bluuebunny/crossref_metadata_2025 huggingface dataset:
Cloud Computing in Bioinformatics: current solutions and challenges
Authors: Calabrese Barbara , Cannataro Mario
Published: January 2018

Abstract truncated at 3,000 characters - the full version is available in the pdf file

MOTIVATIONS The availability of high-throughput technologies and the application of genomics and pharmacogenomics studies of large populations, are producing an increasing amount of experimental and clinical data, as well as specialized databases spread over the Internet. The storage, preprocessing and analysis of experimental data is becoming the main bottleneck of the analysis pipeline. Managing omics data requires both space for data storing as well as services for data preprocessing, analysis, and sharing. The resulting scenario comprises a set of bioinformatics tools, often implemented as web services, for the management and analysis of data stored in geographically distributed biological databases [1]. Cloud computing may play an important role in many phases of the bioinformatics analysis pipeline, from data management and processing, to data integration and analysis, including data exploration and visualization because it offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, thus it may represent the key technology for facing those issues [2]. METHODS This work reviews main academic and industrial cloud-based bioinformatics solutions developed in the recent years; moreover, it underlines main issues and problems related to the use of such platforms for the storage and analysis of patients’ data. Specifically, the analysed solutions regard: - Data as a Service (DaaS): it provides data storage in a dynamic virtual space hosted by the cloud and allows to have updated data that are accessible from a wide range of connected devices on the web. - Software as a Service (SaaS): several cloud-based tools to execute different bioinformatics tasks, e.g. mapping applications, sequences alignment, gene expression analysis have been proposed and made available. - Platform as a Service (PaaS): unlike SaaS solutions, PaaS solutions allow users to customize the deployment of bioinformatics applications as well as to retain complete control over their instances and associated data. - Infrastructure as a Service (IaaS): this service model is offered in a computing infrastructure that includes servers (typically virtualized) with specific computational capability and/or storage. The user controls all the deployed storage resources, operating systems and bioinformatics applications. For each analysed solution, main technical characteristics as well as security and privacy issues arising when storing and analysing patients data, are reported. RESULTS The application of cloud computing in bioinformatics regards the efficient storage, retrieval and integration of experimental data and their efficient and high-throughput preprocessing and analysis.
Familiar face + novel face = familiar face? Representational bias in the perception of morphed faces in chimpanzee
Authors: Matsuda Yoshi-Taka , Myowa-Yamakoshi Masako , Hirata Satoshi
Published: January 2018

Highly social animals possess a well-developed ability to distinguish the faces of familiar from novel conspecifics to induce distinct behaviors for maintaining society. However, the behaviors of animals when they encounter ambiguous faces of familiar yet novel conspecifics, e.g., strangers with faces resembling known individuals, have not been well characterised. Using a morphing technique and preferential-looking paradigm, we address this question via the chimpanzee’s facial–recognition abilities. We presented eight subjects with three types of stimuli: (1) familiar faces, (2) novel faces and (3) intermediate morphed faces that were 50% familiar and 50% novel faces of conspecifics. We found that chimpanzees spent more time looking at novel faces and scanned novel faces more extensively than familiar or intermediate faces. Interestingly, chimpanzees looked at intermediate faces in a manner similar to familiar faces with regards to the fixation duration, fixation count, and saccade length for facial scanning, even though the participant was encountering the intermediate faces for the first time. We excluded the possibility that subjects merely detected and avoided traces of morphing in the intermediate faces. These findings suggest a bias for a feeling-of-familiarity that chimpanzees perceive familiarity with an intermediate face by detecting traces of a known individual, as 50% alternation is sufficient to perceive familiarity.
Accurate stratification of patients with neuroblastoma by application of the reject option paradigm to outcome prediction
Authors: Cangelosi Davide , Morini Martina , Eva Alessandra , Bosco Maria Carla , Conte Massimo , Varesio Luigi
Published: January 2018

Motivation

Neuroblastoma (NB) is the most common solid pediatric tumor, deriving from ganglionic lineage precursors of the sympathetic nervous system. Half of the patients with high-risk NB die despite treatment and more accurate outcome prediction models are needed to direct effective therapies. To limit the therapy's side effects, a highly accurate classification of a limited number of patients is preferable to a broader classification with greater error. We aimed at improving the classifier's accuracy and establishing the criteria for confident selection of classification rules by applying the reject option technique (RO).

