bluuebunny/crossref_metadata_2025 huggingface dataset:
How does paw pad of Canine attenuate ground impacts: a micromechanical finite element study
Authors: Miao Huaibin , Fu Jun , Qian Zhihui , Ren Luquan , Ren Lei
Published: January 2018

Background. Digitigraded mammals, e.g. dogs and cats, stand or walk on their digits or toes. Their paw pads beneath the digits or toes, rather than the entire sole of the foot, are in contact with the ground surface during locomotion. Digitigrades generally move more quickly and quietly than other animals. So far, little is known about the micro-scale structural characteristics of digitigrades' paw pads and its connection with the superior biomechanical functioning of their feet.

Methods. In this study, we investigated the micro-structure of the paw pad of German shepherd dog (GSD) using SEM and histological examination, and assessed the biomechanical functions of the micro-structured epidermis layer by using dynamic finite element (FE) simulations.

Results. We found that there exists a thick layer of stratified epithelium of a honeycomb like structure with conical protuberances (i.e. dermal papilla) embedded in each cell unit. Our FE simulation analyses revealed that this specially structured layer is capable of effectively attenuating the ground impact across a range of impact velocities. Moreover, this cushioning capacity becomes more pronounced with increased impact velocity. More importantly, this layer can also significantly reduce the mechanical stress transmitting to the soft dermal papillae and dermis by using an off-loading mechanism.

Discussion. This would provide more insights into the biomechanical functioning of the digitigrade's paw pads, and also facilitate the development of bio-inspired ground contacting components of robots and machines, and also the design of footwear and orthotics devices.
CartograTree: Enabling landscape genomics for forest trees
Authors: Herndon Nic , Grau Emily S , Batra Iman , Demurjian Jr. Steven A , Vasquez-Gross Hans A , Staton Margaret E , Wegrzyn Jill L
Published: January 2018

Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated for hundreds of species. These long-lived and immobile individuals serve as ideal models to assess population structure and adaptation to environment. Despite the availability of comprehensive data, researchers are challenged to integrate genotype, phenotype, and environment in one place. Towards this goal, CartograTree was designed and implemented as a repository and analytic framework for genomic, phenotypic, and environmental data for forest trees. One of key components, the integration of geospatial data, allows the display of environmental layers and acquisition of environmental metrics relative to the positions of georeferenced individuals.
Lactobacillus plantarum immobilized onto soymilk residue (Okara) for the enhancement of soymilk fermentation and cell survival under simulated gastrointestinal conditions
Authors: Xiudong Xia , Ying Wang , Xiaoli Liu , Ying Li , Jianzhong Zhou
Published: January 2018

Cell immobilization is an alternative to microencapsulation for the maintenance of cells in a liquid medium. However, artificial immobilization carriers are expensive and pose a high safety risk. This study aimed to evaluate the potential of okara, a food-grade byproduct from soymilk production, as a natural immobilizer for L. plantarum 70810 cells. The study also aimed to evaluate the effects of okara-immobilized L. plantarum 70810 cells on soymilk fermentation, glucosidic isoflavone bioconversion, and cell resistance to gastrointestinal (GI) stress. Scanning electron microscopy revealed that the lactobacilli cells attached and bound to okara’s surface. Compared with the free cells (FL), immobilized Lactobacillus plantarum (IL) cells exhibited a significantly higher specific growth rate and shorter lag phase of growth, a faster decrease in pH and increase in titrable acidity, and a higher soymilk viscosity. Similarly, IL in soymilk showed higher productions of daizein and genistein compared with the control. Compared with FL, IL showed reinforced resistance to simulatedGI stress in vitro that included low pH, low pH plus pepsin, pancreatin, and bile salt. Our results indicate that okara is a new potential immobilization carrier to enhance the growth and glucosidic isoflavone bioconversion activities of L. plantarum in soymilk and improve cell survivability following GI transit.
A clinical audit cycle of post-operative hypothermia in dogs
Authors: Rose Nicole , Kwong Grace PS , Pang Daniel SJ
Published: January 2018

