bluuebunny/crossref_metadata_2025 huggingface dataset:
Response of endemic and exotic earthworm communities to ecological restoration
Authors: Boyer Stéphane , Kim Young-Nam , Bowie Mike H , Lefort Marie-Caroline , Dickinson Nicholas M
Published: January 2018

New Zealand has 23 exotic and more than 200 endemic earthworm species. Endemic earthworms disappeared quickly after vegetation clearance and land conversion to agriculture from the early C19th. Environmental changes associated with agronomic practices are believed to have been the main drivers for their disappearance. Exotic earthworms introduced from Europe have since largely replaced endemic earthworms into farming systems and have been intentionally propagated to increase production. Little is known about potential competition between endemic and exotic earthworms in New Zealand, and the capacity of exotic earthworms to extend their range into native habitats. Using two sites in the South Island of New Zealand, we investigated the impact of restoring native vegetation on earthworm communities. The study sites were Quail Island (Banks Peninsula), which has been undergoing native plant restoration for more than 30 years, and the Punakaiki Coastal Restoration Project (West Coast) where 130,000 native trees have been planted in retired pasture in the last seven years. At each site, soil samples (20 x 20 x 20 cm) were collected and hand sorted for earthworms. Sequential restoration plantings revealed that recolonisation by endemic earthworms increases with time after restoration at the two sample sites. With increasing age of the restoration, the biomass of endemic earthworm significantly increased, as did abundance at Punakaiki. However, exotic species did not disappear after restoration of native vegetation, even after 30 years in Quail Island. The persistence of exotic species leads to the cohabitation of the two communities and potential for interspecific competition.
Web servers energy efficiency under HTTP/2
Authors: Sapra Varun , Hindle Abram
Published: January 2018

Server energy consumption has been a subject of research for more than a decade now. With Internet scaling rapidly all over the world, more servers are being added continuously. With global warming and financial cost associated with running servers, it has now become a more pressing concern to optimize the power consumption of these servers while still not affecting the performance. The optimization that can be carried out at the hardware level has its limits and therefore the onus comes on to the software developers as well to optimize their web interacting services and use protocols that are more efficient. Recently, Internet Engineering Task Force (IETF) formalized the specification for the successor of HTTP/1.1 protocol. Named HTTP/2, it has been projected to overcome all the limitations of HTTP/1.1 protocol for which web services developers have to optimize their applications. Understandably, HTTP/2 has been drawing a lot of interest from users, web administrators to big organizations. With HTTP/2 as the future of the Internet communication and servers acting as the backbone of the Internet, we are interested in knowing if HTTP/2 will provide energy efficiency benefits to servers or it will just improve users web experience. In this paper, we evaluate the energy efficiency of two web servers while they communicate over HTTP/1.1 and HTTP/2 protocol. We also investigate how Transport layer security (TLS) affects the power consumption of the servers. In our tests, we have introduced HTTP/2 features one by one so that readers can see for themselves what benefits the HTTP/2 over HTTP/1.1. Our study suggests that multiplexing and Round Trip time (RTT) are the biggest factors helping HTTP/2 achieve its design goals. We conclude that even with huge TLS associated cost with HTTP/2, on high latency networks it can help servers to be more energy efficient while improving their performance as well.
Requirements engineering practice and problems in agile projects: results from an international survey
Authors: Wagner Stefan , Méndez Fernández Daniel , Felderer Michael , Kalinowski Marcos
Published: January 2018

Requirements engineering (RE) is considerably different in agile development than in traditional processes. Yet, there is little empirical knowledge on the state of the practice and contemporary problems in agile RE. As part of a bigger survey initiative (Naming the Pain in Requirements Engineering), we build an empirical basis on such aspects of agile RE. Based on the responses from 92 people representing 92 organizations, we found that agile RE concentrates on free-text documentation of requirements elicited with a variety of techniques. Many manage explicit traces between requirements and code. Furthermore, the continuous improvement of RE is done because of intrinsic motivation. Important experienced problems include unclear requirements and communication flaws. Hence, agile RE is in several aspects not so different from RE in other development processes. We plan to investigate specific techniques, such as acceptance-test-driven development, in a future survey to better capture what is special in agile RE.
Collaboro: A collaborative (Meta) modeling tool
Authors: Cánovas Izquierdo Javier Luis , Cabot Jordi
Published: January 2018

