bluuebunny/crossref_metadata_2025 huggingface dataset:
Cigarette smoking as a risk factor for acute respiratory distress syndrome: a systematic review and meta-analysis
Authors: Zhang Zhongheng
Published: January 2018

Background and objectives: Numerous experimental studies have linked cigarette smoking to lung injury. However, it is still debated on whether cigarette smoking is a risk factor for the development of acute lung injury/acute respiratory distress syndrome (ALI/ARDS). The study aimed to solve the controversy by performing systematic review and meta-analysis. Methods: Electronic databases including Pubmed, Google scholar, Embase and Scopus were searched from inception to April 2014. Studies investigated the association of cigarette smoking and ALI/ARDS were included. Non-randomized studies were assessment for their methodological quality by using Newcastle-Ottawa scale. Meta-analysis was performed by using random effects model and subgroup analyses were performed to address the clinical heterogeneity. Publication bias was assessed by using Egger’s test. Main result: Of the 17 studies included in our analysis, 15 provided data on effect size and were meta-analyzable. Component studies involved heterogeneous populations including major surgery, trauma, septic shock, general population, influenza A infection and transfusion. The combined results showed that cigarette smoking was not a risk factor for the development of ALI/ARDS (OR: 1.00, 95% CI: 0.99-1.01). In subgroup analysis, the same result was obtained in general population (OR: 2.03, 95% CI: 0.06-4.01), patients with major surgery or trauma (OR: 1.20, 95% CI: 0.48-1.93) and patients with other risks of ALI/ARDS (OR: 1.00, 95% CI: 0.99-1.01). Conclusion: Our study demonstrates that cigarette smoking is not associated with increased risk of ALI/ARDS in critically ill patients. However, the relationship in general population is still controversial and requires further confirmation.
Self-generated morphology in lagoon reefs
Authors: Blakeway David , Hamblin Michael G
Published: January 2018

The three-dimensional form of a coral reef develops through interactions and feedbacks between its constituent organisms and their environment. Reef morphology therefore contains a potential wealth of ecological information, accessible if the relationships between morphology and ecology can be decoded. Traditionally, reef morphology has been attributed to external controls such as substrate topography or hydrodynamic influences. Little is known about inherent reef morphology in the absence of external control. Here we use reef growth simulations, based on observations in the cellular reefs of Western Australia’s Houtman Abrolhos Islands, to show that reef morphology is fundamentally determined by the mechanical behaviour of the reef-building organisms themselves—specifically their tendency to either remain in place or to collapse. Reef-building organisms that tend to remain in place, such as massive and encrusting corals or coralline algae, produce nodular reefs, whereas those that tend to collapse, such as branching Acropora, produce cellular reefs. The purest reef growth forms arise in sheltered lagoons dominated by a single type of reef builder, as in the branching Acropora-dominated lagoons of the Abrolhos. In these situations reef morphology can be considered a phenotype of the predominant reef building organism. The capacity to infer coral type from reef morphology can potentially be used to identify and map specific coral habitat in remotely sensed images. More generally, identifying ecological mechanisms underlying other examples of self-generated reef morphology can potentially improve our understanding of present-day reef ecology, because any ecological process capable of shaping a reef will almost invariably be an important process in real time on the living reef.
The effects of venting and decompression on Yellow Tang (Zebrasoma flavescens) in the ornamental aquarium fish trade
Authors: Munday Emily S , Tissot Brian N , Heidel Jerry R , Miller-Morgan Tim
Published: January 2018

Each year, over 45 countries export 30 million fish from coral reefs as part of the global marine ornamental aquarium trade. This catch volume is affected by collection methods that cause mortality. Barotrauma caused by forced ascent of collected fish from depth has been determined to be a cause of post-collection mortality. The detrimental effects of barotrauma can be prevented by decompression, or mitigated with venting (puncturing the swim bladder to release expanded internal gas). To further evaluate the effects of collection methods on fish stress and mortality, we conducted the first comprehensive study on the effects of barotrauma prevention and mitigation practices on marine ornamental fish. We examined the effects of three ascent treatments, each with decompression stops of different frequency and duration coupled with or without venting, on sublethal effects and mortality in yellow tang (Zebrasoma flavescens), using histology and serum cortisol measurements. In Z. flavescens subjected to ascent without decompression stops or venting, a mean post-collection mortality of 6.2% occurred within 24h of capture. Common collection methods in the fishery, ascent without or with one decompression stop followed by venting, resulted in no mortality. Histopathologic examination of heart, liver, head kidney, and swim bladder tissues in fish 0d and 21d post-collection revealed no significant lesions in any treatment group. Ascent without decompression stops resulted in significantly higher serum cortisol than ascent with many decompression stops, and venting alone did not affect cortisol. Future work should examine links in the supply chain following collection to determine if further handling and transport stressors affect survivorship and sublethal effects.
Comparing two models that reduce the number of nephrology fellowship positions in the United States
Authors: Desai Tejas
Published: January 2018

