bluuebunny/crossref_metadata_2025 huggingface dataset:
An explanation of the relationship between mass, metabolic rate and characteristic length for placental mammals
Authors: Frasier Charles
Published: January 2018

The Mass, Metabolism and Length Explanation (MMLE) was advanced in 1984 to explain the relationship between metabolic rate and body mass for birds and mammals. This paper reports on a modernized version of MMLE. MMLE predicts the absolute value of Basal Metabolic Rate (BMR) for individual animals rather than parameters in the power law relationship BMR = a(body mass)b. Beginning with the proposition that BMR is proportional to the number of mitochondria in an animal, two primary equations are derived that predict BMR and body mass as functions of an individual animal’s characteristic length and sturdiness factor. The characteristic length is a measureable skeletal length associated with an animal’s means of propulsion. The sturdiness factor expresses how sturdy or gracile an animal is. Eight other parameters occur in the equations that vary little among animals in the same phylogenetic group. The present paper modernizes MMLE by explicitly treating Froude and Strouhal dynamic similarity of mammals’ skeletal musculature, revising the treatment of BMR and using new data to estimate numerical values for the parameters that occur in the equations. A mass and length data set with 575 entries from the orders Rodentia, Chiroptera, Artiodactyla, Carnivora, Perissodactyla and Proboscidae is used. A BMR and mass data set with 436 entries from the orders Rodentia, Chiroptera, Artiodactyla and Carnivora is also used. With the estimated parameter values MMLE can exactly predict every BMR and mass datum from the BMR and mass data set without any unexplained variance. Furthermore MMLE can exactly predict every body mass and length datum from the mass and length data set without any unexplained variance. Whether or not MMLE can simultaneously exactly predict an individual animal’s BMR and body mass given its characteristic length awaits analysis of a data set that simultaneously reports all three of these items for individual animals.
An explanation of the relationship between mass, metabolic rate and characteristic length for placental mammals
Authors: Frasier Charles
Published: January 2018

The Mass, Metabolism and Length Explanation (MMLE) was advanced in 1984 to explain the relationship between metabolic rate and body mass for birds and mammals. This paper reports on a modernized version of MMLE. MMLE deterministically predicts the absolute value of Basal Metabolic Rate (BMR) and body mass for individual animals. MMLE is thus distinct from other examinations of these topics that use species-averaged data to estimate the parameters in a statistically best fit power law relationship such as BMR = a(body mass)b. Beginning with the proposition that BMR is proportional to the number of mitochondria in an animal, two primary equations are derived that predict BMR and body mass as functions of an individual animal’s characteristic length and sturdiness factor. The characteristic length is a measurable skeletal length associated with an animal’s means of propulsion. The sturdiness factor expresses how sturdy or gracile an animal is. Eight other parameters occur in the equations that vary little among animals in the same phylogenetic group. The present paper modernizes MMLE by explicitly treating Froude and Strouhal dynamic similarity of mammals’ skeletal musculature, revising the treatment of BMR and using new data to estimate numerical values for the parameters that occur in the equations. A mass and length data set with 575 entries from the orders Rodentia, Chiroptera, Artiodactyla, Carnivora, Perissodactyla and Proboscidae is used. A BMR and mass data set with 436 entries from the orders Rodentia, Chiroptera, Artiodactyla and Carnivora is also used. With the estimated parameter values MMLE can exactly predict every BMR and mass datum from the BMR and mass data set with no error and thus no unexplained variance. Furthermore MMLE can exactly predict every body mass and length datum from the mass and length data set with no error and thus no unexplained variance. Whether or not MMLE can simultaneously exactly predict an individual animal’s BMR and body mass given its characteristic length awaits analysis of a data set that simultaneously reports all three of these items for individual animals. However for many of the addressed phylogenetic homogeneous groups, MMLE can predict the exponent obtained by regression analysis of the BMR and mass data using the exponent obtained by regression analysis of the mass and length data. This argues that MMLE may be able to accurately simultaneously predict BMR and mass for an individual animal.
Comparing the influence of ecology journals using citation-based indices: making sense of a multitude of metrics
Authors: Hocking Daniel J.
Published: January 2018