Methods

We evaluated outcome prediction by BFTree, ID3, J48, REPTree, SimpleCART decision-tree algorithms utilizing a 182 patients’ dataset. Fifty percent of the patients were utilized for model selection, and the remaining 50% for independent validation. The risk factors were: NB-hypo, age at diagnosis, stage and MYCN amplification. Accuracy of the classification was measured by Matthew’s Correlation Coefficient and assessed by 2 fold cross validation analysis repeated 1000 times. Trade-off between confidence and accuracy was estimated by the RO technique utilizing the accuracy/rejection plot. Kaplan-Meier estimate and log-rank test assessed overall survival.

Results

Every decision tree classified the patients' outcome with a confidence >0.6. Only ID3, utilizing all risk factors, stratified stage 4 patients and was chosen for further analysis. Application of RO raised the ID3 accuracy from 69% to 92%. This result was obtained because of accuracy/rejection plot identified a threshold confidence of 0.66 at which 71% of the patients, classified by highly reliable rules, were accepted. The trade-off was the exclusion from classification of 29% of patients falling in low represented and ambiguous rules. Kaplan-Meier curves showed a significant stratification of stage 4 patients following RO application. In conclusion, we demonstrated that application of the RO improves the classification performance of ID3 decision tree. Stage 4 patients can be stratified in significant groups characterized by the high confidence rules needed for making clinical decisions.
Building size modelization
Authors: Antoni Arlette , Dhorne Thierry
Published: January 2018

New challenges in the efficient management of cities depend on a deep knowledge of their inner structures. It is therefore very important to have access to reliable models of cities characteristics and organization. This paper aims at providing and validating a stochastic modelization based on statistical data of buildings parameters which can be useful as an entry for many other models considered in a wide range of fields where buildings structure is a main factor of a thorough modelization of cities. The interest of such an approach is highlighted through the detection of errors in the data or as a tool for visual clustering.
Open source geoprocessing tools and meteorological satellite data for crop risk zones monitoring in Sub-Saharan Africa
Authors: De Filippis Tiziana , Rocchi Leandro , Vignaroli Patrizio , Bacci Maurizio , Tarchiani Vieri , Rapisardi Elena
Published: January 2018

In Sub-Saharan Africa analysis tools and models based on meteorological satellites data have been developed within different national and international cooperation initiatives, with the aim of allowing a better monitoring of the cropping season. In most cases, the software was a stand-alone application and the upgrading, in terms of analysis functions, database and hardware maintenance, was difficult for the National Meteorological Services (NMSs) in charge of agro-hydro-meteorological monitoring. The web-based solution proposed in this work intends to improve and ensure the sustainability of applications to support national Early Warning Systems (EWSs) for food security. The Crop Risk Zones (CRZ) model for Niger and Mali, integrated in a web-based open source framework, has been implemented using PL/pgSQL & PostGIS functions to process different meteorological data sets: a) the rainfall precipitation forecast images from Global Forecast System (GFS) b) the Climate Prediction Center (CPC) Rainfall Estimation (RFE) for Africa c) Multi-Sensor Precipitation Estimate (MPE) images from EUMETSAT Earth Observation Portal d) the MOD16 Global Terrestrial Evapotranspiration Data Set. Restful Web Services upload raster images into the PostgreSQL/PostGIS database. PL/pgSQL functions are used to run the CRZ model to identify installation and phenological phases of the main crops in the Region and to create crop risk zones images. This model is focused on the early identification of risks and the production of information for food security within the time prescribed for decision-making. The challenge and the objective of this work is to set up an open access monitoring system, based on meteorological open data providers, targeting NMSs and any other local decision makers for drought risk reduction and resilience improvement.
Increased root hair density by loss of WRKY6 in Arabidopsis thaliana
Authors: Stetter Markus G , Benz Martin , Ludewig Uwe
Published: January 2018

Root hairs are unicellular elongations of certain rhizodermal cells that improve the uptake of sparingly soluble and immobile soil nutrients. Among different Arabidopsis thaliana genotypes, root hair density, length and the local acclimation to low inorganic phosphate (Pi) differs considerably, when analyzed on split agar plates. Here, genome-wide association fine mapping identified significant single nucleotide polymorphisms associated with the increased root hair density in the absence of local phosphate on chromosome 1. A loss-of-function mutant of the candidate transcription factor gene WRKY6, which is involved in the acclimation of plants to low phosphorus, had increased root hair density. This is partially explained by a reduced cortical cell diameter in wrky6-3, reducing the rhizodermal cell numbers adjacent to the cortical cells. As a consequence, rhizodermal cells in positions that are in contact with two cortical cells are found more often, leading to higher hair density. Distinct cortical cell diameters and epidermal cell lengths distinguish other Arabidopsis accessions with distinct root hair density and -Pi response from diploid Col-0, while tetraploid Col-0 had generally larger root cell sizes, which explain longer hairs. A distinct radial root morphology within Arabidopsis accessions and wrky6-3 explains some, but not all, differences in the root hair acclimation to –Pi.
Psychometric properties of the perceived stress scale (PSS): measurement invariance between athletes and non-athletes and construct validity
Authors: Chiu Yi-Hsiang , Lu Frank Jing-Horng , Lin Ju-Han , Nien Chiao-Lin , Hsu Ya-Wen , Liu Hong-Yu
Published: January 2018

