bluuebunny/crossref_metadata_2025 huggingface dataset:
To investigate the antimicrobial effects of extracted polyphenols from green tea (Camellia sinensis) and banana (Musa sp.) leaves
Authors: Ng Qin Xiang
Published: January 2018

In recent years, there is an emergence of antibiotic-resistant bacterial strains due to the indiscriminate use of antibiotics, commonly prescribed to treat infectious diseases. The increasing occurrence of antibiotic resistance has undoubtedly made bacterial infections a greater health risk and threat than before. In this project, the use of natural polyphenolic compounds, extracted from green tea (Camellia sinensis) and banana (Musa sp.) leaves, as a novel antimicrobial chemotherapeutic agent was investigated. This study examined their bactericidal effects on Escherichia coli and Micrococcus luteus, and also evaluated the potential synergistic ability of these polyphenol-rich extracts when used alongside the beta-lactam antibiotic ampicillin. For the same dry mass of plant material used (3g), the prepared green tea extract had a higher total polyphenol concentration than that of banana leaves extract (495.1mg/L as compared to 221.6mg/L respectively). Subsequently, bacterial broth of 105 colony forming units/ml was mixed with varying concentrations of the different test compounds before plating 10µl of the mixture and quantifying the compounds’ bactericidal effect by doing a viable count after overnight incubation. The green tea extract showed the greatest bactericidal effect on E. coli and M. luteus as compared to the banana leaves extract and ampicillin. Against E. coli, this difference was confirmed to be significant (p<0.05) using one-way ANOVA and Tukey’s post-hoc analysis. Furthermore, by applying ampicillin in close association with polyphenol-rich extracts of green tea or banana leaves, there was an enhanced bactericidal effect on the tested bacterial strains. This interaction was categorized as synergistic by the fractional bactericidal concentration index calculated (≤0.5). Ultimately, the plant polyphenols studied in this research could provide a potential adjuvant to currently-produced antibiotics and help to reduce antibiotic application concentrations; as well as prolong the effective lifespan of antibiotics through its synergistic action.
Reproductive biology of the biofuel plant Jatropha curcas in its center of origin
Authors: Rincón-Rabanales Manuel , Vargas-López Laura I. , Adriano-Anaya Lourdes , Vázquez-Ovando Alfredo , Salvador-Figueroa Miguel , Ovando-Medina Isidro
Published: January 2018

In this work, we studied the main characteristics of flowering, reproductive system and diversity of pollinators for the biofuel plant Jatropha curcas (L.) in a site of tropical southeastern Mexico. The plants were monoecious with inflorescences of unisexual flowers. The male flowers produced from 3062 to 5016 pollen grains (266-647 per anther). The plants produced fruits with both geitonogamy and xenogamy, although insect pollination significantly increased the number and quality of fruits. A high diversity of flower visiting insects (36 species) was found, of which nine were classified as efficient pollinators. The native stingless bees Scaptotrigona mexicana (Guérin-Meneville) and Trigona (Tetragonisca) angustula (Latreille) were the most frequent visitors and their presence coincided with the hours when the stigma was receptive. It is noteworthy that the female flowers open before the male flowers, favoring xenogamy, which may explain the high genetic variability reported in J. curcas for this region of the world.
The perception of shape from shading in a new light
Authors: Proulx Michael J
Published: January 2018

How do humans see three-dimensional shape based on two-dimensional shading? Much research has assumed that a ‘light from above’ bias solves the ambiguity of shape from shading. Counter to the ‘light from above’ bias, studies of Bayesian priors have found that such a bias can be swayed by other light cues. Despite the persuasive power of the Bayesian models, many new studies and books cite the original ‘light from above’ findings. Here I present a version of the Bayesian result that can be experienced. The perception of shape-from-shading based was found here to be influenced by an external light source, even when the light was obstructed and did not directly illuminate a two-dimensional stimulus. The results imply that this effect is robust and not low-level in nature. The perception of shape from shading is not necessarily based on a hard-wired internal representation of lighting direction, but rather assesses the direction of lighting in the scene adaptively. Here, for the first time, is an experiential opportunity to see what the Bayesian models have supported all along.
GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework
Authors: Beiko Robert G , Parks Donovan H , Mankowski Timothy , Zangooei Somayyeh , Porter Michael S , Armanini David G , Baird Donald J , Langille Morgan G I
Published: January 2018

GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada.GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.
The rediscovery and redescription of the holotype of the Late Jurassic turtle Plesiochelys etalloni
Authors: Anquetin Jérémy , Deschamps Sylvie , Claude Julien
Published: January 2018

Plesiochelyidae are a major component of Late Jurassic shallow marine environments throughout Europe. However, the taxonomy of the plesiochelyid turtles is rather confused. Over the years, many taxa have been synonymized with Plesiochelys etalloni, one of the first described species. However, the holotype of P. etalloni (and only specimen known from the type locality) was lost for more than 150 years. This specimen has been recently rediscovered in the collections of the Musée d'archéologie du Jura in Lons-le-Saunier, France. For the first time since its original description in 1857, the holotype of P. etalloni is redescribed and compared to relevant material. The taxonomical status of this taxon is revised accordingly. Based on the morphology of the newly rediscovered holotype, the species P. solodurensis, P. sanctaeverenae and P. langii are synonymized with P. etalloni. Known skull-shell associations for P. etalloni are re-evaluated in light of the new morphological information available since the rediscovery of this holotype specimen. Finally, we confirm that Plesiochelys is represented by a single species in Solothurn, Switzerland.
The feature of morphological traits and their effects on body weight in the red crab (Charybdis feriata)
Authors: Zou Xiong , Ma Hongyu , Lu Jianxue , Gong Yangyang , Xia Lianjun
Published: January 2018

The red crab (Charybdis feriata) is one of most important fishery resources in China. In the present study, we first measured 17 morphological traits and body weight of C. feriata, characterized these 18 traits, and then estimated the effects of morphological traits on body weight by statistical methods including correlation coefficients, determination coefficients, path coefficients, and regression equation. All correlation coefficients between 17 morphological traits and body weight reached an extremely significant level (P<0.01). Determination and path coefficients analysis revealed the real correlation relationship between the independent variables and the dependent variable. Significant path coefficients were found between three morphological traits (stemum width, X8; meropodite length of pereopod 3, X16; meropodite length of pereopod 4, X17) and body weight that suggested these three traits were the key traits directly influence body weight. Multiple correlation index (R2) between above three morphological traits and body weight was of 0.977, which indicated that the main independent variables influencing body weight has been found. Finally a best-fit linear regression equation was established as Y = 13.078 X8 + 7.048 X16 - 4.902 X17 - 576.635, which provided an ideal model for better understanding the feature of morphological traits and body weight of C. feriata.
Natural occurrence of the entomopathogenic fungi Beauveria bassiana as a vertically transmitted endophyte of Pinus radiata and its effect on above- and below-ground insect pests
Authors: Lefort Marie-Caroline , McKinnon Aimee C , Nelson Tracey L , Glare Travis R
Published: January 2018

Background. The New Zealand forest industry would greatly benefit from a successful way of controlling insect pests. The entomopathogenic fungus, Beauveria bassiana could hold such potential and has previously been shown to be capable of endophytic colonisation of the Monterey pine Pinus radiata. Nevertheless clarifications on its mode of transmission, persistence and action in this plant are required. In this study we investigated B. bassiana transmission and persitence in P. radiata and whether this fungus is beneficial to P. radiata by testing its effect as a plant endophyte on the fitness performance of above and belowground insect feeders. Methods. Both culturing and molecular approaches were used to detect the occurrence B. bassiana in pines. Transmission electron microscopy of positive germinating seeds was also used to locate the fungus. Bioassays were conducted on root and needle feeding insects using Beauveria positive and endophyte free pine seedlings. Results. Beauveria bassiana was detected in seedlings which had not previously been exposed to the fungus, indicating a vertical mode of transmission. The fungus could colonise all parts of the pines, but did not always persist. We found that the presence of the fungus negatively affects the fitness of the below-ground insect feeding on the plant by reducing their survival by over 10% and their weight by 5%. This study also showed that the mode of action of endophytic B. bassiana in pine is likely to be by feeding deterrence of insects induced locally by fungal metabolites, rather than by direct fungal infection of the insects. Discussion. A vertically transmitted beneficial endophyte of pine could be used as a cost effective approach to control insect pest in these commercially grown trees.
Flower color preferences of insects and livestock: effects on Gentiana lutea reproductive success
Authors: Sobral Mar , Losada María , Veiga Tania , Guitián Javier , Guitián José , Guitián Pablo
Published: January 2018

