bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioral decoding of Drosophila locomotion in a circular arena
Authors: Qiu Shuang , Xiao Chengfeng
Published: January 2018

Motion detection and position tracking of animal behavior over a period of time produce massive amount of information, but analysis and interpretation of such huge datasets are challenging. Here we describe statistical methods to extract major movement structures of Drosophila locomotion in a circular arena, and examine the effects of pulsed light stimulation on these identified locomotor structures. Drosophila adults performed exploratory behavior when restrained individually in the circular arenas (1.27 cm diameter 0.3 cm depth). Measures of the distance to the center of the arena followed a gumbel distribution with mixed components. Representation learning of distance to center from 177,000 observations (from 63 controls and 55 flies with pulsed light stimulation) revealed three major movement components, indicating three locomotor structures characterized as: side-wall walk, angle walk and cross of the central region. Pulsed flies showed reduced cross of the central region compared with controls. We also showed that counter-clockwise walk and clockwise walk were the two major rotation behaviors with equal time proportion. There was a peak relative turning angle at 25.6o for counter-clockwise walk, and 334.4o for clockwise walk. Regression analysis of relative turning angle as a function of distance to center indicated that as distance to center increased, flies switched turning from directions for perimeter-returning to directions for major rotation. Pulsed flies reduced trajectories that had irregular circle-shape and increased trajectories with regular circle-shape during rotation. Taken together, we present a feasible approach to extract major locomotor structures of Drosophila locomotion in a circular arena, and demonstrate how pulsed light stimulation increased the regularity of locomotor trajectory.
The biochronology and palaeobiogeography of Baru (Crocodilia: Mekosuchinae) based on new specimens from the Northern Territory and Queensland, Australia
Authors: Yates Adam M
Published: January 2018

New records of the Oligo-Miocene mekosuchine crocodilian, Baru, from Queensland and the Northern Territory are described. B. wickeni and B. darrowi are accepted as valid species in the genus and their diagnoses are revised. Both species are present in Queensland and the Northern Territory but are restricted in time, with B. wickeni known from the late Oligocene and B. darrowi from the middle Miocene. The broad geographic distributions and restricted time spans of these species indicate that this genus is useful for biochronology. The record of B. wickeni from the Pwerte Marnte Marnte Local Fauna in the Northern Territory establishes that the species inhabited the north-western margin of the Lake Eyre Basin drainage system. More southerly Oligo-Miocene sites in the Lake Eyre Basin contain only one crocodilian species, Australosuchus clarkae. The Pwerte Marnte Marnte occurrence of B. wickeni indicates that the separation of Baru and Australosuchus did not correspond with the boundaries of drainage basins and that palaeolatitude was a more likely segregating factor.
Factors influencing healthcare provider respondent fatigue answering a globally administered in-app survey
Authors: O'Reilly-Shah Vikas N
Published: January 2018

Background: Respondent fatigue, also known as survey fatigue, is a common problem in the collection of survey data. Factors that are known to influence respondent fatigue include survey length, survey topic, question complexity, and open-ended question type. There is a great deal of interest in understanding the drivers of physician survey responsiveness due to the value of information received from these practitioners. With the recent explosion of mobile smartphone technology 7, it has been possible to obtain survey data from users of mobile applications (apps) on a question-by-question basis. We obtained basic demographic survey data as well as survey data related to an anesthesiology-specific drug called sugammadex and leveraged nonresponse rates to examine factors that influenced respondent fatigue.

Methods: Primary data were collected between December 2015 and February 2017. Surveys and in-app analytics were collected from global users of a mobile anesthesia calculator app. Key independent variables were user country, healthcare provider role, rating of importance of the app to personal practice, length of time in practice, and frequency of app use. Key dependent variable was the metric of respondent fatigue.