Background: Although Perceived Stress Scale (PSS, Cohen, Kamarack, Mermelstein, 1983) has been validated and widely used in many domains, there is still no validation in sport by comparing athletes and non-athletes and examination of related psychometric indices. Purpose: The purpose of this study was to examine the measurement invariance of PSS between athletes and non-athletes, and examine construct validity in the sport contexts. Methods: Study 1 sampled 359 college student-athletes (males = 233; females = 126) and 242 non-athletes (males=124; females=118) and examined factorial structure, measurement invariance and internal consistency. Study 2 sampled 196 student-athletes (males = 139, females = 57, Mage =19.88 yrs, SD = 1.35) and examined discriminant validity and convergent validity of PSS. Results: Results found that 2-factor PSS-10 fitted the model the best and had appropriate reliability. Also, there was a measurement invariance between athletes and non-athletes; and PSS positively correlated with athlete burnout and life stress but negatively correlated with coping efficacy provided evidences of discriminant validity and convergent validity. Discussion: It is suggested that 2-factor PSS-10 can be a useful tool in assessing perceived stress either in sport or non-sport settings. We suggest future study may use 2-factor PSS-10 in examining the effects of stress on athletic injury, burnout, and psychiatry disorders.
Exploiting freely available imagery to improve land cover characterization and shallow landslide detection
Authors: Crema Stefano , Cavalli Marco , Bossi Giulia , Schenato Luca , Frigerio Simone , Marchi Lorenzo
Published: January 2018

Natural hazards and land management issues can benefit nowadays from the increasing availability of free, high-resolution satellite imagery that opens the way to fine scale detailed investigations. In high elevation catchments the analysis of vegetation dynamics deserves particular attention since little climatic modifications can be amplified in such fragile systems. For the same reasons, the dynamic of instability phenomena as response to an input hydrological forcing, requires a meticulous spatial representation in order to better represent the active processes at catchment scale. The present work focuses on the analysis of high-resolution freely available imagery (Microsoft® Bing Maps™ Platform) that enables the characterization of vegetation cover and the automatic mapping of shallow landslides in an alpine catchment. Semi-automatic detection of vegetation is carried out at the fine scale using both orthophotos and freely available satellite imagery. The analysis based on the satellite imagery showed a better accuracy in respect to the one based on the orthophotos. In particular, satellite imagery analysis showed high sensitivity and high specificity even in low illumination conditions, while, for the same circumstances, orthophotos-based analysis shows a significant wrong detection rate. In the framework of a long term, multi-temporal and high-resolution characterization of vegetation cover and for a rapid mapping of shallow instability phenomena, the effectiveness of the proposed approach can speed up the representation of the local conditions towards an improvement of land management strategies and hazard and risk assessment.
Analysis of the interactions of a novel cephalosporin derivative with its potential targets penicillin-binding proteins from different sources using a covalent docking approac
Authors: Verdino Anna , De Rosa Margherita , Soriente Annunziata , Marabotti Anna
Published: January 2018

Motivation. Cephalosporins are a class of beta-lactam antibiotics widely used in clinics for their antibacterial activity. Their mode of action, common to other beta lactam antibiotics such as penicillins, is the impairment of the synthesis of the peptidoglycan forming the bacterial cell wall. This polymer, essential for bacterium survival, is made by aminosugars connected by glycosidic bonds to form linear chains, and by short peptides forming cross-links between the linear chains. The enzymes catalyzing the creation of these cross-links are transpeptidases, also called penicillin binding proteins (PBPs) for their ability to interact with penicillins and other beta lactam antibiotics. These molecules mimic the D-Ala-D-Ala terminus of the peptides, therefore they competitively inactivate the PBPs by binding covalently to the Ser residue responsible for the catalysis and stopping the transpeptidation. This results in cell lysis and bacterial death. One of the main problems to face when using cephalosporins is the development of several mechanisms of resistance, either for the reduced affinity of PBPs to the beta lactams, or for the selection of new beta-lactam-insensitive PBPs, or for the production of beta lactamases, enzymes able to hydrolyze the beta lactam ring, thus deactivating the antibiotics. Additionally, most cephalosporins have a limited spectrum of action, against only Gram+ or Gram- bacteria. Therefore, during the time, many new beta lactam antibiotics have been synthesized with the aim of broadening the spectrum of action and/or overcoming the resistance. The prototype of a new group of cephalosporins is AMA-10, in which another beta lactam ring bound to a short alkyl chain has been linked to the aminocephalosporanic ring by means of an amidic bond. In order to develop other molecules, however, it is essential to understand how they interact with their target. Therefore, to apply a rational approach for the design of new derivatives, we have performed a computational study by simulating the binding of AMA-10 to selected PBPs of different species, whose crystallographic structures were available, using a particular approach, covalent docking, able to take into account the covalent bond formed between the antibiotic and the enzyme.