Angiosperms diversification was primarily driven by pollinator agents, but non-pollinator agents also promoted floral evolution. Gentiana lutea shows pollinator driven flower color variation in NW Spain. We test whether insect herbivores and livestock, which frequently feed in G.lutea, play a role in G. lutea flower color variation, by answering the following questions: i) Do insect herbivores and grazing livestock show flower color preferences when feeding on G. lutea? ii) Do mutualists (pollinators) and antagonists (seed predators, insect herbivores and livestock) jointly affect G. lutea reproductive success? Insect herbivores fed more often on yellow flowering individuals but they did not affect seed production whereas livestock affected seed production but did not show clear color preferences. Our data indicate that flower color variation of G. lutea is not affected by insect herbivores or grazing livestock.
A comparison of tree community assemblage and diversity of secondary forests between the birch and pine-oak belts in the mid-altitude zone of the Qinling Mountains, China
Authors: Chai Zongzheng , Wang Dexiang
Published: January 2018

Deforestation is a major driver of forest loss and fragmentation, threatening forest biodiversity worldwide. The conservation and restoration of secondary vegetation is thus an important developmental goal. Birch and pine-oak belts have been the two main types of vegetation in the mid-altitude zone of the Qinling Mountains in China but are now mainly covered by secondary growth following large-scale deforestation. Assessing the recovery and sustainability of these forests is essential for their management and restoration. We investigated and compared the tree community assemblages and diversity patterns of secondary forests between birch and pine-oak belts in the Huoditang forest region of the Qinling Mountains after identical natural recoveries. Both the birch and pine-oak belts had richspeciescompositions and similar floristiccomponents but clearly different tree community structures. Niche and neutral processes simultaneously influenced the distribution of species and the community dynamics of the belts. Tree diversity was significantly higher for the birch than the pine-oak belt. Monitoring biodiversity is essential for the recovery and development of forest resources in the Qinling Mountains to safeguard biodiversity, especially tree diversity.
Red deer synchronise their activity with close neighbours
Authors: Rands Sean A , Terry Naomi , Muir Hayley
Published: January 2018

Models of collective animal behaviour frequently make assumptions about the effects of neighbours on the behaviour of focal individuals, but these assumptions are rarely tested. One such set of assumptions is that the switch between active and inactive behaviour seen in herding animals is influenced by the activity of close neighbours, where neighbouring animals show a higher degree of behavioural synchrony than would be expected by chance. We tested this assumption by observing the simultaneous behaviour of paired individuals within a herd of red deer Cervus elaphus. Focal individuals were more synchronised with their two closest neighbours than with the third closest or randomly selected individuals from the herd. Our results suggest that the behaviour of individual deer is influenced by immediate neighbours. Even if we assume that there are no social relationships between individuals, this suggests that the assumptions made in models about the influence of neighbours may be appropriate.
Open access as a mechanism of revolutionary science and the limitations of data
Authors: Vakalopoulos Costa
Published: January 2018

Data is the cornerstone of the modern academic industry, like a constant production line of consumable goods packaged with a veneer of statistical techniques. Biomedical and psychological sciences invert the traditional logic of the physical sciences where hypotheses were tested against data rather than data against hypotheses. This is likely to reflect the immaturity of the new paradigms that barely cope with the data output of a precocious enterprise. However, the current state leads to distortions of the practice of science and entrenchment of its dysfunctional politics reflected in the science itself. With the debate now on the reproduction of data and statistical sleights of hand accompanying many if not most studies, what is lost in the debate is the preeminent role of good theoretical discovery. This is partly as a result of the structure of funding, the nature of reporting in biomedical fields based on the symbiotic relationship of high ranking institutions and journals. Open access could fill a gap in traditional publishing literature which has entrenched a culture of highly restrictive practices at a time when revolutionary science is required. OA is not in danger of lowering the standards of science as its critics claim, but because it is ‘open’ to new and radical ideas that would never see the light of day otherwise, it may well provide a rejuvenating energy. OA is a self-regulatory response to the consequences of the distorted and inhibitory contemporary practice of science.
Open access as a mechanism of revolutionary science and the limitations of data
Authors: Vakalopoulos Costa
Published: January 2018