Software development processes are collaborative in nature. Neglecting the key role of end-users leads to software unlikely to satisfy their needs. This collaboration becomes specially important when creating Domain-Specific Modeling Languages (DSMLs), which are (modeling) languages specifically designed to carry out the tasks of a particular domain. While end-users are actually the experts of the domain for which a DSML is developed, their participation in the DSML specification process is still rather limited nowadays. In this paper, we propose a more community-aware language development process by enabling the active participation of all community members (both developers and end-users of the DSML) from the very beginning. Our proposal is based on a DSML itself, called Collaboro, which allows representing change proposals on the DSML design and discussing (and tracing back) possible solutions, comments and decisions arisen during the collaboration. Collaboro also incorporates a metric-based recommender system to help community members to define high-quality notations for the DSMLs. We also show how Collaboro can be used at the model-level to facilitate the collaborative specification of software models.
Properties of distance spaces with power triangle inequalities
Authors: Greenhoe Daniel J
Published: January 2018

Metric spaces provide a framework for analysis and have several very useful properties. Many of these properties follow in part from the triangle inequality. However, there are several applications in which the triangle inequality does not hold but in which we may still like to perform analysis. This paper investigates what happens if the triangle inequality is removed all together, leaving what is called a distance space, and also what happens if the triangle inequality is replaced with a much more general two parameter relation, which is herein called the "power triangle inequality". The power triangle inequality represents an uncountably large class of inequalities, and includes the triangle inequality, relaxed triangle inequality, and inframetric inequality as special cases. The power triangle inequality is defined in terms of a function that is herein called the power triangle function. The power triangle function is itself a power mean, and as such is continuous and monotone with respect to its exponential parameter, and also includes the operations of maximum, minimum, mean square, arithmetic mean, geometric mean, and harmonic mean as special cases.
Mathematical models are a powerful method to understand and control the spread of Huanglongbing
Authors: Taylor Rachel A , Mordecai Erin , Gilligan Christopher A , Rohr Jason R , Johnson Leah R
Published: January 2018

Huanglongbing, or citrus greening, is a global citrus disease occurring in almost all citrus growing regions and causing substantial economic burdens to individual growers, citrus industries and governments. Successful management strategies to reduce disease burden are desperately needed but with so many possible interventions and combinations thereof, it is difficult to know which are worthwhile or cost-effective. We review how mathematical models have yielded useful insights into controlling disease spread for other vector-borne plant diseases, and the small number of mathematical models of Huanglongbing. We adapt a malaria model to Huanglongbing, by including temperature-dependent psyllid traits and economic costs, to show how models can be used to highlight which parameters require more data collection or which should be targeted for intervention. We analyze the most common intervention strategy, insecticide spraying, to determine the most cost-effective spraying strategy. We found that fecundity and feeding rate of the vector require more experimental data collection, for wider temperatures ranges. The best strategy for insecticide intervention was to spray for more days rather than pay extra for a more efficient spray. We conclude that mathematical models are able to provide useful recommendations for managing Huanglongbing spread.
Heterochronic shifts in germband movements contribute to the rapid embryonic development of the coffin fly Megaselia scalaris
Authors: Wotton Karl R
Published: January 2018

The coffin fly, Megaselia scalaris, is a species of medical and forensic importance and is increasingly being used for the study of genetics. Postmortem interval can be estimated based on the life stage of M. scalaris recovered from corpses, therefore many studies have addressed the duration of each life stage. These studies demonstrate that embryogenesis completes significantly faster in M. scalaris than in the congener Megaselia abdita and faster even than the 24 hours needed for Drosophila melanogaster embryogenesis. However, until now it has been unclear if this increased speed is achieved by reducing developmental time across all embryonic stages or by the acceleration of individual stages and processes. Here I use time-lapse imaging to create a staging scheme for M. scalaris embryogenesis. Comparison of stages between D. melanogaster and both Megaselia species reveals that heterochronic shifts, simultaneous morphogenetic movements and compression of individual stages all contribute to the rapid development of M. scalaris.
mockrobiota: a public resource for microbiome bioinformatics benchmarking
Authors: Bokulich Nicholas A , Rideout Jai Ram , Mercurio William G , Wolfe Benjamin , Maurice Corinne F , Dutton Rachel J , Turnbaugh Peter J , Knight Rob , Caporaso J. Gregory
Published: January 2018

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at https://github.com/caporaso-lab/mockrobiota. The materials contained in mockrobiota include dataset and sample metadata, expected composition data, which are annotated based on one or more reference taxonomies, links to raw data (e.g., raw sequence data) for each mock community dataset, and optional reference sequences for mock community members. mockrobiota does not supply physical sample materials directly, but the dataset metadata included for each mock community indicate whether physical sample materials are available (and associated contact information). At the time of this writing, mockrobiota contains 11 mock community datasets with known species compositions (including bacterial, archaeal, and eukaryotic mock communities), analyzed by high-throughput marker-gene sequencing. The availability of standard, public mock community data will facilitate ongoing methods optimizations; comparisons across studies that share source data; greater transparency and access; and eliminate redundancy. This dynamic resource is intended to expand and evolve to meet the changing needs of the ‘omics community.
The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance
Authors: Tanaka Katherine H , Vincent Antony T , Trudel Mélanie V , Paquet Valérie E , Frenette Michel , Charette Steve J
Published: January 2018

Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistances genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Isolates from Canada and Europe that bore similar antibiotic resistance patterns than pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A.salmonicida subsp. salmonicida bacteria.
Diarrhoea and acute respiratory infections among under-five children in slums: Evidence from India
Authors: Singh Aditya , Singh Mahesh Nath
Published: January 2018

Background: In the wake of burgeoning slum population, a substantial reduction in the prevalence of diarrhea and acute respiratory infections (ARI) is necessary for to achieve necessary reduction in child mortality in urban India. To achieve this, we need evidence based public health interventions and programs. However, a review of previous studies indicate that national level studies focused on slum population are very few. Therefore, the present study aims to study differentials and determinants of diarrhea and ARI in urban slums of India. Methodology: Using data obtained from the third round of National Family Health Survey conducted in 2005-06, we analyzed information on 2687 under-5 children living in urban slums located in eight selected India cities. Apart from bivariate analysis, logistic regression analysis was performed to identify factor associated with diarrhea and ARI among slum children. Results: The prevalence diarrhea and ARI is about 8% and 8.5%, respectively. Age, birth weight, access to safe water and improved toilet and region emerge as main factors affecting prevalence of diarrhea among slum children. Safe drinking water reduces the likelihood of getting diarrhea by about 19% compared to unsafe water [CI=0.563-1.151]. Children with normal birth are about 51% less likely to suffer from diarrhea compared to those with unknown birth weight [CI=0.368-0.814]. Older children are about 63% less likely to suffer from diarrhea [CI=0.274-0.502]. Children from Southern cities are about half as likely to have diarrhea as children from slums in Northern cities. ARI is associated with age, birth weight, religion, caste, education, family type, safe water, improved toilet, mass-media exposure, region and separate kitchen. Older children and children with normal birth weight are less likely to suffer from ARI. Children from ‘Other’ religions and OBC are 39% [CI=1.000-1.924] and 49% [CI=1.008-2.190], respectively, more likely to suffer from ARI. Parents’ education is strongly associated with prevalence of ARI. Exposure to mass media reduces the likelihood of ARI to 50% compared to the situation when mother of the child did not have any exposure to mass-media [CI=0.324-0.819]. Non-flush toilet and lack of separate kitchen increase the likelihood of ARI. Children from slums located in Southern region are less likely to suffer from ARI. Conclusion: The findings call for dedicated programs and policies, in line with those already existing ones such as RAY, IHSDP, NUHM, ICDS and JNNURM, for the development of urban slums through provision of affordable housing, improved sanitation, safe water and clean fuel. Adequate nutrition to mothers and their children should be ensured and vulnerable groups identified in the analysis should be the focus of future public health intervention and strategies. The use of mass-media to change health behavior should also be considered.
Complexity curve: a graphical measure of data complexity and classifier performance
Authors: Zubek Julian , Plewczynski Dariusz M
Published: January 2018

We describe a method for assessing data set complexity based on the estimation of the underlining probability distribution and Hellinger distance. Contrary to some popular measures it is not focused on the shape of decision boundary in a classification task but on the amount of available data with respect to attribute structure. Complexity is expressed in terms of graphical plot, which we call complexity curve. We use it to propose a new variant of learning curve plot called generalisation curve. Generalisation curve is a standard learning curve with x-axis rescaled according to the data set complexity curve. It is a classifier performance measure, which shows how well the information present in the data is utilised. We perform theoretical and experimental examination of properties of the introduced complexity measure and show its relation to the variance component of classification error. We compare it with popular data complexity measures on 81 diverse data sets and show that it can contribute to explaining the performance of specific classifiers on these sets. Then we apply our methodology to a panel of benchmarks of standard machine learning algorithms on typical data sets, demonstrating how it can be used in practice to gain insights into data characteristics and classifier behaviour. Moreover, we show that complexity curve is an effective tool for reducing the size of the training set (data pruning), allowing to significantly speed up the learning process without reducing classification accuracy. Associated code is available to download at: https://github.com/zubekj/complexity_curve (open source Python implementation).
Impact of agricultural management on bacterial laccase-encoding genes with possible implications for soil carbon storage in semi-arid Mediterranean olive farming
Authors: Moreno Beatriz , Benitez Emilio
Published: January 2018

Background . Laccases, mostly laccase-like multicopper oxidases (LMCO), are probably the most common ligninolytic enzymes in soil. Although, in recent studies, laccase-encoding genes have been successfully used as molecular markers in order to elucidate the role of bacteria in soil organic C cycling , further research in this field is necessary . In this study, using rainfed olive farming as an experimental model, we determined the stability and accumulation levels of humic substances and appliedthese data to bacterial laccase-encoding gene expression and diversity in soils under four different agricultural management systems (bare soils under tillage/no tillage and vegetation cover under chemical/mechanical management).