Objectives: Use of clinical audits to assess and improve perioperative hypothermia management in client-owned dogs. Methods: Two clinical audits were performed. Audit 1: data were collected to determine the incidence and duration of perioperative hypothermia (defined rectal temperatures < 37.5˚C). The results from Audit 1 were presented to clinic staff and a consensus reached on changes to be implemented to improve temperature management. Following one month with the changes in place, Audit 2 was performed to assess performance. Results: Audit 1 revealed a high incidence of post-operative hypothermia (88.9%) and prolonged time periods for animals to reach normothermia. Following discussion, a consensus was reached to: 1. measure rectal temperatures hourly post-operatively until a temperature ≥ 37.5˚C was achieved and 2. use a forced air warmer on all dogs until rectal temperature was ≥ 37˚5. After one month with the implemented changes, Audit 2 identified a significant reduction in the time to achieve a rectal temperature of ≥ 37.5˚C, with 75% of dogs achieving this goal by 3.5 hours (7.5 hours for Audit 1, p = 0.01). The incidence of hypothermia at extubation remained high in Audit 2 (97.3% with a rectal temperature < 37.5˚C). Clinical significance: Post-operative hypothermia was improved through simple changes in practice, showing that clinical audit is a useful tool for monitoring post-operative hypothermia and improving patient care. Overall management of perioperative hypothermia could be further improved with earlier intervention.
PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers
Authors: Elbrecht Vasco , Leese Florian
Published: January 2018

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers for communities or taxa under study in a certain geographic region and/or ecosystems is of critical importance. However, no tool for obtaining and processing of reference sequence data in bulk that serve as a backbone for primer design is currently available.

2) We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species. Additionally, PrimerMiner offers functionalities to evaluate primers in silico, which are in our opinion more realistic then the strategy employed in another available software for that purpose, ecoPCR.

3) We used PrimerMiner to download cytochrome c oxidase subunit I (COI) sequences for 15 important freshwater invertebrate groups, relevant for ecosystem assessment. By processing COI markers from both databases, we were able to increase the amount of reference data 249-fold on average, compared to using complete mitochondrial genomes alone. Furthermore, we visualized the generated OTU sequence alignments and describe how to evaluate primers in silico using PrimerMiner.

4) With PrimerMiner we provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. The OTU based reference alignments generated with PrimerMiner can be used for manual primer design, or processed with bioinformatic tools for primer development.
Genetic signatures of ecological diversity along an urbanization gradient
Authors: Kelly Ryan P. , O'Donnell James L , Lowell Natalie C. , Shelton Andrew O. , Samhouri Jameal F. , Hennessey Shannon M. , Feist Blake E. , Williams Gregory D.
Published: January 2018

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.
Determination of the optimal bacteriophage dose to control Pseudomonas aeruginosa using evolutionary programming and stochastic kinetics
Authors: Ardila Diana C , Castro Juan D , Holguín Angela V , Clavijo Viviana , Prada Catalina , Vives Martha J , Gonzalez Barrios Andres F Andres
Published: January 2018

Phage-therapy is a promising alternative against pathogenic, multiple drug resistant bacteria. In this work we propose an algorithm to determine the optimal bacteriophage dose able to minimize a population of Pseudomonas aeruginosa. Reverse engineering was used to determine the kinetic parameters; subsequently, a bi-level optimization platform was implemented for a model based on evolutionary programming. Our prediction of optimal dose was tested in vitro with planktonic cultures of P. aeruginosa. From the data obtained, we conclude that reverse engineering and stochastic simulations are a useful approach to find optimal phage doses against pathogenic bacteria, an important step for the implementation of phage-therapy.
Neogene amphibians and reptiles (Caudata, Anura, Gekotta, Lacertilia, Testudines) from south of Western Siberia, Russia and Northeastern Kazakhstan
Authors: Vasilyan Davit , Zazhigin Vladimir , Böhme Madelaine
Published: January 2018

Background. Now-a-day territory of Western Siberia has the poorest diversity of amphibians and reptiles within the Palaearctic Realm, influenced by unfavourable climate. Less is known about the origin and emergence of it. Aside from better-explored European Neogene records of amphibians and reptiles, the Neogene herpetofauna of Western Asia is understudied. The few available studies on amphibian and reptile fossil assemblages need critical reviews and new interpretations considering the latest knowledge of the European record. The comparison with European record will provide data on palaeobiogeographic affiliations of the region as well as origin and emergence of the now-a-day fauna of Western Siberia. Beside these, a study providing overview about the earliest occurences of certain amphibian linages, that can be used for the calibration of the molecular clocks, is missing.

Methods and Results. The amphibian and reptile fauna from over 40 Western Siberian, Russia and Northeastern Kazakhian localities ranging from Middle Miocene to Early Pleistocene has been studied. In the study the published data has been considered and critically reviewed and newly interpreted. More then 50 amphibian and reptile taxa has been identified belonging to families Hynobiidae, Cryptobranchidae, Salamandridae, Palaeobatrachidae, Bombinatoridae, Pelobatidae, Hylidae, Bufonidae, Ranidae, Gekkonidae, Lacertidae and Emydidae. Palaeobiogeographic analysis for those group has been done. For 12 localities, palaeoprecipitation values have been estimated using the bioclimatic analysis of herpetofaunal assemblage.

