label emotions in the self and others is crucial for successful social interactions and good mental health. In the current study we tested the longitudinal relationship between early language skills and recognition of facial and vocal emotion cues in a representative UK population cohort with diverse language and cognitive skills (N = 369), including a large sample of children that met criteria for Developmental Language Disorder (DLD, N = 97). Language skills, but not non-verbal cognitive ability, at age 5–6 predicted emotion recognition at age 10–12. Children that met the criteria for DLD showed a large deficit in recognition of facial and vocal emotion cues. The results highlight the importance of language in supporting identification of emotions from non-verbal cues. Impairments in emotion identification may be one mechanism by which language disorder in early childhood predisposes children to later adverse social and mental health outcomes.
Griffiths et al. (2020) Early language competence, but not general cognitive ability, predicts children’s recognition of emotion from facial and vocal cues. PeerJ 8:e9118 https://doi.org/10.7717/peerj.9118
Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing
“Yibin Baijiu” (YB) is a special Chinese strong-aroma Baijiu (CSAB) that originated in Yibin, a city in western China. YB is fermented in cellars lined with pit mud (PM), the microbiota in which may affect YB quality. In this study, high throughput sequencing of the 16S rRNA gene was used to demonstrate the bacterial community structure and diversity in PM of YB. In addition, the physicochemical characteristics of PM were also analyzed, including moisture content, pH, and available phosphorous, ammonia nitrogen, and humic acid levels. Results showed that Firmicutes was the dominant phylum in all PM samples with abundance > 70.0%, followed by Euryarchaeota (11.3%), Bacteroidetes (6.5%), Synergistetes (3.0%), Actinobacteria (1.4%), and Proteobacteria (1.2%). Furthermore, 14 different genera with average relative abundance of > 1% were detected. The Chao1 and Shannon indexes did not vary significantly between the sub-layer and middle-layer PM (P > 0.05). However, Linear discriminant analysis Effect Size (LEfSe) analysis showed that the relative abundance of Lactobacillus in the sub-layer PM was significantly higher than in middle-layer PM. pH differed significantly (P < 0.05) between the two groups. Canonical correspondence analysis revealed that bacterial community in PM correlated significantly with available phosphorous content and pH. Our study provides basic data for further elucidating the diversity of microbiota in the PM of YB and the potential mechanism of Baijiu production.
Chen et al. (2020) Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing. PeerJ 8:e9122 https://doi.org/10.7717/peerj.9122
Community science participants gain environmental awareness and contribute high quality data but improvements are needed: insights from Bumble Bee Watch
Bumble Bee Watch is a community science program where participants submit photos of bumble bees from across Canada and the United States for expert verification. The data can be used to help better understand bumble bee biology and aid in their conservation. Yet for community science programs like this to be successful and sustainable, it is important to understand the participant demographics, what motivates them, and the outcomes of their participation, as well as areas that are working well or could be improved. It is also important to understand who verifies the submissions, who uses the data and their views on the program. Of the surveyed users, most participate to contribute to scientific data collection (88%), because of a worry about bees and a desire to help save them (80%), to learn more about species in their property (63%) or region (56%), and because of a personal interest (59%). About 77% report increased awareness of species diversity, while 84% report improvement in their identification skills. We found that 81% had at least one college or university degree. There were more respondents from suburban and rural areas than urban areas, but area did not affect numbers of submissions. While half were between 45 and 64 years of age, age did not influence motivation or number of submissions. Respondents were happy with the program, particularly the website resources, the contribution to knowledge and conservation efforts, the educational values, and the ability to get identifications. Areas for improvement included app and website functionality, faster and more detailed feedback, localized resources, and more communication. Most respondents participate rarely and have submitted fewer than ten records, although about five percent are super users who participate often and submit more than fifty records. Suggested improvements to the program may increase this participation rate. Indeed, increased recruitment and retention of users in general is important, and advertising should promote the outcomes of participation. Fifteen experts responded to a separate survey and were favorable of the program although there were suggestions on how to improve the verification process and the quality of the submitted data. Suggested research questions that could be asked or answered from the data included filling knowledge gaps (species diversity, ranges, habitat, phenology, floral associations, etc.), supporting species status assessments, effecting policy and legislation, encouraging habitat restoration and management efforts, and guiding further research. However, only about half have used data from the project to date. Further promotion of Bumble Bee Watch and community science programs in general should occur amongst academia, conservationists, policy makers, and the general public. This would help to increase the number and scope of submissions, knowledge of these species, interest in conserving them, and the overall program impact.