Methods. The structures of PBP3 and PBP4 from both Gram+ (S. aureus, B. subtilis) and Gram- (E. coli, P. aeruginosae) organisms were downloaded from Protein Data Bank (PDB) database, as well as the structures of beta-lactamase from S. aureus and from E. coli. The representative structures were selected on the basis of their quality. Then, covalent docking was made by using a modified version of the program AutoDock 4.2, using the flexible side chain method [Bianco et al, 2016]. [Abstract truncated at 3,000 characters - the full version is available in the pdf file].
Changes in understory species occurrence of a secondary broadleaved forest after mass mortality of oak trees under deer foraging pressure
Authors: Itô Hiroki
Published: January 2018

The epidemic of mass mortality of oak trees has affected secondary deciduous broadleaved forests that have been used as coppices in Japan. The dieback of oak trees formed gaps in the crown that would be expected to enhance the regeneration of shade-intolerant pioneer species. However, foraging by sika deer Cervus nippon has also affected forest vegetation, and the compound effects of both on forest regeneration should be considered when they simultaneously occur. A field study was conducted in Kyôto City, Japan, to investigate how these compound effects affected the vegetation of the understory layer of such a forest. The presence/absence of seedlings and saplings was observed for 200 quadrats sized 5 m × 5 m for each species in 1992, before the mass mortality and deer encroachment, and in 2014 after these effects. A hierarchical Bayesian model was constructed to explain the occurrence, survival, and colonization of each species with their responses to the gaps created or affected by the mass mortality of oak trees. The species that occurred most frequently in 1992, Eurya japonica, Quercus glauca, and Cleyera japonica, also had the highest survival probability. Deer-unpalatable species such as Symplocos prunifolia and Triadica sebifera had higher colonization rates in the gaps, while the deer-palatable species Aucuba japonica had the smallest survival probability. The gaps thus resulted in promoting the colonization of deer-unpalatable plant species such as Symplocos prunifolia and Triadica sebifera. It might be forecasted that such deer-unpalatable species will dominate the gaps created or affected by the mass mortality of oak trees.
Crowdsourcing with mobile techniques for crisis support
Authors: Frigerio Simone , Schenato Luca , Bossi Giulia
Published: January 2018

The responsibilities deployed from the central authorities to local levels acting as first actors of civil protection are a changing pattern in natural hazard management. Prevention and preparedness are long-term goals, rooted in the competence of volunteers, and on the awareness of the citizens as local inhabitants. MAppERS (Mobile Application for Emergency Response and Support) relies on people as “crowd-sourced mappers” through mobiles application. The feedback received from testing and training courses aims to raise participation in a networked disaster response. The goal was to design a mobile application with a real-time dashboard for public citizens and volunteers of civil protection. Two pilot study cases were selected that included trainings on modules, verification of the usability and the quality of the product. The synchronized platform shows the activity of the cloud data collection with a central data dashboard. A first section of the application focuses on floods processes by gathering data from local population, and contributes to awareness and long-term preparedness. The second section of the application tests pre-emergency actions on field with rescue teams, collecting the condition of the hazards.
Suspected anaphylaxis from intravenous cefazolin during general anaesthesia in a dog
Authors: Prebble Melanie , Pang Daniel SJ
Published: January 2018

A 6-year-old female Shetland Sheepdog with a history of cardiorespiratory compromise during general anaesthesia was referred for ovariohysterectomy surgery. Clinical examination was unremarkable at presentation and physiologic parameters under general anaesthesia were within expected ranges during preparation for surgery. Shortly after completion of an intravenous injection of cefazolin, the audible signal from the Doppler ultrasound unit stopped. A rapid survey of the patient revealed tachycardia with weak femoral pulses, tachypnoea, hyperpnoea and substantially increased resistance to manual positive pressure ventilation. Stopping inhalant anaesthesia, administering salbutamol, corticosteroids and diphenhydramine were associated with resolution of clinical signs. However, marked hypotension and resistance to ventilation recurred approximately 25 minutes later. Low dose intravenous epinephrine (5 mcg/kg) was effective at increasing arterial blood pressure and reversing respiratory dysfunction. Surgery was completed and the patient recovered uneventfully. Initial reliance on second line therapy and delay in administering epinephrine, the recommended treatment for anaphylaxis, may have slowed resolution of clinical signs.
MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes
Authors: Moller Abraham G , Liang Chun
Published: January 2018

