Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles
Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.
Yeoh et al. (2019) Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles. PeerJ 7:e6172 https://doi.org/10.7717/peerj.6172
Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis
Background Researches on artificial livers greatly contribute to the clinical treatments for liver failure. This study aimed to evaluate the research output of artificial livers and citations from 2004 to 2017 through a bibliometric analysis. Methods A list of included articles on artificial livers were generated after a comprehensive search of the Web of Science Core Collection (from 2004 to 2017) with the following basic information: number of publications, citations, publication year, country of origin, authors and authorship, funding source, journals, institutions, keywords, and research area. Results A total of 968 included articles ranged from 47 citations to 394 citations with a fluctuation. The publications were distributed in 12 countries, led by China (n = 212) and the US (n = 207). There were strong correlations of the number of citations with authors (r2 = 0.133, p < 0.001), and countries (r2 = 0.275, p < 0.001), while no correlations of the number of citations with the years since publication (r2 = 0.016, p = 0.216), and funding (r2 < 0.001, p = 0.770) were identified. Keyword analysis demonstrated that with the specific change of “acute liver failure,” decrease in “bioartificial livers” and “hepatocyte,” and increase in “tissue engineering” were identified. The top 53 cited keyword and keyword plus (including some duplicates counts) were identified, led by bioartificial liver (405 citations) and hepatocyte (248 citations). The top 50 cited keywords bursts were mainly “Blood” (2004–2008), “hepatocyte like cell” (2008–2015), and “tissue engineering” (2014–2017). All keywords could be classified into four categories: bioartificial livers (57.40%), blood purification (25.00%), clinical (14.81%), and other artificial organs (2.78%). Discussion This study shows the process and tendency of artificial liver research with a comprehensive analysis on artificial livers. However, although it seems that the future of artificial livers seems brighter for hepatocyte transplantation, the systems of artificial livers now are inclined on focusing on blood purification, plasma exchange, etc.
Li et al. (2019) Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis. PeerJ 6:e6178 https://doi.org/10.7717/peerj.6178
Non-H3 CDR template selection in antibody modeling through machine learning
Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1, H2, H3, L1, L2 and L3), which also makes accurate structural modeling of CDRs challenging. Both homology and de novo modeling approaches have been used; to date, the former has achieved greater accuracy for the non-H3 loops. The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters. Most antibody-modeling suites utilize homology modeling for the non-H3 CDRs, differing only in the alignment algorithm and how/if they utilize structural clusters. While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to clusters. While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody structures and are infrequently updated. In this study, we propose a machine learning approach (Gradient Boosting Machine [GBM]) to learn the structural clusters of non-H3 CDRs from sequence alone. The GBM method simplifies feature selection and can easily integrate new data, compared to manual sequence rule curation. We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe an improvement in the classification accuracy of the concerned loops from 84.5% ± 0.24% to 88.16% ± 0.056%. The GBM models reduce the errors in specific cluster membership misclassifications when the involved clusters have relatively abundant data. Based on the factors identified, we suggest methods that can enrich structural classes with sparse data to further improve prediction accuracy in future studies.
Long et al. (2019) Non-H3 CDR template selection in antibody modeling through machine learning. PeerJ 7:e6179 https://doi.org/10.7717/peerj.6179
Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia
Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
Sun et al. (2019) Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia. PeerJ 7:e6194 https://doi.org/10.7717/peerj.6194
Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal
Proponents of artificial reef (AR) deployment are often motivated by the usefulness of such structures. The usefulness of ARs is related to their capability of providing ecosystem services/additional functions. We present two distinct Portuguese AR case studies: (1) The Nazaré reef off the central coast of Portugal and (2) the Oura reef off the Algarve coast. Semi-structured interviews were conducted with local fishermen in the fishing towns of Nazaré and Quarteira pre-and post-AR deployment. The main focus of the interviews was to understand fishermen’s perception of AR usefulness (or lack thereof) in terms of nine ecosystem services/additional functions potentially provided by the ARs. We tested the null hypothesis that ARs do not provide additional ecosystem services/additional functions. When queried pre-AR deployment, fishermen indicated that ARs are most likely to provide three ecosystem services: “habitat and refuge,” “biodiversity preservation” and “food production.” Fishermen had similar perceptions post-deployment. For the Nazaré reef, fishermen tended to have a positive or neutral perception of ecosystem services/additional functions being provided by ARs. For the Oura reef, fishermen tended to have a mostly neutral perception of AR ecosystem services; however, there were also some positive and other negative perceptions. It was difficult for stakeholders to conceptualize some of the ecosystem services/additional functions provided by ARs prior to actively using them. As a result, some stakeholders changed their perception of the ecosystem services/additional functions after using the structures. These results indicate that stakeholders likely need to perceive ARs as useful in order for them to provide their support for AR installation. Likewise, their support is often needed to justify the use of public funds to install ARs, therefore making it imperative for resource managers to undertake similar interviews with fishermen when considering the use of ARs in other areas.