Results: Provider role and World Bank country income level were predictive of the rate of respondent fatigue for this in-app survey. Importance of the app to the provider and length of time in practice were moderately associated with fatigue. Frequency of app use was not associated. This study focused on a survey with a topic closely related to the subject area of the app. Respondent fatigue rates will likely change dramatically if the topic does not align closely,

Discussion: Although apps may serve as powerful platforms for data collection, responses rates to in-app surveys may differ on the basis of important respondent characteristics. Studies should be carefully designed to mitigate fatigue as well as powered with the understanding of the respondent characteristics that may have higher rates of respondent fatigue.
The salivary gland salivation stimulating peptide from Locusta migratoria (Lom-SG-SASP) is not a neuropeptide
Authors: Veenstra Jan A
Published: January 2018

A salivary gland salivation stimulating peptide was identified from the salivary glands of the migratory locust by its ability to stimulate cAMP production in the same tissue. The gene coding for this peptide has recently been shown to code for a precursor consisting of a signal peptide, several copies of the peptide separated by Lys-Arg doublets and a few other peptides. These data are consistent with it being a neuropeptide. However, antiserum raised to this peptide labels the acini of the salivary glands while RT-PCR only gives positive results in the salivary gland, but not in any ganglion of the central nervous system. Thus, this peptide is not a neuropeptide as previously assumed.
Cross-institutional evaluation of a mastoidectomy assessment 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: 65 mastoidectomy performances were evaluated coming from 37 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.
Methodological considerations in assessment of language lateralisation with fMRI: a systematic review
Authors: Bradshaw Abigail R. , Bishop Dorothy V. M. , Woodhead Zoe V. J.
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.
Transcriptomic effects of dispersed oil in a non-model decapod crustacean
Authors: Vazquez-Miranda Hernan , Thoma Brent P , Wong Juliet M , Felder Darryl L , Crandall Keith A , Bracken-Grissom Heather D
Published: January 2018

Background. Oil spills are major environmental disasters. Dispersants help control spills, as they emulsify oil into droplets to speed bioremediation. Although dispersant toxicity is controversial, the genetic consequences and damages of dispersed oil exposure are poorly understood. We used RNA-seq to measure gene expression of flatback mudcrabs (Eurypanopeus depressus, Decapoda, Brachyura, Panopeidae) exposed to dispersed oil. Methods. Our experimental design included two control types, oil-only, and oil-dispersant treatments with three replicates each. We prepared 100 base pair-ended libraries from total RNA and sequenced them in one Illumina HiSeq2000 lane. We assembled a reference transcriptome with all replicates per treatment, assessed quality with novel metrics, identified transcripts, and quantified gene expression with open source software. Results. Our mudcrab transcriptome included 500,008 transcripts from 347,082,962 pair-end raw reads. In oil-only treatments, we found few significant differences. However, in oil-dispersant treatments, over 4000 genes involved with cellular differentiation, primordial cellular component upkeep, apoptosis, and immune response were downregulated. A few muscle structure and development genes were upregulated. Discussion. Our results provide evidence that exposure to chemically dispersed oil causes a generalized cellular shutdown and muscular repair attempts. Our results suggest current oil-spill treatment procedures could be detrimental to crustaceans and indicate additional research is needed to evaluate the impact of oil spills in gene expression. Finally, traditional quality metrics such as N50s have limitations to explain the nature of RNA-seq compared to new methods in non-model decapod crustaceans.
Long-term changes in the susceptibility of corals to thermal stress around Phuket, Thailand
Authors: Putchim Lalita , Phongsuwan Niphon , Yaemarunpattana Chaimongkol , Thongtham Nalinee , Richter Claudio
Published: January 2018

The bleaching susceptibility of 28 coral taxa around southern Phuket was examined in four natural major bleaching events, in 1991, 1995, 2010, and 2016. Surveys were conducted by line intercept and belt transect methods. All coral colonies were identified to genus or species-level and their pigmentation status was assessed as: (1) fully pigmented (i.e. no bleaching), (2) pale (loss of colour), (3) fully bleached, and (4) recently dead as a result of bleaching-induced mortality. Bleaching and mortality indices were calculated to compare bleaching susceptibility among coral taxa. In 2016 some of the formerly bleaching susceptible coral taxa (e.g. Acropora, Montipora, Echinopora, and Pocillopora damicornis) showed far greater tolerance to elevated sea water temperature than in previous years. In P. damicornis the higher bleaching resistance encompassed all sizes from juveniles (<5cm) to adults (>30cm). In contrast, some of the formerly bleaching-resistant corals (e.g. the massive Porites, Goniastrea, Dipsastraea, and Favites) became more susceptible to bleaching over repeated thermal stress events. Our results support the hypothesis that some of the fast-growing branching corals (Acropora, Montipora, and Pocillopora) may have life-history traits that lead to more rapid adaptation to a changed environment than certain growing massive species.
First de-novo transcriptome assembly of a South American frog, Oreobates cruralis, enables population genomic studies of Neotropical amphibians
Authors: Montero-Mendieta Santiago , Grabherr Manfred , Lantz Henrik , De la Riva Ignacio , Leonard Jennifer A , Webster Matthew T , Vilà Carles
Published: January 2018

Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome to facilitate assembly and the transcriptome sequence must be assembled de-novo. We used RNA-seq to obtain the transcriptome profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a workflow to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our workflow guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/PRACTICAL-GUIDE-TO-BUILD-DE-NOVO-TRANSCRIPTOME-ASSEMBLIES-FOR-NON-MODEL-ORGANISMS/wiki
Detection of waterholes by Vegetation Index in the habitat of bighorn sheep (Ovis Canadensis) in Baja California
Authors: Escobar-Flores Jonathan Gabriel , Torres Jorge , Valdez Raúl , Álvarez Cárdenas Sergio , Galina Tessaro Patricia , Sandoval Sarahi
Published: January 2018

The desert bighorn sheep is adapted to the extreme conditions of arid ecosystems. The amount and distribution of watering holes is an essential component of the habitat of this species. With information provided by people in Sierra Santa Isabel a database of potential sites watering sites was obtained, which was taken as reference of spectral information for water and vegetation. Two images of Landsat 8-OLI were processed; the first corresponded to the end of the drought and the second rainy season of 2013. A false-color composite was made between bands where water has an absorption behavior (band 5 and 7) and a Normalized Difference Vegetation Index (NDVI). Field visits to the existence of 15 watering holes of which 11 had evidence of use by the bighorn were confirmed. The abundance of plant species Tamarix ramosissima, Juncus acutus, Typha domingensis and Psorathamnus spinosus contributed substantially NDVI values and facilitated the detection of watering holes.
Integrating active learning and crowdsourcing into large-scale supervised landcover mapping algorithms
Authors: Debats Stephanie R , Estes Lyndon D , Thompson David R , Caylor Kelly K
Published: January 2018

Sub-Saharan Africa and other developing regions of the world are dominated by smallholder farms, which are characterized by small, heterogeneous, and often indistinct field patterns. In previous work, we developed an algorithm for mapping both smallholder and commercial agricultural fields that includes efficient extraction of a vast set of simple, highly correlated, and interdependent features, followed by a random forest classifier. In this paper, we demonstrated how active learning can be incorporated in the algorithm to create smaller, more efficient training data sets, which reduced computational resources, minimized the need for humans to hand-label data, and boosted performance. We designed a patch-based uncertainty metric to drive the active learning framework, based on the regular grid of a crowdsourcing platform, and demonstrated how subject matter experts can be replaced with fleets of crowdsourcing workers. Our active learning algorithm achieved similar performance as an algorithm trained with randomly selected data, but with 62% less data samples.
Can editors save peer review from peer reviewers?
Authors: D'Andrea Rafael , O'Dwyer James P
Published: January 2018

Peer review is the gold standard for scientific communication, but its ability to guarantee the quality of published research remains difficult to verify. Recent modeling studies suggest that peer review is sensitive to reviewer misbehavior, and it has been claimed that referees who sabotage work they perceive as competition may severely undermine the quality of publications. Here we examine which aspects of suboptimal reviewing practices most strongly impact quality, and test different mitigating strategies that editors may employ to counter them. We find that the biggest hazard to the quality of published literature is not selfish rejection of high-quality manuscripts but indifferent acceptance of low-quality ones. Bypassing or blacklisting bad reviewers and consulting additional reviewers to settle disagreements can reduce but not eliminate the impact. The other editorial strategies we tested do not significantly improve quality, but pairing manuscripts to reviewers unlikely to selfishly reject them and allowing revision of rejected manuscripts minimize rejection of above-average manuscripts. In its current form, peer review offers few incentives for impartial reviewing efforts. Editors can help, but structural changes are more likely to have a stronger impact.
A possible linear filtering model to explain White’s illusion at different grating widths
Authors: Mitra Soma , Mazumdar Deabasis , Ghosh Kuntal , Bhaumik Kamales
Published: January 2018