There has been a steady decline in the number of applications to nephrology training programs. One solution is to decrease the number of available fellowship positions. Proponents believe that training programs have grown too big but the method for reduction has not been established. This investigation analyzes two models that decrease the number of available training positions and compares them head-to-head to identify the least burdensome method by which this reduction should occur. In the survival of the fittest model (SotFM) fellowship positions are eliminated if they were unfilled in the National Residency Match Program’s (NRMP) 2013 Specialty Match. In the equal proportions model (EPM) a formula is used to calculate a priority score using ESRD prevalence data from the 2013 USRDS Report and the geometric mean between a given jurisdiction’s current apportionment (n) and its next position (n+1). The least burdensome model is that which results in the 1) least number of jurisdictions losing fellow positions and 2) lowest percent reduction for any single jurisdiction. There were 416 nephrology positions offered and 47 unfilled in 2013. In the SotFM, 23 jurisdictions would sacrifice these 47 positions. In the EPM, 369 positions were apportioned (=416-47); only 9 jurisdictions would experience a reduction. The largest single-jurisdiction reduction in fellow positions was 67% (SotFM) and 50% (EPM). The EPM results in a less burdensome reduction of fellow positions nationwide. The EPM is a time-tested model that injects fairness into the painful process of reducing the total number of fellow positions across America.
Validation of the Emotiv EPOC EEG system for research quality auditory event-related potentials in children
Authors: Badcock Nicholas A , Preece Kathryn A , de Wit Bianca , Glenn Katharine , Fieder Nora , Thie Johnson , McArthur Genevieve
Published: January 2018

Background. Previous work has demonstrated that a commercial gaming electroencephalography (EEG) system, Emotiv EPOC, can be adjusted to provide valid auditory event-related potentials (ERPs) in adults that are comparable to ERPs recorded by a research-grade EEG system, Neuroscan. The aim of the current study was to determine if the same was true for children. Method. An adapted Emotive EPOC system and Neuroscan system were used to make simultaneous EEG recordings in nineteen 6- to 12-year-old children under “passive” and “active” listening conditions. In the passive condition, children were instructed to watch a silent DVD and ignore 566 standard (1000 Hz) and 100 deviant (1200 Hz) tones. In the active condition, they listened to the same stimuli, and were asked to count the number of ‘high’ (i.e. deviant) tones. Results. Intraclass correlations (ICCs) indicated that the ERP morphology recorded with the two systems was very similar for the P1, N1, P2, P2, and P3 ERP peaks (r = .78 to .95) in both passive and active conditions, but was poor for the mismatch negativity ERP component (MMN; r < .30). There were few differences between peak amplitude and latency estimates for the two systems. Conclusions. An adapted EPOC EEG system can be used to index children’s late auditory ERP peaks (i.e. P1, N1, P2, N2, P3) but not their MMN ERP component. Subjects: Psychiatry and Psychology Keywords: EEG, ERP, Emotiv EPOC, Validation, Mismatchnegativity, MMN, Intraclass correlation, Methods, Signal processing, Auditory odd-ball, Children
A research data sharing game
Authors: Pronk Tessa E , Wiersma Paulien H , van Weerden Anne , Schieving Feike
Published: January 2018

While reusing research data has evident benefits for the scientific community as a whole, decisions to archive and share these data are primarily made by individual researchers. In this paper we analyse, within a game theoretical framework, how sharing and reuse of research data affect individuals who share or do not share their datasets. We construct a model in which there is a cost associated with sharing datasets whereas reusing such sets implies a benefit. In our calculations conflicting interests appeared for researchers. Individual researchers are always better off not sharing and omitting the sharing cost, at the same time both sharing and not sharing researchers are better off if (almost) all researchers share. Namely, the more researchers share, the more benefit can be gained by the reuse of those datasets. We simulated several policy measures to increase benefits for researchers sharing or reusing datasets. Results point out that, although policies should be able to increase the rate of sharing researchers, and increased discoverability and dataset quality could partly compensate for costs, a better measure would be to directly lower the costs for sharing, or even turn it into a (citation-) benefit. Making data available would in that case become the most profitable, and therefore stable, strategy. This means researchers would willingly make their datasets available, and arguably in the best possible way to enable reuse, making other policy measures less pressing.
Construction of microRNA functional families by a mixture model of position weight matrices
Authors: Rhee Je-Keun , Shin Soo-Yong , Zhang Byoung-Tak
Published: January 2018