Summary: Clustered regularly interspaced palindromic repeat (CRISPR) systems are prokaryotic adaptive immune systems against viral infection. CRISPR spacer sequences can provide valuable ecological insights by linking environmental viruses to microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool - MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to de novo CRISPR detection methods. Simulations show it performs better than de novo tools for Illumina metagenomes.

Availability and implementation: MetaCRAST is implemented in Perl and takes metagenomic sequence reads and direct repeat queries (FASTA) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.
MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes
Authors: Moller Abraham G , Liang Chun
Published: January 2018

Summary: Clustered regularly interspaced palindromic repeat (CRISPR) systems are prokaryotic adaptive immune systems against viral infection. CRISPR spacer sequences can provide valuable ecological insights by linking environmental viruses to microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool - MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to de novo CRISPR detection methods. Simulations show it performs better than de novo tools for Illumina metagenomes.

Availability and implementation: MetaCRAST is implemented in Perl and takes metagenomic sequence reads and direct repeat queries (FASTA) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.[p]
The northernmost occurrence of Chelydra serpentina in the eastern US during the Pleistocene
Authors: Brownstein Chase
Published: January 2018

The snapping turtle species Chelydra serpentina, which has a wide range across North America, is extremely tolerant to cold and even freezing conditions. Here, I describe a single caudal vertebrae referred to Chelydra serpentina from the Late Pleistocene of New Jersey which represents the northernmost known occurrence of the species in eastern North America and the closest known occurrence of the species to a glacier or ice sheet in the continent during the Pleistocene. The specimen, which was collected at Ramanessin Brook in Holmdel, New Jersey, affirms that the Pleistocene deposits which line the banks of the popular Cretaceous site are not taphonomically biased to preserving larger fossils and in the future may yield an assemblage of small vertebrates.
XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves
Authors: Thomas Nicholas C , Schwessinger Benjamin , Liu Furong , Chen Huamin , Wei Tong , Nguyen Yen P , Shaker Isaac WF , Ronald Pamela C
Published: January 2018

The rice XA21 receptor kinase confers robust resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). We developed a detached leaf infection assay to quickly and reliably measure activation of the XA21-mediated immune response using genetic markers. We used RNA sequencing of elf18 treated EFR:XA21:GFP plants to identify candidate genes that could serve as markers for XA21 activation. From this analysis we identified 8 genes that are up-regulated in both in elf18 treated EFR:XA21:GFP rice leaves and Xoo infected XA21 rice leaves. These results provide a rapid and reliable method to assess bacterial-rice interactions.
Identification of canine papillomavirus by PCR in Greyhound dogs
Authors: Anis Eman A , Frank Linda A , Francisco Raquel , Kania Stephen A
Published: January 2018

Background – Corns are hard protuberances that occur on the digital footpads of Greyhound dogs. The cause of these lesions is unknown and there is little information about them in the veterinary literature. We received anecdotal examples of dog to dog spread of corns suggesting an infectious cause. The aim of this study was to determine if papillomavirus (PV) is associated with Greyhound corns. Methods – We examined four corns from two unrelated adult Greyhound dogs that resided in Florida and Washington, respectively, for PV by PCR. The samples were obtained by owner coring of two lesions from one dog and laser removal of two lesions from the other dog. Total nucleic acid was extracted and DNA was amplified using two PCR primer sets that have been shown to amplify a broad range of PVs from humans and animals: FAP59/ FAP64 and MY11/ MY09. The DNA sequences were compared with all sequences in GenBank. Formalin-fixed, paraffin-embedded tissue from the footpads of four dogs with other inflammatory dermatoses were also examined. Results – PV DNA was amplified from all four corn lesions, while no PV DNA was amplified from other tissues. Comparison of the 300-400-bp sequences amplified by the MY11/ MY09 primers identified two different PVs. One showed 96% nucleotide sequence homology with the L1 gene of canine PV type 12. The other showed 78% homology to canine PV type 16, and, therefore, represents a novel PV. In one of the corns, infection by two of the identified PVs was found. Discussion – These results suggest PV infection could be involved in the pathogenesis of corns in Greyhound dogs.
Enhancing fisheries education through the Canadian Fisheries Research Network: a student perspective on interdisciplinarity, collaboration and inclusivity
Authors: Turgeon Katrine , Hawkshaw Sarah C.F. , Dinning Kristin M. , Quinn Brady K. , Edwards Danielle N. , Wor Catarina , Parlee Courtenay E. , Debertin Allan , Hawkshaw Mike , Nelson Benjamin W. , Zhang Fan , Benestan Laura M , Angel Eric , Morse Bryan L. , Mombourquette Daniel
Published: January 2018

