bluuebunny/crossref_metadata_2025 huggingface dataset:
A comprehensive simulation study on classification of RNA-Seq data
Authors: Zararsiz Gokmen , Göksülük Dinçer , Korkmaz Selçuk , Eldem Vahap , Ertürk Zararsız Gözde , Duru İzzet Parug , Unver Turgay , Öztürk Ahmet
Published: January 2018

Background RNA sequencing (RNA-Seq) is a powerful technique for transcriptome profiling of the organisms that uses the capabilities of next-generation sequencing (NGS) technologies. Recent advances in NGS let to measure the expression levels of tens to thousands of transcripts simultaneously. Using such information, developing expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of disease. Microarray based classifiers cannot be directly applied due to the discrete nature of RNA-Seq data. One way is to develop count-based classifiers, such as poisson linear discriminant analysis (PLDA) and negative binomial linear discriminant analysis (NBLDA). Other way is to transform the data hierarchically closer to microarrays and apply microarray-based classifiers. In most of the studies, the data overdispersion seems to be an another challenge in modeling RNA-Seq data. In this study, we aimed to examine the effect of dispersion parameter and classification algorithms on RNA-Seq classification. We also considered the effect of other parameters (i) sample size, (ii) number of genes, (iii) number of class, (iv) DE (differential expression) rate, (v) transformation method on classification performance.

Methods We designed a comprehensive simulation study, also used two miRNA and two mRNA experimental datasets. Simulated datasets are generated from negative binomial distribution under different scenarios and real datasets are obtained from publicly available resources. We compared the results of several classifiers including PLDA with and without power transformation, NBLDA, single SVM, bagging SVM (bagSVM), classification and regression trees (CART), and random forests (RF).

Results Results from the simulated and real datasets revealed that increasing the sample size, differential expression rate, number of genes and decreasing the dispersion parameter and number of groups lead to an increase in the classification accuracy. To make an overall assessment, power transformed PLDA, RF and SVM classifiers performed the highest classification accuracies.

Discussion Overdispersion seems to be an important challenge in RNA-Seq classification studies. Similar with differential expression studies, classification of RNA-Seq data requires careful attention on handling data overdispersion. We conclude that, as a count-based classifier, power transformed PLDA; as a microarray based classifier vst or rlog transformed RF and SVM (bagSVM for high sample sized data) classifiers may be a good choice for classification. However, there is still a need to develop novel classifiers or transformation approaches for classification of RNA-Seq data. An R/BIOCONDUCTOR package MLSeq with a vignette is freely available at http://www.bioconductor.org/packages/2.14/bioc/html/MLSeq.html .
Angle stability and outflow in excisional ab interno trabeculectomy with active versus passive chamber management
Authors: Wang Chao , Dang Yalong , Waxman Susannah , Xia Xiaobo , Weinreb Robert N , Loewen Nils A
Published: January 2018

Purpose: To compare the intraoperative angle stability and the postoperative outflow of two ab interno trabeculectomy devices that excise the trabecular meshwork. The newer device has an active aspiration and irrigation port while the older requires viscoelastic to maintain the anterior chamber. We hypothesized that anterior segment optical coherence tomography (ASOCT) allows quantifying the intraoperative behavior in a microincisional glaucoma surgery (MIGS) pig eye training model.

Methods: Twelve freshly enucleated porcine eyes were measured with ASOCT at baseline, at the beginning of the procedure and at its conclusion to determine the anterior chamber depth (ACD) and the nasal angle in degrees. The right and left eye of pairs were randomly assigned 24 to an active dual blade goniectome (aDBG) and a passive dual blade goniectome (pDBG) group, 25 respectively. The aDBG had an irrigation and aspiration port while the pDBG required surgery 26 under viscoelastic. We performed the procedures using our MIGS training system with a 27 standard, motorized ophthalmic operating microscope. We estimated outflow by obtaining 28 canalograms with fluorescent spheres.

Results: In aDBG, the nasal angle remained wide open during the procedure at above 90° and 30 did not change towards the end (100±10%, p=0.9). In contrast, in pDBG, ACD decreased by 31 51±19% to 21% below baseline (p<0.01) while the angle progressively narrowed by 40±12% 32 (p<0.001). Canalograms showed a similar extent of access to the outflow tract with the aDBG 33 and the pDBG (p=0.513). The average increase for the aDBG in the superonasal and inferonasal 34 quadrants was between 27 to 31% and for the pDBG between 15 to 18%.

