bluuebunny/crossref_metadata_2025 huggingface dataset:
Strong genetic structure among coral populations within a conservation priority region, the Bird's Head Seascape (Papua and West Papua, Indonesia)
Authors: Starger Craig J , Barber Paul H , Erdmann Mark V , Toha Abdul H. A. , Baker Andrew C
Published: January 2018

Marine Protected Areas (MPAs) are widely considered to be one of the best strategies available for protecting species diversity and ecosystem processes in marine environments, particularly in developing, tropical nations. While data on connectivity and genetic structure of marine populations are critical to designing appropriately sized and spaced networks of MPAs, such data are rarely available. Here we present an assessment of genetic structure in reef-building corals from Papua and West Papua, Indonesia, among the most biologically diverse and least disturbed coral reef regions in the world, and the focus of the multi-institutional Bird's Head Seascape initiative to design and implement a functional network of MPAs. Microsatellite variation was assessed within and among populations of Pocillopora damicornis (Linnaeus , 1758) and Seriatopora hystrix (Dana 1846) (family: Pocilloporidae) from three regions, each currently under a different conservation regime: Teluk Cenderawasih, Raja Ampat, and southwest Papua. Analyses of molecular variance, assignment tests, and genetical bandwidth mapping revealed significant local-scale structure in both species, and a lack of regional filters to gene flow. Overall, P. damicornis populations were less structured (FST = 0.139, p < 0.00001) than those of S. hystrix (FST = 0.357, p < 0.00001). In order to maintain connectivity within and among regions, coral reef conservation on the local scale is needed. These data have been directly applied to the design of a MPA network in the Bird’s Head Seascape.
Phylogeny of water birds inferred from mitochondrial DNA sequences of nine protein coding genes
Authors: Lkhagvajav Treutlein Tsendsesmee , Gonzalez Javier , Wink Michael
Published: January 2018

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides in length) of 14 water birds, and reconstructed their phylogeny in the context of other taxa across the whole class of birds for which complete mitochondrial DNA (mtDNA) sequences were available. Results: The water bird clade, as defined by Hackett et al. (2008) based on nuclear DNA (ncDNA) sequences, was also found in our study by Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. In both reconstruction methods, genera belonging to the same family generally clustered together with moderate to high statistical support. Above the family level, we identified three monophyletic groups: one clade consisting of Procellariidae, Hydrobatidae and Diomedeidae, and a second clade consisting of Sulidae, Anhingidae and Phalacrocoracidae, and a third clade consisting of Ardeidae and Threskiornithidae. Discussion: Based on our mtDNA sequence data, we recovered a robust direct sister relationship between Ardeidae and Threskiornithidae for the first time for mtDNA. Our comprehensive phylogenetic reconstructions contribute to the knowledge of higher level relationships within the water birds and provide evolutionary hypotheses for further studies.
Eleutherodactylus frogs show frequency but no temporal partitioning: implications for the acoustic niche hypothesis
Authors: Villanueva-Rivera Luis J
Published: January 2018

Individuals in acoustic communities compete for the use of the sound resource for communication, a problem that can be studied as niche competition. The acoustic niche hypothesis presents a way to study the partitioning of the resource, but the studies have to take into account the three dimensions of this niche: time, acoustic frequency, and space. I used an Automated Digital Recording System to determine the partitioning of time and acoustic frequency of eight frogs of the genus Eleutherodactylus from Puerto Rico. The calling activity was measured using a calling index. The community exhibited no temporal partitioning since most species called at the same time, between sunset and midnight. The species partitioned the acoustic frequency of their signals, which, in addition to the microhabitat partitioning, can provide some insight into how these species deal with the problem. This data also suggest that monitoring projects with this group should take place only before midnight to avoid false negatives.
Data-mining of potential antitubercular activities from molecular ingredients of Traditional Chinese Medicines
Authors: Jamal Salma , Scaria Vinod ,   Open Source Drug Discovery Consortium
Published: January 2018

Background Traditional Chinese medicine encompasses a well established alternate system of medicine based on a broad range of herbal formulations and is practiced extensively in the region for the treatment of a wide variety of diseases. In recent years, several reports describe in depth studies of the molecular ingredients of Traditional Chinese Medicines on the biological activities including anti-bacterial activities. The availability of a well-curated dataset of molecular ingredients of Traditional Chinese Medicines and accurate in-silico cheminformatics models for data mining for antitubercular agents and computational filters to prioritize molecules has prompted us to search for potential hits from these datasets.

