Mental disorder recovery correlated with centralities and interactions on an online social network
Recent research has established both a theoretical basis and strong empirical evidence that effective social behavior plays a beneficial role in the maintenance of physical and psychological well-being of people. To test whether social behavior and well-being are also associated in online communities, we studied the correlations between the recovery of patients with mental disorders and their behaviors in online social media. As the source of the data related to the social behavior and progress of mental recovery, we used PatientsLikeMe (PLM), the world’s first open-participation research platform for the development of patient-centered health outcome measures. We first constructed an online social network structure based on patient-to-patient ties among 200 patients obtained from PLM. We then characterized patients’ online social activities by measuring the numbers of “posts and views” and “helpful marks” each patient obtained. The patients’ recovery data were obtained from their self-reported status information that was also available on PLM. We found that some node properties (in-degree, eigenvector centrality and PageRank) and the two online social activity measures were significantly correlated with patients’ recovery. Furthermore, we re-collected the patients’ recovery data two months after the first data collection. We found significant correlations between the patients’ social behaviors and the second recovery data, which were collected two months apart. Our results indicated that social interactions in online communities such as PLM were significantly associated with the current and future recoveries of patients with mental disorders.
Ma et al. (2015) Mental disorder recovery correlated with centralities and interactions on an online social network. PeerJ 3:e1163 https://doi.org/10.7717/peerj.1163
Environmental influences on the Indo–Pacific octocoral Isis hippuris Linnaeus 1758 (Alcyonacea: Isididae): genetic fixation or phenotypic plasticity?
As conspicuous modular components of benthic marine habitats, gorgonian (sea fan) octocorals have perplexed taxonomists for centuries through their shear diversity, particularly throughout the Indo–Pacific. Phenotypic incongruence within and between seemingly unitary lineages across contrasting environments can provide the raw material to investigate processes of disruptive selection. Two distinct phenotypes of the Isidid Isis hippuris Linnaeus, 1758 partition between differing reef environments: long-branched bushy colonies on degraded reefs, and short-branched multi/planar colonies on healthy reefs within the Wakatobi Marine National Park (WMNP), Indonesia. Multivariate analyses reveal phenotypic traits between morphotypes were likely integrated primarily at the colony level with increased polyp density and consistently smaller sclerite dimensions at the degraded site. Sediment load and turbidity, hence light availability, primarily influenced phenotypic differences between the two sites. This distinct morphological dissimilarity between the two sites is a reliable indicator of reef health; selection primarily acting on colony morphology, porosity through branching structure, as well as sclerite diversity and size. ITS2 sequence and predicted RNA secondary structure further revealed intraspecific variation between I. hippuris morphotypes relative to such environments (ΦST = 0.7683, P < 0.001). This evidence suggests—but does not confirm—that I. hippuris morphotypes within the WMNP are two separate species; however, to what extent and taxonomic assignment requires further investigation across its full geographic distribution. Incongruence between colonies present in the WMNP with tenuously described Isis alternatives (Isis reticulata Nutting, 1910, Isis minorbrachyblasta Zou, Huang & Wang, 1991), questions the validity of such assignments. Furthermore, phylogenetic analyses confirm early taxonomic suggestion that the characteristic jointed axis of the Isididae is in fact a convergent trait. Thus the polyphyletic nature of the Isididae lies in its type species I. hippuris, being unrelated to the rest of its family members.