Data is the cornerstone of the modern academic industry, like a constant production line of consumable goods packaged with a veneer of statistical techniques. Biomedical and psychological sciences invert the traditional logic of the physical sciences where hypotheses were tested against data rather than data against hypotheses. This is likely to reflect the immaturity of the new paradigms that barely cope with the data output of a precocious enterprise. However, the current state leads to distortions of the practice of science and entrenchment of its dysfunctional politics reflected in the science itself. With the debate now on the reproduction of data and statistical sleights of hand accompanying many if not most studies, what is lost in the debate is the preeminent role of good theoretical discovery. This is partly as a result of the structure of funding, the nature of reporting in biomedical fields based on the symbiotic relationship of high ranking institutions and journals. Open access could fill a gap in traditional publishing literature which has entrenched a culture of highly restrictive practices at a time when revolutionary science is required. OA is not in danger of lowering the standards of science as its critics claim as the studies on non replication show that they do not discriminate against OA papers specifically. Because it is ‘open’ to new and radical ideas that would never see the light of day otherwise, it may well provide a rejuvenating energy. OA is a self-regulatory response to the consequences of the distorted and inhibitory contemporary practice of science as the popularity of OA journals testify to.
Peruvians’ sleep duration: analysis of a population-based survey on adolescents and adults
Authors: Carrillo-Larco Rodrigo M. , Bernabé-Ortiz Antonio , Miranda J. Jaime , Rey de Castro Jorge
Published: January 2018

Sleep duration, either short or long, has been associated with diseases such as obesity, type-2 diabetes and cardiovascular diseases. Characterizing the prevalence and patterns of sleep duration at the population-level, especially in resource-constrained settings, will provide informative evidence on a potentially modifiable risk factor. The aim of this study was to explore the patterns of sleep duration in the Peruvian adult and adolescent population, together with its socio-demographic profile. This is a cross-sectional study, secondary analysis of the Use of Time National Survey conducted in 2010. Weighted means and proportions were used to describe sleep duration according to socio-demographic variables. Poisson regressions, taking into account the multistage sampling design of the survey, were used to calculate crude and adjusted prevalence ratios (PR) and 95% confidence intervals (95% CI). Main outcomes were short- (<6 hours) and long-sleep duration (≥9 hours). A total of 12,424 observations, mean age 35.8 years (SD ±17.7), 50.6% males, were included in the analysis. On average, Peruvians slept 7.7 hours (95% CI 7.4-8.0) on weekdays and 8.0 hours (95% CI 7.8-8.1) during weekends. The proportions of short- and long-sleep, during weekdays, were 4.3% (95% CI 2.9%-6.3%) and 22.4% (95% CI 14.9%-32.1%), respectively. Regarding urban and rural areas, a much higher proportion of short-sleep was observed in the former. On the multivariable analysis, compared to regular-sleepers (≥6 to <9 hours), short-sleepers were twice more likely to be older and to have higher educational status, and 50% more likely to be currently employed. Similarly, relative to regular-sleep, long-sleepers were more likely to have a lower socioeconomic status as per educational attainment. In this nationally representative sample, the sociodemographic profile of short-sleep contrasts the long-sleep. These scenarios in Peru, as depicted by sleeping duration, differ from patterns reported in other high-income settings and could serve as the basis to inform and to improve sleep habits in the population.
Evaluation of morphometric characters of honeybee (Apis mellifera L.) populations in Nigeria
Authors: Dukku Usman H
Published: January 2018

Samples of workers of honeybee were collected from 41 colonies in nine localities in Nigeria and analysed using classical morphometry. Measurements of 35 morphological characters of body size, colour and pilosity were taken from 10 workers per colony and the data subjected to one-way analysis of variance (ANOVA) and principal component analysis. Although ANOVA revealed a considerable variation of morphological characters between the sampled localities, principal component analysis indicated that this variation was not sufficient to group the colonies under investigation into geographically separable groups. Based on the agreement between the results of this study and those of previous studies, it is concluded that the honeybees of this area are morphometrically pure populations of sub-Saharan A. mellifera.
Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
Authors: Delmont Tom O , Eren A. Murat
Published: January 2018