The links among scholarly citations creates a tremendous network that reveals patterns of influence and flows of ideas. The systematic evaluation of the networks can be used to create aggregate measures of journal influence. To understand the citation patterns and compare influence among ecology journals, I complied 11 popular metrics for 110 ecology journals: Journal Impact Factor (JIF), 5-year Journal Impact Factor (JIF), Eigenfactor, Article Influence (AI), Source-Normalized Impact per Paper (SNIP), SCImago Journal Report (SJR), h-index, hc-index, e-index, g-index, and AR-index. All metrics were positively correlated among ecology journals; however, there was still considerable variation among metrics. Annual Review of Ecology Evolution, and Systematics, Trends in Ecology and Evolution, and Ecology Letters were the top three journals across metrics on a per article basis. Proceedings of the Royal Society B, Ecology, and Molecular Ecology had the greatest overall influence on science, as indicated by the Eigenfactor. There was much greater variability among the other metrics because they focus on the mostly highly cited papers from each journal. Each influence metric has its own strengths and weaknesses, and therefore its own uses. Researchers interested in average influence of articles in a journal would be best served by referring to the AI scores or possibly SJR values.
Oxygen transport and release of adenosine triphosphate in micro-channels and arterioles in the human microcirculation
Authors: Moschandreou Terry
Published: January 2018

The governing nonlinear equations for oxygen transport and ATP concentration in a microfluidic channel and tube are solved with the aid of Maple and COMSOL Multiphysics simulation software. Considering a cell-rich and cell free region with RBCs and blood plasma, we obtain results showing clearly that there is a significant decrease in oxygen tension in the vicinity of an oxygen permeable membrane placed midway on the upper channel/tube wall and to the right side of it in the downstream field. The purpose of the membrane is to cause a rapid change in oxygen saturation as RBC’s flow through channel/tube. To the right of the membrane downstream the greatest amount of ATP is released. Finally the corresponding time-dependent oxygen transport problem for plug flow in a channel, which has not been simulated in previous models in the literature, is analyzed and different starting times are shown for ATP release at different points in the channel. The FE modelling is very accurate: The time evolution problem is modelled and solved in it`s entirety with exact parameters used in the literature for blood flow and oxygen transport in the microcirculation. A comparison is made between the steady state and time dependent solutions in order to validate the results. The implications of the time dependent model for biological systems such as the human microcirculation requires exact information on release of energy as ATP is released from blood cells and the present work is important in providing this information.
A surge of p-values between 0.040 and 0.049 in recent decades (but negative results are increasing rapidly too)
Authors: de Winter Joost , Dodou Dimitra
Published: January 2018

It is known that statistically significant results are more likely to be published than results that are not statistically significant. However, it is unclear whether negative results are disappearing from papers, and whether there exists a ‘hierarchy of sciences’ with the social sciences publishing more positive results than the physical sciences. Using Scopus, we conducted a search in the abstracts of papers published between 1990 and 2014, and calculated the percentage of papers reporting marginally positive results (i.e., p-values between 0.040 and 0.049) versus the percentage of papers reporting marginally negative results (i.e., p-values between 0.051 and 0.060). The results indicate that negative results are not disappearing, but have actually become 4.3 times more prevalent since 1990. Positive results, on the other hand, have become 13.9 times more prevalent since 1990. We found no consistent support for a ‘hierarchy of sciences’. However, we did find large differences in reporting practices between disciplines, with the reporting of p-values being 60.6 times more frequent in the biological sciences than in the physical sciences. We argue that the observed longitudinal trends may be caused by negative factors, such as an increase of questionable research practices, but also by positive factors, such as an increasingly quantitative research focus.
Beyond xMOOCs in Healthcare Education: Study of the Feasibility in Integrating Virtual Patient Systems and MOOC platforms
Authors: Stathakarou Natalia , Zary Nabil , Kononowicz Andrzej A.
Published: January 2018

Background: Massive Open Online Courses (MOOCs) are an emerging method of online teaching. However in the field of healthcare education their technology is not adopted yet. Reaching beyond the xMOOC type of courses in order to foster interactivity in the healthcare education requires domain specific software. Virtual Patients (VPs) have been integrated in the past with Virtual Learning Environments (VLEs) but extending MOOCs with VPs has not yet been discussed. Objective: To investigate the technical possibilities of integrating VPs with MOOCs for the purpose of discovering a pragmatic basis were the potential pedagogical benefits can be later studied. Methods: We selected OpenEdx and Open Labyrinth as examples of a MOOC platform and of a VP system. We conducted a literature review to identify technical requirements and e-learning standards apt for the integration. One fundamental requirement was prototyped and verified by use cases. Results: A Single–Sign on mechanism connecting Open Labyrinth with OpenEdx, employing the IMS LTI standard, has been successfully implemented and verified. Conclusion: We investigated the technical perspective of integrating VPs in MOOCs, aiming to set a base for future investigation on the topic. The results point out new opportunities arising from the infrastructure of MOOCs for integrating specialized software aiming to support the healthcare education.
On the relationship between native grouper and invasive lionfish in the Caribbean
Authors: Mumby Peter J , Brumbaugh Daniel R , Harborne Alastair R , Roff George
Published: January 2018