Results We used a consensus approach to predict molecules with potential antitubercular activities from a large dataset of molecular ingredients of Traditional Chinese Medicines available in the public domain. We further prioritized 160 molecules based on five computational filters (SMARTSfilter) so as to avoid potentially undesirable molecules. We further examined the molecules for permeability across Mycobacterial cell wall and for potential activities against non-replicating and drug tolerant Mycobacteria. Additional in-depth literature surveys for the reported antitubercular activities of the molecular ingredients and their sources were considered for drawing support to prioritization.

Conclusions Our analysis suggests that datasets of molecular ingredients of Traditional Chinese Medicines offer a new opportunity to mine for potential biological activities. In this report, we suggest a proof-of-concept methodology to prioritize molecules for further experimental assays using a variety of computational tools. We also additionally suggest that a subset of prioritized molecules could be used for evaluation for tuberculosis due to their additional effect against non-replicating tuberculosis as well as the additional hepato-protection offered by the source of these ingredients.
Measurement uncertainties in quantifying aeolian mass flux: Evidence from wind tunnel and field site data
Authors: Poortinga Ate , Keijsers Joep GS , Maroulis Jerry , Visser Saskia M.
Published: January 2018

Aeolian sediment traps are widely used to estimate the total volume of wind-driven sediment transport, but also to study the vertical mass distribution of a saltating sand cloud. The reliability of sediment flux estimations from this data are dependent upon the specific configuration of the measurement compartments and the analysis approach used. In this study, we analyse the uncertainty of these measurements by investigating the vertical cumulative distribution and relative sediment flux derived from both wind tunnel and field studies. Vertical flux data was examined using existing data in combination with a newly acquired dataset; comprising meteorological data and sediment fluxes from six different events, using three customized catchers at Ameland beaches in northern Netherlands. Fast-temporal data collected in a wind tunnel shows that the median transport height has a scattered pattern between impact and fluid threshold, that increases linearly with shear velocities above the fluid threshold. For finer sediment, a larger proportion was transported closer to the surface compared to coarser sediment fractions. It was also shown that errors originating from the distribution of sampling compartments, specifically the location of the lowest sediment trap relative to the surface, can be identified using the relative sediment flux. In the field, surface conditions such as surface moisture, surface crusts or frozen surfaces have a more pronounced but localized effect than shear velocity. Uncertainty in aeolian mass flux estimates can be reduced by placing multiple compartments in closer proximity to the surface.
DNA methylation marks inter-nucleosome linker regions throughout the human genome
Authors: Berman Benjamin P. , Liu Yaping , Kelly Theresa K.
Published: January 2018

Background: Nucleosome organization and DNA methylation are two mechanisms that are important for proper control of mammalian transcription, as well as epigenetic dysregulation associated with cancer. Whole-genome DNA methylation sequencing studies have found that methylation levels in the human genome show periodicities of approximately 190 bp, suggesting a genome-wide relationship between the two marks. A recent report (Chodavarapu et al., 2010) attributed this to higher methylation levels of DNA within nucleosomes. Here, we analyzed a number of published datasets and found a more compelling alternative explanation, namely that methylation levels are highest in linker regions between nucleosomes.

Results: Reanalyzing the data from (Chodavarapu et al., 2010), we found that nucleosome-associated methylation could be strongly confounded by known sequence-related biases of the next-generation sequencing technologies. By accounting for these biases and using an unrelated nucleosome profiling technology, NOMe-seq, we found that genome-wide methylation was actually highest within linker regions occurring between nucleosomes in multi-nucleosome arrays. This effect was consistent among several methylation datasets generated independently using two unrelated methylation assays. Linker-associated methylation was most prominent within long Partially Methylated Domains (PMDs) and the positioned nucleosomes that flank CTCF binding sites. CTCF adjacent nucleosomes retained the correct positioning in regions completely devoid of CpG dinucleotides, suggesting that DNA methylation is not required for proper nucleosomes positioning.