High-throughput sequencing provides a fast and cost effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini using approaches routinely employed by microbial ecologists who reconstruct bacterial and archaeal genomes from metagenomic data. We created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.
The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation
Authors: Huang Jian-Zhi , Lin Chih-Peng , Cheng Ting-Chi , Huang Ya-Wen , Tsai Yi-Jung , Cheng Shu-Yun , Chen Yi-Wen , Lee Chueh-Pai , Chung Wan-Chia , Chang Bill Chia-Han , Chin Shih-Wen , Lee Chen-Yu , Chen Fure-Chyi
Published: January 2018

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.
Sympathy for the devil: a conservation strategy for devil and manta rays
Authors: Lawson Julia M , Walls Rachel HL , Fordham Sonja V , O'Malley Mary P , Heupel Michelle R , Stevens Guy , Fernando Daniel , Budziak Ania , Simpfendorfer Colin A , Davidson Lindsay NK , Ender Isabel , Francis Malcolm P , Notarbartolo di Sciara Giuseppe , Dulvy Nicholas K
Published: January 2018

Background. Increased interest in luxury products and Traditional Chinese Medicine, associated with economic growth in China, has been linked to depletion of both terrestrial and marine wildlife. Among the most rapidly emerging concerns with respect to these markets is the relatively new demand for gill plates, or Peng Yu Sai (“Fish Gills”), from devil and manta rays (subfamily Mobulinae). The high value of gill plates drives international trade supplied by largely unmonitored and unregulated bycatch and target fisheries around the world. Devil and manta rays are especially sensitive to overexploitation because of their exceptionally low productivity (maximum intrinsic rate of population increase). Scientific research, conservation campaigns, as well as international and national protections that restrict fishing or trade have increased in recent years. Many key protections, however, apply only to manta rays. Methods. We review the state of the development of scientific knowledge and capacity for these species, and summarise the geographic ranges, fisheries and national and international protections for these species. We use a conservation planning approach to develop the Global Devil and Manta Ray Conservation Strategy, specifying a vision, goals, objectives, and actions to advance the conservation of both devil and manta rays. Results and Discussion. Generally, there is greater scientific attention and conservation focused on Manta compared to Devil Rays. We discuss how the successes in manta ray conservation can be expanded to benefit devil rays. We also examine solutions for the two leading threats to both devil and manta rays – bycatch and target fisheries. First, we examine how can the impact of bycatch fisheries can be reduced through international measures and best-practice handling techniques. Second, we examine the role that responsible trade and demand can play in reducing target fisheries for gill plates. Our paper suggests that given similarities in sensitivity and appearance, particularly of the dried gill plate product, conservation measures may need to be harmonised particularly for the larger species in this subfamily.
Towards a barrier height benchmark set for biologically relevant systems
Authors: Kromann Jimmy C , Christensen Anders S , Jensen Jan H.
Published: January 2018

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10-15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4-5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process.
Towards a barrier height benchmark set for biologically relevant systems
Authors: Kromann Jimmy C , Christensen Anders S , Cui Qiang , Jensen Jan H.
Published: January 2018

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10-15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4-5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process.
Deep-sea megafaunal response to physical disturbance along the SW Portuguese continental slope
Authors: Ramalho Sofia P , Lins Lidia , Lampadariou Nikolaos , Vanreusel Ann , Cunha Marina R
Published: January 2018

