bluuebunny/crossref_metadata_2025 huggingface dataset:
Missing, delayed, and old: A status review of ESA recovery plans
Authors: Malcom Jacob , Li Ya-Wei
Published: January 2018

Recovery planning is an essential part of implementing the U.S. Endangered Species Act (ESA), but conservationists and government agencies recognize challenges with the current planning process. Common criticisms are that too many species lack recovery plans, plans take too long to write, and they are rarely updated to include new information. Using data from all U.S. domestic and transboundary ESA-listed species—most of which are required to have recovery plans—we quantify these basic characteristics of ESA recovery planning over the past 40 years. We show that nearly 1/4 of eligible listed species (n = 1,503) lack recovery plans; the average recovery plan has taken >5 years to finalize after listing; half of recovery plans are 19 or more years old; and there is significant variation among regions and between agencies in plan completion rates and time-to-completion. These results are not unexpected given dwindling budgets and an increasing number of species to protect, but underscore the need for systematic improvements to recovery planning. We discuss solutions that may address some of the shortcomings we identify here, including a transition to dynamic, web-based recovery plans.
The Furvela tent-trap Mk 1.1 for the collection of outdoor biting mosquitoes
Authors: Charlwood Jacques D , Le Clair Corey
Published: January 2018

Outdoor transmission of malaria and other vector borne diseases remains a problem. Suitable methods for assessing vector density are required and a number of tent-traps, for the collection for outdoor biting mosquitoes, have recently been developed. Only one such trap, the Furvela tent-trap, does not require an ‘entry’ behavior on the part of the mosquito. It remains the cheapest and lightest tent-trap described. It takes less than two minutes to install and is the only trap described that uses readily available components. We also describe recent modifications to the trap, which make it even easier to set up, provide an SOP and describe some recent experiments examining the effect of the addition of light to the trap. We also provide a short review of work so far undertaken with the trap in Mozambique, Ghana and Tanzania. The trap provides the closest approximation to CDC light-traps, widely used to collect indoor biting mosquitoes. This enables the effect of a number of interventions on mosquito density and indoor/outdoor behaviors to be determined.
Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata
Authors: Putnam Hollie , Adams Diane , Zelzion Ehud , Wagner Nicole , Qiu Huan , Mass Tali , Falkowski Paul , Gates Ruth , Bhattacharya Debashish
Published: January 2018

We investigated intra and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2-3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.
Bridging gaps on population knowledge of giant armadillos: importance of intensify sampling efforts in highly-modified landscapes to accurately estimate species occurrence
Authors: Lemos Frederico G , Costa Alan N , Azevedo Fernanda C , Fragoso Carlos E , Freitas-Junior Mozart C , Rocha Ednaldo C
Published: January 2018

Studies on threatened species in highly modified and unprotected landscapes are necessary to the development of appropriate conservation and management policies. This is particularly important for species with large home-ranges, such as the giant armadillo (Priodontes maximus), whose occurrence in anthropogenic landscapes is poorly understood despite its status as endangered to extinction species. We searched for giant armadillos within human-modified areas in Central Brazil using direct and indirect methods (camera trapping, occasional sightings, recovered carcasses of road-killed and poached animals, burrows and tracks) across a wide region dominated by diverse farming environments and scattered natural remnants. We amassed 52 records of giant armadillos during a 13-year period within 10 municipalities of Minas Gerais and Goiás States, constituting the largest sampling effort and scale for this species to date. Records were mostly distributed in private natural fragments, while some were in protected units. Native vegetation covered most of the occurrence points (85%), while a small portion of records (15%) occurred in anthropic environments (pastures and roads). Our results upheld the suggested distribution for P. maximus while amending previous assumptions regarding this species absence in parts of the studied region in Central Brazil. More importantly, we confirmed the presence of giant armadillos within a wide, intensely human-altered region, likely as result of the extinction debt. These results indicate that Cerrado and Atlantic Forest remnants in human-modified landscapes in Central Brazil have been playing an important role as refuges for this armadillo species, as their use of anthropic environments such as pastures is much less frequent as evidenced by the occurrence records and behavioral patterns. As the giant armadillo can serve as prey to large carnivores as well as help controlling the density of herbivore insects while acting as ecosystem engineers, they play an essential role in community dynamics and merit urgent and decisive conservation efforts.
Cloning, expression, purification of active recombinant human 12R-LOX enzyme and its inhibition by Acalypha indica extracts
Authors: Fatima Naireen , P Ramakrishna B , Kumar Naresh , Reddanna Pallu
Published: January 2018