The perceived lightness of a stimulus depends on its background, a phenomenon known as lightness induction. For instance, the same gray stimulus can look light in one background and dark in another. Moreover, such induction can take place in two directions; in one case, it occurs in the direction of the background lightness known as lightness assimilation, while in the other it occurs opposite to that, known as lightness contrast. The White’s illusion is a typical one which does not completely conform to any of these two processes. In this paper, we have quantified the perceptual strength of the White’s illusion as a function of the width of the background square grating. Based on our results which also corroborate some earlier studies, we propose a linear filtering model inspired from an earlier work dealing with varying Mach band widths. Our model assumes that the for the White’s illusion, where the edges are strong and many in number, and as such the spectrum is rich in high frequency components, the inhibitory surround in the classical Difference-of-Gaussians (DoG) filter gets suppressed, so that the filter essentially reduces to a multi-scale Gaussian one. The simulation results with this model support the present as well as earlier experimental results.
Advances in studying brain morphology: The benefits of open-access data
Authors: Madan Christopher R
Published: January 2018

Until recently, neuroimaging data for a research study needed to be collected within one’s own lab. However, when studying inter-individual differences in brain structure, a large sample of participants is necessary. Given the financial costs involved in collecting neuroimaging data from hundreds or thousands of participants, large-scale studies of brain morphology could previously only be conducted by well-funded laboratories with access to MRI facilities and to large samples of participants. With the advent of broad open-access data-sharing initiatives, this has recently changed–here the primary goal of the study is to collect large datasets to be shared, rather than sharing of the data as an afterthought. This paradigm shift is evident as increase in the pace of discovery, leading to a rapid rate of advances in our characterization of brain structure. The utility of open-access brain morphology data is numerous, ranging from observing novel patterns of age-related differences in subcortical structures to the development of more robust cortical parcellation atlases, with these advances being translatable to improved methods for characterizing clinical disorders (see Figure 1 for an illustration). Moreover, structural MRIs are generally more robust than functional MRIs, relative to potential artifacts and in being not task-dependent, resulting in large potential yields. While the benefits of open-access data have been discussed more broadly within the field of cognitive neuroscience elsewhere (Gilmore et al., 2017; Poldrack and Gorgolewski, 2014; Van Horn and Gazzaniga, 2013; Voytek, 2016), as well as in other fields (Ascoli et al., 2017; Choudhury et al., 2014; Davies et al., 2017), the current paper is focused specifically on the implications of open data to brain morphology research.
Influence of sea cucumbers on chromophoric of dissolved organic matter in multitrophic aquaculture tanks
Authors: Sadeghi-Nassaj Seyed Mohammad , Catalá Teresa S. , Álvarez Pedro A. , Reche Isabel
Published: January 2018

Background. The effluents of the mono-specific aquaculture contain high concentrations of dissolved nutrients and organic matter, which affect negatively water quality of the recipient aquatic ecosystems. A key feature of water quality is its transparency. Chromophoric dissolved organic matter (CDOM) determines most of the light transmission in the ultraviolet and blue bands in the aquatic ecosystems. A sustainable alternative to mono-specific aquaculture is the integrated multitrophic aquaculture that includes species trophically complementary named “extractive” species. Sea cucumbers are recognized as efficient extractive species, with a high potential to improve water quality, due to the consumption of particulate organic matter (POM). However, the effects of sea cucumbers on CDOM are still unknown. Methods. During one year, we biweekly monitored CDOM in two aquaculture tanks with different trophic structure. One of the tanks (-holothurian tank) only contained the primary species, Anemonia sulcata, whereas the other tank (+ holothurian tank) also contained individuals of Holothuria tubulosa and H. forskali. We routinely performed CDOM absorption spectra from 200 nm to 750 nm and determined quantitative (absorption coefficients at 325 nm) and qualitative (spectral slopes and molar absorption coefficients at 325 nm) optical parameters in the inlet waters, in the tanks, and in their corresponding effluents. Results. Absorption coefficients at 325 nm (a325) and spectral slopes from 275 to 295 nm (S275-295) were significantly lower in the effluents of the +holothurian tank (average: 0.33 and 16 μm-1, respectively) than in the effluents of the −holothurian tank (average: 0.69 m-1 and 34 μm-1, respectively), being the former similar to those found in the inlet waters (average: 0.32 m-1 and 22 μm-1, respectively). This reduction in CDOM absorption appears to be mediated by the POM consumption by the holothurians. The reduction of POM concentration in the +holothurian tank may weaken the process of POM disaggregation into dissolved organic matter, which ultimately might have generated CDOM in the –holothurian tank. Discussion. Extractive species such as holothurians improve water transparency through POM consumption, likely because reduces POM disaggregation into CDOM. We suggest that CDOM monitoring in aquaculture facilities, using automatic probes or even remote sensing, could be a useful tool to trace the effectiveness of extractive species at large scales of time and space.
Ginsenoside Rk1 bioactivity: A systematic review
Authors: Elshafay Abdelrahman , Tinh Ngo Xuan , Salman Samar , Shaheen Yara Saber , Othman Eman Bashir , Elhady Mohamed Tamer , Kansakar Aswin Ratna , Tran Linh , Van Le , Hirayama Kenji , Huy Nguyen Tien
Published: January 2018