Continental slopes support highly diverse ecosystems strongly influenced by habitat heterogeneity and increasing anthropogenic disturbance, of which bottom trawling fisheries are considered of major importance. Recent studies showed that megafauna assemblages are particularly sensitive to trawling disturbance in hard substrate habitats (e.g. seamounts) but impacts on soft sediments are mostly unknown. Video surveys obtained by Remotely Operated Vehicle (ROV) were used to investigate megafaunal structural and functional diversity in areas subjected to different degrees of disturbance (no, low, medium and high trawl intensity) covering different soft sediment habitats (muddy-sand and sandy bottoms) along the SW Portuguese continental slope. In total, 17 km of video transects were analysed within a bathymetric range of 200m and 700m water depths. All disturbed areas displayed frequent and recent trawl marks (up to 3 marks per 100m), with general flattened seafloor topography and low bioturbation. Additional scattered litter presence was observed. Megafauna abundances were highly variable among habitats, revealing more than 80 morphospecies, belonging to 17 classes. Overall, communities from muddy-sand habitats presented higher species richness in undisturbed locations, where sessile groups such as sponges (Porifera) and soft corals (e.g. Pennatulacea) were predominantly found. In contrast, sandy locations subjected to disturbance showed lower diversity and high abundances of the dominant polychaete Hyalinoecia tubicula. The use of several biological traits (e.g. mobility, living habit, feeding type) will be discussed in relation to the community composition and structural diversity among the different habitats and disturbance pressures to better understand on the vulnerability of the continental slope benthic habitats.
Computational inference of H3K4me3 and H3K27ac domain length
Authors: Zubek Julian , Stitzel Michael L , Ucar Duygu , Plewczynski Dariusz M
Published: January 2018

Background. Recent epigenomic studies have shown that the length of a DNA region covered by an epigenetic mark is not just a byproduct of the assaying technologies and has functional implications for that locus. For example, expanded regions of DNA sequences that are marked by enhancer-specific histone modifications, such as acetylation of histone H3 lysine 27 (H3K27ac) domains coincide with cell-specific enhancers, known as super or stretch enhancers. Similarly, promoters of genes critical for cell-specific functions are marked by expanded H3K4me3 domains in the cognate cell type, and these can span DNA regions from 4-5kb up to 40-50kb in length. These expanded H3K4me3 domains are known as buffer domains or super promoters. Methods. To ask what correlates with—and potentially regulates—the length of loci marked with these two important histone marks, H3K4me3 and H3K27ac, we built Random Forest regression models. With these models we computationally identified genomic and epigenomic patterns that are predictive for the length of these marks in seven ENCODE cell lines. Results. We found that certain epigenetic marks and transcription factors explain the variability of the length of H3K4me3 and H3K27ac marks across different cell types, which implies that the lengths of these two epigenetic marks are tightly regulated in a given cell type. Our source code for the regression models and data can be found at our GitHub page: https://github.com/zubekj/broad_peaks Discussion. Our Random Forest based regression models enabled us to estimate the individual contribution of different epigenetic marks and protein binding patterns to the length of H3K4me3 and H3K27ac deposition patterns; therefore potentially revealing genomic signatures at cell specific regulatory elements.
Selection of reference genes for RT-qPCR studies in blood of beluga whales (Delphinapterus leucas)
Authors: Chen I-Hua , Wang Jiann-Hsiung , Chou Shih-Jen , Wu Yeong-Huey , Li Tsung-Hsien , Leu Ming-Yih , Chang Wen-Been , Yang Wei Cheng
Published: January 2018

Reverse transcription-quantitative PCR (RT-qPCR) is used for research in gene expression, and it is vital to choose appropriate housekeeping genes (HKGs) as reference genes to obtain correct result. The purpose of this study is to determine stably expressed HKGs in blood of beluga whales (Delphinapterus leucas) that can be the appropriate reference genes in relative quantification in gene expression research. Sixty blood samples were taken from 4 beluga whales. Thirteen candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ) were tested using RT-qPCR. The stability values of the HKGs were determined by four different algorithms. Comprehensive analysis of the results revealed that RPL4, PGK1 and ACTB are strongly recommended for use in future RT-qPCR studies in beluga blood samples. This research provides recommendation of reference gene selection, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans. The gene expression assessment of the immune components in blood have potential to serve as important approach to evaluating cetacean health influenced by environmental insults.
Judging a commit by its cover; or can a commit message predict build failure?
Authors: Santos Eddie A , Hindle Abram
Published: January 2018

Developers summarize their changes to code in commit messages. When a message seems “unusual,” however, this puts doubt into the quality of the code contained in the commit. We trained \(n\)-gram language models and used cross-entropy as an indicator of commit message “unusualness” of over 120 000 commits from open source projects. Build statuses collected from Travis-CI were used as a proxy for code quality. We then compared the distributions of failed and successful commits with regards to the “unusualness” of their commit message. Our analysis yielded significant results when correlating cross-entropy with build status.
Oral health status among long-term hospitalized adults: A cross sectional study.
Authors: Bilder Leon , Yavnai Nirit , Zini Avi
Published: January 2018