Conclusion: ASOCT demonstrated that active irrigation and aspiration improved anterior 36 chamber maintenance and ease of handling with the aDBG in this MIGS training model. The 37 immediate postoperative outflow was equally good with both devices.
Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
Authors: Kadlec Malvina , Bellstedt Dirk U , Le Maitre Nicholas C , Pirie Michael D
Published: January 2018

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for “one size fits all” universal markers, we should improve and make more accessible the tools necessary for developing “made to measure” ones.
The abundance and biomass of mesozooplankton and ichthyoplankton in the confluence boundary of the Negro and the Amazon Rivers
Authors: Nakajima Ryota , Rimachi Elvis V , Santos-Silva Edinaldo N , Khen Adi , Yamane Tetsuo , Mazeroll Anthony I , Inuma Jomber C , Utumi Erika YK , Tanaka Akira
Published: January 2018

The boundary zone between two different hydrological regimes is often a biologically enriched environment with distinct planktonic communities. In the center of the Amazon River basin, muddy white water of the Amazon River meets with black water of the Negro River, creating a conspicuous visible boundary spanning over 10 km along the Amazon River. Here, we tested the hypothesis that the confluence boundary between the white and black water rivers concentrates prey and is used as a feeding habitat for juvenile fish by investigating the abundance, biomass and distribution of mesozooplankton and ichthyoplankton communities across the two rivers. Our results show that mesozooplankton abundance and biomass were higher in the black-water river compared to the white-water river; however an exceptionally high mesozooplankton abundance was not observed in the confluence boundary. Nonetheless we found the highest abundance of ichthyoplankton in the confluence boundary, being up to 9-fold higher than in adjacent rivers. The confluence boundary between black and white water rivers may function as a boundary layer that offers benefits of both high zooplankton prey concentrations (black-water) and low predation risk (white-water). This forms a plausible explanation for the high abundance of ichthyoplankton in the confluence zone of black and white water rivers.
Exploring the mitochondrial response to oxidative DNA damage in octocorals
Authors: Shimpi Gaurav G , Vargas Sergio , Wörheide Gert
Published: January 2018

Mitochondrial response to oxidative stress is intricately related to cellular homeostasis due to the high susceptibility of the mitochondrial genome to oxidative damage. Octocoral mitogenomes possess a unique DNA repair gene, mtMutS, potentially capable of counteracting the effects of oxidative stress induced mtDNA damage. Despite this unique feature, the response of octocoral mitochondria to increased oxidative stress remains unexplored. Here we explore the response of the octocoral Sinularia cf. cruciata to elevated temperature and low-pH stress and its ability to reverse acute oxidative mtDNA damage caused by exogenous agents like hydrogen peroxide (H2O2). The differential transcriptional response to these climate change-related stresses was recorded for two mtDNA-encoded genes and three stress biomarkers. Only HSP70 was significantly upregulated during thermal stress whereas significant reduction in the expression levels of HSP70, GPX, and COI was observed along with an increased number of mtMutS transcripts during low-pH stress. Damage to mtDNA was evident, accompanied by changes in mtDNA copy number. Damage caused by H2O2 toxicity was reversed within 5 hours and initial mtDNA copy number apparently influenced damage reversal. Our results indicate that different stress-specific resilience strategies are used by this octocoral species and its mitochondria to reverse oxidative stress and associated mtDNA damage. These experiments provide the first account on the response of octocoral mitochondria with its unique gene repertoire among animals to different stressors and highlight its potential role in conferring resilience to the host cells during different climate change scenarios.
Standardization in next-generation sequencing - Issues and approaches of establishing standards in a highly dynamic environment
Authors: Endrullat Christoph
Published: January 2018

Introduction

2nd generation sequencing or better known as next-generation sequencing (NGS) represents a cutting-edge technology in life sciences and current foundation for unravelling nucleotide sequences. Since advent of first platforms in 2005 the number of different types of NGS platforms increased in the last 10 years in the same manner as the variety of possible applications. Higher throughput, lower cost and better quality of data were the incentive for a range of enterprises developing new NGS devices, whereas economic issues and competitive pressure, based on expensive workflows of obsolete systems and decreasing cost of market leader platforms, resulted simultaneously in accelerated vanishing of several companies. Due to the fast development, NGS is currently characterized by a lack of standard operating procedures, quality management/quality assurance specifications, proficiency testing systems and even less approved standards along with high cost and uncertainty of data quality. On the one hand, appropriate standardization approaches were already performed by different initiatives and projects in the format of accreditation checklists, technical notes and guidelines for validation of NGS workflows. On the other hand, these approaches are exclusively located in the US due to origins of NGS overseas, therefore there exists an obvious lack of European-based standardization initiatives. An additional problem represents the validity of promising standards across different NGS applications. Due to highest demands and regulations in specific areas like clinical diagnostics, the same standards, which will be established there, will not be applicable or reasonable in other applications. These points emphasize the importance of standardization in NGS mainly addressing the laboratory workflows, which are the prerequisite and foundation for sufficient quality of downstream results.