Abstract Ginsenoside Rk1 (G-Rk1) is one of the unique components created by processing ginseng at high temperature, in particular of Sun Ginseng (SG). The aim of our study was to systematically review the pharmacological effects of G-Rk1.we conducted our search in eight databases and searched manually to select in vivo and in vitro original studies that provided information about biological pharmaceutical effects of G-Rk1 and were published up to August 2015 with no restriction in language or study design. We retrieved 21 eligible papers out of 121 identified ones. Some studies confirmed the G-Rk1 anticancer effects by investigating “cell viability”, “cell proliferation inhibition”, “apoptotic activity”, “anticancer activity” and “effects of G-Rk1 on G1 phase and autophagy in tumor cells” either alone or in combination with G-Rg5. Others proved that it has anti-platelet aggregation activities and anti-inflammatory effects, enhances cognitive function, reduces lipid accumulation and prevents osteoporosis. In conclusion, G-Rk1 has a significant anti-tumor effect of liver cancer, melanoma, and gastric cancer. Additionally, G-Rk1 has demonstrated as anti-platelet aggregation, anti-inflammatory, and anti-lipid accumulation. All these results corroborate the clinical effects of G-Rk1 and demonstrate the potential possibility to develop G-Rk1-based treatments, either alone or in combination with G-Rg5, with previously mentioned conditions.
Spider World Records: a resource for using organismal biology as a hook for science learning
Authors: Mammola Stefano , Michalik Peter , Hebets Eileen A , Isaia Marco
Published: January 2018

The public reputation of spiders is that they are deadly poisonous, brown and nondescript, and hairy and ugly. There are tales describing how they lay eggs in human skin, frequent toilet seats in airports, and crawl into your mouth when you are sleeping. Misinformation about spiders in the popular media and on the World Wide Web is rampant, leading to distorted perceptions and negative feelings about spiders. Despite these negative feelings, however, spiders offer intrigue and mystery and can be used to effectively engage even arachnophobic individuals. As such, we contend that spider biology can be a convincing hook for engaging people of all ages in science-related learning. Towards this end, and in order to provide an enthusiastic knowledge base for spider-related learning, we provide essential information about spider biology followed by a compilation of Spider World Records. We choose a world-record style format, as it is known to be an effective tool of engaging youth and adults alike. We group our records into the categories of Taxonomy, Morphology/Physiology and Ecology/Behaviour. We further reported on curiosities and clarify fake news about these underappreciated animals. Our contribution is specifically aimed to raise public awareness and attractiveness of spiders, meanwhile providing the first official knowledge base for world spider records.
Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina
Authors: Blevins William , Albà Mar , Carey Lucas
Published: January 2018

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology with other genes. Furthermore, de novo genes may not initially be under the same selective constraints as other genes. Dozens of de novo genes have recently been identified in many diverse species; however, the mechanisms leading to their appearance are not yet well understood. To study this phenomenon, we have performed deep RNA sequencing (RNA-seq) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. Furthermore, we performed ribosome profiling (Ribo-seq) experiments in both conditions with S. cerevisiae. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (unannotated), and many were identified as putative de novo genes; these candidates were then tested for signals of translation using our Ribo-seq data. We show that putative de novo genes have different properties relative to phylogenetically conserved genes. This comparative phylotranscriptomic analysis advances our understanding of de novo gene origins.
Short COI markers for freshwater macroinvertebrate metabarcoding
Authors: Vamos Ecaterina Edith , Elbrecht Vasco , Leese Florian
Published: January 2018