MicroRNAs (miRNAs) are small regulatory molecules that repress the translational processes of their target genes by binding to their 3' untranslated regions (3' UTRs). Because the target genes are predominantly determined by their sequence complementarity to the miRNA seed regions (nucleotides 2-7) which are evolutionarily conserved, it is inferred that the target relationships and functions of the miRNA family members are conserved across many species. Therefore, detecting the relevant miRNA families with confidence would help to clarify the conserved miRNA functions, and elucidate miRNA-mediated biological processes. We present a mixture model of position weight matrices for constructing miRNA functional families. This model systematically finds not only evolutionarily conserved miRNA family members but also functionally related miRNAs, as it simultaneously generates position weight matrices representing the conserved sequences. Using mammalian miRNA sequences, in our experiments, we identified potential miRNA groups characterized by similar sequence patterns that have common functions. We validated our results using score measures and by the analysis of the conserved targets. Our method would provide a way to comprehensively identify conserved miRNA functions.
Species loss in developed landscapes: an experimental evaluation
Authors: Shepack Alex , Freidenburg Kealoha , Skelly David
Published: January 2018

Conversion of landscapes for human uses is widely associated with loss of biodiversity. Here we focus on limits to distribution defined by intensity of landscape development. Using a translocation experiment, we ask does degradation of wetland habitat contribute to species loss? Wood frog larvae (Rana sylvatica = Lithobates sylvaticus), were reared within enclosures in 7 ponds harboring populations of wood frogs and in 5 ponds where they are absent. Survival, growth rate, and development rate were equivalent between ‘present’ and ‘absent’ ponds. While it is clear that landscapes surrounding ‘absent’ ponds had been heavily influenced by human use, we find no evidence that such wetlands provide inferior habitat for wood frog recruitment. Their absence in human altered landscapes may stem from influences outside of pond basins. The results provide a caution to the typically unexamined presumption that relictual habitats in developed landscapes are degraded in their utility for wildlife.
Population dynamics and orientation of the central Andean cushion Azorella compacta
Authors: Kleier Catherine , Trenary Tim , Graham Eric A , Rundel Philip W
Published: January 2018

Azorella compacta (llareta; Apiaceae), a large woody cushion plant, is a remarkable species forming dense cushions and characterizing the high elevation rocky slopes of the central Andean Altiplano. Field studies of an elevational gradient of A. compacta within Lauca National Park in northern Chile found a reverse J-shape distribution of size classes of individuals with abundant small plants at all elevations. A new elevational limit for A. compacta was found at 5250 m. A series of cushions marked 14 years earlier showed either slight shrinkage or small degrees of growth up to 2.2 cm yr-1. Despite their irregularity in growth, cushions of A. compacta show a strong orientation, centered on a north-facing aspect and angle of about 20o from horizontal. This exposure to maximize solar irradiance closely matches previous observations of a population favoring north-facing slopes at a similar angle. Populations of A. compacta appear to be stable, or even expanding, with young plants abundant and recolonization of disturbed habitats.
A Bayesian approach to optimizing stem cell cryopreservation protocols
Authors: Sambu Sammy
Published: January 2018

Cryopreservation is beset with the challenge of protocol alignment across a wide range of cell types and process variables. By taking a cross-sectional assessment of previously published cryopreservation data (sample means and standard errors) as preliminary meta-data, a decision tree learning analysis (DTLA) was performed to develop an understanding of target survival based on different approaches. Briefly, using a DTLA approach, a clear direction on the decision process for selection of methods was developed with key choices being the cooling rate, plunge temperature on the one hand and biomaterial choice, use of composites (sugars and proteins), loading procedure and cell location in 3D scaffold. Since machine learning and generalized approaches were employed, these metadata could be used to develop posterior probabilities via Naïve Bayes Classification (NBC) for combinatorial approaches that were not initially captured in the metadata. These results showed that newer protocol choices could lead to improved cell survival consistent with physical reports. In conclusion, this article proposes the use of DTLA models and NBC for the improvement of modern cryopreservation techniques through an integrative approach.Keywords: 3D cryopreservation, decision-tree learning (DTL), sugars, mouse embryonic stem cells, meta-data, Naïve Bayes Classifier (NBC)
Myocardial force generation and anoxia tolerance in the common cockle, Cerastoderma edule
Authors: Joyce William , Ozolina Karlina , Shiels Holly A
Published: January 2018