Conclusions. The Neogene assemblage of Westren Sibera is dominated by groups (Palaeobatrachidae, Bombina, Hyla, Bufo bufo) with European affinities. A small part of assemblage includes Eastern Palaearctic taxa (e.g. Hynobiidae, Tylototriton, Bufotes viridis, R. arvalis). For several taxa (e.g. Mioproteus, Hyla, Bombina) the Western Siberian records of represent the most east Eurasian records of these groups. The most divers faunas are found in the Middle Miocene, whereas the poorest towards Early Pleistocene. This tendency could be referred to the progressive global cooling of the climate in Northern Hemisphere. Our results showed higher-amplitude changes of precipitation development in Western Siberia from Early Miocene to Pliocene, than earlier assumed.
Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model
Authors: Johnson Eric G , Swenarton Mary Katherine
Published: January 2018

The effective management of invasive species requires a detailed understanding of the invader’s life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish ( Pterois volitans/miles ) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates, (2) distinct cohorts were clearly identifiable in the length-frequency data suggesting that lionfish arerecruiting during a relatively short period in summer, and (3) the majority of lionfish were less than two years old with no lionfish older than 3 years of age, possibly as a result of an ontogenetic shift to deeper water, which may provide a reservoir of spawning biomass not accessible to recreational or commercial spearfishing.
Ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae
Authors: Pereira Pedro H , Santos Marcus , Lippi Daniel L , Silva Pedro
Published: January 2018

Parrotfish are fundamental species in controlling algae phase-shifts and ensuring the resilience of coral reefs. Nevertheless, little is known on their ecological role in the South-western Atlantic Ocean. The present study analysed the ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae using behavioural observation and benthic composition analyses. We found a significant negative relationship between fish size and feeding rates for S. zelindae individuals. Thus, terminal phase individuals forage with lower feeding rates compared to juveniles and initial phase individuals. The highest relative foraging frequency of S. zelindae was on epilithic algae matrix (EAM) with similar values for juveniles (86.6%), initial phase (88.1%) and terminal phase (88.6%) individuals. The second preferred benthos for juveniles was sponge (11.6%) compared with initial (4.5%) and terminal life phases (1.3%). Different life phases of S. zelindae foraged on different benthos according to their availability. Based on Ivlev's electivity index, juveniles selected EAM and sponge, while initial phase and terminal phase individuals only selected EAM. Our findings demonstrate that the foraging frequency of the endemic parrotfish S. zelindae is reduced according to body size and that there is a slight ontogenetic change in feeding selectivity. Therefore, ecological knowledge of ontogenetic variations on resource use is critical for the remaining parrotfish populations which have been dramatically reduced in the Southwestern Atlantic Ocean.
Regional drivers of clutch loss reveal important trade-offs for beach-nesting birds
Authors: Maslo Brooke , Schlacher Thomas A , Weston Mike A. , Huijbers Chantal M , Anderson Chris , Gilby Ben L , Olds Andrew D , Connolly Rod M , Schoeman David S
Published: January 2018

Coastal birds are critical ecosystem constituents on sandy shores, yet are threatened by depressed reproductive success resulting from direct and indirect anthropogenic and natural pressures. Few studies examine clutch fate across the wide range of environments experienced by birds; instead, most focus at the small site scale. We examine survival of model shorebird clutches as an index of true clutch survival at a regional scale (~ 200 km), encompassing a variety of geomorphologies, predator communities, and human use regimes in southeast Queensland, Australia. Of the 132 model nests deployed and monitored with cameras, 45 (34%) survived the experimental exposure period. Thirty-five (27%) were lost to flooding, 32 (24%) were depredated, 9 (7%) buried by sand, 7 (5%) destroyed by people, 3 (2%) failed by unknown causes, and 1 (0.1%) was destroyed by a dog. Clutch fate differed substantially among regions, particularly with respect to losses from flooding and predation. ‘Topographic’ exposure was the main driver of mortality of nests placed close to the drift line near the base of dunes, which were lost to waves (particularly during storms) and to a lesser extent depredation. Predators determined the fate of clutches not lost to waves, with the depredation probability largely influenced by region. Depredation probability declined as nests were backed by higher dunes and were placed closer to vegetation. This study emphasizes the scale at which clutch fate and survival varies within a regional context, the prominence of corvids as egg predators, the significant role of flooding as a source of nest loss, and the multiple trade-offs faced by beach-nesting birds and those that manage them.
Doubts concerning the analysis of data collected in areas surrounding badger culled areas of the RBCT
Authors: Hendy David
Published: January 2018

In a report issued to the UK government in 2007 on the Randomised Badger Culling Trial (RBCT), it was stated that the incidence of bovine tuberculosis (TB) in cattle increased in areas surrounding where badgers were removed. It is known that badger culling perturbs badgers and this leads to increased TB transmission in and around these treated areas. The increase in TB in the surrounding areas was attributed to this process.