Species diversity of metazoan bulk samples can be rapidly assessed using cytochrome c oxidase I (COI) metabarcoding. However, in some applications often only degraded DNA is available, e.g. from poorly conserved museum specimens, environmental DNA (eDNA) filtered from water or gut content analyses. Here universal primer sets targeting only a short COI fragment are advantageous, as they often can still amplify short DNA fragments. Using PrimerMiner, we optimised two universal primer sets targeting freshwater macroinvertebrates based on NCBI and BOLD reference sequences. The fwh1 and fwh2 primer sets targeting a 178 and 205 bp region were tested in vitro by sequencing previously used freshwater macroinvertebrate mock communities as well as three monitoring samples from Romanian streams of unknown composition. They were further evaluated in silico for their suitability to amplify other insect groups. The fwh1 primer sets showed the most consistent amplification in silico and in vitro , detecting 92% of the taxa present in the mock communities, and allowing clear differentiation between the three macroinvertebrate communities from the Romanian streams. In silico analysis indicates that the short primers are likely to perform well even for non-freshwater insects. Comparing the performance of the new fwh1 primer sets to a highly degenerate primer set targeting a longer fragment (BF2+BR2) revealed that detection efficiency is slightly lower for the new primer set. Nevertheless, the shorter new primer pairs might be useful for studies that have to rely on degraded or poorly conserved DNA and thus be of importance for biomonitoring, conservation biological or molecular ecological studies. Furthermore, our study highlights the need for in silico evaluation of primer sets in order to detect design errors in primers (fwhR2) and find optimal universal primer sets for the target taxa of interest.
The Missing landscape of human genomic diversity in the Arabian Peninsula
Authors: Bakhsh Njlaa , Jackson Fatimah , Jackson Latifa , cross Christopher
Published: January 2018

The Arabian Peninsula (AP) is the first site of human migration and habitation outside of Africa. As a major crossroad for human populations, the AP provides an opportunity to better understand early to modern changes in human demographic patterns through selections, admixture, gene flow, and migration. Dramatic climatic fluctuations have been recorded in the AP that contributed to contractions and expansions in water availability. These climatological perturbations are thought to have shaped genomic variations in this population. Recent reports indicate that a number of Arab nation-states have committed significant resources to genetically type the national population, with the overall goal of determining the degree of genomic diversity in the AP. We sought to characterize currently typed genomic variation in Arabian populations to support the rationale for our proposed analyses of Saudi Arabian genomic diversity. Interestingly, in contrast to published claims , a comprehensive search of peer-reviewed reports on genomic analysis (N=20 papers) revealed no genomic data from four national genomic projects (Qatar, Saudi Arabia, Kuwait, and The United Arab Emirates). Our analysis demonstrates that while much fanfare and presumably resources have been devoted to defining the genomic landscape of the Arabian peoples, little actual data is available to either substantiate or support such an investment.
BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters
Authors: Cheng Gong , Lu Quan , Ma Ling , Zhang Guocai , Xu Liang , Zhou Zongshan
Published: January 2018

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists, and thus its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, governmental, and private owners in Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker to analyze and visualize pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various public biological databases. This step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.
Skin temperature and reproductive condition in wild female chimpanzees
Authors: Dezecache Guillaume , Wilke Claudia , Richi Nathalie , Neumann Christof , Zuberbühler Klaus
Published: January 2018

Infrared thermal imaging has emerged as a valuable tool in veterinary medicine, in particular in evaluating reproductive processes. Here, we explored differences in skin temperature of cycling and pregnant wild chimpanzee females in Budongo Forest, Uganda. Based on previous literature, we predicted increased skin temperature when approaching peak fertility at the area of the reproductive organs of cycling females. For pregnant females, we made the same prediction, mainly because it has been argued that chimpanzee females have evolved mechanisms to conceal pregnancy, including exaggerated sexual swelling and sexually conspicuous vocal behaviour, and to encourage male mating behaviour in order to decrease their infanticidal tendencies by confusing paternity. Overall, we found only small changes in cycling females, with slight temperature increases towards the end of the swelling cycles but no overall increase in skin temperature between oestrous and non-oestrous phases. Interestingly, however, pregnant and cycling females had very similar skin temperatures. These results suggest that males cannot use skin temperature to discriminate between pregnant and non-pregnant/cycling females during maximal swelling, when ovulation is most likely to occur in cycling females. This pattern may be linked to the evolution of physiological means to conceal reproductive state in pregnant females.
Tissue material properties and computational modelling of the human knee: A critical review
Authors: Peters Abby E , Akhtar Riaz , Comerford Eithne J , Bates Karl T
Published: January 2018