Rowley et al. (2015) Environmental influences on the Indo–Pacific octocoral Isis hippuris Linnaeus 1758 (Alcyonacea: Isididae): genetic fixation or phenotypic plasticity?. PeerJ 3:e1128 https://doi.org/10.7717/peerj.1128
In vitro biomechanical evaluation of internal fixation techniques on the canine lumbosacral junction
Few biomechanical studies have evaluated the effect of internal stabilization techniques after decompressive surgery on the stability of the canine lumbosacral junction. The purpose of this canine cadaver study is to evaluate the stability of the canine lumbosacral (LS) spine in flexion and extension following laminectomy and discectomy and then stabilization with each of the three techniques: pins and polymethylmethacrylate (P/PMMA), two dorsal locking plates (SOP) or bilateral transarticular facet screws (FACET).Using a cantilever biomechanical system, bending moments were applied to the LS and range of motion (ROM) was recorded via a rotational potentiometer. With 3 Nm, the ROM (n = 4 in each group) for P/PMMA, SOP and FACET were 1.92 ± 0.96°, 2.56 ± 0.55°and 3.18 ± 1.14°, respectively. With moments up to 35 Nm, the P/PMMA specimens appeared stable. Sacroiliac motion in the SOP and FACET groups invalidated further comparisons. Each of the stabilization techniques (P/PMMA, SOP, and FACET) significantly decreased the range of motion in flexion and extension for low bending moments.
Early et al. (2015) In vitro biomechanical evaluation of internal fixation techniques on the canine lumbosacral junction. PeerJ 3:e1094 https://doi.org/10.7717/peerj.1094
Coalescent: an open-science framework for importance sampling in coalescent theory
Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner. Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable. Conclusions. In coalescent theory, many studies of computational efficiency consider only effective sample size. Here, we evaluate proposals in the coalescent literature, to discover that the order of efficiency among the three importance sampling schemes changes when one considers running time as well as effective sample size. We also describe a computational technique called “just-in-time delegation” available to improve the trade-off between running time and precision by constructing improved importance sampling schemes from existing ones. Thus, our systems approach is a potential solution to the “28 programs problem” highlighted by Felsenstein, because it provides the flexibility to include or exclude various features of similar coalescent models or importance sampling schemes.
Tewari et al. (2015) Coalescent: an open-science framework for importance sampling in coalescent theory. PeerJ 3:e1203 https://doi.org/10.7717/peerj.1203
Biological and ecological traits of marine species
This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the ‘status’ of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them.
Costello et al. (2015) Biological and ecological traits of marine species. PeerJ 3:e1201 https://doi.org/10.7717/peerj.1201
The application of fractional Mel cepstral coefficient in deceptive speech detection
The inconvenience operation of EEG P300 or functional magnetic resonance imaging (FMRI) will be overcome, when the deceptive information can be effectively detected from speech signal analysis. In this paper, the fractional Mel cepstral coefficient (FrCC) is proposed as the speech character for deception detection. The different fractional order can reveal various personalities of the speakers. The linear discriminant analysis (LDA) model (which has the ability of global optimal vector mapping) is introduced, and the performance of FrCC and MFCC in deceptive detection is compared when all the data are mapped to low dimensional. Then, the hidden Markov model (HMM) is introduced as a long-term signal analysis tool. Twenty-five male and 25 female participants are involved in the experiment. The results show that the clustering effect of optimal fractional order FrCC is better than that of MFCC. The average accuracy for male and female speaker is 59.9% and 56.2%, respectively, by using the FrCC under the LDA model. When MFCC is used, the accuracy is reduced by 3.2% and 5.9%, respectively, for male and female. The accuracy can be increased to 71.0% and 70.2% for male and female speakers when HMM is used. Moreover, some individual accuracy is increased over 20%, or even more than 85%, when FrCC is introduced. The results show that the deceptive information is indeed hidden in the speech signals. Therefore, speech-based psychophysiology calculating may be a valuable research field.