Conclusions: The biological mechanisms responsible for DNA methylation patterns outside of gene promoters remain poorly understood. We identified a significant genome-wide relationship between nucleosome organization and DNA methylation, which can be used to more accurately analyze and understand the epigenetic changes that accompany cancer and other diseases.
Challenges in evaluation of pain and a pre-incisional line block
Authors: McKune Carolyn , Pascoe Peter , Kass Philip H , Lascelles B. Duncan X.
Published: January 2018

Background: Our objective was to test the effectiveness of a local anesthetic line block administered before surgery in reducing postoperative pain scores in dogs undergoing ovariohysterectomy (OVHX). This study was a prospective, randomized, blinded, clinical trial involving 59 healthy female dogs. An algometric pressure-measuring device was used to determine nociceptive threshold, and compared to three subjective pain scales. Group L/B received a line block of lidocaine (4 mg/kg) and bupivacaine (1 mg/kg) subcutaneously in the area of the proposed incision and saline subcutaneously as premedication; group L/BM (positive control) received a similar block and morphine (0.5 mg/kg) subcutaneously for premedication; and group SS (negative control) received a saline line block and saline premedication. Criteria for rescue analgesia were defined before the study. Dogs were assessed prior to surgery, at extubation (time 0) and at 2, 4, 6, 8 and 24 hours post-recovery. The data were analyzed with one-way ANOVA, and a repeated measures ANOVA with one grouping factor and one repeat factor (time). P < 0.05 was considered statistically significant. Results: Pain was so subtle that there were no significant differences between treatment groups with any assessment method, and no significant difference between positive and negative controls. Conclusions: Pain in non-verbal responders is subtle, even in animals with a known painful stimulus. Pre-emptive, intraoperative and post-operative analgesia is necessary regardless of pain score within the first 24 hours. None of the pain scales evaluated were sensitive enough to determine pain in all animals in this study.
A complete, multi-level conformational clustering of antibody complementarity-determining regions
Authors: Nikoloudis Dimitris , Pitts Jim E. , Saldanha José W.
Published: January 2018

Classification of antibody Complementarity-Determining Region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation.
The relative roles of politics and science: William Bateson, black slavery, eugenics and speciation
Authors: Forsdyke Donald R
Published: January 2018

William Bateson’s background and training suggest sympathy with the black emancipation movement. Yet the movement’s success is attributed more to battles between political figures, than between scientists with contending views on the biology of racial differences. Perhaps, in the long term, Bateson’s contributions to slavery andeugenic issues will be seen as no less important than those of politicians. Mendel’sdiscovery of what we now know as “genes” languished until seized upon by Bateson in 1900. For six exhausting years he struggled to win scientific acceptance of these biological character-determining units. Later, he pressed the Mendelian message home to the general public, opposing simplistic applications of Mendelian principles to human affairs, and arguing that minor genic differences that distinguished races – e.g. skin colour – can seldom initiate new species. Indeed, the spark that initiates a divergence into two species can be non-genic. We are one reproductively isolated population, the human species.
Perceived extrinsic mortality risk and reported effort in looking after health: Testing a behavioural ecological prediction
Authors: Pepper Gillian V , Nettle Daniel
Published: January 2018

Socioeconomic gradients in health behaviour are pervasive and well documented. Yet, there is little consensus on their causes. Behavioural ecological theory predicts that, if people of lower socioeconomic position (SEP) perceive greater personal extrinsic mortality risk than those of higher SEP, they should disinvest in their future health. We surveyed North American adults for reported effort in looking after health, perceived extrinsic and intrinsic mortality risks, and measures of SEP. We examined the relationships between these variables and found that lower subjective SEP predicted lower reported health effort. Lower subjective SEP was also associated with higher perceived extrinsic mortality risk, which in turn predicted lower reported health effort. The effect of subjective SEP on reported health effort was completely mediated by perceived extrinsic mortality risk. Our findings indicate that perceived extrinsic mortality risk may be a key factor underlying SEP gradients in motivation to invest in future health.
A marker circuit to enable recording of auditory evoked potential using a wireless EEG system (EPOC) and a portable computer
Authors: Thie Johnson
Published: January 2018

This paper describes a circuit that enables auditory evoked potential recordings using a wireless EEG device (Emotiv EPOC) and a portable computer as the stimulus machine. The need arises since neither the portable computer nor EPOC has serial/parallel ports to send/receive marker signals that indicate the stimulus onset. The circuit produces a pulse on the EEG channels when it detects an audio stimulus. First it amplifies the audio tones produced by the stimulus machine and detects their envelope. If the envelope exceeds the threshold, it will activate the emitter side of an optocoupler. This in turn switches on the photo-transistor of the optocoupler and produces a pulse that is electrically isolated from the stimulus machine. The pulse's amplitude is reduced to at most 300 microvolts using a voltage divider and is fed to a pair of the EEG channels. The delay between the output pulse and the onset of the 1 kHz audio tone is under 1 ms when the tone is instantly switched on and hence insignificant. Each of the two EEG channels was also biased to DRL via a 4.7 kohm resistor so that it is free from EEG and movement artifact.
With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase
Authors: Silva Pedro J
Published: January 2018