In this study of the RBCT analysis it was found that large TB increases in areas surrounding proactively treated areas depended heavily on adjustments made for pre-cull history. This work looks at the basis for applying these adjustments. Since it is not possible to remove statistical error in the data, which confidence intervals suggest may have been large, it is argued that it was unsafe to apply these adjustments. As such it is argued that TB increases due to perturbation in the report presented to the UK government in 2007 may have been grossly over-estimated.
Multitask regression for condition-specific prioritization of miRNA targets in transcripts
Authors: Dehghani Amirabad Azim , Schulz Marcel H
Published: January 2018

Deregulation of miRNAs is implicated in many diseases in particular cancer, where miRNAs can act as tumour suppressors or oncogenes. As sequence-based miRNA target predictions do not provide condition-specific information, many algorithms combine expression data for miRNAs and genes for prioritization of miRNA targets. However, common strategies prioritize miRNA-gene as- sociations, although a miRNA may only target a subset of the alternative transcripts produced by a gene. Thus, current approaches are suboptimal. Here we address the problem of transcript and not gene based miRNA target prioritization. We show how to leverage methods that were developed for gene expression based miRNA-target prioritization for transcripts. In addition, we introduce a new multitasking based learning (MTL) method that uses structured-sparsity inducing regularization to improve accuracy of the learning. The new MTL approach performs especially favorable in small sample size settings, for genes with many transcripts and with noisy transcript expression level es- timates as shown with simulated data. In an analysis of real liver cancer RNA-seq data we show that the MTL approach better predicts transcript expression and outperforms simpler approaches for miRNA-target prediction.
Multitask regression for condition-specific prioritization of miRNA targets in transcripts
Authors: Dehghani Amirabad Azim , Schulz Marcel H
Published: January 2018

Deregulation of miRNAs is implicated in many diseases in particular cancer, where miRNAs can act as tumour suppressors or oncogenes. As sequence-based miRNA target predictions do not provide condition-specific information, many algorithms combine expression data for miRNAs and genes for prioritization of miRNA targets. However, common strategies prioritize miRNA-gene associations, although a miRNA may only target a subset of the alternative transcripts produced by a gene. Thus, current approaches are suboptimal. Here we address the problem of transcript and not gene based miRNA target prioritization. We show how to leverage methods that were developed for gene expression based miRNA-target prioritization for transcripts. In addition, we introduce a new multitasking based learning (MTL) method that uses structured-sparsity inducing regularization to improve accuracy of the learning. The new MTL approach performs especially favorable in small sample size settings, for genes with many transcripts and with noisy transcript expression level estimates as shown with simulated data. In an analysis of real liver cancer RNA-seq data we show that the MTL approach better predicts transcript expression and outperforms simpler approaches for miRNA-target prediction.
Prediction of amyloidogenicity based on the n-gram analysis
Authors: Burdukiewicz Michał Jan , Sobczyk Piotr , Rödiger Stefan , Duda-Madej Anna , Mackiewicz Paweł , Kotulska Małgorzata
Published: January 2018

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots. To find the patterns defining the hot-spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers, based on data collected in the AmyLoad database. Only the most informative n-grams, selected by our Quick Permutation Test, were considered. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on more general properties of amino acids, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids, which are strongly correlated with hydrophobicity, a tendency to form ß-sheets and rigidity of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were already confirmed experimentally. AmyloGram is available as a web-server: www.smorfland.uni.wroc.pl/amylogram/. The code and results are publicly available at: www.github.com/michbur/prediction_amyloidogenicity_ngram/.
MARCARviz: Interactive web-platform for exploratory analysis of toxicogenomics data for nongenotoxic hepatocarcinogenesis
Authors: Römer Michael , Ellinger-Ziegelbauer Heidrun , Grasl-Kraupp Bettina , Schwarz Michael , Zell Andreas
Published: January 2018