Fisheries sciences and management involve complex problems not easily addressed by a single set of stakeholders or methodologies from one discipline; accordingly, the Canadian Fisheries Research Network (CFRN) was initiated to increase fisheries research capacity in Canada through interdisciplinary and inclusive research collaborations. We compared the value of the CFRN students’ learning experience to that offered in traditional fisheries programs at Canadian universities in training post-graduate students to tackle complex fisheries problems. This paper presents 1) a review of the current state of fisheries education across Canada and 2) reflections on our training within the CFRN, and challenges to implementing its innovative approach to fisheries education. We found few dedicated fisheries programs in Canada and concluded that fisheries research typically relies on securing a supervisor with an interest in fisheries. In contrast, the CFRN enhanced our university training through interdisciplinary and inclusive research collaborations, and by exposure to the realities of industry, government and academics collaborating for sustainable fisheries. We propose a new approach to post-graduate level fisheries education, one that combines interdisciplinarity, collaboration, and inclusivity to produce more capable fisheries scientists and managers. Furthermore, we made recommendations on how universities, researchers, and funding agencies can successfully incorporate these themes into fisheries education.
Conserved domain and structure analysis of a putative polyphosphate kinase from Buruli ulcer causing bacterium
Authors: Basharat Zarrin
Published: January 2018

With increasing sophistication of instruments and techniques, in addition to the increment in intricacies, girth and complexities of the problems being addressed, simple methods (especially computational biology techniques) are being overlooked, replaced or phased out. One such technique on the twilight of survival is simple computational analysis of protein sequence i.e. property determination, homology modeling etc. Manuscripts reporting solely such type of analysis face upfront rejection, although some exceptions might exist. Only some predatory or beginner journals might accept such publications. This continues despite the fact that simple, cost effective, quick computational analysis of protein sequence has its merits and paves way for further research. This report is basically an attempt to keep the dying venture of protein structure modeling alive.
Multiple, independent colonizations of the Hawaiian Archipelago by the family Dolichopodidae (Diptera)
Authors: Goodman Kari Roesch , Evenhuis Neal , Bartošová-Sojková Pavla , O'Grady Patrick Michael
Published: January 2018

The family Dolichopodidae forms two of the four largest evolutionary radiations in the Hawaiian Islands across all flies: Campsicnemus (183 spp) and the Eurynogaster complex (66 spp). They also include a small radiation of Conchopus (6 spp). A handful of other dolichopodid species are native to the islands in singleton lineages or small radiations. This study provides a phylogenetic perspective on the colonization history of the dolichopodid fauna in the islands. We generated a multi gene data set including representatives from 11 of the 14 endemic Hawaiian dolichopodid genera to examine the history of colonization to the islands, and analyzed it using Bayesian and maximum likelihood phylogenetic methods. We used a subset of the data that included Conchopus and the eight genera comprising the Eurynogaster complex to estimate the first phylogenetic hypothesis for these endemic groups, then used Beast to estimate their age of arrival to the archipelago. The Eurynogaster complex, Campsicnemus and Conchopus are clearly the result of independent colonizations. The results strongly support the Eurynogaster complex as a monophyletic group, and also supports the monophyly of 4 of the 8 described genera within the complex (Adachia, Arciellia, Uropachys and Eurynogaster). Members of the family Dolichopodidae have been dispersing over vast distances to colonize the Hawaiian Archipelago for millions of years, leading to multiple independent evolutionary diversification events. The Eurynogaster complex arrived in the Hawaiian Archipelago 11.8 Ma, well before the arrival of Campsicnemus (4.5 Ma), and the even more recent Conchopus (1.8 Ma). Data presented here demonstrate that the Hawaiian Dolichopodidae both disperse and diversify easily, a rare combination that lays the groundwork for field studies on the reproductive isolating mechanisms and ecological partitioning of this group.
Computational characterization and epitope prediction for Bet-v1 like protein of Cannabis sativa
Authors: Basharat Zarrin
Published: January 2018