The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe-4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)// B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe-4S], yielding a negatively-charged intermediate. Depending on the rate of Fe-S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe-S cluster re-reduction should be the rate-limiting stage of the process. Poisson-Boltzmann computations on the full enzyme-substrate complex, followed by Monte Carlo simulations of redox and protonation titrations revealed a hitherto unsuspected pH-dependence of the reaction potential of the Fe-S cluster. Furthermore, the computed distributions of protonation states of the His, Asp and Glu residues were used in conjunction with single-point ONIOM computations to obtain, for the first time, the influence of all protonation states of an enzyme on the reaction it catalyzes. Despite exaggerating the ease of reduction of the substrate, these computations confirmed the broad features of the reaction mechanism obtained with the medium-sized models, and afforded valuable insights on the influence of the titratable amino acids on each reaction step. Additional comparisons of the energetic features of the reaction intermediates with those of common biochemical redox intermediates suggest a surprisingly simple explanation for the mechanistic differences between the dark-catalyzed and light-dependent enzyme reaction mechanisms.
Levodopa-stimulated dopamine release in Tourette syndrome
Authors: Black Kevin J , Piccirillo Marilyn L. , Koller Jonathan M. , Hseih Tiffany , Wang Lei , Mintun Mark A.
Published: January 2018

RATIONALE: Several lines of evidence suggest that dopamine (DA)-influenced neuronal pathways may malfunction in Tourette Syndrome (TS). Some PET studies support the hypothesis of presynaptic abnormalities in levodopa uptake, dopamine synthesis, or dopamine release.

OBJECTIVE: Directly test the presynaptic hypothesis using a new approach.

METHODS: We used positron emission tomography (PET) and [11C]raclopride (RAC*) to measure synaptic dopamine release before and during levodopa and placebo infusions (with carbidopa) in 5neuroleptic-naïve adults with TS and 5 matched control subjects. The primary analysis examined RAC* binding potential (BPND) in predefined volumes of interest (VOIs). A secondary analysis compared BPND voxel by voxel over the entire brain.

RESULTS: (1) Baseline RAC* BPND did not differ significantly between groups, though nucleus accumbens BPND was higher in TS (16%, p=0.051). (2) DA release declined from before to during infusions (p=0.014), including with placebo. (3) This decline was smaller in TS (p=0.080). (4) Levodopa’s effect on BPND differed significantly in right midbrain (p=0.002, corrected), where levodopa displaced RAC* by 59% in control subjects but increased BPND by 74% in TS subjects, and in parahippocampal gyrus (p=0.02, corrected).

DISCUSSION: Our finding that a before/after RAC* design is confounded by time and/or expectation effects may have implications for other RAC* PET studies. The smaller decrease of BPND with time in TS may be attributable to impaired habituation to the scan environment. Levodopa’s opposite effect on RAC* binding in TS dopaminergic midbrain but may signify an abnormal response to dopaminergic stimulation in TS.
Speculation versus data-driven conclusions: A response to Gereau et al.’s "Phylogenetic patterns of extinction risk: the need for critical application of appropriate datasets"
Authors: Daru Barnabas , Yessoufou Kowiyou , Davies Jonathan
Published: January 2018

Gereau et al. (2013) criticized our recent analysis on the phylogenetic patterns of extinction risk in the Eastern Arc biodiversity hotspot (Yessoufou et al. 2012). However, Gereau and colleagues based their critique on preconceptions and speculation rather than data. Here we identify several shortfalls in their lines of argument, and suggest that, given current rates of extinction, it is far more dangerous to wait for complete Red List assessments than to explore patterns of threat using available data. Nonetheless, we agree that all analyses should be based upon the best available data, and we encourage the rapid releases of new data on threat status for the flora of the Eastern Arc.
Disease dynamics and potential mitigation among restored and wild staghorn coral, Acropora cervicornis
Authors: Miller Margaret W. , Lohr Kathryn E. , Cameron Caitlin M. , Williams D. E. , Peters E. C.
Published: January 2018