Ramos et al. (2019) Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal. PeerJ 6:e6206 https://doi.org/10.7717/peerj.6206
Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon
The relationships among the morphoclimatic domains of South America have been a major biogeographical issue of recent years. Palynological, geological and phytogeographical data suggest that the Amazon Forest and the Atlantic Forest were connected during part of the Tertiary and Quaternary periods. This study uses amphibians as model organisms to investigate whether relict northeastern forests are a transition between the Amazon Forest and the Atlantic Forest. We compiled matrices of species composition for four different phytogeographic formations and “Brejos de Altitude,” and analyzed them using clustering methods and Cladistic Analysis of Distributions and Endemism. Our results indicate that the anurofauna of these northeastern forest relicts is most similar in composition to the areas of the Atlantic Forest included in this study, and most dissimilar to the Amazon Forest, which leads us to affirm that events of biotic exchange were more frequent within the Atlantic Forest areas.
Castro et al. (2019) Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon. PeerJ 6:e6208 https://doi.org/10.7717/peerj.6208
Immunohistochemical analysis of cyclin A expression in Wilms tumor
Background Cyclin A overexpression is found in a variety of human tumors and correlates with unfavorable outcome. We analyzed immunohistochemical expression of cyclin A in Wilms tumor (WT) in relation to clinicopathological characteristics, preoperative chemotherapy (PrOpChTh), and overall survival (OS). Methods This retrospective study involved 43 patients who underwent nephrectomy from January 1996 to October 2010. Tumor stage and histological subtype were determined by revised Societé International d’Oncologie Pediatrique protocol, based on histological components/alterations caused by PrOpChTh, within the prognostic group of low, intermediate and high risk, and with criteria for anaplasia. The regressive/necrotic changes in total tumor mass of primary tumor and the proportion of epithelial, blastemal, and stromal components in the remaining viable tumor tissue were also determined. Cyclin A expression was evaluated by immunohistochemistry using a polyclonal rabbit, antihuman antibody (H-432). Results Cyclin A overexpression was found in 34.3% of WTs, with higher frequency in tumors with epithelial (31.3%) and blastemal (37.1%) components than those with stromal component (17.7%). Regarding histological type, cyclin A overexpression was found most often in focal anaplasia (100%), stromal (60%), and diffuse anaplastic (66.7) WTs. The overexpression was also more frequent in stages 3 and 4 (77.8% and 66.7%, respectively) compared to tumors in stages 1 and 2 (13.3% and 12.5%, respectively; p = 0.004) in all components, as well as in blastemal component in stages 3 and 4 (77.8% and 66.7%, respectively) vs. stages 1 and 2 (13.3% and 25%, respectively, p = 0.009). Cyclin A overexpression in all components was 66.7% in WTs with metastasis and 31.3% in WTs without metastasis (p = 0.265, Fisher test). Log-rank testing revealed differences of OS regarding stage (p = 0.000), prognostic groups (p = 0.001), and cyclin A expression in blastemal component (p = 0.025). After univariate analysis, tumor stage (p = 0.001), prognostic group (p = 0.004), and cyclin A expression in blastemal component (p = 0.042) were significant prognostic factors for OS; however, after multivariate analysis, none of these factors were confirmed as independent predictors of survival. Discussion This study showed that cyclin A overexpression might be associated with the development and progression of WT with anaplasia. Also, cyclin A overexpression was more often observed in advanced stages (3 and 4) of WT, in the group of high-risk WTs, and in focal and diffuse anaplasia WTs. There was no relation of cyclin A overexpression and metastatic ability of WT. Although this study has not confirmed the prognostic value of cyclin A overexpression, its association with unfavorable prognosis should be further evaluated.