The myocardium of molluscs exhibits profound anoxia tolerance, however the cellular mechanisms underlying heart performance during normoxia and anoxia are not well understood. In the present study we investigated the role of the sarcoplasmic reticulum (SR) during normoxia and chemical anoxia (2 mM sodium cyanide) in electrically paced ventricle preparations from the common cockle (Cerastoderma edule) at ~19°C. Acute anoxia caused a substantial increase in resting tension but did not significantly affect the force of contraction, rate of contraction or rate of relaxation in myocardial preparations. SR inhibition (ryanodine, 10 µM; thapsigargin, 2 µM) attenuated the increase in resting tension, and also caused a significant decrease in the force of contraction during anoxia. During normoxia, SR inhibition reduced the force and rate of contraction by 20-30 % at contraction frequencies of 0.2 Hz and 0.5 Hz. SR inhibition also elicited an increase in resting tension at 0.5 Hz. Our results suggest that the SR plays a role in maintaining cardiac performance during anoxia in cockle myocardium. Furthermore, the SR is operative during normoxia and is relatively more important in the cockle heart than in many ectothermic vertebrates. As efforts to understand the evolution of the SR are advanced, anoxia tolerant invertebrates may serve as valuable model organisms.
Distinct binding modes and structural changes induced by cAMP and cGMP in the GAF domain of Anabaena adenylyl cyclase, CyaB2
Authors: Biswas Kabir H , Badireddy Suguna , Anand Ganesh S , Visweswariah Sandhya S
Published: January 2018

GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem (GAFab domain). In silico docking and mutational analysis indicated distinct modes of binding of cAMP and cGMP to the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by the highly sensitive Bioluminescence Resonance Energy Transfer (BRET) experiments. Amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments, however, revealed the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the structural changes induced by cAMP and cGMP binding to the GAF domain. Thus, our results provide an insight into structural mechanisms of ligand binding to GAF domains in general, which can be utilized in developing molecules that modulate the allosteric regulation by GAF domains in pharmacologically relevant proteins.
Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes
Authors: Jiang Liang , Zhu Huazhang , Xu Yinzhen , Ni Jiazuan , Zhang Yan , Liu Qiong
Published: January 2018

Background: The selenocysteine(Sec)-containing proteins, selenoproteins, are an important group of proteins present in all three kingdoms of life. Although the selenoproteomes of many organisms have been analyzed, systematic studies on selenoproteins in platyhelminthes are still lacking. Moreover, comparison of selenoproteomes between free-living and parasitic animals is rarely studied. Results: In this study, three representative organisms (Schmidtea mediterranea, Schistosoma japonicum and Taenia solium) were selected for comparative analysis of selenoproteomes in Platyhelminthes. Using a SelGenAmic-based selenoprotein prediction algorithm, a total of 37 selenoprotein genes were identified in these organisms. The size of selenoproteomes and selenoprotein families were found to be associated with different lifestyles: free-living organisms have larger selenoproteome whereas parasitic lifestyle corresponds to reduced selenoproteomes. Five selenoproteins, SelT, Sel15, GPx, SPS2 and TR, were found to be present in all examined platyhelminthes as well as almost all sequenced animals, suggesting their essential role in metazoans. Finally, a new splicing form of SelW that lacked the first exon was found to be present in S. japonicum. Conclusions: Our data provide a first glance into the selenoproteomes of organisms in the phylum Platyhelminthes and may help understand function and evolutionary dynamics of selenium utilization in diversified metazoans.
Using life history trade-offs to understand core-transient structuring of a small mammal community
Authors: Supp Sarah R , Koons David N. , Ernest S. K. Morgan
Published: January 2018