Methods

This work was based on a platform-dependent and -independent systematic literature review as well as personal communications with i.a. Illumina, Inc., ISO/TC 276 as well as DIN NA 057-06-02 AA 'Biotechnology'.

Results

Prior formulation of specific standard proposals and collection of current de facto standards, the problems of standardization in NGS itself were identified and interpreted. Therefore, a variety of different standardization approaches and projects from organizations, societies and companies were reviewed.

Conclusions

There is already a distinct number of NGS standardization efforts present; however, the majority of approaches target the standardization of the bioinformatics processing pipeline in the context of “Big Data”. Therefore, an essential prerequisite is the simplification and standardization of wet laboratory workflows, because respective steps are directly affecting the final data quality and thus there exists the demand to formulate experimental procedures to ensure a sufficient final data output quality.
How long should the fully hillside-closed forest protection be implemented on the Loess Plateau, Shaanxi, China?
Authors: Hou Lin , Hou Sijia
Published: January 2018

Background. Restoration of degraded forest ecosystem is crucial for regional sustainable development. To protect the country’s fragile and fragmented environment, the Chinese government has initiated an ecological engineering, the Natural Forest Protection Program in seventeen provinces in China since 1998. Fully hillside-closed forest protection (vegetation restoration naturally without any artificial disturbance) was one of vital measures of the Natural Forest Protection Program applied national wide. Whether plant diversity, biomass and age structure of dominant tree species and soil nutrients in protected stands may become better with increase of protected period are still open problems. Methods. We investigated community diversity, biomass of dominant tree species, age structures, and analyzed soil chemical properties of a Pinus tabulaeformis population at protected sites representing different protected ages at Huanglongshan Forest Bureau on the Loess Plateau, Shaanxi, China. Results. Plant species richness of Pinus tabulaeformis community was significantly affected (p<0.05) by forest protection and the effect attenuated with protected age.Shannon evenness index of plant species generally increased with protected age. Stands protected for 45 years had the highest tree biomass and considerable natural regeneration capacity. Contents of organic carbon, available phosphorus and available potassium in top soil increased in protected stands less than 45 years, however decreased significantly thereafter. Long-term forest protection also decreased content of mineral nitrogen in top soil. Discussion. We found that richness of shrubs and herbs was significantly affected by forest protection, and evenness indices of tree, shrub and herb increased inconsistently with protected ages. Forest protection created more complex age structures and tree densities with increasing age of protection. Content of soil mineral nitrogen at 0-20 cm soil depth showed a decreasing trend in stands of up to 30 years. Soil available phosphorus and potassium contents were higher in stands with greater proportions of big and middle trees. Long-term protection (> 45 years) of Pinus tabulaeformis stand in southeast Loess Plateau, China, may be associated with decreasing plant species richness, proportion of medium to large trees, dominant biomass of Pinus tabulaeformis and soil nutrients.
Prediction of protein function using a deep convolutional neural network ensemble
Authors: Zacharaki Evangelia I
Published: January 2018

Background. The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function prediction.

Methods. In this work, novel shape features are extracted representing protein structure in the form of local (per amino acid) distribution of angles and amino acid distances, respectively. Each of the multi-channel feature maps is introduced into a deep convolutional neural network (CNN) for function prediction and the outputs are fused through Support Vector Machines (SVM) or a correlation-based k-nearest neighbor classifier. Two different architectures are investigated employing either one CNN per multi-channel feature set, or one CNN per image channel.

Results. Cross validation experiments on enzymes (n = 44,661) from the PDB database achieved 90.1% correct classification demonstrating the effectiveness of the proposed method for automatic function annotation of protein structures.