Materials and Methods. Humic C (>10 4 Da) was subjected to isoelectric focusing. The GC-MS method was used to analyze aromatic hydrocarbons. Real-Time PCR quantification and denaturing gradient gel electrophoresis ( DGGE) of DNA/RNA for functional bacterial laccase-like multicopper oxidase (LMCO)-encoding genes and transcripts were also carried out.

Results. Soils under spontaneous vegetation, eliminated in springtime using mechanical methods, showed the highest humic acid levels as well as the largest bacterial population, rich in laccase genes and transcripts after more than 30 years of experiments. The structure of the bacterial community based on LMCO genes also pointed to phylogenetic differences between these soils due to the impact of different management systems. Soils where herbicides were used to eliminate spontaneous vegetation once a year and those where pre-emergence herbicides resulted in bare soils clustered together for DNA-based DGGEanalysis, which indicated a certain amount of microbial selection due to the application of herbicides. When LMCO-encoding gene expression was studied, soils where cover vegetation was managed either with herbicides or with mechanical methods showed less than 10% similarity, suggesting that the different laccase substrates derived from vegetation cover decay when herbicides are used.

Conclusions. We suggest that the low humic acid content retrieved in the herbicide-treated soils was mainly related to the type (due to vegetal cover specialization ) and smaller quantity (due to lower vegetal biomass levels) of phenolic substrates for laccase enzymes involved in humification processes. We also found that spontaneous vegetal cover managed using mechanical methods could be the best option for achieving C stabilization in rainfed Mediterranean agroecosystems.
Plant spatial patterns and functional traits interaction along a chronosequence of primary succession: evidence from a central Alpine glacier foreland
Authors: Sitzia Tommaso , Dainese Matteo , Krüsi Bertil O. , McCollin Duncan
Published: January 2018

The main aim of this study was to elucidate the roles of terrain age and spatial self-organisation as drivers of primary succession using high-resolution assessment of plant composition, functional traits and landscape metrics. We sampled 46 plots, 1m x 1m each, distributed along a 15-70 year range of terrain ages on the foreland of the Nardis glacier, located in the southern central Alps of Italy. From existing databases, we selected nine quantitative traits for the 16 plant species present, and we measured a set of seven landscape metrics, which described the spatial arrangement of the plant species patches on the study plots, at a 1cm x 1cm resolution. We applied linear models to study the relationships among plant communities, landscape metrics and terrain age. Furthermore, we used RLQ-analysis to examine trait-spatial configuration relations. To assess the effect of terrain age variation on trait performance, we applied a partial-RLQ analysis approach. Finally, we used the fourth-corner statistic to quantify and test relations between traits, landscape metrics and RLQ axes. Surprisingly, linear models revealed that neither the plant composition nor any of the landscape metrics differed among the three classes of terrain age distinguished, viz. 15-41 y, 41-57 y and 57-66 y, respectively. Further, no correlations were detected between trait patterns and terrain age, however, the floristically defined relevé clusters differed significantly with regard to several landscape metrics and suggestive relationships between increasing patch diversity and traits connected to growth rate were detected. We conclude that (i) terrain age below 70 years is not a good predictor for neither plant composition nor spatial configuration on the studied microhabitat and (ii) the small-scale configuration of the plant species patches correlates with certain functional traits and with plant composition, suggesting species-based spatial self-organisation.
A formal approach to the molecular fuzzy lock-and-key
Authors: Wallace Rodrick
Published: January 2018