An emerging conceptual framework suggests that communities are composed of two main groups of species through time: core species that are temporally persistent, and transient species that are temporally intermittent. Core and transient species have been shown to differ in spatiotemporal turnover, diversity patterns, and importantly, survival strategies targeted at local vs. regional habitat use. While the core-transient framework has typically been a site-specific designation for species, we suggest that if core and transient species have local vs. regional survival strategies across sites, and consistently differ in population-level spatial structure and gene flow, they may also exhibit different life-history strategies. Specifically, core species should display relatively low movement rates, low reproductive effort, high ecological specialization and high survival rates compared to transient species, which may display a wider range of traits given that transience may result from source-sink dynamics or from the ability to emigrate readily in a nomadic fashion. We present results from 21 years of capture-mark-recapture data in a diverse rodent community, evaluating the linkages between temporal persistence, local abundance, and trade-offs among life-history traits. Core species at our site conservatively supported our hypotheses, differing in ecological specialization, survival and movement probabilities, and reproductive effort relative to transient species. Transient species exhibited a wider range of characteristics, which likely stems from the multiple processes generating transience in local communities, such as source-sink dynamics at larger regional scales or nomadic life history strategies. We suggest that trait associations among core-transient species may be similar in other systems and warrants further study.
High throughput screening of Toxoplasma gondii clones by PCR after limitation cloning
Authors: Liu Ting-Kai
Published: January 2018

Toxoplasma gondii is a kind of obligate intracellular parasites that are capable of infecting virtually all warm-blooded animals. It is one of the most common parasites in human. Serological studies estimated that up to a third of the global population has been chronically infected with the parsites. Toxoplasma gondii is also used as a model orgnisim of Apicomplexans that includes Plasmodium – the parasites that cause malaria. Gene knockout is a very important way to study gene function in all organisms. When it comes to Toxoplasma, it’s very difficult as this haploid parasite has strong adaptability to circumvent the condition of gene defects by gene duplication. High throughput screening at very early stage of transfection is very important for generating a true knockout of this parasite. For some genes that are required forToxoplasma gondii, the high throughput screening is necessary. Different labs use different protocols. After reading and practicing protocols from different papers or different labs, here I established an efficient pipeline for this purpose.
Nephila clavata L. Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae)
Authors: Hoebeke E. Richard , Huffmaster Wesley , Freeman Byron J
Published: January 2018

Nephila clavata L. Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.
Quantifying the variability of optimal cutpoints and reference values for diagnostic measures
Authors: Hirschfeld Gerrit , Zernikow Boris
Published: January 2018

Aim: Empirical studies in medicine – and most other fields of study - yield results that are uncertain to a certain degree. Medical research on interventions has made tremendous leaps forward by quantifying and reporting this uncertainty using p-values and confidence intervals. In contrast to this, most diagnostic studies that determine optimal cutpoints or reference values for diagnostic measures ignore that their outcomes, i.e. the specific cutpoints or normal ranges they recommend, are subject to chance variability. Methods: In this paper we use a simple simulation approach to quantify the variability of optimal cutpoints for two published studies. The first determined an optimal cutpoint for Becks Depression Inventory (BDI) in adults. The second determined reference values for Quantitative Sensory Testing (QST) in children. Results: We find that frequently employed cutpoints to interpret BDI scores and QST results are highly variable. For the BDI we find that replication of this study may identify values between 14 and 21 as optimal cutpoints. The lower cutpoint results in a misclassification of 15% of the healthy adults as depressed, the upper cutpoint results in a misclassification rate of 2%. For the QST we find that the upper end of the normal range HPT varies between 46.9 and 50.2 degrees Celsius. Conclusions: Based on our results we argue that researchers should be required to estimate and report the variability of reference values and optimal cutpoints for diagnostic tools. This may improve the harmonization of findings across studies and provides a rationale for planning future studies.
A novel approach to assess the dynamics of extra-chromosomal circular ribosomal DNA in human cells
Authors: Leheste Joerg R , Forbes Emily , DiGregorio Kristin , Katz Victoria , Miceli Alyssa , Husko Christopher , Ramos Raddy L , Torres German
Published: January 2018