Background: Many Long-Term Care (LTC) patients suffer from dental neglect due to difficulties in achieving appropriate dental professional care; although oral health has important influence on the quality of life among them. Dental care of the long term institutionalized adults is often limited to emergency and first aid care and there is insufficient data regarding oral health status in this population.Objectives: To describe the oral health status of the long-term hospitalized adults. Materials and methods: A cross-sectional study including clinical oral examinations was carried out among institutionalized LTC patients aged 18 and older in a geriatric - psychiatric Hospital in Israel. Main outcome measures were: edentulousness, presence of dentures, mucosal findings, number of teeth, number of functional teeth, level of dental hygiene and, dental caries. Results: Subjects’ mean age was 65 years; 31.3% of the patients were edentulous, and only 14% had partial or full dentures. Only 17.2% were caries free. Females had significantly higher number of caries cavitation than men (p=0.044). The number of caries cavitation was higher among patients with higher plaque scores (p<0.001) and when taking Clonex (p=0.018). Number of residual teeth in mouth was higher in the low plaque score group (p<0.001). Carious teeth percentage was higher among the high plaque score group (p<0.001)
pyAffy: An efficient Python/Cython implementation of the RMA method for processing raw data from Affymetrix expression microarrays
Authors: Wagner Florian
Published: January 2018

Robust multi-array average (RMA) is a highly successful method for processing raw data from Affymetrix expression microarrays. However, most of the work on microarray data processing predates the widespread use of Python in scientific computing. Here, I describe pyAffy, an efficient implementation of the RMA method in Python/Cython. Using data from the MAQC project, I show that this implementation produces virtually identical results compared to the RMA reference implementation in the affy R package, while running more than five times faster and consuming significantly less memory. I also show how individual steps of the RMA method affect the final expression estimates. The source code for pyAffy is available from PyPI and GitHub (https://github.com/flo-compbio/pyaffy) under an OSI-approved license. I intend to periodically revise this article to ensure that it accurately reflects the functionalities available in the pyAffy Python package.
Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria
Authors: Muthusamy Saraldevi , Lundin Daniel , Branca Rui MM , Baltar Federico , González José M , Lehtiö Janne , Pinhassi Jarone
Published: January 2018

Exponentially growing bacteria are rarely found in nature. Instead, bacteria spend most of their lifetime in a slow- or non-proliferating state, a state that is occasionally interrupted by an increase in accessible nutrients. To successfully compete for pulses of nutrients, copiotrophic marine bacteria have adaptations that allow them to change their metabolism to support exponential growth in response to nutrients and to return to stationary phase when nutrients return to normal scarcity. The molecular details of these adaptations can be observed through proteome profiles, i.e. relative abundances of proteins in cells, and how they change between different conditions. We developed proteome profiles during exponential and stationary phase conditions for three model organisms representing major marine bacterioplankton lineages. 22500-3000 proteins per isolate were detected, representing large proportions of each proteome (67-87%). A shift from protein synthesis and other processes typically associated with active growth, to proteins essential for nutrient scavenging, was observed during transition into stationary phase. The three isolates differed in magnitude of their responses and in how enzymes of different metabolisms responded. Some of the differences can be seen as differences in implementation of a shared strategy, such as an increase in enzymes involved in carbon storage, while other differences are best described as differences in strategy. We thus observed the proteome reflection of “signature metabolisms” in the three isolates – distinct metabolic adaptations to environmental circumstances. These findings have direct implications for the interpretation of proteomic and genetic data from microbes in natural environments.
Absence of Helicobacter pylori is not protective against peptic ulcer bleeding in elderly on offending agents: lessons from an exceptionally low prevalence population
Authors: Lee Yeong Yeh , Noridah Nordin , Syed Hassan Syed Abdul Aziz , Menon Jayaram
Published: January 2018

