title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1639 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples link: https://peerj.com/articles/4040 last-modified: 2017-11-22 description: Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations. creator: Zeeshan Ahmed creator: Duygu Ucar uri: https://doi.org/10.7717/peerj.4040 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ahmed and Ucar title: Assessment of brain functional connectome alternations and correlation with depression and anxiety in major depressive disorders link: https://peerj.com/articles/3147 last-modified: 2017-11-22 description: Major depressive disorder (MDD) is highly prevalent, recurrent, and associated with functional impairment, morbidity, and mortality. Herein, we aimed to identify disruptions in functional connectomics among subjects with MDD by using resting-state functional magnetic resonance imaging (rs-fMRI). Sixteen subjects with MDD and thirty health controls completed resting-state fMRI scans and clinical assessments (e.g., Hamilton Depression Rating Scale (HAMD) and Hospital Anxiety and Depression Scale (HADS)). We found higher amplitude of low frequency fluctuations (ALFF) bilaterally in the hippocampus and amygdala among MDD subjects when compared to healthy controls. Using graph theoretical analysis, we found decreased clustering coefficient, local efficiency, and transitivity in the MDD patients. Our findings suggest a potential biomarker for differentiating individuals with MDD from individuals without MDD. creator: Vincent Chin-Hung Chen creator: Chao-Yu Shen creator: Sophie Hsin-Yi Liang creator: Zhen-Hui Li creator: Ming-Hong Hsieh creator: Yeu-Sheng Tyan creator: Mong-Liang Lu creator: Yena Lee creator: Roger S. McIntyre creator: Jun-Cheng Weng uri: https://doi.org/10.7717/peerj.3147 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chen et al. title: Morphological convergence in ‘river dolphin’ skulls link: https://peerj.com/articles/4090 last-modified: 2017-11-21 description: Convergent evolution can provide insights into the predictability of, and constraints on, the evolution of biodiversity. One striking example of convergence is seen in the ‘river dolphins’. The four dolphin genera that make up the ‘river dolphins’ (Inia geoffrensis, Pontoporia blainvillei, Platanista gangetica and Lipotes vexillifer) do not represent a single monophyletic group, despite being very similar in morphology. This has led many to using the ‘river dolphins’ as an example of convergent evolution. We investigate whether the skulls of the four ‘river dolphin’ genera are convergent when compared to other toothed dolphin taxa in addition to identifying convergent cranial and mandibular features. We use geometric morphometrics to uncover shape variation in the skulls of the ‘river dolphins’ and then apply a number of phylogenetic techniques to test for convergence. We find significant convergence in the skull morphology of the ‘river dolphins’. The four genera seem to have evolved similar skull shapes, leading to a convergent morphotype characterised by elongation of skull features. The cause of this morphological convergence remains unclear. However, the features we uncover as convergent, in particular elongation of the rostrum, support hypotheses of shared feeding mode or diet and thus provide the foundation for future work into convergence within the Odontoceti. creator: Charlotte E. Page creator: Natalie Cooper uri: https://doi.org/10.7717/peerj.4090 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Page and Cooper title: Diversity of bacterial communities on the facial skin of different age-group Thai males link: https://peerj.com/articles/4084 last-modified: 2017-11-21 description: BackgroundSkin microbiome varies from person to person due to a combination of various factors, including age, biogeography, sex, cosmetics and genetics. Many skin disorders appear to be related to the resident microflora, yet databases of facial skin microbiome of many biogeographies, including Thai, are limited.MethodsMetagenomics derived B-RISA and 16S rRNA gene sequencing was utilized to identify the culture-independent bacterial diversity on Thai male faces (cheek and forehead areas). Skin samples were categorized (grouped) into (i) normal (teenage.hea) and (ii) acne-prone (teenage.acn) young adults, and normal (iii) middle-aged (middle.hea) and (iv) elderly (elderly.hea) adults.ResultsThe 16S rRNA gene sequencing was successful as the sequencing depth had an estimated >98% genus coverage of the true community. The major diversity was found between the young and elderly adults in both cheek and forehead areas, followed by that between normal and acne young adults. Detection of representative characteristics indicated that bacteria from the order Rhizobiales, genera Sphingomonas and Pseudoalteromonas, distinguished the elderly.hea microbiota, along the clinical features of wrinkles and pores. Prediction of the metabolic potential revealed reduced metabolic pathways involved in replication and repair, nucleotide metabolism and genetic translation in the elderly.hea compared with that in the teenage.hea. For young adults, some unique compositions such as abundance of Propionibacterium acnes and Staphylococcus epidermidis, with a minor diversity between normal and acne skins, were detected. The metabolic potentials of the acne vs. normal young adults showed that teenage.acn was low in many cellular processes (e.g., cell motility and environmental adaptation), but high in carbohydrate metabolism, which could support acne growth. Moreover, comparison with the age-matched males from the US (Boulder, Colorado) to gain insight into the diversity across national biogeography, revealed differences in the distribution pattern of species, although common bacteria were present in both biogeographical samples. Furthermore, B-RISA served as a crosscheck result to the 16S rRNA gene sequencing (i.e., differences between teenage and elderly microbiota).ConclusionsThis study revealed and compared the microbial diversity on different aged Thai male faces, and included analyses for representing the bacterial flora, the clinical skin characteristics, and comparison with the US age-matched. The results represent the first skin microbiota of Thai males, and helps the design of a large-scale skin microbiome study of Thais. The findings of the diversity among ages, skin type and national biogeography supported the importance of these traits in the skin microbiome and in developing a safe and sustainable treatment for acne and aging skin diseases. creator: Alisa Wilantho creator: Pamornya Deekaew creator: Chutika Srisuttiyakorn creator: Sissades Tongsima creator: Naraporn Somboonna uri: https://doi.org/10.7717/peerj.4084 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wilantho et al. title: Development of medical informatics in China over the past 30 years from a conference perspective and a Sino-American comparison link: https://peerj.com/articles/4082 last-modified: 2017-11-21 description: BackgroundAs the world’s second-largest economy, China has launched health reforms for the second time and invested significant funding in medical informatics (MI) since 2010; however, few studies have been conducted on the outcomes of this ambitious cause.ObjectiveThis study analyzed the features of major MI meetings held in China and compared them with similar MI conferences in the United States, aiming at informing researchers on the outcomes of MI in China and the US from the professional conference perspective and encouraging greater international cooperation for the advancement of the field of medical informatics in China and, ultimately, the promotion of China’s health reform.MethodsQualitative and quantitative analyses of four MI meetings in China (i.e., CMIAAS, CHINC, CHITEC, and CPMI) and two in the US (i.e., AMIA and HIMSS) were conducted. Furthermore, the size, constituent parts and regional allocation of participants, topics, and fields of research for each meeting were determined and compared.ResultsFrom 1985 to 2016, approximately 45,000 individuals attended the CMIAAS and CPMI (academic), CHINC and CHITEC (industry), resulting in 5,085 documented articles. In contrast, in 2015, 38,000 and 3,700 individuals, respectively, attended the American HIMSS (industry) and AMIA (academic) conferences and published 1,926 papers in the latter. Compared to those of HIMSS in 2015, the meeting duration of Chinese industry CHITEC was 3 vs. 5 days, the number of vendors was 100 vs. 1,500+, the number of sub-forums was 10 vs. 250; while compared to those of AMIA, the meeting duration of Chinese CMIAAS was 2 vs. 8 days, the number of vendors was 5 vs. 65+, the number of sub-forums was 4 vs. 26. HIMSS and AMIA were more open, international, and comprehensive in comparison to the aforementioned Chinese conferences.ConclusionsThe current MI in China can be characterized as “hot in industry application, and cold in academic research.” Taking into consideration the economic scale together with the huge investment in MI, conference yield and attendee diversity are still low in China. This study demonstrates an urgent necessity to elevate the medical informatics discipline in China and to expand research fields in order to maintain pace with the development of medical informatics in the US and other countries. creator: Jun Liang creator: Kunyan Wei creator: Qun Meng creator: Zhenying Chen creator: Jiajie Zhang creator: Jianbo Lei uri: https://doi.org/10.7717/peerj.4082 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liang et al. title: Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata link: https://peerj.com/articles/4077 last-modified: 2017-11-21 description: The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species. creator: Meghann K. Devlin-Durante creator: Iliana B. Baums uri: https://doi.org/10.7717/peerj.4077 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Devlin-Durante and Baums title: The ability of laying pullets to negotiate two ramp designs as measured by bird preference and behaviour link: https://peerj.com/articles/4069 last-modified: 2017-11-21 description: BackgroundLaying hens are often kept in barn or free-range systems where they must negotiate level changes in the house to access resources. However, collisions and resultant keel fractures are commonplace. Producers sometimes add ramps to make raised areas more accessible but designs vary and very little research has investigated bird preference or behaviour when using different ramp designs, or the effect of ramp design on falls and collisions.MethodsTwo ramp designs were studied in an experimental setting—a ramp made of plastic poultry slats (grid ramp, GR) and a ramp made of wooden rungs (ladder ramp, LR). Sixty-four young female hens were trained to move to a food reward and this was used to test their behavioural responses when first negotiating the two different ramps during individual tests. Both upward and downward transitions were studied. Ramp preference was also tested using a room that replicated a commercial single-tier system with both types of ramp available. Birds were placed in this room in groups of 16 for three days and their use of the ramps studied.ResultsA greater percentage of birds