The Indo-Pacific lionfish, Pterois volitans, has invaded most of the Tropical Western Atlantic in the last few years. The degree to which populations of this invasive species can be controlled by native predatory fish (mostly grouper), is controversial with conflicting reports. Here, we review the evidence of two recent papers and point out some of the difficulties in inferring predator-limitation purely from observational data. A negative relationship has been found between large-bodied grouper and lionfish during early colonisation though the degree to which this is caused by direct predation versus behavioural mechanisms is unclear. Evidence to the contrary from a recent study suffers confounding effects of habitat quality, fishing, and dispersal and therefore remains equivocal.
Habitat creation and biodiversity maintenance in mangrove forests: Teredinid bivalves as ecosystem engineers
Authors: Hendy Ian W , Michie Laura A , Taylor Benjamin W
Published: January 2018

Substantial amounts of dead wood in the intertidal zone of mature mangrove forests are tunnelled by teredinid bivalves. When the tunnels are exposed, animals are able to use tunnels as refuges. In this study, the effect of teredinid tunnelling upon mangrove forest faunal diversity was investigated. Mangrove wood not containing teredinid tunnels had very few species and abundance of animals. However, with a greater cross-sectional surface area of teredinid tunnels, the numbers of species and abundance of animals was significantly higher. Temperatures within teredinid-attacked wood were significantly cooler compared with air temperatures, and the animals in tunnels inside the wood may avoid desiccation by escaping the higher temperatures. Animals co-existing in teredinid tunnelled wood ranged from animals found in terrestrial ecosystems including centipedes, crickets and spiders, and animals found in subtidal marine ecosystems such as fish, octopods and polychaetes. There was also evidence of breeding within teredinid-attacked wood, as many juvenile individuals were found, and they may also benefit from the cooler wood temperatures. Teredinid tunnelled wood is a key low-tide refuge for cryptic animals, which would otherwise be exposed to piscivorous fishes and birds, and higher external temperatures. This study provides evidence that teredinids are ecosystem engineers and also provides an example of a mechanism whereby mangrove forests support intertidal biodiversity and nurseries through the wood-boring activity of teredinids.
Mapping of dextral : sinistral proportions in the chirally dimorphic land snail Amphidromus inversus
Authors: Schilthuizen Menno , Looijestijn Sylvia , Chua Sek Chuan , Castillo Cajas Ruth F.
Published: January 2018

One of the very few snail taxa that display genetic antisymmetry (that is, roughly even mixes of genetically determined clockwise and anticlockwise individuals within a single population) are the circa 35 species of the tropical tree snail subgenus Amphidromus. Previous work has shown that this may be due to a particular type of sexual selection, in which sperm transfer is improved in copulations between the two mirror-image morphs. However, it is not yet clear why so often significant deviations from 50:50 proportions are found. Modelling studies show that population structure will affect the degree by which the dimorphism is skewed towards the morph associated with the recessive allele. In this study, we mapped the proportions of sinistrals (PropS) in 56 demes in A. inversus on the Malaysian island of Kapas. We also mapped population density, predation rates, and several measures of vegetation structure. Our results show that PropS amounts on average to 0.65, but across the island varies from 0.30 to 0.85. Density and overall predation are inversely correlated, but neither predicts PropS. Vegetation parameters also do not correlate with the proportion of sinistrals. We do, however, find a negative correlation between the predation rate on sinistrals and PropS, a finding which may warrant further study.
Fibrochondrogenic potential of synoviocytes from osteoarthritic and normal joints cultured as tensioned bioscaffolds for meniscal tissue engineering in dogs
Authors: Warnock Jennifer J , Bobe Gerd , Duesterdieck-Zellmer Katja F.
Published: January 2018