Discussion. The automatic prediction of protein function can provide quick annotations on extensive datasets opening the path for relevant applications, such as pharmacological target identification.
Imagining tomorrow's university: open science and its impact
Authors: Howe Adina , Howe Michael D. , Kaleita Amy L , Raman D. Raj
Published: January 2018

As part of a recent workshop entitled "Imagining Tomorrow's University”, we were asked to visualize the future of universities as research becomes increasingly data- and computation-driven and identify a set of principles characterizing pertinent opportunities and obstacles presented by this shift. In order to establish a holistic view, we take a multilevel approach and examine the impact of open science on individual scholars as well as the university as a whole. At the university level, open science presents a double-edged sword: when well executed, open science can accelerate the rate of scientific inquiry across the institution and beyond; however, haphazard or half-hearted efforts are likely to squander valuable resources, diminish university productivity and prestige, and potentially do more harm than good. We present our prespective on the role of open science at the university.
Glycaspis brimblecombei (Hemiptera: Psyllidae) attack patterns on different Eucalyptus genotypes
Authors: Tuller Juliana , Oliveira Karla Nunes , Silva Jhonathan Oliveira , de Faria Maurício Lopes , do Espírito-Santo Mario Marcos , Serrão José Eduardo , Zanuncio José Cola
Published: January 2018

Background. The red gum lerp psyllid Glycaspis brimblecombei Moore (Hemiptera: Psyllidae), an eucalypt insect pest from Australia, was reported in Brazil in 2003. This study evaluated damage patterns of this pest and the parasitism rates of Psyllaephagus bliteus (Hymenoptera: Encyrtidae) on E. camaldulensis and its hybrids E. urophylla X E. camaldulensis and E. urophylla X E. grandis. Methods. Plantation plots of three eucalypt genotypes were evaluated over one year. The eucalypt leaves were collected and examined. Results. Damage by G. brimblecombei was lower on the hybrid genotypes and on the adaxial surface of the eucalypt leaves. Glycaspis brimblecombei egg and nymph density correlated negatively with monthly rainfall. Nymph parasitism by P. bliteus was low (2.9%) independent of genotype and did not vary throughout the year. Discussion. The use of less susceptible eucalypt genotypes (e.g., hybrids) seems to be an alternative to G. brimblecombei management because mortality rates for this pest resulting from P. bliteus parasitism were low.
How do they cope with the situation when the caterpillars of beet armyworms, Spodoptera exigua, attack their host plant under different fertilization conditions?
Authors: Wang Sifang , Ding Tianbo , Xu Manlin , Zhang Bin
Published: January 2018

Fertilizer with different ration of nitrogen (N) to phosphorus (P) could influence performance of plants including crops and vegetables. Spodoptera exigua is an important agriculture pest that has caused serious economic loss especially recent decades. In the present study, we explored that the response of host plants and S. exigua after S. exigua caterpillars damaged on the way of different level intensity and frequency under five fertilizer treatments with different ratio of N to P. The results indicated that fertilizer can significantly influence the interaction between host plants and caterpillars. Compensatory growth was detected under definite fertilizer with N : P = 3 : 1. Higher N proportion in fertilizer appears to contribute to maintain similar stem biomass in defoliated seedlings to control ones. Root biomass had almost no significant difference between defoliation and control, but it can not compensate under definite fertilizer. Higher proportion of N in fertilizer also contributed to enhance antioxidant enzymes activities: antioxidase catalase (CAT), superoxide dismutase (SOD), at low-level intensity caterpillars on host plants.However, when the herbivorous intensity was increasing, higher proportion of P in fertilizer seemed to play more important role on increase the activities of CAT and SOD. Higher phosphorus likely contributes to enhance acetylcholin esterase (AChE) activity at lower degree of defoliation, but higher nitrogen proportion could result in higher AChE activity at higher degree of defoliation. Higher content of nitrogen in definite range contributed to reduce the carboxylesterase (CarE) activity at high intensity within short-term defoliation. However, when defoliation intensity enhanced, the difference of CarE activity between fertilizer categories was small.
Evaluating the environmental hazard of industrial chemicals from data collected during the REACH registration process
Authors: Gustavsson Mikael B , Hellohf Andreas , Backhaus Thomas
Published: January 2018