The fuzzy lock-and-key (FLK) powers a vast array of sophisticated logic gates at inter- and intra-cellular levels. We invoke representations of groupoid tiling wreath products - analogous to the study of nonrigid molecules - or the syntopy group and related fuzzy symmetry extensions, to build a Morse Function that can describe spontaneous symmetry breaking phase transitions driven by information catalysis. The Function can, however, also be used to construct an Onsager-like stochastic dynamics, linked to the phase transition approach by the rich stability criteria associated with stochastic differential equations. The two methods provide complementary ways of looking at the FLK. A limit condition emerging from the stochastic dynamics gives insight into a cellular 'generalized inflammation' requiring progressively higher commitment of metabolic free energy for maintenance of basic FLK processes. These results suggest that more systematic study may illuminate pathologies associated with the failure of the FLK, a centrally-important but enigmatic biological process.
Modeling potential distribution of Indo-Pacific humpback dolphins (Sousa chinensis) in the Beibu Gulf, China
Authors: Chen Mei , Song Yuqin , Qin Dagong
Published: January 2018

Background. Mapping key habitats of marine mega-vertebrates with high mobility is crucial for species conservation. Due to difficulties in obtaining sound data in the field, Species Distribution Modeling (SDM) provides an effective alternative to identify habitats. As a keystone and flagship species in inshore waters in southern China, Indo-Pacific humpback dolphins (Sousa chinensis) play an important role in coastal ecosystems. However, our knowledge on their key habitats remained unclear in some waters including the Beibu Gulf of South China Sea.

Methods. We used a maximum entropy (Maxent) modeling approach to predict potential habitats for Sousa chinensis in the Beibu Gulf of China. Models were based on eight independent oceanographic variables derived from Google Earth Digital Elevation Model (DEM) and Landsat images, and presence-only sighting data from boat-based surveys and literatures during 2003-2013.

Results. Three variables, distance to major river mouths, to coast and to 10-m isobaths, were the strongest predictors, consistent with other studies on the dolphin habitat selection. Furthermore, we confirmed that influence of estuaries was the most important and irreplaceable. Besides two known distribution areas as well as data sources, a new area close to the boundary of China and Vietnam, Beilunhe Estuary (BE), was predicted as a potential habitat.

Discussion. Influence of estuaries is likely to indicate feeding preference of the humpback dolphins. The “new” habitat BE should be a key area connecting China and Vietnam dolphins, and deserved to be examined and preserved.
Historical reconstruction of the community response, and related epidemiology, of a suspected biological weapon attack in Ningpo, Manchuria (1940)
Authors: Wilson James M , Daniel Mari
Published: January 2018

After the conclusion of World War II, members of the Imperial Japanese Army biological warfare Unit 731 testified to a Soviet military court they conducted a live test deployment of plague-infected fleas in Ningpo, Zhejiang Province, a city south of Shanghai with a population of approximately 300,000. The deployment triggered an outbreak involving 78 cases and 74 fatalities (case fatality rate 95%) that included the death of seven families. Children and young adults aged 11-30 were most severely effected. Despite lack of access to effective medical countermeasures, the Ningpo community exhibited a high degree of social cohesion and resilience in the context of effective public health response.
Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB)
Authors: Joshi Amar , Esteve Vicent , Buckroyd Adrian N , Blatter Markus , Allain Frédéric HT , Curry Stephen
Published: January 2018

The eukaryotic polypyrimidine tract binding protein (PTB) serves primarily as a regulator of alternative splicing of messenger RNA, but is also co-opted to other roles such as RNA localisation and translation initiation from internal ribosome entry sites. The neuronal paralogue of PTB (nPTB) protein is 75% identical in amino acid sequence with PTB. Although the two proteins have broadly similar RNA binding specificities and effects on RNA splicing, differential expression of PTB and nPTB can lead to the generation of alternatively spliced mRNAs. RNA binding by PTB and nPTB is mediated by four RNA recognition motifs (RRMs). We present here the crystal and solution structures of the C-terminal domain of nPTB (nPTB34) which contains RRMs 3 and 4. As expected the structures are similar to each other and to the solution structure of the equivalent fragment from PTB (PTB34). The result confirms that, as found for PTB, RRMs 3 and 4 of nPTB interact with one another to form a stable unit that presents the RNA-binding surfaces of the component RRMs on opposing sides. The major differences between PTB34 and nPTB34 arise from amino acid side chain substitutions on the exposed β-sheet surfaces and adjoining loops of each RRM, which are likely to modulate interactions with RNA.
Hierarchical multistate models from population data: An application to parity statuses
Authors: Schoen Robert
Published: January 2018

Hierarchical models are characterized by having N living states connected by N–1 rates of transfer. Demographic measures for such models can be calculated directly from counts of the number of persons in each state at two nearby points in time. Exploiting the ability of population stocks to determine the flows in hierarchical models expands the range of demographic analysis.