Cannabis sativa encodes a Bet-v1 like protein is an allergen and a causuative agent of pollen allergy. Multiple sequence alignment of this protein revealed conserved residues in Betv1 domain. Identification of linear epitopes of this protein was done after preliminary bioinformatics characterization and structure prediction. Structure prediction was done using Modeller software and minimized using Swiss PDBViewer. Six linear epitopes were then, predicted using EMBOSS antigenic program. Phylogenetic analysis of Bet-v1 with other sequences demonstrated divergence patterns with allergens of other species but revealed conserved residues in allergenic epitopes. This study can serve as an informational aid in the development of hypoallergenic vaccine for Cannabis sativa allergy.
How are topics born? Understanding the research dynamics preceding the emergence of new areas
Authors: Salatino Angelo A , Osborne Francesco , Motta Enrico
Published: January 2018

The ability to recognise new research trends early is strategic for many stakeholders, such as academics, institutional funding bodies, academic publishers and companies. While the state of the art presents several works on the identification of novel research topics, detecting the emergence of a new research area at a very early stage, i.e., when the area has not been even explicitly labelled and is associated with very few publications, is still an open challenge. This limitation hinders the ability of the aforementioned stakeholders to timely react to the emergence of new areas in the research landscape. In this paper, we address this issue by hypothesising the existence of an embryonic stage for research topics and by suggesting that topics in this phase can actually be detected by analysing diachronically the co-occurrence graph of already established topics. To confirm our hypothesis, we performed a study of the dynamics preceding the creation of novel topics. This analysis showed that the emergence of new topics is actually anticipated by a significant increase of the pace of collaboration and density in the co-occurrence graphs of related research areas. These findings are very relevant to a number of research communities and stakeholders. Firstly, they confirm the existence of an embryonic phase in the development of research topics and suggest that it might be possible to perform very early detection of research topics by taking into account the aforementioned dynamics. Secondly, they bring new empirical evidence to related theories in Philosophy of Science. Finally, they suggest that significant new topics tend to emerge in an environment in which previously less interconnected research areas start cross-fertilising.
Demographic, ecological and physiological responses of ringed seals to an abrupt decline in sea ice availability
Authors: Ferguson Steven H , Young Brent G , Yurkowski David J , Anderson Randi , Willing Cornelia , Nielsen Ole
Published: January 2018

To assess whether demographic declines of Arctic species at the southern limit of their range will be gradual or punctuated, we compared large-scale environmental patterns including sea ice dynamics to ringed seal (Pusa hispida ) reproduction, body condition, recruitment, and stress in Hudson Bay from 2003-2013. Aerial surveys suggested a gradual decline in seal density from 1995-2013, with the lowest density occurring in 2013. Body condition decreased and stress (cortisol) increased over time in relation to longer open waterperiods. The 2010 open water period in Hudson Bay coincided with extremes in large-scale atmospheric patterns (NAO, AO, ENSO) resulting in the earliest spring breakup and the latest ice formation on record. The warming event was coincident with the highest stress levels and the lowest recorded ovulation rate and low pregnancy rate, few pups in the Inuit harvest, and observations of sick seals. We conclude that although negative demographic responses of Hudson Bay seals are occurring gradually with diminishing sea ice, a recent episodic environmental event played a significant role in a punctuated population decline.
Seasonal shifts in accumulation of glycerol biosynthetic gene transcripts in mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae), larvae
Authors: Fraser Jordie D , Bonnett Tiffany R , Keeling Christopher I , Huber Dezene P
Published: January 2018

Winter mortality is a major factor regulating population size of the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). Glycerol is the major cryoprotectant in this freeze intolerant insect. We report findings from a gene expression study on an overwintering mountain pine beetle population over the course of 35 weeks. mRNA transcript levels suggest glycerol production in the mountain pine beetle occurs through glycogenolytic, gluconeogenic and potentially glyceroneogenic pathways, but not from metabolism of lipids. A two-week lag period between fall glycogen phosphorylase transcript and phosphoenolpyruvate carboxykinase transcript up-regulation suggests that gluconeogenesis serves as a secondary glycerol-production process, subsequent to exhaustion of the primary glycogenolytic source. These results provide a first look at the details of seasonal gene expression related to the production of glycerol in the mountain pine beetle.
Aspects of the gorgonopsian paleobiology: insights from the basicranium, occiput, osseous labyrinth and neuroanatomy of the immature gorgonopsian skull of Aloposaurus gracilis (Therapsida: Theriodontia: Gorgonopsia)
Authors: Araujo Ricardo M , Fernandez Vincent , Polcyn Michael J , Fröbisch Jörg , Martins Rui M.S.
Published: January 2018