12R-LOX over-expression has been reported in various pathologies such as psoriasis, proliferative dermatitis as well as pulmonary obstructive diseases indicating that this enzyme plays significant role in pathogenesis of inflammatory diseases. 12R-LOX, therefore, is a suitable target for therapeutic intervention with potential application of its inhibitors in the treatment of skin and other inflammatory disorders. Identification of such inhibitors requires sufficient quantity of active enzyme to be produced by an easy and cost effective expression systems and further development of a robust assay system to screen inhibitors against the 12R-LOX enzyme. Therefore, in the present study, a prokaryotic expression system was developed to over-express and purify active human 12R-LOX enzyme by a single step purification process. We have further standardized an HPLC based assay system to assess the activity of purified human 12R-LOX enzyme. We show here that purified 12R-LOX preferentially utilizes free arachidonic acid as the substrate but it is also active on methyl ester of arachidonic acid, albeit less efficiently. Additionally, using this assay system we observed the potent inhibition of human 12R-LOX enzyme activity by the ethyl acetate and aqueous sub-fractions of Acalypha indica leaves, which is widely used in traditional medicines for the treatment of various skin ailments
AnnotationBustR: An R package to extract subsequences from GenBank annotations
Authors: Borstein Samuel R. , O'Meara Brian C.
Published: January 2018

Background. DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequences on GenBank contain more than one gene or are portions of genomes, and inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from multiple GenBank accessions based on annotations where gene names may vary extensively. Results. The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts portions of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion. FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.
The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillos (Dasypus novemcinctus)
Authors: Billet Guillaume , Hautier Lionel , de Thoisy Benoit , Delsuc Frédéric
Published: January 2018

Background. With their Pan-American distribution, long-nosed armadillos (genus Dasypus) constitute an understudied model for Neotropical biogeography. This genus currently comprises seven recognized species, the nine-banded armadillo (D. novemcinctus) having the widest distribution ranging from Northern Argentina to the South-Eastern US. With their broad diversity of habitats, nine-banded armadillos provide a useful model to explore the effects of climatic and biogeographic events on morphological diversity at a continental scale.

Methods. Based on a sample of 136 skulls of Dasypus spp., including 112 specimens identified as D. novemcinctus, we studied the diversity and pattern of variation of internal paranasal cavities, which were reconstructed virtually using µCT-scanning or observed through bone transparency.

Results. Our qualitative analyses of paranasal sinuses and recesses successfully retrieved a taxonomic differentiation between the traditional species D. kappleri, D. pilosus and D. novemcinctus but failed to recover diagnostic features between the disputed and morphologically similar D. septemcinctus and D. hybridus. Most interestingly, the high variation detected in our large sample of D. novemcinctus showed a clear geographical patterning, with the recognition of three well-separated morphotypes: one ranging from North and Central America and parts of northern South America west of the Andes, one distributed across the Amazonian Basin and central South America, and one restricted to the Guiana Shield.

Discussion. The question as to whether these paranasal morphotypes may represent previously unrecognized species is to be evaluated through a thorough revision of the Dasypus species complex integrating molecular and morphological data. Remarkably, our recognition of a distinct morphotype in the Guiana Shield area is congruent with the recent discovery of a divergent mitogenomic lineage in French Guiana. The inflation of the second medialmost pair of caudal frontal sinuses constitutes an unexpected morphological diagnostic feature for this potentially distinct species. Our results demonstrate the benefits of studying overlooked internal morphological structures in supposedly cryptic species revealed by molecular data. It also illustrates the under-exploited potential of the highly variable paranasal sinuses of armadillos for systematic studies.
Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, U.S. Virgin Islands
Authors: Cunning Ross , Gates Ruth D , Edmunds Peter J
Published: January 2018

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this 'within-sample clustering' to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying 'dominant' and 'background' niches, and coral hosts that are more 'flexible' or 'specific' in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.
Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies
Authors: Xiao Jun , Li Xiaowei , Liu Juan , Fan Xiu , Lei Huifen , Li Cuiying
Published: January 2018