Meniscal tears are a common cause of stifle lameness in dogs. Use of autologous synoviocytes from the affected stifle is an attractive cell source for tissue engineering replacement fibrocartilage. However, the diseased state of these cells may impede in vitro fibrocartilage formation. Synoviocytes from 12 osteoarthritic (“oaTSB”) and 6 normal joints (“nTSB”) were cultured as tensioned bioscaffolds and compared for their ability to synthesize fibrocartilage sheets. Gene expression of collagens type I and II were higher and expression of interleukin-6 was lower in oaTSB versus nTSB. Compared with nTSB, oaTSB had more glycosaminoglycan and alpha smooth muscle staining and less collagen I and II staining on histologic analysis, whereas collagen and glycosaminoglycan quantities were similar. In conclusion, osteoarthritic joint-origin synoviocytes can produce extracellular matrix components of meniscal fibrocartilage at similar levels to normal joint-origin synoviocytes, which makes them a potential cell source for canine meniscal tissue engineering.
Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer
Authors: Doughty Emma L , Sergeant Martin J , Adetifa Ifedayo M.O , Antonio Martin , Pallen Mark J
Published: January 2018

Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of “modern” M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence-based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplification steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.
Heterotrophic and mixotrophic cultivation of Chlorella pyrenoidosa and the enzymatic hydrolysis of its biomass for the synthesis of third generation bioethanol
Authors: Dhull Nisha Phour , Gupta Kshitiz , Soni Sanjeev Kumar
Published: January 2018

The present study has been carried out with a view of evaluating a green alga Chlorella pyrenoidosa as a potential candidate for the production of reducing sugars using an enzyme cocktail of multiple carbohydrates produced on site for the fermentation into bioethanol. The ability of C. pyrenoidosa to grow similarly fast on different carbon sources and light has been studied in Fog’s medium in heterotrophic and mixotrophic cultures. The high cells densities of mixotrophic cultures demonstrated that the growth-stimulating effects of light and carbon utilization were better as compared to the effects of glucose in heterotrophic condition. Maximum biomass yield of 1.2 g/l was achieved with 1% Glucose and 0.2% KNO3 after 7 days of incubation at 28oC. The algal biomass was steam pretreated and hydrolyzed by a cocktail of multiple carbohydrases produced by solid state culture of a laboratory isolate belonging to Aspergillus sp. on wheat bran exhibiting the yields of 86, 35, 74, 1947, 61, 17000 and 1388 IU/g dry wheat bran for CMCase, FPase, β-glucosidase, xylanase, mannanase, α-amylase and glucoamylase respectively. The enzyme cocktail worked well in the hydrolysis of algal biomass at 50oC and produced total reducing sugars amounting to 429 mg/g of dried biomass revealing carbohydrate conversion efficiency of 96% after 48 h of hydrolysis. The released sugars may be fermented using suitable yeast strains for the production of third generation bioethanol.
The physiologic and therapeutic role of Heparin in implantation and placentation
Authors: Quaranta Michela , Erez Offer , Mastrolia Salvatore Andrea , Koifman Arie , Leron Elad , Eshkoli Tamar , Mazor Moshe , Holcberg Gershon
Published: January 2018

Implantation, trophoblast development and placentation are crucial processes in the establishment and development of normal pregnancy. Abnormalities of these processes can lead to pregnancy complications named the great obstetrical syndromes (preeclampsia, intrauterine growth restriction, fetal demise, premature prelabor rupture or membranes, preterm labor, and recurrent pregnancy loss). There is mounting evidence regarding the physiological and therapeutic role of heparins in the establishment of normal gestation and as a modality for treatment and prevention of pregnancy complications. In this review we will summarize the properties and the physiological contribute of heparins to the success of implantation and placentation and normal pregnancy.
A statistical assessment of population trends for data deficient Mexican amphibians
Authors: Quintero Esther , Thessen Anne E. , Arias-Caballero Paulina , Ayala-Orozco Bárbara
Published: January 2018

Background: Mexico is the fourth richest country in amphibians and the second country with the highest quantity of threatened amphibian species, and this number could be higher as many species are too poorly known to be accurately assigned to a risk category. The absence of a risk status or an unknown population trend can slow or halt conservation action, so it is vital to develop tools that in the absence of specific demographic data can assess a species’ risk of extinction, population trend, and to better understand which variables increase their vulnerability. Recent studies have demonstrated that the risk of species decline depends on extrinsic and intrinsic trait, thus including both of them for assessing extinction might render more accurate assessment of threat. Methods: In this study harvested data from the Encyclopedia of Life (EOL) and the published literature for Mexican amphibians and used these data to assess the population trend of some of the Mexican species that have been assigned to the Data Deficient category of the IUCN using Random Forests, a Machine Learning method that gives a prediction of complex processes and identifies the most important variables that account for the predictions. Results: Our results show that most data deficient Mexican amphibians have decreasing population trends. We found that Random Forests is a solid and accurate way to identify species with decreasing population trends when no demographic data is available. Moreover, we point the most important variables that make species more vulnerable for extinction. This exercise is a very valuable first step in assigning conservation priorities for poorly known species.
A process to support species conservation planning and climate change readiness in protected areas
Authors: Angeli Nicole F. , Otegui Javier , Wood Margot , Gomez-Ruiz Emma P.
Published: January 2018

