title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1794 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Muscle size explains low passive skeletal muscle force in heart failure patients link: https://peerj.com/articles/2447 last-modified: 2016-09-15 description: BackgroundAlterations in skeletal muscle function and architecture have been linked to the compromised exercise capacity characterizing chronic heart failure (CHF). However, how passive skeletal muscle force is affected in CHF is not clear. Understanding passive force characteristics in CHF can help further elucidate the extent to which altered contractile properties and/or architecture might affect muscle and locomotor function. Therefore, the aim of this study was to investigate passive force in a single muscle for which non-invasive measures of muscle size and estimates of fiber force are possible, the soleus (SOL), both in CHF patients and age- and physical activity-matched control participants.MethodsPassive SOL muscle force and size were obtained by means of a novel approach combining experimental data (dynamometry, electromyography, ultrasound imaging) with a musculoskeletal model.ResultsWe found reduced passive SOL forces (∼30%) (at the same relative levels of muscle stretch) in CHF vs. healthy individuals. This difference was eliminated when force was normalized by physiological cross sectional area, indicating that reduced force output may be most strongly associated with muscle size. Nevertheless, passive force was significantly higher in CHF at a given absolute muscle length (non length-normalized) and likely explained by the shorter muscle slack lengths and optimal muscle lengths measured in CHF compared to the control participants. This later factor may lead to altered performance of the SOL in functional tasks such gait.DiscussionThese findings suggest introducing exercise rehabilitation targeting muscle hypertrophy and, specifically for the calf muscles, exercise that promotes muscle lengthening. creator: Fausto Antonio Panizzolo creator: Andrew J. Maiorana creator: Louise H. Naylor creator: Lawrence G. Dembo creator: David G. Lloyd creator: Daniel J. Green creator: Jonas Rubenson uri: https://doi.org/10.7717/peerj.2447 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Panizzolo et al. title: Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea link: https://peerj.com/articles/2387 last-modified: 2016-09-15 description: Biodiversity is well studied in ecology and the concept has been developed to include traits of species, rather than solely taxonomy, to better reflect the functional diversity of a system. The deep sea provides a natural environmental gradient within which to study changes in different diversity metrics, but traits of deep-sea fish are not widely known, hampering the application of functional diversity to this globally important system. We used morphological traits to determine the functional richness and functional divergence of demersal fish assemblages along the continental slope in the Northeast Atlantic, at depths of 300–2,000 m. We compared these metrics to size diversity based on individual body size and species richness. Functional richness and size diversity showed similar patterns, with the highest diversity at intermediate depths; functional divergence showed the opposite pattern, with the highest values at the shallowest and deepest parts of the study site. Species richness increased with depth. The functional implications of these patterns were deduced by examining depth-related changes in morphological traits and the dominance of feeding guilds as illustrated by stable isotope analyses. The patterns in diversity and the variation in certain morphological traits can potentially be explained by changes in the relative dominance of pelagic and benthic feeding guilds. All measures of diversity examined here suggest that the deep areas of the continental slope may be equally or more diverse than assemblages just beyond the continental shelf. creator: Beth L. Mindel creator: Francis C. Neat creator: Clive N. Trueman creator: Thomas J. Webb creator: Julia L. Blanchard uri: https://doi.org/10.7717/peerj.2387 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mindel et al. title: The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets link: https://peerj.com/articles/2443 last-modified: 2016-09-15 description: An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%–99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development. creator: Zi Li creator: Wenqi He creator: Yungang Lan creator: Kui Zhao creator: Xiaoling Lv creator: Huijun Lu creator: Ning Ding creator: Jing Zhang creator: Junchao Shi creator: Changjian Shan creator: Feng Gao uri: https://doi.org/10.7717/peerj.2443 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Li et al. title: Emotion recognition using Kinect motion capture data of human gaits link: https://peerj.com/articles/2364 last-modified: 2016-09-15 description: Automatic emotion recognition is of great value in many applications, however, to fully display the application value of emotion recognition, more portable, non-intrusive, inexpensive technologies need to be developed. Human gaits could reflect the walker’s emotional state, and could be an information source for emotion recognition. This paper proposed a novel method to recognize emotional state through human gaits by using Microsoft Kinect, a low-cost, portable, camera-based sensor. Fifty-nine participants’ gaits under neutral state, induced anger and induced happiness were recorded by two Kinect cameras, and the original data were processed through joint selection, coordinate system transformation, sliding window gauss filtering, differential operation, and data segmentation. Features of gait patterns were extracted from 3-dimentional coordinates of 14 main body joints by Fourier transformation and Principal Component Analysis (PCA). The classifiers NaiveBayes, RandomForests, LibSVM and SMO (Sequential Minimal Optimization) were trained and evaluated, and the accuracy of recognizing anger and