Background: Tibetans have lived at high altitudes for thousands of years, and they have a unique composition of physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to select potential reference genes. Results: Eight candidate reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) from humans were selected to assess their expression levels in blood under hypoxic environments. The expression stabilities of these candidate reference genes were evaluated using BestKeeper, geNorm and NormFinder programs. Interestingly, RPL13A was selected as the ideal reference gene to normalize the target gene expression in human blood before and after moving to the plateau. Conclusion: These results indicate that different reference genes should be selected for the normalization of gene expression in blood based on the environmental setting.
Multi-institutional development of a mastoidectomy performance evaluation instrument
Authors: Kerwin Thomas , Hittle Brad , Stredney Don , De Boeck Paul , Wiet Gregory
Published: January 2018

A method for rating surgical performance of a mastoidectomy procedure that is shown to apply universally across teaching institutions has not yet been devised. This work describes the development of a rating instrument created from a multi-institutional consortium. Using a participatory design and a modified Delphi approach, a multi-institutional group of expert otologists constructed a 15 element task-based checklist for evaluating mastoidectomy performance. This instrument was further refined into a 14 element checklist focusing on the concept of safety after using it to rate a large and varied population of performances. By using 14 experts from 12 different institutions and a literature review, individual metrics were identified, rated as to the level of importance and operationally defined to create a rating scale for mastoidectomy performance. Initial use of the rating scale showed modest rater agreement. The operational definitions of individual metrics were modified to emphasize “safe” as opposed to “proper” technique. A second rating instrument was developed based on this feedback. Using a consensus building approach with multiple rounds of communication between experts is a feasible way to construct a rating instrument for mastoidectomy. Expert opinion alone using a Delphi method provides face and content validity evidence, however, this is not sufficient to develop a universally acceptable rating instrument. A continued process of development and experimentation to demonstrate evidence for reliability and validity making use of a large population of raters and performances is necessary to achieve universal acceptance.
Evaluation of a multi-institution mastoidectomy performance instrument
Authors: Kerwin Thomas , Hittle Brad , Stredney Don , De Boeck Paul , Wiet Gregory
Published: January 2018

Objective: The objective of this work is to obtain validity evidence for an evaluation instrument used to assess the performance level of a mastoidectomy. The instrument has been previously described and had been formulated by a multi-institutional consortium.

Design: Mastoidectomies were performed on a virtual temporal bone system and then rated by experts using a previously described 15 element task-based checklist. Based on the results, a second, similar checklist was created and a second round of rating was performed.

Setting: Twelve otolaryngological surgical training programs in the United States. Participants 66 individuals with a variety of temporal bone dissection experience, from medical students to attending physicians. Raters were attending surgeons from 12 different institutions.

Results: Intraclass correlation (ICC) scores varied greatly between items in the checklist with some being low and some being high. Percentage agreement scores were similar to previous rating instruments. There is strong evidence that a high score on the task- based checklist is necessary for a rater to consider a mastoidectomy to be performed at the level of an expert but a high score is not a sufficient condition.

Conclusions: Rewording of the instrument items to focus on safety does not result in increased reliability of the instrument. The strong result of the Necessary Condition Analysis suggests that going beyond simple correlation measures can give extra insight into grading results. Additionally, we suggest using a multiple point scale instead of a binary pass/fail question combined with descriptive mastery levels.
The Ax21 protein influences virulence and biofilm formation in the nosocomial pathogen Stenotrophomonas maltophilia
Authors: An Shi-qi , Tang Ji-liang
Published: January 2018

Stenotrophomonas maltophilia is an antibiotic resistant Gram-negative pathogen, which is associated with hospital-acquired infection. The genome encodes a protein highly related to the Ax21 protein of Xanthomonas oryzae pv. oryzae that is implicated in interactions of this plant pathogen with rice. Here we show that loss by mutation of Ax21 influences a variety of functions in Stenotrophomonas maltophilia, to include virulence, antibiotic resistance and biofilm formation in this nosocomial pathogen.
Methodological considerations in assessment of language lateralisation with fMRI: a systematic review
Authors: Bradshaw Abigail R. , Woodhead Zoe V. J. , Bishop Dorothy V. M.
Published: January 2018

The involvement of the right and left hemispheres in mediating language functions has been measured in a variety of ways over the centuries since the relative dominance of the left hemisphere was first known. Functional magnetic resonance imaging (fMRI) presents a useful non-invasive method of assessing lateralisation that is being increasingly used in clinical practice and research. However, the methods used in the fMRI laterality literature currently are highly variable, making systematic comparisons across studies difficult. Here we consider the different methods of quantifying and classifying laterality that have been used in fMRI studies since 2000, with the aim of determining which give the most robust and reliable measurement. Recommendations are made with a view to informing future research to increase standardisation in fMRI laterality protocols. In particular, the findings reinforce the importance of threshold-independent methods for calculating laterality indices, and the benefits of assessing heterogeneity of language laterality across multiple regions of interest and tasks.
Can squirrel monkeys learn an ABnA grammar? A re-evaluation of Ravignani et al. (2013)
Authors: Ghirlanda Stefano
Published: January 2018