The late detection of non-genotoxic carcinogens in the drug development process can delay drug candidates for unmet medical needs from reaching the market despite considerable investments in their development. To enable faster, safer, and less expensive development of medications for patients, the MARCAR project generated a large set of transcriptomic data to investigate the underlying mechanisms of non-genotoxic hepatocarcinogenesis and to identify potential biomarkers for early detection of tumor formation in the rodent liver. The effective mining of these high-dimensional datasets is a non-trivial task that usually requires bioinformatics support to extract relevant mechanistic patterns and confirm toxicological hypotheses. Here, we present MARCARviz, a web-platform that enables biologists to (a) quickly address the most common questions associated with the MARCAR microarray data, to (b) identify relevant patterns in the data, and to (c) generate or confirm mechanistic hypotheses about non-genotoxic effects leading to cancer formation. The major advantage of MARCARviz is that there is no software or advanced technical knowledge required to perform powerful analyses and generate visualizations of the MARCAR data. MARCARviz greatly facilitates the confirmation of published MARCAR results and generation of new insights from the collected data by the greater public without the requirement for tedious pre-processing steps. MARCARviz is publicly available from https://tea.cs.uni-tuebingen.de/.
The effects of cooling conditions on EDTA whole canine blood samples
Authors: Tobias Karen M , Serrano Leslie , Sun Xiaocun , Flatland Bente
Published: January 2018

Background. Preanalytic factors such as time and temperature can have significant effects on laboratory test results. For example, ammonium concentration will increase 31% in blood samples stored at room temperature for 30 minutes before centrifugation. To reduce preanalytic error, blood samples may be placed in precooled tubes and chilled on ice or in ice water baths; however, the effectiveness of these modalities in cooling blood samples has not been formally evaluated. The purpose of this study was to evaluate the effectiveness of various cooling modalities on reducing temperature of EDTA whole blood samples.

Methods. Pooled samples of canine EDTA whole blood were divided into two aliquots. Saline was added to one aliquot to produce a packed cell volume (PCV) of 40% and to the second aliquot to produce a PCV of 20% (simulated anemia). Thirty samples from each aliquot were warmed to 37.7°C and cooled in 2 ml allotments under one of three conditions: in ice, in ice after transfer to a precooled tube, or in an ice water bath. Temperature of each sample was recorded at one minute intervals for 15 minutes.

Results. Within treatment conditions, sample PCV had no significant effect on cooling. Cooling in ice water was significantly faster than cooling in ice only or transferring the sample to a precooled tube and cooling it on ice. Mean temperature of samples cooled in ice water was significantly lower at 15 minutes than mean temperatures of those cooled in ice, whether or not the tube was precooled. By 4 minutes, samples cooled in an ice water bath had reached mean temperatures less than 4°C (refrigeration temperature), while samples cooled in other conditions remained above 4.0°C for at least 11 minutes. For samples with a PCV of 40%, precooling the tube had no significant effect on rate of cooling on ice. For samples with a PCV of 20%, transfer to a precooled tube resulted in a significantly faster rate of cooling than direct placement of the warmed tube onto ice.

Discussion. Canine EDTA whole blood samples cool most rapidly and to a greater degree when placed in an ice-water bath rather than in ice. Samples stored on ice water can rapidly drop below normal refrigeration temperatures; this should be taken into consideration when using this cooling modality.
EasyMirror and EasyImport: Simplifying the setup of a custom Ensembl database and webserver for any species
Authors: Challis Richard J , Kumar Sujai , Stevens Lewis , Blaxter Mark
Published: January 2018

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive API. Here we introduce the EasyMirror and EasyImport pipelines to facilitate the setup and hosting of custom Ensembl genome browsers.

EasyMirror (https://github.com/lepbase/easy-mirror) makes it possible to set up a mirror of any Ensembl or Ensembl Genomes (including Bacteria, Metazoa, Fungi, Plants and Protists) species in four simple steps that can be run in less than an hour on a fresh Ubuntu installation. This tool exploits the modular nature of the Ensembl codebase to allow a site to be set up with none, some or all of the data hosted locally.

EasyImport (https://github.com/lepbase/easy-mirror) extends this approach to simplify the import of genomic data for any species from standard flat files into the Ensembl database schema, ready to be deployed using EasyMirror. All that is needed to get started is a genome fasta file and the gene models in GFF format.