successfully completed (reached the reward bowl) on the GR than the LR during both upward (58% vs 37%) and downward (83% vs 73%) transitions, and a smaller percentage of birds made zero attempts to use the GR than the LR (upwards: 13% vs 56%, downwards: 8% vs 26%). When making a downward transition, more hesitation behaviours were seen (head orientations, stepping on the spot, moving away) for the LR. However, more head orientations were seen for the GR during the upward transition. Birds were more likely to abort attempts (an attempt began when a bird placed both feet on the ramp) to move up the GR than the LR. Birds took longer to negotiate the LR than the GR in both directions, and more pauses were seen during a successful upward transition on the LR. Birds were more likely to move down the GR by walking/running whereas birds tended to jump over the entire LR. More collisions with the food reward bowl were seen for the LR. In the group tests, birds preferred to use the GR, with more transitions seen at all timepoints. However, in these tests, birds preferred to rest on the LR with greater numbers of birds counted on this type of ramp during scan sampling at all timepoints.DiscussionBehavioural results suggest that the GR was easier for the birds to use than the LR, particularly on the downward transition. The GR was also less likely to result in collisions. However, the upward transition may be more difficult on the GR for some birds, potentially because of the inability to pause on a level surface during the transition. The results suggest that the GR was preferred by pullets for moving between a raised area and the ground but the LR was preferred for resting. creator: Isabelle C. Pettersson creator: Claire A. Weeks creator: Kate I. Norman creator: Christine J. Nicol uri: https://doi.org/10.7717/peerj.4069 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pettersson et al. title: Levels of detail analysis of microwave scattering from human head models for brain stroke detection link: https://peerj.com/articles/4061 last-modified: 2017-11-21 description: In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model.After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to find out the solution of subject microwave scattering problem in a minimum computational time along with memory resources requirement.It is seen from this study that the microwave imaging may effectively be utilized for the detection, localization and differentiation of different types of brain stroke. The simulation results verified that the microwave imaging can be efficiently exploited to study the significant contrast between electric field values of the normal and abnormal brain tissues for the investigation of brain anomalies. In the end, a specific absorption rate analysis was carried out to compare the ionizing effects of microwave signals to different types of head model using a factor of safety for brain tissues. It is also suggested after careful study of various inversion methods in practice for microwave head imaging, that the contrast source inversion method may be more suitable and computationally efficient for such problems. creator: Awais Munawar Qureshi creator: Zartasha Mustansar uri: https://doi.org/10.7717/peerj.4061 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Qureshi and Mustansar title: Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach link: https://peerj.com/articles/4042 last-modified: 2017-11-21 description: BackgroundTartary buckwheat (TB), a crop rich in protein, dietary fiber, and flavonoids, has been reported to have an effect on Type II diabetes (T2D), hypertension (HT), and hyperlipidemia (HL). However, limited information is available about the relationship between Tartary buckwheat and these three diseases. The mechanisms of how TB impacts these diseases are still unclear.MethodsIn this study, network pharmacology was used to investigate the relationship between the herb as well as the diseases and the mechanisms of how TB might impact these diseases.ResultsA total of 97 putative targets of 20 compounds found in TB were obtained. Then, an interaction network of 97 putative targets for these compounds and known therapeutic targets for the treatment of the three diseases was constructed. Based on the constructed network, 28 major nodes were identified as the key targets of TB due to their importance in network topology. The targets of ATK2, IKBKB, RAF1, CHUK, TNF, JUN, and PRKCA were mainly involved in fluid shear stress and the atherosclerosis and PI3K-Akt signaling pathways. Finally, molecular docking simulation showed that 174 pairs of chemical components and the corresponding key targets had strong binding efficiencies.ConclusionFor the first time, a comprehensive systemic approach integrating drug target prediction, network analysis, and molecular docking simulation was developed to reveal the relationships and mechanisms between the putative targets in TB and T2D, HT, and HL. creator: Chao-Long Lu creator: Qi Zheng creator: Qi Shen creator: Chi Song creator: Zhi-Ming Zhang uri: https://doi.org/10.7717/peerj.4042 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lu et al. title: Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta link: https://peerj.com/articles/3998 last-modified: 2017-11-21 description: Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon. creator: Kishor Dhaygude creator: Kalevi Trontti creator: Jenni Paviala creator: Claire Morandin creator: Christopher Wheat creator: Liselotte Sundström creator: Heikki Helanterä uri: https://doi.org/10.7717/peerj.3998 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dhaygude et al.