Ravignani et al. (2013) habituated squirrel monkeys to sound sequences conforming to an ABnB grammar, then tested them for the ability to identify novel grammatical sequences as well as non-grammatical ones. Although they conclude that the monkeys "consistently recognized and generalized the sequence ABnA," the data indicate very poor generalization. Pattern grammaticality accounted for at most 6% of the variance in responding. In addition, the statistical significance of results depends on specific choices of data analysis (dichotomization of the response variable and omission of certain data points) which appear to have a weak rationale. I also suggest that the task used by Ravignani et al. (2013) may be fruitfully analyzed as an auditory sequence discrimination task that does not require specific proto-linguistic abilities.
Understanding evolutionary dynamics of phosphorylation with fungal species as model system
Authors: Ng Wenfa
Published: January 2018

Movement in proteins requires energy. To this end, natural selection has selected phosphate as the principal energy currency in cells. On the other hand, depicting the state of transcription could come in the form of epigenetic markers, which are modifications on nucleotide residues. But, what are the deeper evolutionary forces that underpin the selection of phosphorylation as a key process for translating molecular information of cellular state into specific phenotype in movement and metabolism at the cellular level? From another perspective, what are the factors that guide the selection of particular phosphosites as principal phosphorylation sites? Seeking answers to the latter question, Villen and coworkers (“Evolution of protein phosphorylation across 18 fungal species”, Science, Link ) used mass spectrometry to profile the phosphoproteome of 18 fungal species and employed discovery science approaches to elucidate specific phosphosite highly conserved for particular functions such as transcription and translation. Using histone protein (H2) and transcription initiator factor (eIF4E) as model proteins for gaining a deeper understanding of the evolutionary forces that shape the annotation of specific phosphosite (from a large library of possible phosphosites) as key molecular effectors of cellular processes such as conformational changes in enzymes and ion channels. Results obtained suggests possible selection forces that define particular phosphosite for function, which are corroborated through assessing kinase motif usage and biochemical assays for the binding affinity between peptide libraries and cell lysates. Looking at a broader landscape of protein phosphorylation, the paper, however, does not yield sufficient insights to answer questions such as how protein phosphorylation first emerged as a defining mechanism for translating stored cellular energy in phosphate groups into movement necessary for protein function and, by extension, that of the cell. Understanding the evolutionary processes that first potentiated protein phosphorylation as well as the specific natural selection factors that resulted in the definition of specific phosphosite for particular function are fundamental questions important to understanding how biology utilizes chemical and physical principles for powering life.
Cuticle hydrocarbons in saline aquatic beetles
Authors: Botella-Cruz María , Villastrigo Adrián , Pallarés Susana , López-Gallego Elena , Millán Andrés , Velasco Josefa
Published: January 2018

Hydrocarbons are the principal component of insects cuticle and play an important role in maintaining water balance. Cuticular impermeability could be an adaptative response to salinity and desiccation in aquatic insects; however, cuticular hydrocarbons have been poorly explored in this group and there are no previous data on saline species. We characterized cuticular hydrocarbons of adults and larvae of two saline aquatic beetles, namely Nebrioporus baeticus (Dytiscidae) and Enochrus jesusarribasi (Hydrophilidae), using a gas chromatograph coupled to a mass spectrometer. The CHC profile of adults of both species, characterized by a high abundance of branched alkanes and low of unsaturated alkenes, seems to be more similar to that of some terrestrial beetles (e.g. desert Tenebrionidae) compared with other aquatic Coleoptera (freshwater Dytiscidae). Adults of E. jesusarribasi had longer chain compounds than N. baeticus, in agreement with their higher resistance to salinity and desiccation. The more permeable cuticle of larvae was characterized by a lower diversity in compounds, shorter carbon chain length and a higher proportion of unsaturated hydrocarbons compared with that of the adults. These results suggest that osmotic stress on aquatic insects could exert a selection pressure on CHC profile similar to aridity in terrestrial species.
Vertical handoff algorithm for different wireless technologies
Authors: Abdullah Radhwan Mohamed , Zukarnain Zuriati Ahmad
Published: January 2018