Global change will causes species range shifts, affecting species interactions. The conservation implications of species range shifts are widely unknown. Through forming an ecology-bioinformatics partnership at the National Evolutionary Synthesis Center-Encyclopedia of Life-Biodiversity Heritage Library Research Sprint, we developed an analytical pipeline to test whether global trends are forcing shifts of mutually dependent species in different spatial directions. We calculated potential overlap between dependent species across climate scenarios within protected areas. We selected the Great Green Macaw (Ara ambiguus) and its nesting host tree the Giant Almendro (Dipteryx panamensis) as a proof-of-concept species pair that will be affected by range shifts. We demonstrate with modeling that the Great Green Macaw will lose approximately 64.0% of suitable habitat in future scenarios, while the Giant Almendro will lose 59.7% of suitable habitat. Species habitat overlaps across 85.3 % of its currently predicted distribution and 69.07% of the remaining habitat predicted in future scenarios. After accounting for spatially explicit protected areas networks, only 20.3% and 40.2 % of remaining habitat persists within protected areas across climate scenarios for the Almendro and Macaw, respectively, and 19.9 % of that habitat overlaps between the species. Currently, we are conducting a literature review to select and expand our list of species for use in the pipeline to detect trends for climate readiness planning in protected areas networks. The analytical pipeline will produce habitat suitability maps for multiple climate scenarios based on current distributions, and these maps will potentially be embedded into the Encyclopedia of Life as free, downloadable files. This is just one of several broader impact products from the research. This work demonstrates that modeling the future distribution of species is limited by biotic interactions and conservation planning should account for climate change scenarios.
EOL-BHL-NESCent Research Sprint Report
Authors: Parr Cynthia S , McClain Craig R
Published: January 2018

There are exciting biological questions which require programming and large online data resources to address, yet many traditionally-trained biologists lack the informatics skills needed for successful analysis. In the last decade, new aggregated, open data resources have become available, but these are not often being leveraged effectively for big data research. Using a new hackathon-inspired format, the EOL-BHL-NESCent Research Sprint facilitated scientific discovery by supporting teams to use online data resources such as the Encyclopedia of Life and Biodiversity Heritage Library to answer their biological questions. We describe the methods of the research sprint and present results indicating its success in producing publications, in introducing scientists to large-scale informatics resources and approaches, and in encouraging new collaborations.
Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species
Authors: Lowe Elijah K , Swalla Billie J , Brown C. Titus
Published: January 2018

De novo transcriptome sequencing and assembly for non-model organisms has become prevalent in the past decade. However, most assembly approaches are computationally expensive, and little in-depth evaluation has been done to compare de novo approaches. We sequenced several developmental stages of two free-spawning marine species—Molgula occulta and Molgula oculata—assembled their transcriptomes using four different combinations of preprocessing and assembly approaches, and evaluated the quality of the assembly. We present a straightforward and reproducible mRNAseq assembly protocol that combines quality filtering, digital normalization, and assembly, together with several metrics to evaluate our de novo assemblies. The use of digital normalization in the protocol reduces the time and memory needed to complete the assembly and makes this pipeline available to labs without large computing infrastructure. Despite varying widely in basic assembly statistics, all of the assembled transcriptomes evaluate well in metrics such as gene recovery and estimated completeness.
Ontogenetic scaling patterns and functional anatomy of the pelvic limb musculature in emus (Dromaius novaehollandiae)
Authors: Lamas Luis P , Main Russell P , Hutchinson John R.
Published: January 2018