happiness from neutral state achieved 80.5% and 75.4%. Although the results of distinguishing angry and happiness states were not ideal in current study, it showed the feasibility of automatically recognizing emotional states from gaits, with the characteristics meeting the application requirements. creator: Shun Li creator: Liqing Cui creator: Changye Zhu creator: Baobin Li creator: Nan Zhao creator: Tingshao Zhu uri: https://doi.org/10.7717/peerj.2364 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Li et al. title: A juvenile subfossil crocodylian from Anjohibe Cave, Northwestern Madagascar link: https://peerj.com/articles/2296 last-modified: 2016-09-15 description: Madagascar’s subfossil record preserves a diverse community of animals including elephant birds, pygmy hippopotamus, giant lemurs, turtles, crocodiles, bats, rodents, and carnivorans. These fossil accumulations give us a window into the island’s past from 80,000 years ago to a mere few hundred years ago, recording the extinction of some groups and the persistence of others. The crocodylian subfossil record is limited to two taxa, Voay robustus and Crocodylus niloticus, found at sites distributed throughout the island. V. robustus is extinct while C. niloticus is still found on the island today, but whether these two species overlapped temporally, or if Voay was driven to extinction by competing with Crocodylus remains unknown. While their size and presumed behavior was similar to each other, nearly nothing is known about the growth and development of Voay, as the overwhelming majority of fossil specimens represent mature adult individuals. Here we describe a nearly complete juvenile crocodylian specimen from Anjohibe Cave, northwestern Madagascar. The specimen is referred to Crocodylus based on the presence of caviconchal recesses on the medial wall of the maxillae, and to C. niloticus based on the presence of an oval shaped internal choana, lack of rostral ornamentation and a long narrow snout. However, as there are currently no described juvenile specimens of Voay robustus, it is important to recognize that some of the defining characteristics of that genus may have changed through ontogeny. Elements include a nearly complete skull and many postcranial elements (cervical, thoracic, sacral, and caudal vertebrae, pectoral elements, pelvic elements, forelimb and hindlimb elements, osteoderms). Crocodylus niloticus currently inhabits Madagascar but is locally extinct from this particular region; radiometric dating indicates an age of ∼460–310 years before present (BP). This specimen clearly represents a juvenile based on the extremely small size and open sutures/detached neural arches; total body length is estimated to be ∼1.1 m (modern adults of this species range from ∼4–6 m). This fossil represents the only juvenile subfossil crocodylian specimen reported from Madagascar. creator: Joshua C. Mathews creator: Karen E. Samonds uri: https://doi.org/10.7717/peerj.2296 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Mathews and Samonds title: Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline link: https://peerj.com/articles/2477 last-modified: 2016-09-14 description: Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective. This study describes the analysis of the S. pneumoniae capsular operon genetic sequence to determine serotype distinguishing features and the development, evaluation and verification of an automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT (Pneumococcal Capsule Typing). Initially, WGS data from 871 S. pneumoniae isolates were mapped to reference cps locus sequences for the 92 serotypes. Thirty-two of 92 serotypes could be unambiguously identified based on sequence similarities within the cps operon. The remaining 60 were allocated to one of 20 ‘genogroups’ that broadly correspond to the immunologically defined serogroups. By comparing the cps reference sequences for each genogroup, unique molecular differences were determined for serotypes within 18 of the 20 genogroups and verified using the set of 871 isolates. This information was used to design a decision-tree style algorithm within the PneumoCaT bioinformatics tool to predict to serotype level for 89/94 (92 + 2 molecular types/subtypes) from WGS data and to serogroup level for serogroups 24 and 32, which currently comprise 2.1% of UK referred, invasive isolates submitted to the National Reference Laboratory (NRL), Public Health England (June 2014–July 2015). PneumoCaT was evaluated with an internal validation set of 2065 UK isolates covering 72/92 serotypes, including 19 non-typeable isolates and an external validation set of 2964 isolates from Thailand (n = 2,531), USA (n = 181) and Iceland (n = 252). PneumoCaT was able to predict serotype in 99.1% of the typeable UK isolates and in 99.0% of the non-UK isolates. Concordance was evaluated in UK isolates where further investigation was possible; in 91.5% of the cases the predicted capsular type was concordant with the serologically derived serotype. Following retesting, concordance increased to 99.3% and in most resolved cases (97.8%; 135/138) discordance was shown to be caused by errors in original serotyping. Replicate testing demonstrated that PneumoCaT gave 100% reproducibility of the predicted serotype result. In summary, we have developed a WGS-based serotyping method that can predict capsular type to serotype level for 89/94 serotypes and to serogroup level for the remaining four. This approach could be integrated into routine typing workflows in reference laboratories, reducing the need for phenotypic immunological testing. creator: Georgia Kapatai creator: Carmen L. Sheppard creator: Ali Al-Shahib creator: David J. Litt creator: Anthony P. Underwood creator: Timothy G. Harrison creator: Norman K. Fry uri: https://doi.org/10.7717/peerj.2477 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kapatai et al. title: Gua Sha, a press-stroke treatment of the skin, boosts the immune response to intradermal vaccination link: https://peerj.com/articles/2451 last-modified: 2016-09-14 