Transferring a huge amount of data between different network locations over the network links depends on the heterogeneous wireless network. Such a network consists of several networks with different access technologies. Traditionally, a mobile device may be moved to achieve the operations of vertical handover, considering only one criterion, that is, the received signal strength (RSS). The use of a single criterion may cause service interruption, an unbalanced network load, and an inefficient vertical handover. In this paper, we propose enhanced vertical handover decision algorithm based on multiple criteria in the heterogeneous wireless network. The algorithm consists of three technology interfaces: Long-Term Evolution (LTE), Worldwide interoperability for Microwave Access (WiMAX), and Wireless Local Area Network (WLAN). It also employs three types of the vertical handover decision algorithms: equal priority, mobile priority, and network priority. The simulation results illustrate that the proposed handover decision algorithm outperforms the traditional network decision algorithm in terms of handover number probability and the handover failure probability. In addition, it is noticed that the network priority handover decision algorithm produces better results compared to equal priority and mobile priority handover decision algorithm. Finally, the simulation results are validated by the analytical model.
Structure and properties of slow-resorbing nanofibers obtained by (co-axial) electrospinning as tissue scaffolds in regenerative medicine
Authors: Hudecki Andrzej , Gola Joanna , Ghavami Saeid , Skonieczna Magdalena , Markowski Jarosław , Likus Wirginia , Lewandowska Magdalena , Maziarz Wojciech , Los Marek J.
Published: January 2018

We investigated the structure and properties of PCL10 nanofiber, PCL5/PCL10 core-shell type nanofibers, as well as PCL5/PCLAg nanofibres prepared by electrospinning. For the production of the fibre variants, a 5-10% solution of polycaprolactone (Mw = 70000-90000), dissolved in a mixture of formic acid and acetic acid at a ratio of 70:30 m/m was used. In order to obtain fibres containing PCLAg 1% of silver nanoparticles was added. The electrospin was conducted using the above-described solutions at the electrostatic field. The subsequent bio-analysis shows that synthesis of core-shell nanofibers PCL5/PCL10, and the silver-doped variant nanofiber core shell PCL5/PCLAg by using organic acids as solvents is a robust technique. Such way obtained nanofibres may then be used in regenerative medicine for extracellular scaffolds: (i) for controlled bone regeneration due to the long decay time of the PCL, (ii) and as carriers of drug delivery nanocapsules. Furthermore, the used solvents are significantly less toxic than the solvents for polycaprolactone currently commonly used in electrospin, like for example chloroform (CHCl3), methanol (CH3OH), dimethylformamide (C3H7NO) or tetrahyfrofurna (C4H8O), hence the presented here electrospin technique may allow for the production of multilayer nanofibres more suitable for the use in medical field.
Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families
Authors: Vining Kelly J , Salinas Natalia , Tennessen Jacob A , Zurn Jason D , Sargent Daniel James , Hancock James , Bassil Nahla V
Published: January 2018

With the goal of evaluating genotyping-by-sequencing (GBS) in a species with a complex octoploid genome, GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria ×ananassa) populations. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30-65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. ×ananassa chromosomal regions derived from diploid ancestor F. vesca.
Lionfish (Pterois sp.) invade the upper bathyal zone in the western Atlantic
Authors: Gress Erika , Andradi-Brown Dominic A , Woodall Lucy , Schofield Pamela J , Stanley Karl , Rogers Alex D
Published: January 2018

Non-native lionfish have been widely recorded throughout the western Atlantic on both shallow and mesophotic reefs, where they have been linked to declines in reef health. In this study we report the first lionfish observations from the deep sea (>200 m) in Bermuda and Roatan, Honduras, with lionfish observed to a maximum depth of 304 m off the Bermuda platform, and 250 m off West End, Roatan. Placed in the context of other deeper lionfish observations and records, our results imply that lionfish may be found more widely in the 200-300 m depth range of the upper bathyal zone across the western Atlantic, but currently are under sampled compared to shallow habitats. We highlight the need for considering deep-sea lionfish populations in future invasive lionfish management.
The Chinese colossus: an evaluation of the phylogeny of Ruyangosaurus giganteus and its implications for titanosaur evolution
Authors: Sassani Nima , Bivens Gunnar T
Published: January 2018