Documentation for both pipelines is available at http://easy-import.readme.io
High unexpected genetic diversity of a narrow endemic terrestrial mollusc
Authors: Madeira Pedro M , Chefaoui Rosa M. , Cunha Regina L , Moreira Francisco , Dias Susana , Calado Gonçalo , Castilho Rita
Published: January 2018

A large array of species and species complexes from the Iberian Peninsula display strong genetic subdivisions indicative of past population isolation in separate glacial refugia as a result of survival throughout the Pleistocene ice ages. We used mitochondrial and nuclear sequence data to analyse phylogeographic patterns in a group of endemic land snails of the genus Candidula from a valley of central Portugal (Vale da Couda) showing an exceptionally narrow distributional range. Phylogenetic analyses recovered Vale da Couda specimens in two main clades that do not share a common ancestry. Considering the restricted geographic distribution, an unusual high number of haplotypes was found. These haplotypes were unevenly distributed among the sampling sites. Our results show a departure from the expectation that species with restricted distributions have low genetic variability. The putative past and contemporary models of geographic distribution of Vale da Couda lineages are compatible with a scenario of species co-existence in more southern locations during the last glacial maximum (LGM) followed by a post-LGM northern dispersal tracking the species optimal thermal, humidity and soil physical conditions. Mismatch analysis indicated a population expansion during the LGM, which corroborates our biogeographic scenario.
RNA interference as a gene silencing tool to control Tuta absoluta in tomato (Solanum lycopersicum)
Authors: Camargo Roberto A , Barbosa Guilherme O , Possignolo Isabella Presotto , Peres Lazaro E. P. , Lam Eric , Lima Joni E , Figueira Antonio V. O. , Marques-Souza Henrique
Published: January 2018

RNA interference (RNAi), a gene-silencing mechanism that involves providing double-stranded RNA molecules that match a specific target gene sequence, is now widely used in functional genetic studies. The potential application of RNAi-mediated control of agricultural insect pests has rapidly become evident. The production of transgenic plants expressing dsRNA molecules that target essential insect genes could provide a means of specific gene silencing in larvae that feed on these plants, resulting in larval phenotypes that range from loss of appetite to death. In this report, we show that the tomato leafminer (Tuta absoluta), a major threat to commercial tomato production, can be targeted by RNAi. We selected two target genes [Vacuolar ATPase-A and Arginine kinase] based on the RNAi response reported for these genes in other pest species. In view of the lack of an artificial diet for T. absoluta, we used two approaches to deliver dsRNA into tomato leaflets. The first approach was based on the uptake of dsRNA by leaflets and the second was based on “in planta-induced transient gene silencing” (PITGS), a well-established method for silencing plant genes, used here for the first time to deliver in planta-transcribed dsRNA to target insect genes. Tuta absoluta larvae that fed on leaves containing dsRNA of the target genes showed an ~60% reduction in target gene transcript accumulation, an increase in larval mortality and less leaf damage. We then generated transgenic ‘Micro-Tom’ tomato plants that expressed hairpin sequences for both genes and observed a reduction in foliar damage by T. absoluta in these plants. Our results demonstrate the feasibility of RNAi as an alternative method for controlling this critical tomato pest.
What is the best way for developers to learn new software tools? An empirical comparison between a text and a video tutorial
Authors: Käfer Verena , Kulesz Daniel , Wagner Stefan
Published: January 2018

Tutorials for software developers are supposed to help them to adapt to new tools quickly. While in the early days of computing, mostly text tutorials were available, nowadays software developers can choose among a huge number of tutorials for almost any popular software tool. However, almost no research was conducted to understand how text tutorials differ from other tutorials, which tutorial types are preferred and, especially, which tutorial types yield the best learning experience in terms of efficiency and effectiveness.

To evaluate these questions, we converted a “proven” video tutorial for a novel software tool into a content-equivalent text tutorial. We then conducted an experiment in three groups where 42 undergraduate students from a software engineering course were commissioned to operate the software tool after using a tutorial: the first group was provided only with the video tutorial, the second group only with the text tutorial and the third group with both.

Surprisingly, the differences in terms of efficiency are almost negligible: we could observe that participants using only the text tutorial completed the tutorial faster than the participants with the video tutorial. However, the participants using only the video tutorial applied the learned content faster, achieving roughly the same bottom line performance. We also found that if both tutorial types are offered, participants clearly prefer video tutorials for learning new content but text tutorials for looking up “missed” information. So while it would be ideal if software tool makers would offer both tutorial types, we think that it is more efficient to produce only text tutorials – provided you manage to motivate developers to use them.
GRIND-FREE: Gaming-resistant index for research evaluation
Authors: Belikov Aleksey V
Published: January 2018