description: ObjectiveThe skin is an important immunological barrier of the body as well as an optimal route for vaccine administration. Gua Sha, which involves press-stroke treatment of the skin, is an effective folk therapy, widely accepted in East Asia, for various symptoms; however, the mechanisms underlying its therapeutic effects have not been clarified. We investigated the influence of Gua Sha on the immunological features of the skin.MethodsGua Sha was performed on BALB/c mice and the effects were evaluated using anatomical, histological, and cytometric methods as well as cytokine determination locally and systemically. The effect on intradermal vaccination was assessed with antigen-specific subtype antibody responses.ResultsBlood vessel expansion, erythrocyte extravasation, and increased ratios of immune active cells were observed in the skin tissue following the treatment. Pro-inflammatory cytokines were up-regulated, and immunosuppressive cytokines, down-regulated, in the treated and untreated skin and systemic circulation; no obvious variations were detected in case of anti-inflammatory cytokines. Interestingly, intradermal delivery of a model vaccine following Gua Sha induced about three-fold higher IgG titers with a more Th1-biased antibody subtype profile.ConclusionGua Sha treatment can up-regulate the innate and adaptive immune functions of the skin and boost the response against intradermal antigens. Thus, Gua Sha may serve as a safe, inexpensive, and independent physical adjuvant for intradermal vaccination. creator: Tingting Chen creator: Ninghua Liu creator: Jinxuan Liu creator: Xiaoying Zhang creator: Zhen Huang creator: Yuhui Zang creator: Jiangning Chen creator: Lei Dong creator: Junfeng Zhang creator: Zhi Ding uri: https://doi.org/10.7717/peerj.2451 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chen et al. title: Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls link: https://peerj.com/articles/2433 last-modified: 2016-09-14 description: BackgroundThe composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals.MethodsStimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode.ResultsWe identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease.ConclusionsOverexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity. creator: Daniel Belstrøm creator: Rosa R. Jersie-Christensen creator: David Lyon creator: Christian Damgaard creator: Lars J. Jensen creator: Palle Holmstrup creator: Jesper V. Olsen uri: https://doi.org/10.7717/peerj.2433 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Belstrøm et al. title: Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV link: https://peerj.com/articles/2464 last-modified: 2016-09-13 description: Pain burden is high in people living with HIV (PLWH), but the effect of this pain on functionality is equivocal. Resilience, the ability to cope with adversity, may promote adaptation to pain, so we hypothesised that higher resilience would correlate with less pain-related impairment of activity. We recruited 197 black South African PLWH, 99 with chronic pain (CP) and 98 patients without. We measured pain intensity and interference using the Brief Pain Inventory, and resilience using the Resilience Scale. Participants were generally highly resilient. Greater resilience correlated with better health-related quality of life, but not with pain intensity or interference. We also measured physical activity objectively, by actigraphy, in a subset of patients (37 with chronic pain and 31 without chronic pain), who wore accelerometers for two weeks. There was no difference in duration or intensity of activity between those with and without pain, and activity was not associated with resilience. In this sample, pain was not associated with altered physical activity. Resilience did not explain differences in pain intensity or pain interference but was associated with improved quality of life. Financial stresses and the fear of HIV stigma may have driven patients to conceal pain and to suppress its expected impairment of activity. creator: Antonia L. Wadley creator: Duncan Mitchell creator: Peter R. Kamerman uri: https://doi.org/10.7717/peerj.2464 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Wadley et al. title: Lowland tapir distribution and habitat loss in South America link: https://peerj.com/articles/2456 last-modified: 2016-09-13 description: The development of species distribution models (SDMs) can help conservation efforts by generating potential distributions and identifying areas of high environmental suitability for protection. Our study presents a distribution and habitat map for lowland tapir in South America. We also describe the potential habitat suitability of various geographical regions and habitat loss, inside and outside of protected areas network. Two different SDM approaches, MAXENT and ENFA, produced relative different Habitat Suitability Maps for the lowland tapir. While MAXENT was efficient at identifying areas as suitable or unsuitable, it was less efficient (when compared to the results by ENFA) at identifying the gradient of habitat suitability. MAXENT is a more multifaceted technique that establishes more complex relationships between dependent and independent variables. Our results demonstrate that for at least one species, the lowland tapir, the use of a simple consensual approach (average of ENFA and MAXENT models outputs) better reflected its current distribution patterns. The Brazilian ecoregions have the highest habitat loss for the tapir. Cerrado and Atlantic Forest account for nearly half (48.19%) of the total area lost. The Amazon region contains the largest area under protection, and the most extensive remaining habitat for the tapir, but also showed high levels of habitat loss outside protected areas, which increases the importance of support for proper management. creator: Jose Luis Passos Cordeiro creator: José M.V. Fragoso creator: Danielle Crawshaw creator: Luiz Flamarion B. Oliveira uri: https://doi.org/10.7717/peerj.2456 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cordeiro et al.