For many years the precise taxonomy of Titanosauria has been a puzzle, and even today only certain segments of this vast clade are well-understood. The phylogenetic positions of many titanosaurs are murky, though specimens often still await rigorous analysis. One of the largest examples is the massive Chinese titanosaur Ruyangosaurus giganteus – though largely incomplete, the holotype is distinct enough to indicate strong phylogenetic affinities with a specific subgroup of titanosaurs. A review of previous literature on Ruyangosaurus, referred tentatively to Andesauridae, shows that this classification is based on three weak, non-diagnostic characters. Ruyangosaurus differs from taxa traditionally included in Andesauridae in at least 20 characters of the torso, femur, and tibia. Several plesiomorphies of Ruyangosaurus are extremely rare in titanosauria except for the clade Lognkosauria and its close relatives. The vertebra initially described as a posterior cervical is most likely an anterior dorsal, with a strong resemblance to that of Puertasaurus. The posterior dorsal of Ruyangosaurus shares synapomorphies with Mendozasaurus and Dreadnoughtus. The femur clusters close to the femora of Malawisaurus, Traukutitan, and Pitekunsaurus. Ruyangosaurus is here recovered as a lognkosaurian, with significant implications for the distribution and evolution of that group and the paleobiology of Mid-Cretaceous China.
Multi-label classification of frog species via deep learning
Authors: Xie Jie
Published: January 2018

Acoustic classification of frogs has received increasing attention for its promising application in ecological studies. Various studies have been proposed for classifying frog species, but most recordings are assumed to have only a single species. In this study, a method to classify multiple frog species in an audio clip is presented. To be specific, continuous frog recordings are first cropped into audio clips (10 seconds). Then, various time-frequency representations are generated for each 10-s recording. Next, instead of using traditional hand-crafted features, a deep learning algorithm is used to find the most important feature. Finally, a binary relevance based multi-label classification approach is proposed to classify simultaneously vocalizing frog species with our proposed features. Experimental results show that our proposed features extracted using deep learning can achieve better classification performance when compared to hand-crafted features for frog call classification.
Assessing vision in young children: Communication skills
Authors: Paudel Nabin
Published: January 2018

Measurement of visual functions is critical to the detection and diagnosis of eye disease, particularly in children where eliciting symptomology can be challenging. An effective practitioner-patient relationship is crucial in optometric practice and has numerous benefits such as increased satisfaction, good compliance to assessment and treatment. The aim of this work is to share my experience of assessing visual functions (visual acuity, stereopsis, and computer-based visual psychophysical testing) in infants and children. I will discuss some unique strategies in order gain attention of children ranging from infants to preschoolers. The importance of the waiting area, use of colorful toys, appropriate use of tests and language are a few among many strategies for getting through a pediatric vision assessment. Based on my 9 years experience as a pediatric optometrist and a child vision researcher, these approaches has been quite successful in conducting hundreds of pediatric vision assessments. A friendly clinician equipped with interesting age appropriate tests and colorful toys along with some essential communication skills can easily conduct a thorough and efficient pediatric vision assessment.
Statistical infarction: A postmortem of the Cornell Food and Brand Lab pizza publications
Authors: Anaya Jordan , van der Zee Tim , Brown Nick
Published: January 2018

We previously reported over 150 inconsistencies in a series of four articles (the "pizza papers") from the Cornell Food and Brand Lab that described a study of eating habits at an all-you-can-eat pizza buffet. The lab's initial response led us to investigate more of their work, and our investigation has now identified issues with at least 45 publications from this lab. Perhaps because of the growing media attention, Cornell and the lab have released a statement concerning the pizza papers, which included a response to the inconsistencies, along with data and code. Many of the inconsistencies were identified with the new technique of granularity testing, and this case has the highest density of granularity inconsistencies that we know of. This is also the first time a data set has been made public after granularity concerns were raised, making it a highly suitable case study for showing the accuracy and potential of this technique. It is also important that a third party audit the lab's response, given the continuing investigation of misconduct and presumably future reports and data releases. Our careful inspection of the data set suggests no evidence of fabrication, but we found the lab's report confusing, incomplete, and error prone. In addition, we found the number of missing, unusual, and logically impossible responses in the data set highly concerning. Unfortunately, given the unsound theory, poor methodology, questionable data, and countless errors, we find it remarkable that these four papers were published and recommend retraction of all four papers.
Short-term effect of reduction in forced vital capacity after diving exposure
Authors: Cheng Hua
Published: January 2018