The value of such analyses is illustrated by an application to childbearing, where the states of interest reflect the number of children a woman has born. Using Census data on the distribution of women by age and parity, a parity status life table for U.S. Women, 2005-2010, is constructed. That analysis shows that nearly a quarter of American women are likely to remain childless, with a 0-3 child pattern replacing the 2-4 child pattern of the past.
Open technologies for monitoring systems aimed at disaster risk reduction
Authors: Cannata Massimiliano , Chemin Yann , Antonovic Milan Petar , Wijesinghe Lahiru , Deparday Vivien
Published: January 2018

This research is spearheading the integration of Free and Open Source Software (FOSS) and Open Source Hardware (OSHW) in the field of agri-meteorology applications to disaster risk reduction, flood and droughts. A Do-It-Yourself weather station based on OSHW standards has been developed from local sources in Sri Lanka, reporting by SMS to tank/reservoir managers when rainfall is higher than 10mm/h. These weather stations are soon going to be reprogrammed to report to istSOS, a FOSS web-based Sensor-Observation-Service compliant system, which will collate live reporting of rainfall every hour and before if intensities are dimmed worrying for flood risks. This is both a scientific, technological, and practical challenge toward a very low cost real time disaster risk notification system in places where climate, economy and maintenance supports are themselves other challenges.
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
Authors: Sahl Jason W , Caporaso Greg , Rasko David A , Keim Paul S
Published: January 2018

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the large-scale, flexible, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 minutes using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.
Exploring complex disease gene relationships using simultaneous analysis
Authors: Romano Joseph D , Tharp William G , Sarkar Indra N
Published: January 2018

The characterization of complex diseases remains a great challenge for biomedical researchers due to the myriad interactions of genetic and environmental factors. Adaptation of phylogenomic techniques to increasingly available genomic data provides an evolutionary perspective that may elucidate important unknown features of complex diseases. Here an automated method is presented that leverages publicly available genomic data and phylogenomic techniques. The approach is tested with nine genes implicated in the development of Alzheimer Disease, a complex neurodegenerative syndrome. The developed technique, implemented through a suite of Ruby scripts entitled “ASAP2,” first compiles a list of sequence-similarity based orthologues using PSI-BLAST and a recursive NCBI BLAST+ search strategy, then constructs maximum parsimony phylogenetic trees for each set of nucleotide and protein sequences, and calculates phylogenetic metrics (partitioned Bremer support values, combined branch scores, and Robinson-Foulds distance) to provide an empirical assessment of evolutionary conservation within a given genetic network. This study demonstrates the potential for using automated simultaneous phylogenetic analysis to uncover previously unknown relationships among disease-associated genes that may not have been apparent using traditional, single-gene methods. Furthermore, the results provide the first integrated evolutionary history of an Alzheimer Disease gene network and identify potentially important co-evolutionary clustering around components of oxidative stress pathways.
Tree mortality from a global-change type drought coupled with a short-duration freezing event in a Southwestern piñon-juniper woodland, USA
Authors: Poulos Helen M
Published: January 2018

This study documents tree mortality in Big Bend National Park in Texas in response to the most acute one-year drought on record, which occurred in conjunction with a five-day winter freeze. I estimated changes in forest stand structure and species composition due to drought in the Chisos Mountains of Big Bend National Park using permanent monitoring plot data. Tree mortality was pervasive, and it occurred across the entire elevation gradient. Significant mortality occurred in trees up to 20 cm diameter (P < 0.05). Pinus cembroides Zucc. experienced the greatest seedling and tree mortality (P < 0.0001), and over five times as many standing dead pines were observed in 2012 than in 2009. Juniperus deppeana vonSteudal and Quercus emoryi Leibmann also experienced significant declines (P < 0.02). Trees probably died as a result of hydraulic failure, however the preferential mortality of P. cembroides relative to other species could also be tied to its adoption of an isohydric drought tolerance strategy. Subsequent droughts under climate change will likely cause even greater damage to trees that survived this record drought, especially if such events are coupled with freezes. The results from this study highlight the vulnerability of trees in the Southwest to climatic change and that future shifts in forest structure can have large-scale community consequences.
Direct-to-consumer genetic testing in the college classroom: Knowledge, attitudes, and concerns of introductory biology students
Authors: Austriaco Nicanor
Published: January 2018