The threatened status (both ecologically and legally) of Caribbean staghorn coral, Acropora cervicornis, has prompted rapidly expanding efforts in culture and restocking, although tissue loss diseases continue to affect populations. In this study, disease surveillance and histopathological characterization were used to compare disease dynamics and conditions in both restored and extant wild populations. Disease had devastating effects on both wild and restored populations, but dynamics were highly variable and appeared to be site-specific with no significant differences in disease prevalence between wild versus restored sites. Disease affected up to 80% of colonies at one site following a tropical storm. A subset of 20 haphazardly selected colonies at each site observed over a single field season revealed widely varying disease incidence, although not in a consistent way between restored and wild sites, and a case fatality rate of 8%. Lastly, two field mitigation techniques, (1) excision of apparently healthy branch tips from a diseased colony, and (2) placement of a band of epoxy fully enclosing the diseased margin, gave equivocal results with no significant benefit detected for either treatment compared to controls. Tissue condition of associated samples was fair to very poor; unsuccessful mitigation treatment samples had severe degeneration of mesenterial filament cnidoglandular bands. Polyp mucocytes in all samples were infected with suspect rickettsia-like organisms; no bacterial aggregates were found. Overall results do not support differing disease quality, quantity, dynamics, or health management strategies between restored and wild colonies of A. cervicornis in the Florida Keys.
Cascading effects of a highly specialized beech-aphid-fungus interaction on forest regeneration
Authors: Cook-Patton Susan Susan , Maynard Lauren , Lemoine Nathan Susan , Shue Jessica Susan , Parker John D
Published: January 2018

Specialist herbivores are often thought to benefit the larger plant community, because they prevent their host species from becoming competitively dominant. In contrast, specialist enemies are not generally expected to have negative impacts on non-hosts. However, we describe a cascade of indirect interactions whereby a specialist sooty mold (Scorias spongiosa) colonizes the honeydew from a specialist beech aphid (Grylloprociphilus imbricator), ultimately decreasing the survival of seedlings beneath American beech trees (Fagus grandifolia). A common garden experiment indicated that this mortality resulted from moldy honeydew impairing leaf function rather than from chemical or microbial changes to the soil. In addition, aphids consistently colonized the same beech trees regardless of host density, suggesting that seedling-depauperate islands may form beneath these trees. Thus this highly specialized three-way beech-aphid-fungus interaction has the potential to impact local forest regeneration via a cascade of indirect effects.
Anatomical and biomechanical traits of broiler chickens across ontogeny. 1. Anatomy of the musculoskeletal respiratory apparatus and changes in organ size.
Authors: Tickle Peter G , Paxton Heather , Rankin Jeffery W , Hutchinson John R. , Codd Jonathan R
Published: January 2018

Genetic selection for improved meat yields, digestive efficiency and growth rates have transformed the biology of broiler chickens. Modern birds undergo a 50-fold multiplication in body mass in just six weeks, from hatching to slaughter weight. However, this selection for rapid growth and improvements in broiler productivity is also widely thought to be associated with increased welfare problems as many birds suffer from leg, circulatory and respiratory diseases. To understand growth-related changes in musculoskeletal and organ morphology and respiratory skeletal development over the standard six-week rearing period, we present data from post-hatch cadaveric commercial broiler chickens aged 0, 2, 4 and 6 weeks. The heart, lungs and intestines decreased in size for hatch to slaughter weight when considered as a proportion of body mass. Proportional liver size increased in the two weeks after hatch but decreased between 2 and 6 weeks. Breast muscle mass on the other hand displayed strong positive allometry, increasing in mass faster than the increase in body mass. Contrastingly, less rapid isometric growth was found in the external oblique muscle, a major respiratory muscle that moves the sternum dorsally during expiration. Considered together with the relatively slow ossification of elements of the respiratory skeleton, it seems that rapid growth of the breast muscles might compromise the efficacy of the respiratory apparatus. Furthermore, the relative reduction in size of the major organs indicates that selective breeding in meat-producing birds has unintended consequences that may bias these birds toward compromised welfare and could limit further improvements in meat-production and feed efficiency.
Revisiting the first case of insect-bacteria cospeciation: phylogenetic incongruence between aphids and their obligate endosymbiont at subfamily level
Authors: Liu Lin , Huang Xiaolei , Wang Yuan , Qiao Gexia
Published: January 2018