To discuss whether there is relationship between short-term and long-time attenuation effects of ventilation caused by diving activity. The ventilation observed before and after hyperbaric exposure for 20min by case-control experiments. Participants of the experimental group (EG) stayed for 20min under 12-m underwater and the control group (CG) stayed in hyperbaric chamber under pressure of 2.2ATA. Immediate effects of pulmonary ventilation detected by the Spirometer and compared by paired T test to reveal the different caused by environmental pressure. The Vital Capacity (VC) rises while the Minute Ventilation (MV), Maximal Voluntary Ventilation (MVV) decreases after the exposure for 20min in both groups. The Forced Vital Capacity (FVC) is detected decreased significantly in EG (t=1.21, P =0.25) while it slightly increased in CG (t=-0.42, P =0.68).The ratio of Forced Expiratory Volume in one second to VC (FEV1.0/VC %) increase in EG (t=-0.73, P=0.48) while decrease in CG (t=0.42, P=0.17). The Ratio of FEV1.0 to FVC (FEV1.0 %) values increase obviously in EG (t=-1.48, P =0.16) and a bit in CG (t=-0.23, P =0.82). High pressure is the common factor in both groups that leads the changes in the same trend in VC, MV and MVV. Extra factors as immersion effect, loading of diving equipment and low temperature underwater, would encounter EG participants. Instant reduced effects of FVC under diving exposure in the study are quite consistent with the long-term cumulative effect of professional divers in previous research, which illustrated even small depth of short-range diving exercise have definite influences on ventilation.
Satellite tagging highlights the importance of productive Mozambican coastal waters to the ecology and conservation of whale sharks
Authors: Rohner Christoph A , Richardson Anthony J , Jaine Fabrice R A , Bennett Michael B , Weeks Scarla J , Cliff Geremy , Robinson David P , Pierce Simon J
Published: January 2018

Recent advances in tracking technologies and analytical approaches allow for deeper insights into the movement ecology of wide-ranging fishes. The whale shark Rhincodon typus is an endangered, highly migratory species with a wide, albeit patchy, distribution through tropical oceans. Aerial surveys along the southern Mozambican coast, conducted over a 5-year period, documented the highest densities of whale sharks to occur within a ~200 km long stretch of the Inhambane Province, with a pronounced hotspot adjacent to Praia do Tofo. We tagged 15 juvenile whale sharks with SPOT5 satellite tags off Praia do Tofo and tracked them for 1–87 days (mean = 26 days) as they dispersed from this area. Sharks travelled between 10 and 2,737 km (mean = 738 km) at a mean horizontal speed of 29 ± 30.7 SD km day-1. While several individuals left shelf waters and travelled across international boundaries, most sharks stayed in Mozambican coastal waters over the tracking period. We tested for whale shark habitat preferences, using sea surface temperature, chlorophyll-a concentration and water depth as variables, by computing 100 random model tracks for each real shark based on their empirical movement characteristics. Whale sharks spent significantly more time in cooler, shallower water with higher chlorophyll-a concentrations than model sharks, suggesting that feeding in productive coastal waters is an important driver of their movements. Our results show that, while whale sharks are capable of long-distance oceanic movements, they can spend a disproportionate amount of time in specific areas. The increasing use of large-mesh gill nets in this coastal hotspot for whale sharks is a clear threat to regional populations of this iconic species.
How do we transition from non-coding to coding?
Authors: Ruiz-Orera Jorge , Villanueva-Cañas José Luis , Blevins William , Albà M.Mar
Published: January 2018

Recent years have witnessed the discovery of protein–coding genes which appear to have evolved de novo from previously non-coding sequences. This has changed the long-standing view that coding sequences can only evolve from other coding sequences. However, there are still many open questions regarding how new protein-coding sequences can arise from non-genic DNA.

Two prerequisites for the birth of a new functional protein-coding gene are that the corresponding DNA fragment is transcribed and that it is also translated. Transcription is known to be pervasive in the genome, producing a large number of transcripts that do not correspond to conserved protein-coding genes, and which are usually annotated as long non-coding RNAs (lncRNA). Recently, sequencing of ribosome protected fragments (Ribo-Seq) has provided evidence that many of these transcripts actually translate small proteins. We have used mouse non-synonymous and synonymous variation data to estimate the strength of purifying selection acting on the translated open reading frames (ORFs). Whereas a subset of the lncRNAs are likely to actually be true protein-coding genes (and thus previously misclassified), the bulk of lncRNAs code for proteins which show variation patterns consistent with neutral evolution. We also show that the ORFs that have a more favorable, coding-like, sequence composition are more likely to be translated than other ORFs in lncRNAs. This study provides strong evidence that there is a large and ever-changing reservoir of lowly abundant proteins; some of these peptides may become useful and act as seeds for de novo gene evolution.
A Virtual Environment-based Training System for the Blind Wheelchair User through use of 3D Audio Supported by EEG
Authors: de Souza Everton S , Lamounier Edgard EL , Cardoso Alexandre AC
Published: January 2018