Several nutrient-signaling pathways that extend life span have been described in model organisms. Thus, parallel and redundant signaling pathways that are similar across species might be subject to experimental manipulation. Here, we develop a PCR-based technique for testing the hypothesis that mitotic accumulation of extra-chromosomal ribosomal DNA circles might also determine life span in human cells. Using resveratrol, a phytochemical that counters age-related signs, we find treatment-dependent subcellular accumulations of extra-chromosomal 5S ribosomal DNA in human cell lines. These data suggest an association between DNA circles and intrinsic aging and demonstrate the utility of a PCR-based technique for studying the accumulation of dysfunctional molecules that promote senescence.
Evidence from studies in rodents and in isolated adipocytes that agonists of the chemerin receptor CMKLR1 may be beneficial in the treatment of type 2 diabetes
Authors: Wargent Ed T , Zaibi Mohamed S , O'Dowd Jacqueline F , Cawthorne Mike A , Wang Steven J Y , Arch Jonathan R S , Stocker Claire J
Published: January 2018

It is unclear whether the adipokine chemerin has pro- or anti-inflammatory properties, plays any role in the aetiology of obesity or type 2 diabetes, or whether agonists or antagonists of the chemerin receptor CMKLR1 have potential in the treatment of these diseases. To address these questions, we investigatedthe metabolic phenotypes of both male and female, CMKLR1 knockout and heterozygote mice; the effects of murine chemerin and some C-terminal peptides on glucose uptake in wild-type and CMKLR1 knockout adipocytes; and plasma chemerin levels and chemerin gene mRNA content in adipose tissue in models ofobesity and diabetes, and in response to fasting or administration of the insulin sensitizing drug rosiglitazone, which also has anti-inflammatory properties. Both male and female, CMKLR1 knockout and heterozygote mice displayed a mild tendency to obesity and impaired glucose homeostasis, but only when they were fed on a high fat, rather than a standard low fat diet. Obesity and impaired glucose homeostasis did not occur concurrently, suggesting that obesity was not the sole cause of impaired glucose homeostasis. Picomolar concentrations of chemerin and its C15- and C19-terminal peptides stimulatedglucose uptake in the presence of insulin by rat and mouse wild-type epididymal adipocytes, but not by murine CMKLR1 knockout adipocytes. The insulin concentration-response curve was shifted to the left in the presence of 40 pM chemerin or its C-15 terminal peptide. The plasma chemerin level was raised in diet-induced obesity and ob/ob but not db/db mice, and reduced by fasting and, in ob/ob mice, by treatment with rosiglitazone. These findings suggest that an agonist of CMKLR1 is more likely than an antagonist to be of value in the treatment of type 2 diabetes and have associated anti-obesity andanti-inflammatory activities. One mechanism by which an agonist of CMKLR1 might improve glucose homeostasis is by increasing insulin-stimulated glucose uptake by adipocytes.
First record of multi-species synchronous coral spawning from Malaysia
Authors: Cheliah Alvin J , Bin Amir Halimi , Hyde Julian , Yewdall Katie , Steinberg Peter D , Guest James R
Published: January 2018

Knowledge about the timing and synchrony of coral spawning has important implications for both the ecology and management of coral reef ecosystems, however,data on spawning timing and extent of synchrony are still lacking for many coral reefs, particularly from equatorial regions and from locations within the coral triangle. Here we present the first documentation of a multi-species coral spawning event from reefs around Pulau Tioman, Peninsular Malaysia, a popular diving and tourist destination located on the edge of the coral triangle. At least 8 coral species from 3 genera and 2 families participated in multi-species spawning over five nights in April 2014, between two nights before and two nights after the full moon. Two Acropora species (A. digitifera and A. tenuis) also spawned one night prior to the full moon in October 2014. While two species of Acropora (A. millepora and A. nasuta) exhibited highly synchronous spawning in April (100% of sampled colonies), two other common species (A. hyacinthus and A. digitifera) did not contain visible eggs in the majority of colonies sampled (i.e., <15% of colonies) in either April or October, suggesting that these species spawn at other times of the year. To the best of our knowledge, this is the first detailed documented observation of multi-species coral spawning from reefs in Malaysia and these data support the contention that this phenomenon is a feature of all speciose coral assemblages. More research is needed, however, to determine the seasonal cycles and extent of spawning synchrony on these reefs and elsewhere in Malaysia.
Trait correlates of distribution trends in the Odonata of Britain and Ireland: Southern species benefit from climate warming
Authors: Powney Gary D , Cham Steve SA , Smallshire Dave , Isaac Nick J B
Published: January 2018