Emus (Dromaius novaehollandiae) are exclusively terrestrial, bipedal and cursorial ratites with some similar biomechanical characteristics to humans. Their growth rates are impressive as their body mass increases eighty-fold from hatching to adulthood whilst maintaining the same mode of locomotion throughout life. These ontogenetic characteristics stimulate biomechanical questions about the strategies that allow emus to cope with their rapid growth and locomotion, which can be partly addressed via scaling (allometric) analysis of morphology. In this study we have collected pelvic limb anatomical data (muscle architecture, tendon length, tendon mass and bone lengths) and calculated muscle physiological cross sectional area (PCSA) and average tendon cross sectional area from emus across three ontogenetic stages (n=17, body masses from 3.6 to 42 kg). The data were analysed by reduced major axis regression to determine how these biomechanically relevant aspects of morphology scaled with body mass. Muscle mass and PCSA showed a marked trend towards positive allometry (26 and 27 out of 34 muscles respectively) and fascicle length showed a more mixed scaling pattern. The long tendons of the main digital flexors scaled with positive allometry for all characteristics whilst other tendons demonstrated a less clear scaling pattern. Finally, the two longer bones of the limb (tibiotarsus and tarsometatarsus) also exhibited positive allometry for length and the two others (femur and first phalanx of digit III) had trends towards isometry. These results indicate that emus experience a relative increase in their muscle force-generating capacities, as well as potentially increasing the force-sustaining capacities of their tendons, as they grow. Furthermore, we have clarified anatomical descriptions and provided illustrations of the pelvic limb muscle-tendon units in emus.
When is a network complex? Connectance drives degree distribution and emerging network properties
Authors: Poisot Timothée , Gravel Dominique
Published: January 2018

Connectance and degree distributions are important components of the structure of ecological networks. In this contribution, we use a statistical argument and simple network generating models to show that properties of the degree distribution are driven by network connectance. We discuss the consequences of this finding for (1) the generation of random networks in null-model analyses, and (2) the interpretation of network structure and ecosystem properties in relationship with degree distribution.
When is an ecological network complex? Connectance drives degree distribution and emerging network properties
Authors: Poisot Timothée , Gravel Dominique
Published: January 2018

Connectance and degree distributions are important components of the structure of ecological networks. In this contribution, we use a statistical argument and simple network generating models to show that properties of the degree distribution are driven by network connectance. We discuss the consequences of this finding for (1) the generation of random networks in null-model analyses, and (2) the interpretation of network structure and ecosystem properties in relationship with degree distribution.
Occurrence of the Megatoothed sharks (Lamniformes:Otodontidae) in Alabama, USA
Authors: Ehret Dana J , Ebersole Jun A.
Published: January 2018

The Otodontidae include some of the largest sharks to ever live in the world’s oceans (i.e. Carcharocles megalodon). Here we report on Paleocene and Eocene occurrences of Otodus obliquus and Carcharocles auriculatus from Alabama, USA. Teeth of Otodus are rarely encountered in the Gulf Coastal Plain and this report is one of the first records for Alabama. Carcharocles auriculatus is more common in the Eocene deposits of Alabama, but its occurrence has been largely overlooked in the literature. We also refute the occurrence of the Oligocene Carcharocles angustidens in the state. Raised awareness and increased collecting of under-sampled geologic formations in Alabama will likely increase sample sizes of O. obliquus and C. auriculatus and also might unearth other otodontids, such as C. megalodon and C. chubutensis.
Are improper kinetic models hampering drug development?
Authors: Walsh Ryan
Published: January 2018

Reproducibility of biological data is a significant problem in research today. One potential contributor to this, which has received little attention, is the over complication of enzyme kinetic inhibition models. This over complication of inhibitory models stems from the common use of the inhibitory term (1+[I]/Ki), an equilibrium binding term that does not distinguish between inhibitor binding and inhibitory effect. Since its initial appearance in the literature, around a century ago, the perceived mechanistic methods used in its production have spurred countless inhibitory equations. These equations are overly complex and are seldom compared to each other, which has destroyed their usefulness resulting in the proliferation and regulatory acceptance of simpler models such as ic50s for drug characterization. However, empirical analysis of inhibitory data recognizing the clear distinctions between inhibitor binding and inhibitory effect can produce simple logical inhibition models. In contrast to the common divergent practice of generating new inhibitory models for every inhibitory situation that presents itself, the empirical approach to inhibition modeling presented here, is broadly applicable allowing easy comparison and rational analysis of drug interactions. To demonstrate this, a simple kinetic model of DAPT, a compound which both activates and inhibits γ-secretase is examined using excel. The empirical kinetic method described here allows for a more in depth understanding of drug interactions and disease mechanism.
Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers
Authors: Lefcheck Jonathan S , Duffy J. Emmett
Published: January 2018