Pioneered by companies like 23andMe.com, deCODEme.com, and Navigenics.com, direct-to-consumer genetic testing refers to genetic tests that are marketed directly to consumers via television, print media, or the Internet. This kind of testing provides access to a customer’s genetic information without necessarily involving either a medical health care professional or a genetic counselor in the process. In recent years, a course offered to medical and graduate students at Stanford University has included an option for students to undergo personal genotyping, raising the possibility that direct-to-consumer genetic testing could also be incorporated into undergraduate biology courses to enhance student learning. In this study, I assess the attitudes and concerns of college students enrolled in the first semester of an introductory majors course in biology, before and after they had completed the course, regarding the availability of this technology and its possible use in the college classroom. The pre-course survey revealed that these students were open to the possibility of using this technology in their courses, but that they had concerns about the confidentiality and the accuracy of their genetic results. Strikingly, however, completing the genetics, molecular and cellular biology semester-long portion of the yearlong introductory sequence in biology appeared to boost student confidence in this technology and its use in the undergraduate classroom.
Area-based sampling for an epidemiological study on injury patterns and risk factors in a low-income urban setting in sub-Saharan Africa
Authors: Wilson Michael L , Seifert Stephen P.
Published: January 2018

Unintentional injuries represent an important health threat to the lives of children and adolescents world-wide. The epidemic of injury and resulting harm such as disability or death, are likely to be the most severe in the low- and middle-income countries of the African continent. The following paper is intended to document an area-based sampling method designed to facilitate an epidemiological study to examine injury patterns among children and adolescents in Dar es Salaam, Tanzania. We used official census data and geographic information system software to create a series of area maps for Dar es Salaam city. Then, based on these maps, we identified population clusters for sampling based on area population density.
Overload injuries in barefoot/minimal footwear running: evidence from crowd sourcing
Authors: Daumer Martin , Kleinmond Christine , Stolle Christoph , Lederer Christian , Hilgers Marc , Walther Markus
Published: January 2018

Background: The incidence of injuries in minimal footwear or barefoot runners compared to runners using conventional running shoes is still being discussed.

Methods: We focus here on methods and results of a online survey in a community of minimal footwear/barefoot (MF/B) runners. The aim of the survey was to investigate the viability of the method and to record first insights on running behavior, distance performance and injuries.

Results: In total 226 runners answered the questionnaire, 15 subjects had to be removed due to invalid data. A total of 211 (94%) subjects (152 male, ages 15-71 years [mean=40]) were included in the analysis. The risk to suffer a running related injury was significantly increased during the time period of changing from shod running to MF/B running (see Table 2). The injury rate per km was markedly lower – about one half - in MF/B than in shod running, but threefold higher during the transition period.

Discussion/Conclusion: Future research into the right “dosage” of barefoot/minimal footwear running in the transition period is warranted. We speculate that special adaptations - which may take years and thousands of kilometers to become effective - of the neuromuscular control play a major role, very similar to the thousands of hours a person needs to play and practice playing the piano before becoming a musician.
Spatial and temporal variability of benthic primary production in upwelling-influenced Colombian Caribbean coral reefs
Authors: Eidens Corvin , Bayraktarov Elisa , Pizarro Valeria , Wilke Thomas , Wild Christian
Published: January 2018

In Tayrona National Natural Park (Colombian Caribbean), abiotic factors such as light intensity, water temperature, and nutrient availability are subjected to high temporal variability due to seasonal coastal upwelling. These factors are major drivers controlling coral reef primary production. This offers the opportunity to assess the effects of abiotic factors on key coral reef ecosystem services in terms of productivity. We therefore quantified primary net (Pn) and gross production (Pg) of the dominant local primary producers (scleractinian corals, macroalgae, algal turfs, crustose coralline algae, and microphytobenthos) at a water current/wave-exposed (EXP) and -sheltered (SHE) site in an exemplary bay of Tayrona National Natural Park. A series of short-term incubations was conducted to quantify O2 fluxes of the different primary producers before and at the end of the upwelling event 2011/2012. At the level of the organism, scleractinian corals showed highest Pn and Pg rates before upwelling (16 and 19 mmol O2 m-2 specimen area h-1), and corals and algal turfs dominated the primary production at the end of upwelling (12 and 19 mmol O2 m-2 specimen area h-1, respectively). At the ecosystem level, corals contributed most to total Pn (EXP: 81 %; SHE: 65 %) and Pg (EXP: 78 %; SHE: 55 %) before the upwelling, while at the end of the upwelling, corals contributed most to Pn and Pg only at EXP (73 and 75 %) and macroalgae at SHE (52 and 46 %, respectively). Despite the significant spatial and temporal differences in individual productivity of investigated groups and their different contribution to reef productivity, no spatial or temporal differences in daily ecosystem Pn and Pg were detected (194 – 218 and 311 – 409 mmol O2 m-2 seafloor area d-1). Our findings therefore indicate that local autotrophic benthic reef communities are well adapted to pronounced fluctuations of environmental key parameters. This might lead to a higher resilience against climate change consequences and anthropogenic disturbances.
Color vision in Attention-Deficit/Hyperactivity Disorder: A pilot visual evoked potential study
Authors: Kim Soyeon , Banaschewski Tobias , Tannock Rosemary
Published: January 2018

Background: Individuals with Attention-Deficit/Hyperactivity Disorder (ADHD) are reported to manifest visual problems (including ophthalmological and color perception problems, particularly for blue-yellow stimuli), but findings are inconsistent. Accordingly, this study investigated visual function and color perception in adolescents with ADHD using VEP.