Pan et al. (2015) The application of fractional Mel cepstral coefficient in deceptive speech detection. PeerJ 3:e1194 https://doi.org/10.7717/peerj.1194
Perivascular mast cells regulate vein graft neointimal formation and remodeling
Objective. Emerging evidence suggests an important role for mast cells in vein graft failure. This study addressed the hypothesis that perivascular mast cells regulate in situ vascular inflammatory and proliferative responses and subsequent vein graft neointimal lesion formation, using an optimized local mast cell reconstitution method. Methods and Results. Neointimal hyperplasia was induced by insertion of a vein graft into the right carotid artery in wild type and mast cell deficient KitW−sh/W−sh mice. In some experiments, mast cells were reconstituted systemically (tail vein injection of bone marrow-derived mast cells) or locally (directly into the right neck area) prior to vein grafting. Vein graft neointimal lesion formation was significantly (P < 0.05) reduced in KitW−sh/W−sh mice. Mast cell deficiency reduced the number of proliferating cells, and inhibited L-selectin, CCL2, M-CSF and MIP-3α expression in the vein grafts. Local but not systemic mast cell reconstitution restored a perivascular mast cell population that subsequently promoted neointimal formation in mast cell deficient mice. Conclusion. Our data demonstrate that perivascular mast cells play a key role in promoting neointima formation by inducing local acute inflammatory and proliferative responses. These results suggest that ex vivo intraoperative targeting of mast cells may have therapeutic potential for the prevention of pathological vein graft remodeling.
Wu et al. (2015) Perivascular mast cells regulate vein graft neointimal formation and remodeling. PeerJ 3:e1192 https://doi.org/10.7717/peerj.1192
Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota
Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of the methods tested here, and base their choice according to practical considerations such as prior use, cost, and availability in the field, although we still advise that all samples within a study be handled in an identical manner when possible. We also suggest that, in large-scale molecular studies of hundreds of insect specimens, surface sterilization may not be worth the time and effort involved. This information should help researchers design sampling strategies and will facilitate cross-comparisons and meta-analyses of microbial community data obtained from insect specimens preserved in different ways.
Hammer et al. (2015) Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota. PeerJ 3:e1190 https://doi.org/10.7717/peerj.1190
Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions
The ichthyoplankton assemblage structure in the Yangtze Estuary was analyzed based on four springs in 1999, 2001, 2004 and 2007 in order to provide detailed characterizations of the ichthyoplankton assemblage in springs, examine the long-term dynamics of spring ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. Forty-two ichthyoplankton species belonging to 23 families were collected. Engraulidae was the most abundant family, including six species and comprising 67.91% of the total catch. Only four species (Coilia mystus, Engraulis japonicus, Trachidermis fasciatus and Allanetta bleekeri) could be considered dominant, accounting for 88.70% of total abundance. The structure of the ichthyoplankton spring assemblage persisted on an annual basis, with the dominant species reappearing consistently even though their abundance fluctuated from year to year. This inter-annual variation probably reflects variable environmental conditions influenced by jellyfish blooms, declining river flow, and overfishing. Canonical correspondence analysis indicated aspatial structure of the ichthyoplankton assemblage in three areas: (1) an inner assemblage dominated by C. mystus; (2) a central assemblage dominated by A. bleekeri and T. fasciatus; and (3) a shelf assemblage featuring E. japonicus. The observed ichthyoplankton assemblage structure appears to be strongly influenced by depth, salinity and suspended particulate matter gradients.
Zhang et al. (2015) Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions. PeerJ 3:e1186 https://doi.org/10.7717/peerj.1186
Face matching in a long task: enforced rest and desk-switching cannot maintain identification accuracy
In face matching, observers have to decide whether two photographs depict the same person or different people. This task is not only remarkably difficult but accuracy declines further during prolonged testing. The current study investigated whether this decline in long tasks can be eliminated with regular rest-breaks (Experiment 1) or room-switching (Experiment 2). Both experiments replicated the accuracy decline for long face-matching tasks and showed that this could not be eliminated with rest or room-switching. These findings suggest that person identification in applied settings, such as passport control, might be particularly error-prone due to the long and repetitive nature of the task. The experiments also show that it is difficult to counteract these problems.
Alenezi et al. (2015) Face matching in a long task: enforced rest and desk-switching cannot maintain identification accuracy. PeerJ 3:e1184 https://doi.org/10.7717/peerj.1184