The use of functional traits to explain biodiversity effects on ecosystem functioning has attracted intense recent interest, yet very few a priori manipulations of functional diversity have been attempted to date, especially from a food web perspective. Here, we simultaneously manipulated multiple functional traits of estuarine grazers and predators within multiple levels of species richness to test whether species richness or functional diversity is a better predictor of ecosystem functioning in multitrophic estuarine food webs. Community functional diversity better predicted the majority of ecosystem responses based on results from generalized linear mixed effects models. Structural equation modeling revealed that this outcome was independently attributable to functional diversity of both trophic levels, with stronger effects observed for predators. Functional complementarity was also important, as species with different combinations of traits influenced different ecosystem functions. Our study is the first to extend experimental investigations of functional diversity to a multilevel food web, and demonstrates that functional diversity is more effective than species richness in predicting ecosystem functioning in a food web context.
Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers
Authors: Lefcheck Jonathan S , Duffy J. Emmett
Published: January 2018

The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on general linear mixed effects models. Combining inferences from 8 traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.
Possible odour-mediated attraction of flies to Bacillus subtilis NRS-762 stationary phase culture
Authors: Ng Wenfa
Published: January 2018

Signalling helps connects different organisms in the biosphere. This research note describes the possible concentration-dependent odour mediated attraction of flies to stationary phase aerobic liquid cultures of Bacillus subtilis NRS-762 cultivated on an open orbital shaker at 25 oC. Greater odour pungency correlated with more intense “foraging” attempts, which suggested the compounds’ possible behaviour modifying effects. Additionally, co-occurrence of optical density decline and increase in odour pungency suggested volatile compound(s) secretion might be a cell survival response mediated by a cell density-based signalling mechanism. Flies were not attracted to odourous stationary phase cultures of other common bacteria (Escherichia coli DH5α, Pseudomonas aeruginosa PRD-10, and Pseudomonas protegens Pf-5, which suggested species-specificity of the volatile compound(s)). Altogether, volatile compound(s) might serve as interkingdom messengers to enlist flies for dispersing B. subtilis to habitats with more favourable conditions in coping with possible irreversible decline in habitability, and operate in parallel with other in situ mechanisms such as cannibalism and sporulation that help B. subtilis ride out short- and long-term environmental fluctuations, respectively. Interested researchers are invited to build upon the preliminary findings.
Estimation of predator-prey mass ratios using stable isotopes: sources of errors
Authors: Hertz Eric , Robinson James , Trudel Marc , Mazumder Asit , Baum Julia K
Published: January 2018

In aquatic systems, the ratio of predator mass to prey mass (PPMR) is an important constraint on food web structure, and has been correlated with environmental stability. One common approach of estimating PPMR uses nitrogen stable isotopes (δ15N) as an indicator of trophic position, under the assumption that the discrimination between diet and tissue is constant with increasing diet δ15N (an additive approach). However, recent studies have shown that this assumption may not be valid, and that there is a negative trend between the δ15N of the diet and the discrimination value (a scaled approach). We estimated PPMR for a simulated food web using the traditional additive approach and improved scaled approach, before testing our predictions with isotope samples from a North Sea food web. Our simulations show that the additive approach gives incorrect estimates of PPMR, and these biases are reflected in North Sea PPMR estimates. The extent of the bias is dependent on the baseline δ15N and trophic level sampled, with the greatest differences for samples with low baseline δ15N sampled at lower trophic levels. The scaled approach allows for the comparison of PPMR across varying δ15N baselines and trophic levels, and will refine estimates of PPMR.
Profile analysis of hepatic porcine and murine brain tissue slices obtained with a vibratome
Authors: Mattei Giorgio , Cristiani Irene , Magliaro Chiara , Ahluwalia Arti
Published: January 2018

This study is aimed at characterizing soft tissue slices using a vibratome. In particular, the effect of two sectioning parameters (i.e. step size and sectioning speed) on resultant slice thickness was investigated for fresh porcine liver as well as for paraformaldehyde-fixed (PFA-fixed) and fresh murine brain. A simple framework for embedding, sectioning and imaging the slices was established to derive their thickness, which was evaluated through a purposely developed graphical user interface. Sectioning speed and step size had little effect on the thickness of fresh liver slices. Conversely, the thickness of PFA-fixed murine brain slices was found to be dependent on the step size, but not on the sectioning speed. In view of these results, fresh brain tissue was sliced varying the step size only, which was found to have a significant effect on resultant slice thickness. Although precision-cut slices (i.e. with regular thickness) were obtained for all the tissues, slice accuracy (defined as the match between the nominal step size chosen and the actual slice thickness obtained) was found to increase with tissue stiffness from fresh liver to PFA-fixed brain. This quantitative investigation can be very helpful for establishing the most suitable slicing setup for a given tissue.
Urinary nucleic acids can be concentrated, dried on membranes and stored at room temperature in vacuum bags
Authors: Zhang Fanshuang , Yuan Yuan , Wu Jianqiang , Gao Youhe
Published: January 2018