Synapsida, the clade including therapsids and thus also mammals, is one of the two major branches of amniotes. Organismal design, with modularity as a concept, offers insights into the evolution of therapsids, a group that experienced profound anatomical transformations throughout the past 270Ma, eventually leading to the evolution of the mammalian bauplan. However, the anatomy of some therapsid groups remains obscure. Gorgonopsian braincase anatomy remains poorly known, and aspects of their brain anatomy, cranial nerves and vasculature, osseous labyrinth persist unknown. By using propagation phase contrast synchrotron micro-computed tomography, we scanned GPIT/RE/7124, a specimen previously reported as Aloposaurus gracilis. We explored the anatomy of the braincase and rendered the anatomy of the various skull cavities. Notably, we found that there is a separate ossification between what was previously referred as the “parasphenoid” and the basioccipital. This element is reinterpreted as a posterior ossification of the basisphenoid, the basi-postsphenoid. Additionally the previously called “parasphenoid” is in fact the co-ossification of the dermal parasphenoid and the endochondral basi-presphenoid. The anatomy of the osseous labyrinth is rendered in detail, revealing a unique discoid morphology of the horizontal semicircular canal, rather than toroidal, probably due to architectural contraints of the ossification of the opisthotic and supraoccipital. In addition, the orientation of the horizontal semicircular canal suggests an anteriorly tilted alert head posture. The morphology of the brain endocast is in accordance with the more reptilian endocast shape of other non-mammaliaform neotherapsids.
Gene discovery in Atlantic Forest plant species using GR-RSC simplified genomes
Authors: Detoni Marcella A A , Cardenas Raony G C C L , Uliano-Silva Marcela , de Freitas Rebelo Mauro
Published: January 2018

The Atlantic Forest is one of the most import biodiversity hotspots in the world, nevertheless, its 20,000 plant species are poorly characterized genetically, what could undermine conservational efforts and bioprospection of natural products. We used a genome reduction using restriction site conservation (GR-RSC) technique to minimize sequencing effort and build in a short period a data bank of gene sequences from 35 plant species from the Atlantic Forest in a private natural protected area in Southwest Brazil. After Illumina sequencing and standard bioinformatics, we produced more than 66 million super reads, of which 11 million (17\%) were annotated using Diamond and UNIREF90 database and 55 million were 'No hit'. We picked 17 enzymes from 2 secondary metabolite synthesis pathways that are both important representatives of biological processes for plants and also of industrial interest, to test the usefulness of the databank we created for gene discovery. All 17 genes were detected in at least one of the 35 species and all species exhibited at least one of the genes. Eight of the 35 species exhibited all 17 genes. These results shows that genome simplification by restriction enzyme can be applied to preliminary screen thousands of species in tropical forests, generating useful databanks for scientific and entreprenurial activities both in conservational biology and bioprospection.
Seqenv: linking sequences to environments through text mining
Authors: Sinclair Lucas , Ijaz Umer Z , Jensen Lars , Coolen Marco JL , Gubry-Rangin Cecile , Chroňáková Alica , Oulas Anastasis , Pavloudi Christina , Schnetzer Julia , Weimann Aaron , Ijaz Ali , Eiler Alexander , Quince Christopher , Pafilis Evangelos
Published: January 2018

Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts – if it is available – the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install, go to: https://github.com/xapple/seqenv
Angiosperm Phylogeny Poster – Flowering Plant Systematics
Authors: Cole Theodor C. H. , Hilger Hartmut H
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.

Translations of the poster by internationally renown botanists are now available in more than a dozen world languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.

This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Microscale insight into microbial seed banks
Authors: Locey Kenneth J , Fisk Melany C , Lennon Jay T
Published: January 2018

Dormancy is a general microbial life-history trait that leads to the emergence of seed banks across diverse ecosystems. While the primary forces driving seed banks include macroscale factors like resource supply, the importance of microscale factors such as individual encounters with resource molecules are often overlooked. Here, we used >10,000 individual based models (IBMs) to simulate energetic, physiological, and ecological processes across combinations of resource-, spatial-, and trophic-complexity. We found that increasing rates of encounter of individual organisms with resource molecules led to greater abundance, greater productivity, and larger seed banks. We also found that the chemical complexity of resource molecules reduced encounter rates, which led to increased variability in the size of seed banks. Encounter-driven ‘boom and bust’ dynamics also caused resource-rich environments to simultaneously host large seed banks and serve as hotbeds of microbial activity. In conclusion, microscale phenomena appear to be essential for understanding the emergence of seed banks, the energetic basis of microbial life history trade-offs, and variation in the abundance and activity of microbial communities.