Understanding how structural and functional alterations of individual tissues impact on whole-joint function is challenging, particularly in humans where direct invasive experimentation is difficult. Finite element computational models produce quantitative predictions of the mechanical and physiological behaviour of multiple tissues simultaneously, thereby providing a means to study changes that occur through healthy ageing and disease such as osteoarthritis. As a result significant research investment has been placed in developing such models of the human knee. Previous work has highlighted that model predictions are highly sensitive to the various inputs used to build them, particularly the mathematical definition of material properties of biological tissues. The goal of this systematic review is two-fold. First, we provide a comprehensive summation and evaluation of existing material property data for human knee joint tissues, tabulating numerical values as a reference resource for future studies. Second, we review efforts to model whole-knee joint mechanical behaviour through finite element modelling with particular focus on how studies have sourced tissue material properties. The last decade has seen a renaissance in material testing fueled by development of a variety of new engineering techniques that allow the mechanical behaviour of both soft and hard tissues to be characterised at a spectrum of scales from nano- to bulk tissue level. As a result there now exists an extremely broad range of published values for human knee tissues. However, our systematic review highlights gaps and ambiguities that mean quantitative understanding of how tissue material properties alter with age and osteoarthritis is limited. It is therefore currently challenging to construct finite element models of the knee that are truly representative of a specific age or disease-state. Consequently, recent whole-joint finite element models have been highly generic in terms of material properties even relying on non-human data from multiple species. We highlight this by critically evaluating current ability to quantitatively compare and model 1) young and old and 2) healthy and osteoarthritis human knee joints. We suggest that future research into both healthy and diseased knee function will benefit greatly from a subject- or cohort-specific approach in which finite element models are constructed using material properties, medical imagery and loading data from cohorts with consistent demographics and/or disease states.
Steep declines in sightings of manta rays and devilrays (Mobulidae) in southern Mozambique
Authors: Rohner Christoph A. , Flam Anna L , Pierce Simon J , Marshall Andrea D
Published: January 2018

Mobulid rays are one of the most vulnerable chondrichthyan groups due to their low population growth rates and high susceptibility to fisheries. While estimates of human-induced mortality are lacking, sighting trend data can provide an index of their status. We recorded underwater sightings data of Mobula alfredi, M. birostris and M. kuhlii over a 14-year period in southern Mozambique. Generalised linear models were used to standardise sightings and adjust for influences other than time. Standardised sightings of the three species, individually, declined by >90%. Declines in sightings were driven primarily by a rapid decrease between 2003–2007, although the declines continued to 2016. While environmental variables did influence sightings, they did not explain this steep decline over time. Increasing mortality from fisheries is likely to have played a significant role in the declining sightings of these vulnerable species.
North Atlantic Oscillation drives the annual occurrence of an isolated, peripheral population of the brown seaweed Fucus guiryi in the Western Mediterranean Sea
Authors: Melero Ignacio , Salvo A. Enrique , Báez José Carlos , Bañares-España Elena , Reul Andreas , Flores-Moya Antonio
Published: January 2018