MacPhail et al. (2020) Community science participants gain environmental awareness and contribute high quality data but improvements are needed: insights from Bumble Bee Watch. PeerJ 8:e9141 https://doi.org/10.7717/peerj.9141
Long-term outcomes of repaired and unrepaired truncus arteriosus: 20-year, single-center experience in Thailand
Background Truncus arteriosus (TA) is a complex congenital heart disease that carries morbidities in the first year of life. Previous authors have reported an operative mortality of 50%. In this report, we aim to report on the survival of patients with TA in our medical center in the recent era. Methods A retrospective review of all patients diagnosed with TA in Siriraj Hospital, Thailand from August 1995 to March 2018 was performed. Patients with single ventricle, hemiTA were excluded. The characteristics and outcomes of repaired and unrepaired TA patients with a known recent functional status in 2018 were reviewed. Operative mortality risks were analyzed using a multivariate model. Results A total of 74 patients (median age at referral: 70 days) were included in the cohort. One-third of the patients had associated anomalies including DiGeorge syndrome (13.5%). Anatomical repair was not performed in 22 patients (29.7%). The median age at time of repair for the 52 patients was 133 days (range: 22 days to 16.7 years). Complex TA was 10%. Early mortality occurred in 16 patients (30.8%). Five patients (9.6%) had late deaths at 0.3–1.2 years. Significant mortality risk was weight at time of operation <4 kg (HR 3.05, 95% CI [1.05–8.74], p-value 0.041). Of the 31 operation survivors, 17 required re-intervention within 0.4–11.4 years. Eight patients had reoperation at 8.7 years (range: 2.7–14.6 years) post-repair. Freedom from reoperation was 93%, 70.4%, and 31%, at 5, 10, and 15 years, respectively. All late survivors were in functional class I–II. Of the 22 unrepaired TA patients, 11 patients (50%) died (median age: 13.6 years; range: 14 days–32.8 years). Survival of unrepaired TA patients was 68.2%, 68.2%, and 56.8, at 5, 10, and 15 years of age, respectively. At the end of study, 11 survivors of TA with palliative treatment had a recent mean oxygen saturation value of 84.1 ± 4.8% and a mean weight for height of 81.4 ± 12.7%, which were significantly lower than those of 31 late-survivors who had undergone anatomical repair. Conclusion Contemporary survival rates of patients with TA following operation in the center has been gradually improved over time. Most of the operative mortality occurs in the early postoperative period. Compared to patients with TA who had palliative treatment, operative survivors have a better functional status even though they carry a risk for re-intervention.
Dangrungroj et al. (2020) Long-term outcomes of repaired and unrepaired truncus arteriosus: 20-year, single-center experience in Thailand. PeerJ 8:e9148 https://doi.org/10.7717/peerj.9148
High type I collagen density fails to increase breast cancer stem cell phenotype
Breast cancer is a highly frequent and lethal malignancy which metastasis and relapse frequently associates with the existence of breast cancer stem cells (CSCs). CSCs are undifferentiated, aggressive and highly resistant to therapy, with traits modulated by microenvironmental cells and the extracellular matrix (ECM), a biologically complex and dynamic structure composed mainly by type I collagen (Col-I). Col-I enrichment in the tumor-associated ECM leads to microenvironment stiffness and higher tumor aggressiveness and metastatic potential. While Col-I is also known to induce tumor stemness, it is unknown if such effect is dependent of Col-I density. To answer this question, we evaluated the stemness phenotype of MDA-MB-231 and MCF-7 human breast cancer cells cultured within gels of varying Col-I densities. High Col-I density increased CD44+CD24− breast cancer stem cell (BCSC) immunophenotype but failed to potentiate Col-I fiber alignment, cell self-renewal and clonogenicity in MDA-MB-231 cells. In MCF-7 cells, high Col-I density decreased total levels of variant CD44 (CD44v). Common to both cell types, high Col-I density induced neither markers related to CSC nor those related with mechanically-induced cell response. We conclude that high Col-I density per se is not sufficient to fully develop the BCSC phenotype.
Valadão et al. (2020) High type I collagen density fails to increase breast cancer stem cell phenotype. PeerJ 8:e9153 https://doi.org/10.7717/peerj.9153
Exploring the interactions among SNARC effect, finger counting direction and embodied cognition
The Spatial Numerical Association of Response Code (SNARC) is the preferential association between smaller/larger magnitudes and left/right side, respectively. Some evidence suggest a link between SNARC and a left-to-right finger counting habit. We asked 268 participants to show how they use the hands to count from 1 to 10. By means of this ecological task, 80% of the sample use first the right hand (to count from 1 to 5) and the majority of them use a palm-up posture. In Experiment 2 (N = 46) right-starters were asked to categorize 1-to-5 magnitudes as even or odd, using the left and right hand. Stimuli were presented both as Arabic numbers and by means of left and right hand photographs in palm-up and palm-down posture. Results confirmed the expected SNARC effect in the Arabic condition. With hand images we found that right hand responses were better for larger than for smaller magnitudes (SNARC, mainly for left hand palm-up stimuli), showing that the SNARC can be generalized to different codes. Finally, the interactions between magnitudes and left/right hand images in palm-up and palm-down posture suggest that embodied cognition can influence numerical processing.
Prete et al. (2020) Exploring the interactions among SNARC effect, finger counting direction and embodied cognition. PeerJ 8:e9155 https://doi.org/10.7717/peerj.9155
Ontogeny of a sexually selected structure in an extant archosaur Gavialis gangeticus (Pseudosuchia: Crocodylia) with implications for sexual dimorphism in dinosaurs
Despite strong evidence for sexual selection in various display traits and other exaggerated structures in large extinct reptiles, such as dinosaurs, detecting sexual dimorphism in them remains difficult. Their relatively small sample sizes, long growth periods, and difficulties distinguishing the sexes of fossil specimens mean that there are little compelling data on dimorphism in these animals. The extant gharial (Gavialis gangeticus) is a large and endangered crocodylian that is sexually dimorphic in size, but males also possesses a sexually selected structure, the ghara, which has an osteological correlate in the presence of a fossa associated with the nares. This makes the species a unique model for potentially assessing dimorphism in fossil lineages, such as dinosaurs and pterosaurs, because it is a large, slow-growing, egg-laying archosaur. Here we assess the dimorphism of G. gangeticus across 106 specimens and show that the presence of a narial fossa diagnoses adult male gharials. Males are larger than females, but the level of size dimorphism, and that of other cranial features, is low and difficult to detect without a priori knowledge of the sexes, even with this large dataset. By extension, dimorphism in extinct reptiles is very difficult to detect in the absence of sex specific characters, such as the narial fossa.
Hone et al. (2020) Ontogeny of a sexually selected structure in an extant archosaur Gavialis gangeticus (Pseudosuchia: Crocodylia) with implications for sexual dimorphism in dinosaurs. PeerJ 8:e9134 https://doi.org/10.7717/peerj.9134