Aim Helicobacter pylori (H. pylori) infection is exceptionally rare in population from the north-eastern region of Peninsular Malaysia. This provides us an opportunity to contemplate the future without H. pylori in acute non-variceal upper gastrointestinal (GI) bleeding.Methods All prospective cases in the GI database registry with GI bleeding between 2003 and 2006 were reviewed. Cases with confirmed non-variceal aetiology were analysed. Rockall score > 5 was considered high risk for bleeding and primary outcomes studied were in-hospital mortality, recurrent bleeding and need for surgery. Results The incidence of non-variceal upper GI bleeding was 2.2/100,000 person-years. Peptic ulcer bleeding was the most common aetiology (1.8/100,000 person-years). In-hospital mortality (3.6%), recurrent bleeding (9.6%) and need for surgery (4.0%) were uncommon in this population with a largely low risk score (85.2% with score ≤ 5). Elderly were at greater risk for bleeding (mean 68.5 years, P = 0.01) especially in the presence of duodenal ulcers (P = 0.04) despite gastric ulcers being more common. NSAIDs (34%) and aspirin (22.8%) were the main risk factors. Conclusions The absence of H. pylori infection may not reduce the risk of peptic ulcer bleeding in the presence of risk factors especially offending drugs in the elderly.
Zika virus impairs growth in human neurospheres and brain organoids
Authors: Garcez Patricia P , Loiola Erick C , Madeiro da Costa Rodrigo F , Higa Luiza , Trindade Pablo , Delvecchio Rodrigo , Nascimento Juliana M , Brindeiro Rodrigo M , Tanuri Almicar , Rehen Stevens K
Published: January 2018

Since the emergence of Zika virus (ZIKV), reports of microcephaly have increased dramatically in Brazil; however, causality between the widespread epidemic and malformations in fetal brains has not been confirmed. Here, we examine the effects of ZIKV infection in human neural stem cells growing as neurospheres and cerebral organoids. Using immunocytochemistry and electron microscopy, we show that ZIKV targets human brain cells, reducing their viability and growth as neurospheres and cerebral organoids. These results suggest that ZIKV abrogates neurogenesis during human brain development.
Microbes in deionized water: Implications for maintenance of laboratory water production system
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Microbes, with their diverse metabolic capabilities and great adaptability, occupy almost every conceivable ecological niche on Earth – thus, could they survive in the oligotrophic (i.e., nutrient-poor) deionized (DI) water that we use for our experiments? Observations of white cauliflower-like lumps and black specks in salt solutions after months of storage in plastic bottles prompted the inquisition concerning the origin and nature of the “contaminants.” Hypothesising that the “contaminants” may be microbes from DI water, a series of growth experiments was conducted to detect and profile the microbial diversity in fresh DI water - produced on a just-in-time basis by a filter-cum-ion-exchange system with tap water as feed. While microbes could also be present on the surfaces and headspace of the unsterilized polyethylene bottles, investigating whether microbes are present in freshly produced DI water provides a more stringent performance test of the production system. Inoculation of DI water on R2A agar followed by multi-day aerobic cultivation revealed the presence of a wide variety of microbes (total viable cell concentration of ~103 colony forming units (CFU) per mL) with differing pigmentations, growth rates as well as colony sizes and morphologies. Additionally, greater abundance and diversity of microbes was recovered at 30 oC relative to 25 and 37 oC; most probably due to adaptation of microbes to tropical ambient water temperatures of 25 to 30 oC. Comparative experiments with tap water as inoculum recovered a significantly smaller number and diversity of microbes; thereby, suggesting that monochloramine residual disinfectant in tap water was effective in inhibiting cell viability. In contrast, possible removal of monochloramine by adsorption onto ion-exchange resins – and thus, alleviation of a source of environmental stress - might explain the observed greater diversity and abundance of viable microbes in DI water. Collectively, this study confirmed the presence of microbes in fresh DI water – and suggested a possible source for the “contaminants” in prepared salt solutions. Propensity of microbes for forming biofilm on various surfaces suggested that intermittent flow in just-in-time DI water production provided opportunities for cell attachment and biofilm formation in the system during water stagnation, and subsequent dislodgement and resuspension of cells upon water flow. Thus, regular maintenance and cleaning of the production system should help reduce DI water’s microbial load. Additionally, simple and low-cost culture experiments on agar medium can provide a qualitative and semi-quantitative estimate of microbial diversity and viable cell concentration in DI water, respectively; which, along with regular monitoring of water resistivity or conductivity, comprise a trio of tests useful for detecting possible contamination or, deterioration of DI water’s chemical and microbiological quality.