It has been widely accepted that aphids and their primary endosymbiotic bacteria Buchnera have strictly parallel diversification relationship. As the first reported case of insect-bacteria cospeciation, this parallel diversification hypothesis has been prevalent, in spite of its basis of limited taxonomic sampling and recent doubts. Here we revisit the evolutionary relationships between aphids and Buchnera by using much more taxa and genomic data (16S rDNA, ATP synthase β-subunit gene, and gluconate-6-phosphate dehydrogenase gene) to reconstruct the Buchnera phylogeny and test its congruence with the host phylogeny. Comparisons of the Buchnera phylogeny with morphology- and molecular-based aphid phylogenies indicate phylogenetic incongruence between aphids and Buchnera at subfamily level. Current empirical and theoretical evidence indicate two potential mechanisms underlying this incongruence: one is variation in evolutionary rates of Buchnera genomes among different aphid lineages; the other is horizontal transmission of Buchnera during the radiation of extant aphid subfamilies and tribes from their common ancestor.
Stream grazers determine their crawling direction on the basis of chemical and visual/tactile microalgal cues
Authors: Katano Izumi , Doi Hideyuki
Published: January 2018

This study aimed to determine the association of herbivore behavior with cues from producers. We used stream grazer Glossosoma larvae and determined their crawling direction in relation to the chemical and visual cues from microalgae. The experimental treatments included control (no cue), particulate (chemical and visual/tactile cues), and dissolved (chemical cue) cues from microalgae. The experimental water samples were randomly placed into either arms of a Y-shaped channel, and the crawling direction of the grazers was determined. Although the grazers crawled toward the arm containing either particulate or dissolved cues, they preferred the arm with particulate cues. This suggested that grazers responded well when both visual/tactile (i.e., drifting algal cells) and chemical cues (algal smell) were present, and that visual/tactile cues were more important for foraging. In natural habitats, grazers detect cues from both producers and predators and use them to maximize fitness by avoiding predation and obtaining food.
A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+
Authors: Kromann Jimmy Charnley , Christensen Anders , Steinmann Casper , Korth Martin , Jensen Jan H.
Published: January 2018

We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and $\ge$ 3 imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g. when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.
The limitations of diversity metrics in directing global marine conservation
Authors: Robinson James PW , White Easton R , Wiwchar Logan D , Claar Danielle C , Suraci Justin P , Baum Julia K
Published: January 2018

Biodiversity hotspots have been used extensively in setting conservation priorities for reef ecosystems. A recent Nature publication claims to have uncovered new hotspots based on global comparisons of functional diversity. Simulation models show that the purported novel evenness pattern is a mathematical inevitability of differences in species richness, as well as an artefact of differences in detectability between vastly different marine ecosystems. Constraints on evenness, along with disparity among communities in possible functional traits, cast doubt on the utility of global functional diversity comparisons for management of marine systems.
Visitation and economic impact of whale shark tourism in a Maldivian marine protected area
Authors: Cagua Edgar Fernando , Collins Neal M , Hancock James , Rees Richard
Published: January 2018

Whale sharks are a major attraction for tourist divers and snorkelers in South Ari Atoll, Maldives. Yet without information regarding the use and economic extent of the attraction, it is difficult to prioritize conservation or implement effective management plans. Using empirical recreational data and generalized mixed models, this study provides the first economic valuation—via direct spend—of whale shark tourism in Maldives. We estimate that direct expenditure on whale shark excursions in the South Ari Marine Protected Area for 2012–2013 at US$7.6 and $9.4 million, respectively. These expenditures are based on an estimate of 72 to 78 thousand tourists who are involved in whale shark excursions annually. This level of visitation and expenditure highlights the need to implement regulations and management which can safeguard the sustainability of the industry through ensuring guest satisfaction and whale shark conservation.
Combining computational models, semantic annotations, and associated simulation experiments in a graph database
Authors: Henkel Ron , Wolkenhauer Olaf , Walthemath Dagmar
Published: January 2018

Model repositories such as the BioModels Database or the CellML Model Repository are frequently accessed to retrieve computational models describing biological systems. However, the current designs of these databases limit the types of supported queries, and many data in these repositories cannot easily be accessed. Computational methods for model retrieval cannot be applied. In this paper we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models' structure, incorporates semantic annotations and experiment descriptions, and ultimately connects different types of model-related data.The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features such as network structure.The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching, filtering etc.We exemplify how CellML- and SBML-encoded models can be maintained in one database, how these models can be linked via annotations, and queried.
The nonavian theropod quadrate II: systematic usefulness, major trends and cladistic and phylogenetic morphometrics analyses
Authors: Hendrickx Christophe , Araújo Ricardo , Mateus Octávio
Published: January 2018