A major challenge in ecology is understanding what enables certain species to persist, while others decline, in response to environmental change. Trait-based comparative analyses are useful in this regard as they can help identify the key drivers of decline, and highlight traits that promote resistance to change. Despite their popularity trait-based comparative analyses tend to focus on explaining variation in range shift and extinction risk, seldom being applied to actual measures of species decline. Furthermore they have tended to be taxonomically restricted to birds, mammals, plants and butterflies. Here we utilise a novel approach to estimate trends for the Odonata in Britain and Ireland, and examine trait correlates of these trends using a recently available trait dataset. We found the dragonfly fauna in Britain and Ireland has undergone considerable change between 1980 and 2012, with 33 and 39% of species showing significant declines and increases respectively. Distribution type was the key trait associated with these trends, where southern species showed significantly higher trends than widespread and northern species. We believe this reflects the impact of climate change as the increased ambient temperature in Britain and Ireland better suits species that are adapted to warmer conditions. We conclude that northern species are particularly vulnerable to climate change due to the combined pressures of a decline in climate suitability, and competition from species that were previously limited by lower thermal tolerance.
No evidence for differential biomass and mineral content in adult plants grown from dimorphic seeds of Suaeda aralocaspica
Authors: Wang Lei , Tian Chang-Yan , Huang Zhen-Ying
Published: January 2018

Producing two or more types of seeds by a single plant is known as seed heteromorphism. Comparison of seed traits or growth between plants grown from heteromorphic seeds has received considerable attention. However, information is scarce regarding the comparison of mineral content of adult plants from heteromorphic seeds. Here we present biomass and mineral profiles (Nitrogen, Phosphorus, Potassium, Sodium and Chloride) of adult plants grown from dimorphic seeds (non-dormant brown seeds and black seeds with non-deep physiological dormancy) of annual desert halophyte Suaeda aralocaspica at different levels of nutrient and salinity. The results showed that, although nutrient and salinity could affect dry weigh and mineral content, seed-dimorphic plants of S. aralocaspica did not show significant difference under the same experimental conditions. This study is one of the few to compare the physiological responses between seed-heteromorphic plants and suggests that mineral status is exactly consistent with growth performance for these plants.
Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing
Authors: Ashton Philip , Perry Neil , Ellis Richard J , Petrovska Liljana , Wain John , Grant Kathie , Jenkins Claire , Dallman Tim
Published: January 2018

The ability of Shiga toxin-producing Escherichia coli (STEC) to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx) subtype. Given the link between Stx2a subtype and disease severity, we sought to identify the stx subtypes present in whole genome sequences (WGS) of 444 isolates of STEC O157. Difficulties in assembling the stx genes in some strains, were overcome by using two complementary bioinformatics methods; mapping and de novo assembly. We compared the WGS analysis with the results obtained using a PCR approach and investigated the diversity within and between the subtypes. All strains of STEC O157 in this study had stx1a, stx2a or stx2c or a combination of these three genes. There was over 99% (442/444) concordance between PCR and WGS. When common source strains were excluded, 236/349 strains of STEC O157 had multiple copies of different Stx subtypes and 54 had multiple copies of the same Stx subtype. Of those strains harbouring multiple copies of the same Stx subtype, 33 had variants between the alleles while 21 had identical copies. Strains harbouring Stx2a only were most commonly found to have multiple alleles of the same subtype (42%). Both the PCR and WGS approach to stx subtyping provided a good level of sensitivity and specificity. In addition, the WGS data also showed there were a significant proportion of strains harbouring multiple alleles of the same Stx subtype associated with clinical disease in England.
Disentangling the sense of agency and the sense of ownership in the virtual hand illusion paradigm
Authors: Zhang Jing , Chen Wei , Li Hengwei , Hommel Bernhard , Yuan Tifei
Published: January 2018

We used the virtual hand illusion paradigm to study the relationship between two aspects of the minimal self: the sense of agency and the sense of (body) ownership. Converging evidence for the (at least) partial independence of agency and ownership was found. For instance, sense of agency was a better predictor of individual anxiety levels than sense of ownership, and males showed stronger effects related to agency, presumably due to gender-specific attribution styles and empathy skills. Taken together, our findings suggest that the sense of agency and the sense of ownership are driven by different kinds of information and related to different psychological functions.
Super-individual based model for fish migration
Authors: Babak Petro
Published: January 2018