Registration dossiers for 11678 industrial chemicals were retrieved from the database of the European Chemicals Agency, of which 3566 provided a numerical entry for the corresponding predicted no effect concentration for the freshwater environment (PNEC). A distribution-based examination of 2244 of these entries reveals that the average PNEC of an industrial chemical in Europe is 238 nmol/L, covering a span of 9 orders of magnitude. A comparison with biocides, pesticides, pharmaceuticals and WFD-priority pollutants reveals that, in average, industrial chemicals are least hazardous (hazard ranking: industrial chemicals << pharmaceuticals < pesticides < Water Framework Directive priority pollutants < biocides). However, 280 industrial chemicals have a lower environmental threshold than the median pesticide and 73 have a lower environmental threshold than even the median biocide. Industrial chemicals produced and/or imported in higher tonnages have, on average, higher PNECs which most likely is due to the lower assessment factors used for the PNEC determination. This pattern indicates that the initial AF of 1000 comprises a measure of conservatism. The vast majority of PNEC values are driven by EC50 and NOEC data from tests with Daphnia magna. Tests with marine species are rarely provided for the hazard characterization of industrial chemicals.
pISA-tree: standard directory tree as a support for reproducible research
Authors: Blejec Andrej , Gruden Kristina
Published: January 2018

Basic idea of science is reproducibility of phenomena and experiments. Reproducibility of data analyses and reports is becoming more and more important. It requires structured organization of data, augmented with enought metadata for future re-use of data. Our aim is to provide a system to store data in a way that can be used for small and moderate size projects and fulfill minimal requirements of ISA-tab and FAIR paradigm.

Standard directory trees are applicable to research data storage. The main condition is that information is organized in files and we are not interested in the system that enables access to individual line/record or column/variable in a tabular data structure in the file. The tree structure is generated on the fly by use of batch files (on Windows platform) that generate necessary folders and meta-data template files.

We implemented the system of standard directory trees for support of the research in our research unit. Most often, our research projects can be hierarchically structured into, what can be called, Investigation which is composed of several Studies. Each individual study can have one or more Assays. To reflect this hierarchy, we named such directory tree the pISA-tree. To make new levels we provide three batch files: makeInvestigation, makeStudy, and makeAssay. Special attention is given to Description files that contain meta-information about research, protocols, samples, features et cetera. They are in line with the standards accepted for particular assays (e.g. MIQE, MIAMI, MIRIAM,...) which allow exchange of data with other data management services. In particular, we have in mind FAIRdom platform and some digital notebooks (e.g. SciNote).

pISA-tree structure rely on directories that are readily available on any computer platform and familiar to use by the researchers. Since the translation of meta-data into ISA-tab standard format is not too complex, pISA-tree is a step towards the FAIR paradigm.
Colonizer: Anandroid OS based automated microbial colony counter
Authors: Kumar Shashwat , Vaswata Roy Choudhury Rudra , Laxman Sunil
Published: January 2018

Colony counting to estimate colony forming units (CFUs) is a standard microbiology procedure used for determining the number of viable microbes in a system. Typically this process is done manually, which is time consuming, tedious, and sometimes error prone. Alternate image analysis based systems are also time consuming. In this paper we develop and demonstrate a simpleandroid based automated colony counter, called Colonizer, also made freely available on Google Playstore. Our algorithm can also threshold and segment overlapping colonies and thus provide rapid, accurate counts across a wide range of colony densities (from 50-500 colonies/plate), for different microbes, using any android based phone or device.
A survey of the World Wide Web evolution with respect to security issues
Authors: Lee Cheng
Published: January 2018

Recently, we hear more about web generations and its role in current web technologies we are using. Most of people know Web 2.0 and how the huge transformation changed from the previous version (Web 1.0). Web 2.0 is the style that became standard in the late 1990s and includes all the features that have allowed web pages to move beyond static documents. Web 2.0 marked a cultural shift in how web pages were developed, designed, and used from static era to dynamic one. It saw the meteoric rise of social media, including Facebook and Twitter, and user-generated content such as blogs, wikis, Wikipedia being perhaps the most famous and video-sharing sites such as YouTube. Its features made it very attractive for people to be familiar with it and learn to work with it. In this paper, we will go through some aspects of Web Generations from 1.0 to 3.0 and focus on some security issues for each generation.
Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map a nascent insect symbiont
Authors: Renoz François , Champagne Antoine , Degand Hervé , Faber Anne-Marie , Morsomme Pierre , Foray Vincent , Hance Thierry
Published: January 2018

Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deployed at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.
Transmissible cancer in marine bivalves: Implications for mode of cancer transmission
Authors: Ng Wenfa
Published: January 2018