The skull-bone quadrate in nonavian theropods is very diverse morphologically alongside the disparity of the group as a whole. However this disparity has been underestimated for taxonomic purposes. In order to evaluate the phylogenetic potential and investigate the evolutionary transformations of the quadrate, we conducted a Catalano-Goloboff phylogenetic morphometric analysis as well as a cladistic analysis using 98 discrete quadrate related characters. The cladistic analysis provides a fully resolved tree mirroring to some degree the classification of nonavian theropods. The quadrate morphology by its own provides a wealth of data with strong phylogenetic signal and allows inference of major trends in the evolution of this bone. Important synapomorphies include: for Abelisauroidea, a lateral ramus extending to the ectocondyle; for Tetanurae, the absence of the lateral process; for Spinosauridae, a medial curvature of the ventral part of the pterygoid ramus occurring just above the mandibular articulation; for Avetheropoda, an anterior margin of the pterygoid flange formed by a roughly parabolic margin; and for Tyrannosauroidea, a semi-oval pterygoid flange shape in medial view. The Catalano-Goloboff phylogenetic morphometric analysis reveals two main morphotypes of the mandibular articulation of the quadrate linked to function. The first morphotype, characterized by an anteroposteriorly broad mandibular articulation with two ovoid/subcircular condyles roughly subequal in size, is found in Ceratosauria, Tyrannosauroidea and Oviraptorosauria. This morphotype allows a very weak displacement of the mandible laterally. The second morphotype is characterized by an elongate and anteroposteriorly narrow mandibular articulation and a long and parabolic/sigmoid ectocondyle. Present in Megalosauroidea, Carcharodontosauridae and Dromaeosauridae, this morphotype permits the lower jaw rami to be displaced laterally when the mouth opened.
Rape and the Prevalence of Hybrids in Broadly Sympatric Species: a Case Study using Albatrosses
Authors: Rohwer Sievert , Harris Rebecca B. , Walsh Hollie E.
Published: January 2018

Conspecific rape often increases male reproductive success. However, the haste and aggression of forced copulations suggests that males may sometimes rape heterospecific females, thus making rape a likely, but undocumented, source of hybrids between broadly sympatric species. We present evidence that heterospecific rape may be the source of hybrids between Black-footed and Laysan Albatrosses (Phoebastria nigripes, and P. immutabilis, respectively). Extensive field studies have shown that paired (but not unpaired) males of both of these albatross species use rape as a supplemental reproductive strategy. Between species differences in size, timing of laying, and aggressiveness suggest that Black-footed Albatrosses should be more successful than Laysan Albatrosses in heteropspecific rape attempts, and male Black-footed Albatrosses have been observed attempting to force copulations on female Laysan Albatrosses. Nuclear markers showed that the six hybrids we studied were F1s and mitochondrial markers showed that male Black-footed Albatrosses sired all six hybrids. The siring asymmetry found in our hybrids may have long persisted because an IM analysis suggests that long-term gene exchange between these species has been from Black-footed Albatrosses into Laysan Albatrosses. If hybrids are sired in heterospecific rapes, they presumably would be raised and sexually imprinted on Laysan Albatrosses, and two unmated hybrids in a previous study courted only Laysan Albatrosses.
Swarm: robust and fast clustering method for amplicon-based studies
Authors: Mahé Frédéric , Rognes Torbjørn , Quince Christopher , de Vargas Colomban , Dunthorn Micah
Published: January 2018

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units, improving the amount of meaningful biological information that can be extracted from amplicon-based studies.
How to critically read ecological meta-analyses.
Authors: Lortie Christopher J. , Stewart Gavin , Rothstein Hannah , Lau Joseph
Published: January 2018