Radojević-Škodrić et al. (2019) Immunohistochemical analysis of cyclin A expression in Wilms tumor. PeerJ 6:e6212 https://doi.org/10.7717/peerj.6212
Detection and variability analyses of CRISPR-like loci in the H. pylori genome
Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
García-Zea et al. (2019) Detection and variability analyses of CRISPR-like loci in the H. pylori genome. PeerJ 7:e6221 https://doi.org/10.7717/peerj.6221
Grazing by large savanna herbivores indirectly alters ant diversity and promotes resource monopolisation
In savannas, grazing is an important disturbance that modifies the grass layer structure and composition. Habitat structural complexity influences species diversity and assemblage functioning. By using a combination of natural sites and manipulated experiments, we explored how habitat structure (grazing lawns and adjacent bunch grass) affects ant diversity and foraging behaviour, specifically the efficiency of resource acquisition, resource monopolisation and ant body size. We found that in the natural sites there was no difference in the amount of time ants took to locate resources, but in the manipulated experiments, ants were faster at locating resources and were more abundant in the simple treatments than in the more complex treatments. Ant body size was only affected by the manipulated experiments, with smaller ants found in the more complex treatments. In both the grazing lawn and bunch grass habitats there were differences in assemblage patterns of ants discovering resources and those dominating them. Seasonality, which was predicted to affect the speed at which ants discovered resources and the intensity of resource monopolisation, also played a role. We show that ants in winter monopolised more baits and discovered resources at a slower rate, but only at certain times within the experiment. Grazing in conjunction with season thus had a significant effect on ant diversity and foraging behaviour, with dominant ants promoted where habitat complexity was simplified when temperatures were low. Our results indicate that structural complexity plays a major role in determining ant assemblage structure and function in African savannas.
Purdon et al. (2019) Grazing by large savanna herbivores indirectly alters ant diversity and promotes resource monopolisation. PeerJ 7:e6226 https://doi.org/10.7717/peerj.6226
Individual tree crown delineation and tree species classification with hyperspectral and LiDAR data
An international data science challenge, called National Ecological Observatory Network—National Institute of Standards and Technology data science evaluation, was set up in autumn 2017 with the goal to improve the use of remote sensing data in ecological applications. The competition was divided into three tasks: (1) individual tree crown (ITC) delineation, for identifying the location and size of individual trees; (2) alignment between field surveyed trees and ITCs delineated on remote sensing data; and (3) tree species classification. In this paper, the methods and results of team Fondazione Edmund Mach (FEM) are presented. The ITC delineation (Task 1 of the challenge) was done using a region growing method applied to a near-infrared band of the hyperspectral images. The optimization of the parameters of the delineation algorithm was done in a supervised way on the basis of the Jaccard score using the training set provided by the organizers. The alignment (Task 2) between the delineated ITCs and the field surveyed trees was done using the Euclidean distance among the position, the height, and the crown radius of the ITCs and the field surveyed trees. The classification (Task 3) was performed using a support vector machine classifier applied to a selection of the hyperspectral bands and the canopy height model. The selection of the bands was done using the sequential forward floating selection method and the Jeffries Matusita distance. The results of the three tasks were very promising: team FEM ranked first in the data science competition in Task 1 and 2, and second in Task 3. The Jaccard score of the delineated crowns was 0.3402, and the results showed that the proposed approach delineated both small and large crowns. The alignment was correctly done for all the test samples. The classification results were good (overall accuracy of 88.1%, kappa accuracy of 75.7%, and mean class accuracy of 61.5%), although the accuracy was biased toward the most represented species.
Spatial and Geographic Information Science
Dalponte et al. (2019) Individual tree crown delineation and tree species classification with hyperspectral and LiDAR data. PeerJ 6:e6227 https://doi.org/10.7717/peerj.6227