Method: Participants were 31 adolescents (aged 13-18); 16 with a confirmed diagnosis of ADHD, and 15 healthy peers, matched for age, gender, and IQ. All underwent ophthalmological exam, color vision testing (Mollon-Reffin Minimalist Colour Vision Test), as well as electrophysiological testing (color Visual Evoked Potentials; cVEP) which measured the latency and amplitude of the neural P1 response to chromatic stimuli (Blue-Yellow, Red-Green).

Result: No group differences were found in clinical measure of color perception or opthalmological exam. However, significantly larger P1 amplitude was found for blue and yellow stimuli, but not red/green stimuli, in the ADHD group compared to controls.

Discussion: Larger amplitude in the P1 component for blue-yellow in ADHD group compared to control group may account for no difference in colour perception task. Perhaps activating more resources in early sensory processing (P1) compensated for any underlying problems including compromised retinal input of s-cones due to hypo-dopaminergic tone.
Characterisation of the horse transcriptome from immunologically active tissues
Authors: Moreton Joanna , Malla Sunir , Aboobaker Aziz , Tarlinton Rachael , Emes Richard D
Published: January 2018

The immune system of the horse has not been well studied, despite the fact that the horse displays several features such as sensitivity to bacterial lipopolysaccharide that make them in many ways a more suitable model of some human disorders than the current rodent models. The difficulty of working with large animal models has however limited characterisation of gene expression in the horse immune system with current annotations for the equine genome restricted to predictions from other mammals and the few described horse proteins. This paper outlines sequencing of 184 million transcriptome short reads from immunologically active tissues of three horses including the genome reference “Twilight”. In a comparison with the Ensembl horse genome annotation, we found 8,763 potentially novel isoforms.
SHAPS-C: The Snaith-Hamilton Pleasure Scale modified for clinician administration
Authors: Ameil Rezvan , Luckenbaugh David A , Gould Neda F , Holmes M. Kathleen , Lally Níall , Ballard Elizabeth D , Zarate Jr. Carlos A
Published: January 2018

Anhedonia, a diminished or lack of ability to experience and anticipate pleasure represents a core psychiatric symptom in depression. Current clinician assessment of anhedonia is generally limited to one or two all-purpose questions and most well-known psychometric scales of anhedonia are relatively long, self-administered, typically not state sensitive, and are unsuitable for use in clinical settings. A user-friendly tool for a more in-depth clinician assessment of hedonic capacity is needed. The present study assessed the validity and reliability of a clinician administered version of the Snaith-Hamilton Pleasure Scale, the SHAPS-C, in 34 depressed subjects. We compared total and specific item scores on the SHAPS-C, SHAPS (self-report version), Montgomery-Åsberg Depression Rating Scale (MADRS), and the Inventory of Depressive Symptomatology-Self Rating version (IDS-SR). We also examined construct, content, concurrent, convergent, and discriminant validity, internal consistency, and split-half reliability of the SHAPS-C. The SHAPS-C was found to be valid and reliable. The SHAPS and the SHAPS-C were positively correlated with one another, with levels of depression severity, as measured by the MADRS, and the IDS-SR total scores, and with specific items of the MADRS and IDS-SR sensitive to measuring hedonic capacity. Our investigation indicates that the SHAPS-C is a user friendly, reliable, and valid tool for clinician assessment of hedonic capacity in depressed bipolar and unipolar patients.
Modified generalized method of moments for a robust estimation of polytomous logistic model
Authors: Wang Xiaoshan
Published: January 2018

The maximum likelihood estimation (MLE) method, typically used for polytomous logistic regression, is prone to bias due to both misclassification in outcome and contamination in the design matrix. Hence, robust estimators are needed. In this study, we propose such a method for nominal response data with continuous covariates. A generalized method of weighted moments (GMWM) approach is developed for dealing with contaminated polytomous response data. In this approach, distances are calculated based on individual sample moments. And Huber weights are applied to those observations with large distances. Mellow-type weights are also used to downplay leverage points. We describe theoretical properties of the proposed approach. Simulations suggest that the GMWM performs very well in correcting contamination-caused biases. An empirical application of the GMWM estimator on data from a survet demonstrates its usefulness.