Meta-analysis offers ecologists a powerful tool for knowledge synthesis. Albeit a form of review, it also shares many similarities with primary empirical research. Consequently, critical reading of meta-analyses incorporates criteria from both sets of approaches particularly because ecology is a discipline that embraces heterogeneity and broad methodologies. The most important issues in critically assessing a meta-analysis initially include transparency, replicability, and clear statement of purpose by the authors. Specific to ecology more so than other disciplines, tests of the same hypothesis are generally conducted at different study sites, have variable ecological contexts (i.e., seasonality), and use very different methods. Clear reporting and careful examination of heterogeneity in ecological meta-analyses is thus crucial. Ecologists often also test similar hypotheses with different species, and in these meta-analyses, the reader should expect exploration of phylogenetic dependencies. Finally, observational studies not only provide the substrate for potential current manipulative experiments in this discipline but also form an important body of literature historically for synthesis. Sensitivity analyses of observational versus manipulative experiments when aggregated in the same ecological meta-analysis are also frequent and appropriate. This brief conceptual review is not intended as an instrument to rate meta-analyses for ecologists but does provide the appropriate framing for those purposes and directs the reader to ongoing developments in this direction in other disciplines.
Scaling of olfactory antennae of the terrestrial hermit crabs Coenobita rugosus and Coenobita perlatus during ontogeny
Authors: Waldrop Lindsay D , Bantay Roxanne M , Nguyen Quang V
Published: January 2018

Although many lineages of terrestrialized crustaceans have poor olfactory capabilities, crabs in the family Coenobitidae, including the terrestrial hermit crabs in the genus Coenobita, are able to locate food and water using olfactory antennae (antennules) to capture odors from the surrounding air. Terrestrial hermit crabs begin their lives as small marine larvae and must find a suitable place to undergo metamorphosis into a juvenile form, which initiates their transition to land. Juveniles increase in size by more than an order of magnitude to reach adult size. Since odor capture is a process heavily dependent on the size and speed of the antennules and physical properties of the fluid, both the transition from water to air and the large increase in size during ontogeny could impact odor capture. In this study, we examine two species of terrestrial hermit crabs, Coenobita perlatus H. Milne-Edwards and Coenobita rugosus H. Milne-Edwards, to determine how the antennule morphometrics and kinematics of flicking change in comparison to body size during ontogeny, and how this scaling relationship could impact odor capture by using a simple model of mass transport in flow. Many features of the antennules, including the chemosensory sensilla, scaled allometrically with carapace width and increased slower than expected by isometry, resulting in relatively larger antennules on juvenile animals. Flicking speed scaled as expected with isometry. Our mass-transport model showed that allometric scaling of antennule morphometrics and kinematics leads to thinner boundary layers of attached fluid around the antennule during flicking and higher odorant capture rates as compared to antennules which scaled isometrically. There were no significant differences in morphometric or kinematic measurements between the two species.
Formalized synthesis opportunities for ecology: systematic reviews and meta-analyses
Authors: Lortie Christopher J.
Published: January 2018

Narrative reviews are dead. Long live systematic reviews (and meta-analyses). Synthesis in many forms is now a driving force in ecology. Advances in open big data for ecology and new tools provide vastly improved capacity for novel, emergent knowledge synthesis in our discipline. Systematic reviews and meta-analyses are two formal synthesis opportunities for ecologists. To date, systematic reviews are rarely used whilst the rate of meta-analyses published in ecological journals is increasing exponentially. Systematic reviews provide an overview of the literature landscape for a topic, and meta-analyses examine the strength of evidence integrated across different studies. Effective synthesis benefits from both approaches, but better data reporting and more rapid changes in the culture of data sharing will further energize these efforts. At this junction, synthetic efforts that include systematic reviews and meta-analyses should continue as stand-alone publications. This is a necessary step in the evolution of synthesis in our discipline. Nonetheless, they are still evolving tools, and meta-analyses in particular are simply an extended set of statistical tests. Admittedly, understanding the statistics and assumptions influence how we conduct synthesis much as statistical choices often shape experimental design, i.e. ANOVA versus regression-based experiments, but statistics do not make the paper. Clear ideas and excellent questions do. Titles with ‘a meta-analysis of…’ in them may have their days numbered as these tools become more widely adopted and as we seek to integrate evidence across many scales not just between studies. Approaches associated with both sets will inevitably and appropriately also become routine mechanisms to contrast primary study-level research to the work of others. For instance, in the Introduction of a primary study, formal systematic review techniques are applied, the authors identify a gap that they proceed to examine within that particular study via an experiment, and in the Discussion, the strength of the evidence is linked to other effect size estimates reported in the literature. This is already occurring but will certainly become more frequent. First steps, primary research articles need to more effectively report evidence, we need to continue to share data, and systematic reviews and meta-analyses should be used to identify research gaps and examine patterns in evidence to further predictive ecology.