Cancer spread away from the primary tumour towards other parts of the body is what is most feared in cancer treatment, and is the leading cause of relapse for patients who are in remission after initial rounds of treatment with surgery, radiation or chemotherapy. Typically more aggressive than the primary tumour, secondary tumours developed through the process of metastasis are seeded by circulating tumour cells that migrate away from solid tumours to distant body sites. But increasingly, there is another method by which cancer is able to spread: transmission between members of the same or different species. Dangerous for the implications that it portends, the intra- and interspecies transmission of cancer highlights the potential infectious nature of the disease of neoplastic cell growth, and the implications it may have on transmission of cancer through the food chain, even though the latter link find no verifiable reported episode, but which remains a possibility to be vigilant for. Currently, transmissible cancers have been detected in dogs, Tasmanian devils, and molluscs. In a recent report in Nature, Goff and coworkers reported the widespread transmission of independent cancer lineages within and between marine bivalves species (“Widespread transmission of independent cancer lineage within multiple bivalve species”). Field studies conducted along the Pacific Northwest coast led to the identification of neoplastic bivalves, which upon sequencing of the mitochondrial cytochrome c oxidase gene proffer a set of single nucleotide polymorphisms (SNP) that could be clustered into distinct cancer lineages in a phylogenetic tree. Using sequence information as guide and histology observations as clues, clear evidence of cancer transmission between and within bivalves species were confirmed, with affected bivalves showing clear phenotypic neoplasms. Given that bivalves are a source of nutrients and vitamins in the delicacy segment of Asian cuisine, possible transmission of cancer between bivalves and humans as well as mammals such as bears that feed on them is an important direction for future research.
Effect of achievement motive on purpose in life, social participation, role expectation, self-efficacy, and physical function by a longitudinal research study in Japan: using multilevel structural equation modeling
Authors: Sano Nobuyuki , Kyougoku Makoto
Published: January 2018

Objective: The purpose of this study was to demonstrate the effects of the achievement motive on important variables such as the purpose in life and social participation with objective physical functions in predicting within-person fluctuations and between-person differences using longitudinal research in community-dwelling Japanese elderly people.

Methods: The final dataset consisted of 227 persons (men: 109, women: 118) from day-service centers through testing at three time points. The tests comprised a questionnaire on the achievement motive, purpose in life and so on and the measurement of physical functions. We verified the following hypothesis model; 1) achievement motive works on improvement of the purpose in life, social participation, self-efficacy, and role expectation, 2) social participation and role expectation improve the purpose in life, 3) hobbies and going out affect the purpose in life, 4) social participation and physical function affect the increase in going out, 5) achievement motive and social participation improve physical function and increase role expectation and hobbies, and 6) self-efficacy improves social participation and the purpose in life. Our hypothesized model was based on previous research and was analyzed using a multilevel structural equation modeling approach.

Results: The modified hypothesis model without hobby, grip strength, and gait speed exhibited an adequate model fit: comparative fit index = 0.904, Tucker-Lewis index = 0.775, root mean square error of approximation = 0.064, Akaike’s information criterion = 25201.17, Bayesian information criterion = 25389.59, and adjusted BIC = 25256.24. Within level, the achievement motive had significant direct effects on the purpose in life, social participation, and self-efficacy. In addition, there were significant indirect effects of the achievement motive on the purpose in life through social participation and on social participation through self-efficacy. Between level, the achievement motive had significant direct effects on all variables and significant indirect effects on the purpose in life, social participation, and going out.

Conclusion: Our findings highlight the implications of achievement motive for the purpose in life, social participation and self-efficacy of the participation at the within person and between people levels. Consequently, we understood that the achievement motive could strongly affect between-person differences more than within-person fluctuations during a short period of six months.
De novo assembly of expressed transcripts and analysis of pistil to identify genes involved in early stage of pollination in Liriodendron chinense
Authors: Li Ming , Wang Kun , Damaris Rebecca Njeri , Yang Pingfang
Published: January 2018

Plant sexual reproduction is a complicated and a key biological process with profuse interactions between pollen and pistil. This process determines whether fertilization will be successful or not and thus affect the seed setting. To explore the reason why L. chinense has a low seed setting ratio, transcriptome analysis on pistils of L. chinense during pollination were conducted. After analyzing the sequencing data, 206,858 unigenes with an average length of 646 bp were generated using the assembled transcripts. Among total unigenes, 3844 genes which expression fold change during early stage of pollination was higher or lower than 10 were selected as significant differentially expressed genes. 54 differentially expressed genes involved in sexual reproduction processes including the regulation of pollen tube growth process and double fertilization process might be partially causing the low seed setting in L. chinense. These results indicated that the barrier between pollen tube and pistil might be the reason why L. chinense have low seed setting. This study might be helpful to understand why L. chinense has such a low seed setting ratio.
Prevalence and seroepidemiology of Haemophilus parasuis in Sichuan province, China
Authors: Wang Zhenghao , Zhao Qin , Wei Hailin , Wen Xintian , Cao Sanjie , Huang Xiaobo , Wu Rui , Yan Qigui , Huang Yong , Wen Yiping
Published: January 2018