Many difficulties are encountered by people with disabilities, especially when a diagnosis is made up of more than one dysfunction, as is the case of visually impaired wheelchair users. In fact, this scenario generates a degree of incapacity in terms of the performing of basic activities on the part of the wheelchair user. The treatment of disabled patients is performed in an individualized manner according to their particular clinical aspects. People with visual and motor disabilities are restricted in independent navigation. In this navigation scenario, there is a requirement for interaction, this requirement justifies the use of Virtual Reality (VR). In addition, locomotion needs to possess natural control, in order to be successfully incorporated. Based on such a condition, Electroencephalography (EEG) has shown great advances in the area of health, concerning spontaneous brain signals. This research demonstrates through experiment, the use of a wheelchair adapted with support of VR and EEG for the training of locomotion and individualized interaction of wheelchair users with visual impairment. The objective being to provide efficient interactions, thus allowing social inclusion of patients considered otherwise incapacitated. This project was based on the following criteria natural control, feedback, stimuli and safety. A multi-layer computer rehabilitation system was developed incorporating natural interaction supported by EEG, which activates the movements in the Virtual Environment and real wheelchair through adequately performed experiments. This research consists of elaborating a suitable approach for blind wheelchair user patients. The results demonstrated that the use of Virtual Reality with EEG signals has the potential for improving the quality of life and independence of blind wheelchair users.
Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches
Authors: Woon James Sy-Keen , Mackeen Mukram M , Illias Rosli M , Mahadi Nor M , Broughton William J , Abdul Murad Abdul Munir , Abu Bakar Farah Diba
Published: January 2018

Background. Aspergillus niger along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e. β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A. niger CBH is desirable to increase CBH production yield and also to allow biochemical characterisation of the recombinant CBH from A. niger.

Methods. In this study, the gene encoding a cellobiohydrolase B (cbhB) from A. niger ATCC 10574 was cloned and expressed in the methylotrophic yeast Pichia pastoris X-33. The recombinant CbhB was purified and characterised to study its biochemical and kinetic characteristics. To evaluate the potential of CbhB in assisting biomass conversion, CbhB was supplemented into a commercial cellulase preparation (Cellic® CTec2) and was used to hydrolyse oil palm empty fruit bunch (OPEFB), one of the most abundant lignocellulosic waste from the palm oil industry. To attain maximum saccharification, enzyme loadings were optimised by response surface methodology and the optimum point was validated experimentally. Hydrolysed OPEFB samples were analysed using attenuated total reflectance FTIR spectroscopy (ATR-FTIR) to screen for any compositional changes upon enzymatic treatment.

Results. Recombinant CbhB was over-expressed as a hyperglycosylated protein attached to N-glycans. CbhB was enzymatically active towards soluble substrates such as 4-methylumbelliferyl-β-D-cellobioside (MUC), p-nitrophenyl-cellobioside (pNPC) and p-nitrophenyl-cellobiotrioside (pNPG3) but was not active towards crystalline substrates like Avicel® and Sigmacell cellulose. Characterisation of purified CbhB using MUC as the model substrate revealed that optimum catalysis occurred at 50 oC and pH 4 but the enzyme was stable between pH 3 to 10 and 30 to 80 oC. Although CbhB on its own was unable to digest crystalline substrates, supplementation of CbhB (0.37%) with Cellic® CTec2 (30%) increased saccharification of OPEFB by 27%. Compositional analyses of the treated OPEFB samples revealed that CbhB complementation reduced peak intensities of both crystalline cellulose Iα and Iβ in the treated OPEFB samples.

Discussion. Since CbhB alone was inactive against crystalline cellulose, these data suggested that it might work synergistically with other components of Cellic® CTec2. CbhB supplements were desirable as they further increased hydrolysis of OPEFB when the performance of Cellic® CTec2 was theoretically capped at an enzyme loading of 34% in this study. Hence, A. niger CbhB was identified as a potential supplementary enzyme for the enzymatic hydrolysis of OPEFB.