The ever-growing need to evaluate researchers without actually reading their work has fertilized the soil for the appearance of hundreds of scientometric indicators. The reason why they continue to emerge is simple: no perfect one has been found yet. The major problem is that any indicator which starts to dominate the evaluation practices causes the evaluated to adjust their behavior accordingly, leading to depreciation of the indicator and diverse scientific malpractice, such as excessive self-citation, self-plagiarism, salami-slicing of publications, guest authorships, and so on. Hence, an indicator is needed that cannot be affected by the evaluated researchers at will, but still captures scientific excellence. Such an indicator is proposed here.
New records of predation on eggs of Bemisia tabaci (Hemiptera: Aleyrodidae) by Chrysopodes (Chrysopodes) lineafrons (Neuroptera: Chrysopidae) in Northwestern Argentina
Authors: Ortega Eugenia S. , Veggiani Cecilia A. , Avila Ana L. , Reguilon Carmen
Published: January 2018

Bemisia tabaci has become a major economic importance pest, affecting several crops worldwide. Among their natural enemies, species of Chrysopidae family, with larvae predators of different pests, are a very effective biological control agent. The developmental time and survival of the immature stages of Chrysopodes (Chrysopodes) lineafrons, and the longevity and oviposition of adults fed with eggs of B. tabaci was determined. C. (C.) lineafrons adults were collected in tomato crops in Lules department, Tucumán province. To determine the developmental duration of each instar, and larvae survival, 90 eggs of C. (C.) lineafrons were randomly selected, of which only 71 eggs hatched; of these, 34 larvae were fed with B. tabaci eggs and 37 with Sitotroga cerealella eggs, used as control. Oviposition and longevity of adults fed with the two preys were recorded. C. (C.) lineafrons larvae consumed an average of 127.04 B. tabaci eggs and 44 S. cerealella eggs per day. Mean developmental time of C. (C.) lineafrons fed with B. tabaci eggs was 45 days; while for those fed with S. cerealella eggs it was 35 days. Immature stages survival, number of eggs per adults and longevity were higher when C. (C.) lineafrons were fed with S. cerealella eggs than with B. tabaci eggs. C. (C.) lineafrons proved to be an efficient predator, thus representing an excellent tool for the biological control of B. tabaci in tomato crops .
Actin-dependence of the chloroplast cold positioning response in the liverwort Marchantia polymorpha L
Authors: Kimura Shun , Kodama Yutaka
Published: January 2018

The subcellular positioning of chloroplasts can be changed by alterations in the environment such as light and temperature. For example, in leaf mesophyll cells, chloroplasts localize along anticlinal cell walls under high-intensity light, and along periclinal cell walls under low-intensity light. These types of positioning responses are involved in photosynthetic optimization. In light-mediated chloroplast positioning responses, chloroplasts move to the appropriate positions in an actin-dependent manner, although some exceptions also depend on microtubule. Even under low-intensity light, at low temperature (e.g., 5°C), chloroplasts localize along anticlinal cell walls; this phenomenon is termed chloroplast cold positioning. In this study, we analyzed whether chloroplast cold positioning is dependent on actin filaments and/or microtubules in the liverwort Marchantia polymorpha L. When liverwort cells were treated with drugs for the de-polymerization of actin filaments, chloroplast cold positioning was completely inhibited. In contrast, chloroplast cold positioning was not affected by treatment with a drug for the de-polymerization of microtubules. These observations indicate the actin-dependence of chloroplast cold positioning in M. polymorpha. Actin filaments during the chloroplast cold positioning response were visualized by using fluorescent probes based on fluorescent proteins in living liverwort cells, and thus, their behavior during the chloroplast cold positioning response was documented.
10 simple rules for best experimental design in ecology
Authors: Sajadi Farwa
Published: January 2018

A quick set of rules on how best to execute an experimental design in ecology. From having a clear hypothesis to obtaining accurate statistics, this guide will help make sure authors are on the right track before publishing. The 10 simple rules are based on articles written to help readers and editors learn more about experimental design and how to avoid any unseeable pitfalls. These rules act as a checklist for authors to go through to make sure they have created the best experimental design for their procedure.
Complexity in a facilitative behavior web of piscivores and associated species at Isla del Coco National Park (Eastern Tropical Pacific)
Authors: Auster Peter J , Cortés Jorge
Published: January 2018