Haemophilus parasuis, the causative agent of Glässer’s disease, has been reported widely, but seldom is known about its epidemiology in Sichuan province, China. The objective was to reveal the prevalence and distribution of H.parasuis in the area. Widely sampling and isolation was performed initially and following serotyping multiplex PCR (serotyping-mPCR) combined with agar gel diffusion (GD) was subjected to these strains. From January 2014 to May 2016, 254 H.parasuis field strains were isolated from 576 pigs with clinical symptoms, for the frequence of 44.10%. Statistically significant differences of infection incidence were found in three age groups and seasons. Serovars 5(25.98%) and 4(23.62%) were the most prevalent and non-typeable isolates accounted for 7.87%. In geographical distribution, serovars 5 and 4 were prepotent in both major two parts of Sichuan province. The results confirmed the compound approach was dependable and revealed the diversity and distribution of serovars in Sichuan province, which was promising to know relevant vaccinal candidates and further prevention.
Individual-level movement bias leads to the formation of higher-order social structure in a mobile group of baboons
Authors: Bonnell Tyler R , Clarke Parry M. , Henzi S. Peter , Barrett Louise
Published: January 2018

In mobile social groups, influence patterns driving group movement can vary between democratic and despotic. The arrival at any single pattern of influence is thought to be underpinned by environmental factors and group composition. To determine the specific patterns of influence in a chacma baboon troop we used spatially explicit data to identify patterns of individual movement bias on travel decision-making. We scaled these estimates of individual-level bias to the group as a whole by constructing an influence network, and assess its emergent structural properties. Our results suggest that individual animals respond consistently to specific group members, and that higher-ranking animals are more likely to influence the movement of others. At the group level, we identified a network structure with a single core and two outer shells. The presence of a core in this troop suggests that a set of highly inter-dependent individuals drive routine group movements. Our findings suggest that heterogeneity in individual level movement bias can lead to group level influence structures, and that movement patterns in mobile social groups can add to the exploration of both how social influence patterns develop (i.e., mechanistic aspects) and their linkages to individual and group level outcomes (i.e., functional aspects).
Within outlying mean indexes: refining the OMI analysis for the realized niche decomposition
Authors: Karasiewicz Stéphane , Dolédec Sylvain , Lefebvre Sébastien
Published: January 2018

The ecological niche concept has a revival interest under climate change, especially to study its impact on niche shift and/or conservatism. Here, we propose the Within Outlying Mean Indexes (WitOMI), which refines the Outlying Mean Index (OMI) analysis by using its properties in combination with the K-select analysis species marginality decomposition. The purpose is to decompose the ecological niche, into subniches associated to the experimental design, i.e. taking into account temporal or spatial subsets. WitOMI emphasizes the habitat conditions that contribute 1) to the definition of species’ niches using all available conditions and, at the same time, 2) to the delineation of species’ subniches according to given subsets of dates or sites. This latter aspect allows addressing niche dynamics by highlighting the influence of atypical habitat conditions on species at a given time or space. 3) Then, the biological constraint exerted on the species subniche becomes observable within the Euclidean space as the difference between the potential subniche and the realized subniche. We illustrate the decomposition of published OMI analysis, using spatial and temporal examples. The species assemblage’s subniches are comparable to the same environmental gradient, producing a more accurate and precise description of the assemblage niche distribution under climate change.
Designing the MIRRI information system
Authors: Romano Paolo DM , Smith David , Bunk Boyke , Vasilenko Alexander , Glöckner Frank Oliver
Published: January 2018

Culture collections (CCs) manage fundamental data about preserved microorganisms. To enable the exploitation of these resources requires standardized, and simplified, access to the associated information. To this end, a European Microbial Resource Research Infrastructure, MIRRI, was established. A prime objective of MIRRI is to unite and provide universal access to the information available in European public collections of microorganisms through a dynamic Information System, the MIRRI-IS. In this context, the desired outcome would include a repository for microbial domain Biological Resource Centre (mBRC) catalogues in a common format, the validation of catalogue contents to provide quality data, the interconnection of domain information systems for data extension, a unique portal for catalogues and associated data and an interoperable system based on Application Programming Interfaces (APIs) and service based interfaces and workflows.