The intertidal brown seaweed Fucus guiryi is distributed in the cold-temperate and warm-temperate coasts of Europe and North Africa. Curiously, an isolated population develops at Punta Calaburras (Alboran Sea, Western Mediterranean) but its presence is not permanent throughout the years, unlike the closest (ca. 80 km), perennial populations at the Strait of Gibraltar. The presence of the alga at Punta Calaburras is supposed to be due to the influence of the permanent Atlantic jet coming from the Atlantic Ocean into the Mediterranean. A twenty six years’ time series (from 1990 to 2015) of occurrence of F. guiryi at Punta Calaburras has been analysed by correlating with oceanographic (sea surface temperature, an estimator of the Atlantic jet power) and climatic factors (air temperature, rainfall, and North Atlantic Oscillation –NAO-, and Arctic Oscillation –AO- indexes). The occurrence of the alga aggregated from 1990-1994 and 1999-2004, with sporadic events in 2006 and 2011. Binary logistic regression showed that the occurrence of the alga at Punta Calaburras is favoured under positive NAO index from April to June. It has been hypothesized that the isolated population of F. guiryi should show greater stress than their congeners of permanent populations, and to this end, two approaches were used to evaluate stress: one based on the integrated response to ontogeny (developmental instability, based on measurements of the fractral pattern of algal thalli) and another based on the photosynthetic response. However, the only significant differences detected were in photosynthetic quantum yield and water loss under emersion conditions. In conclusion, this study demonstrates the teleconnection between atmospheric oscillations and survival and proliferation of marine macroalgae, an aspect practically unknown before.
Use and misuse of temperature normalisation in meta-analyses of thermal responses of biological traits
Authors: Kontopoulos Dimitrios - Georgios , García-Carreras Bernardo , Sal Sofía , Smith Thomas P. , Pawar Samraat
Published: January 2018

There is currently unprecedented interest in quantifying variation in thermal physiology among organisms in order to understand and predict the biological impacts of climate change. A key parameter in this quantification of thermal physiology is the performance or value of a trait, across individuals or species, at a common temperature (temperature normalisation). An increasingly popular model for fitting thermal performance curves to data – the Sharpe-Schoolfield equation – can yield strongly inflated estimates of temperature-normalised trait values. These deviations occur whenever a key thermodynamic assumption of the model is violated, i.e. when the enzyme governing the performance of the trait is not fully functional at the chosen reference temperature. Using data on 1,758 thermal performance curves across a wide range of species, we identify the conditions that exacerbate this inflation. We then demonstrate that these biases can compromise tests to detect metabolic cold adaptation, which requires comparison of fitness or trait performance of different species or genotypes at some fixed low temperature. Finally, we suggest alternative methods for obtaining unbiased estimates of temperature-normalised trait values for meta-analyses of thermal performance across species in climate change impact studies.
Patterns in artisanal coral reef fisheries reveal best practices for monitoring and management
Authors: Delaney David G , Teneva Lida T , Stamoulis Kostantinos A , Giddens Jonatha L , Koike Haruko , Ogawa Tom , Friedlander Alan M , Kittinger John N
Published: January 2018

Sustainable fisheries management is key to restoring and maintaining ecological function and benefits to people, but it requires accurate information about patterns in resource use, particularly fishing pressure. In most coral reef fisheries and other data-poor contexts, obtaining such information is challenging and remains an impediment to effective management. We developed the most comprehensive regional view of shore-based fishing effort and catch for the Hawaiian Islands to show detailed fishing patterns from across the main Hawaiian Islands (MHI). We reveal these regional patterns through fisher “creel” surveys conducted through collaborative efforts by local communities, state agencies, academics, and environmental organizations, at 18 sites and comprising >10,000 hr of monitoring across a range of habitats and human influences throughout the MHI. Here, we document spatial patterns in nearshore fisheries catch, effort, catch rates (i.e., catch-per-unit-effort [CPUE]), and catch disposition (i.e., use of fish after catch is landed). Line fishing was consistently the most commonly employed gear type (94%), followed by net fishing. The most efficient gear types (i.e., higher CPUE) were spear (0.64 kg hr-1), followed closely by net (0.61 kg hr-1), with CPUE for line (0.16 kg hr-1) 3.9 times lower than spear and 3.7 times lower than net. Creel surveys also reveal rampant illegal fishing activity across the studied locations. Surprisingly, overall, most of the catch was not sold, but rather retained for home consumption or given away to extended family, which indicates that cultural and food security may be stronger drivers of fishing effort than commercial exploitation for nearshore coral reef fisheries in Hawai‘i. Increased monitoring of spatial patterns in nearshore fisheries can inform targeted management, in order to maintain these fisheries for local communities’ food security, cultural, and ecological value.
Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary
Authors: Wu Dong-Mei , Wang Jian-Xin , Liu Xiao-Hui , Fan Ying-Ping , Jiang Ran , Liu Ming-Hua , Wang Shuai-Bing , Liu Xue-Zhu ,   Zhejiang Ocean University
Marine Science and Technology College
No.1, Haida South Road, Lincheng Changzhi Island
Published: January 2018

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.