Discerning the role that facilitative behavioral interactions in mixed species groups of hunting piscivores play in growth and survivorship is important both in our fundamental understanding of fish community dynamics and for developing conservation strategies. In this study we collected data on mixed-species hunting groups (species composition, numbers, behavioral interactions) and used both multivariate and network analyses to quantify pair-wise and guild level behavioral relationships. Our results demonstrate that collective behaviors in mixed species hunting groups exhibit consistent patterns of associations within a set of dominant species (10 of 32 species within the network) and are a common attribute of this functional guild within the shallow fish community at Isla del Coco (to 80 m depth), Pacific Costa Rica. Indeed the removal of only a few dominant species from the behavior web model, to simulate overfishing, reduced the number of pair-wise linkages by 57% (32 species with 282 pair-wise links to 28 species with 122 links). The identification of these patterns, assuming they are persistent features of these communities, can be used as a foundation for time-series monitoring to assess status and change in ecological interactions within the higher trophic level guild of fishes. That said, more work is needed to understand the temporal dynamics of network linkages and intensity of interactions as prey resources vary in distribution and abundance. Such information could be used to interpret the nature of multispecies interactions within predator communities and serve as an aid in conservation and management.
Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire
Authors: Lee Sang-Hoon , Sorensen Jackson W , Grady Keara L , Tobin Tammy C , Shade Ashley
Published: January 2018

Press disturbances are stressors that are extended or ongoing relative to the generation times of community members, and, due to their longevity, have the potential to alter communities beyond the possibility of recovery. They also provide key opportunities to investigate ecological resilience and to probe biological limits in the face of prolonged stressors. The underground coal mine fire in Centralia, Pennsylvania has been burning since 1962 and severely alters the overlying surface soils by elevating temperatures and depositing coal combustion pollutants. As the fire burns along the coal seams to disturb new soils, previously disturbed soils return to ambient temperatures, resulting in a chronosequence of fire impact. We used 16S rRNA gene sequencing to investigate bacterial and archaeal soil community responses along two active fire fronts in Centralia, and investigated the influences of assembly processes (selection, dispersal and drift) on community outcomes. The hottest soils harbored the most variable and divergent communities, despite their reduced diversity. Recovered soils converged toward similar community structures, demonstrating resilience within 10-20 years and exhibiting near-complete return to reference communities. Measured soil properties (selection), local dispersal, and neutral community assembly models could not explain the divergences of communities observed at temperature extremes. We hypothesize that transitions between the seed bank and the active community, which would manifest as drift processes, are key in explaining these divergences. These results suggest that soils generally have an intrinsic capacity for robustness to varied disturbances, even to press disturbances considered to be “extreme”, compounded, or incongruent with natural conditions.
Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire
Authors: Lee Sang-Hoon , Sorensen Jackson W , Grady Keara L , Tobin Tammy C , Shade Ashley
Published: January 2018

Press disturbances are stressors that are extended or ongoing relative to the generation times of community members, and, due to their longevity, have the potential to alter communities beyond the possibility of recovery. They also provide key opportunities to investigate ecological resilience and to probe biological limits in the face of prolonged stressors. The underground coal mine fire in Centralia, Pennsylvania has been burning since 1962 and severely alters the overlying surface soils by elevating temperatures and depositing coal combustion pollutants. As the fire burns along the coal seams to disturb new soils, previously disturbed soils return to ambient temperatures, resulting in a chronosequence of fire impact. We used 16S rRNA gene sequencing to examine bacterial and archaeal soil community responses along two active fire fronts in Centralia, and investigated the influences of assembly processes (selection, dispersal and drift) on community outcomes. The hottest soils harbored the most variable and divergent communities, despite their reduced diversity. Recovered soils converged toward similar community structures, demonstrating resilience within 10-20 years and exhibiting near-complete return to reference communities. Measured soil properties (selection), local dispersal, and neutral community assembly models could not explain the divergences of communities observed at temperature extremes, yet beta-null modeling suggested that communities at temperature extremes follow niche-based processes rather than null. We hypothesize that priority effects from responsive seed bank transitions may be key in explaining the multiple equilibria observed among communities at extreme temperatures. These results suggest that soils generally have an intrinsic capacity for robustness to varied disturbances, even to press disturbances considered to be “extreme”, compounded, or incongruent with natural conditions.
Engineering permanence in finite systems
Authors: Bilar Daniel
Published: January 2018

The man-machine integration era (MMIE) is marked by sensor ubiquity, whose readings map human beings to finite numbers. These numbers - processed by continuously changing, optimizing/learning, finite precision, closed loop, distributed systems - are used to drive decisions such as insurance rates, prison sentencing, health care allocations and probation guidelines. Optimization and system parameter tuning is increasingly left to machine learning and applied AI. One challenges we face is thus: Ensuring the indelibility, the permanence, the infinite value of human beings as optimization-resistant invariants in such system environments.