The architectural design of the system foresees the adoption of a standard format for exchanging data between CCs, a Minimum Data Set for essential data, to evolve into Minimum Information about Biological Resources (MIaBRe), a user-friendly interface, as well as APIs and services/workflows for integration software.

Three systems were developed in the MIRRI preparatory phase. They have been developed to cope with distinct issues. The BacDive demonstrator aims at extending the contents of catalogues with a greater number of better defined data. The StrainInfo demonstrator is targeted towards a better integration among collection catalogues through the identification of common strains. It makes some order in strains available in various collections and makes possible the re-organization of collections and the sharing of data between catalogues. The USMI Galaxy demonstrator is aimed at supporting data curation and at integrating catalogues with external resources. It makes it possible to integrate collections' data with other bioinformatics databases by leveraging on existing tools and with little development requirements. Moreover, it allows the improvement of a collection’s data by automating links to external databases.

A five-year plan for the implementation of the MIRRI-IS has been defined. The four main lines included in the plan are data curation, interoperability, applications development and IT competence. Data curation is meant to be developed by the progressive adoption of Standard Operating Procedures, able to lead user catalogues from the current Minimum Data Set to a structured extended data set and finally to data sets fully compliant with Minimum Information about Biological Resources (MIaBRE) guidelines, still under definition. Interoperability will lead current separated catalogues to interact with an integrated repository of reference data which will finally allow user access to all catalogues through a common portal.
Milky way analysis through a Science Gateway: workflows and resource monitoring
Authors: Sciacca Eva , Vitello Fabio , Hajnal Akos , Becciani Ugo , Costa Alessandro , Kacsuk Peter
Published: January 2018

This paper presents the latest developments on the VIALACTEA Science Gateway in the context of the FP7 VIALACTEA project. This Science Gateway operates as a central workbench for the VIALACTEA community in order to allow astronomers to process the new-generation (from Infrared to Radio) surveys of the Galactic Plane to build and deliver a quantitative 3D model of our Milky Way Galaxy. The final model will be used as a template for external galaxies to study star formation across the cosmic time. The adopted AGILE software development process allowed to fulfill the community needs in terms of required workflows and underlying resources monitoring. The scientific requirements arose during the process highlighted the needs for easy parameter setting, fully embarrassingly parallel computations and large-scale input dataset processing. Therefore the Science Gateway based on the WS-PGRADE/gUSE framework has been able to fulfill the requirements mainly exploiting the parameter sweep paradigm and parallel jobs execution of the workflow management system. Moving from the development to the production environment an efficient resource monitoring system has been implemented to easily analyse and debug sources of failure of workflows computations exploitable not only for IT experts administrators and workflow developers but also for the final users of the gateway. The affiliation to the STARnet Gateway Federation ensures the sustainability of the whole products after the end of the project, allowing the usage of VIALACTEA Science Gateway to all the stakeholders and not only to the community members.
Milky way analysis through a Science Gateway: workflows and resource monitoring
Authors: Sciacca Eva , Vitello Fabio , Becciani Ugo , Costa Alessandro , Hajnal Akos , Kacsuk Peter , Molinari Sergio , Di Giorgio Anna M , Schisano Eugenio , Liu Scige John , Elia Davide , Cavuoti Stefano , Riccio Giuseppe , Brescia Massimo
Published: January 2018

This paper presents the latest developments on the VIALACTEA Science Gateway in the context of the FP7 VIALACTEA project. This science gateway operates as a central workbench for the VIALACTEA community in order to allow astronomers to process the new-generation (from Infrared to Radio) surveys of the Galactic Plane to build and deliver a quantitative 3D model of our Milky Way Galaxy. The final model will be used as a template for external galaxies to study star formation across the cosmic time. The adopted AGILE software development process allowed to fulfill the community needs in terms of required workflows and underlying resources monitoring. The scientific requirements arose during the process highlighted the needs for easy parameter setting, fully embarrassingly parallel computations and large-scale input dataset processing. Therefore the science gateway based on the WS-PGRADE/gUSE framework has been able to fulfill the requirements mainly exploiting the parameter sweep paradigm and parallel jobs execution of the workflow management system. Moving from the development to the production environment an efficient resource monitoring system has been implemented to easily analyse and debug sources of failure due to workflows computations. The results of the resource monitoring system are exploitable not only for IT experts administrators and workflow developers but also for the final users of the gateway. The affiliation to the STARnet Gateway Federation ensures the sustainability of the presented products after the end of the project, allowing the usage of VIALACTEA Science Gateway to all the stakeholders and not only to the community members.