Urine accumulates traces of changes that occur in the body and can potentially serve as a better biomarker source. Urinary nucleic acids are a promising class of non-invasive disease biomarkers. However, long-term frozen human urine samples are not a good source for the extraction of nucleic acids. In this paper, we demonstrate that urinary nucleic acids can be concentrated, dried on membranes and stored in vacuum bags at room temperature for several months. The amount of total RNA on the membranes after storage at room temperature for three months was unchanged. The levels of miR-16 and miR-21 exhibited no significant differences (P = 0.564, 0.386). This simple and economical method makes the large-scale storage of clinical samples of urinary nucleic acids possible.
First photographic records of the giant manta ray Manta birostris off eastern Australia
Authors: Couturier Lydie I. E. , Jaine Fabrice R. A. , Kashiwagi Tom
Published: January 2018

We present the first photographic evidence of the presence of the giant manta ray Manta birostris in east Australian waters. Two individuals were photographed off Montague Island in New South Wales and off the north east coast of Tasmania, during summer 2012 and 2014, respectively. These sightings confirm previous unverified reports on the species occurrence and extending the range of M. birostris to 40ºS. We discuss these findings in the context of the species’ migratory ecology, the regional oceanography along the south eastern Australian coastline and local productivity events.
Oviposition interval and gonotrophic concordance in Southeast Asian anophelines
Authors: Charlwood Jacques Derek D , Phala Nep , Sovannaroth Siv , Morgan John , Hemingway Janet , Chitnis Nakul , Briët Olivier JT
Published: January 2018

Mosquito survival and oviposition interval are important disease vector’s determinants that may vary within species depending on the environment. The length of the oviposition interval may be estimated by the proportion of mosquito ovaries with sacs. Fourteen species of Anopheles were collected from four locations in Cambodia and 1965 specimens were dissected. Both the number and predominant species collected varied according to location and trapping method. Five species were collected in sufficient numbers to allow comparisons between locations Sac rates differed between species but not within species between locations. Anopheles minimus had a higher sac rate in weeks leading up to a full moon. The more preserved environments supported more diverse anopheline fauna than the degraded environments. Despite the fact that many of the species occurred at very low densities there was no evidence of gonotrophic dissociation in any of the species. The principal malaria vector, An. dirus, was only common in one location where it was collected in miniature light-traps. It is suggested that a nationwide survey using such traps may help in determining patterns of malaria transmission in Cambodia.
CauseMap: Fast inference of causality from complex time series
Authors: Maher M. Cyrus , Hernandez Ryan D.
Published: January 2018

Background: Establishing health-related causal relationships is a central pursuit in biomedical research. Yet, the interdependent non-linearity of biological systems renders causal dynamics laborious and at times impractical to disentangle. This pursuit is further impeded by the dearth of time series that are sufficiently long to observe and understand recurrent patterns of flux. However, as data generation costs plummet and technologies like wearable devices democratize data collection, we anticipate a coming surge in the availability of biomedically-relevant time series data. Given the life-saving potential of these burgeoning resources, it is critical to invest in the development of open source software tools that are capable of drawing meaningful insight from vast amounts of time series data.

Results: Here we present CauseMap, the first open source implementation of convergent cross mapping (CCM), a method for establishing causality from long time series data (> ~25 observations). Compared to existing time series methods, CCM has the advantage of being model-free and robust to unmeasured confounding that could otherwise induce spurious associations. CCM builds on Takens’ Theorem, a well-established result from dynamical systems theory that requires only mild assumptions. This theorem allows us to reconstruct high dimensional system dynamics using a time series of only a single variable. These reconstructions can be thought of as shadows of the true causal system. If the reconstructed shadows can predict points from the opposing time series, we can infer that the corresponding variables are providing views of the same causal system, and so are causally related. Unlike traditional metrics, this test can establish the directionality of causation, even in the presence of feedback loops. Furthermore, since CCM can extract causal relationships from times series of, e.g. a single individual, it may be a valuable tool to personalized medicine. We implement CCM in Julia, a high-performance programming language designed for facile technical computing. Our software package, CauseMap, is platform-independent and freely available as an official Julia package.

Conclusions: CauseMap is an efficient implementation of a state-of-the-art algorithm for detecting causality from time series data. We believe this tool will be a valuable resource for biomedical research and personalized medicine.