One of the most remarkable characteristics of collective motion of fish is the emergence of complex migration patterns in which swimming fish are synchronised by remaining together and moving in the same direction. These migration patterns, referred to as fish schools, are often explained using individual based models (IBM’s) that focus on interactions between single individuals. The IBM’s appear to be realistic and robust; however, they are computationally unable to efficiently describe migration of large groups of fish. Here, an approach for developing computationally efficient super-individual based models from simple individual based models for fish migration is proposed. This approach accentuates on ecological mechanisms underlying collective motion of fish, and interaction between them; it explicitly incorporates such important mechanisms in collective motion of fish as fish school splitting and merging.
Early archosauromorph remains from the Permo-Triassic Buena Vista formation of NorthEastern Uruguay
Authors: Ezcurra Martin , Velozo Pablo , Meneghel Melitta , Piñeiro Graciela
Published: January 2018

The Permo-Triassic archosauromorph record is crucial to understand the impact of the Permo-Triassic mass extinction on the early evolution of the group and its subsequent dominance in Mesozoic terrestrial ecosystems. However, the Permo-Triassic archosauromorph record is still very poor in most continents and hampers the identification of global macroevolutionary patterns. Here we describe cranial and postcranial bones from the Permo-Triassic Buena Vista Formation of northeastern Uruguay that contribute to increase the meagre early archosauromorph record from South America. A basioccipital fused to both partial exoccipitals and three cervical vertebrae are assigned to Archosauromorpha based on apomorphies or a unique combination of characters. The archosauromorph remains of the Buena Vista Formation probably represent a multi-taxonomic assemblage composed of non-archosauriform archosauromorphs and a ‘proterosuchid-grade’ animal. This assemblage does not contribute in the discussion of a Late Permian or Early Triassic age for the Buena Vista Formation, but reinforces the broad palaeobiogeographic distribution of ‘proterosuchid grade’ diapsids in Permo-Triassic beds worldwide.
The neck of Barosaurus: longer, wider and weirder than those of Diplodocus and other diplodocines
Authors: Taylor Michael P , Wedel Mathew J
Published: January 2018

Barosaurus is a diplodocid sauropod from the Upper Jurassic Morrison Formation of the western United States, and is known for its very long neck. It is closely related to the sympatric Diplodocus, and often thought of as more or less identical except with a longer neck. The holotype YPM 429 includes three and a half posterior cervical vertebrae, somewhat distorted and damaged, which are nevertheless very distinctive and quite different from those of Diplodocus. The cervicals of the better known and more complete referred Barosaurus specimen AMNH 6341 show the same characteristic features as the holotype, though not to the same extent: transversely broad but anteroposteriorly short zygapophyseal facets; prezygapophyses carried on broad, squared-off rami; zygapophyses shifted forward relative to the centrum; diapophyses, parapophyses and neural spines shifted backwards; and broad diapophyseal “wings”. These features form a single functional complex, enabling great lateral flexibility, but restricting vertical flexibility. This may indicate that Barosaurus used a different feeding style from other sauropods perhaps sweeping out long arcs at ground level. The Morrison Formation contains at least nine diplodocid species in six to eight genera whose relationships are not yet fully understood, but Barosaurus remains distinct from its relatives.
Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)
Authors: Vann Laura , Kono Thomas , Pyhäjärvi Tanja , Hufford Matthew B. , Ross-Ibarra Jeffrey
Published: January 2018

The teosinte branched1 (tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maize tb1 allele in teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in teosinte. We assessed the prevalence of the Hopscotch element across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Additionally, we calculated population genetic summaries using sequence data from a subset of individuals from four teosinte populations and collected phenotypic data using seed from a single teosinte population where Hopscotch was found segregating at high frequency. Genotyping results indicate the Hopscotch element is found in a number of teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on the tb1 locus revealing a potential ecological role, but a greenhouse experiment does not detect a strong association between the Hopscotch and tillering in teosinte. Our findings suggest the role of Hopscotch differs between maize and teosinte. Future work should assess tb1 expression levels in teosinte with and without the Hopscotch and more comprehensively phenotype teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in teosinte.
Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours
Authors: Howlin Jill , Cirenajwis Helena , Lettiero Barbara. , Staaf Johan , Lauss Martin , Saal Lao , Borg Åke , Gruvberger-Saal Sofia K , Jönsson Göran B
Published: January 2018

CITED1 is a non-DNA binding transcriptional co-regulator whose expression can distinguish the ‘proliferative’ from ‘invasive’ signature in the phenotype-switching model of melanoma. We have found that, in addition to other 'proliferative' signature genes, CITED1 expression is repressed by TGFβ while the ‘invasive’ signature genes are upregulated. In agreement, CITED1 positively correlates with MITF expression and can discriminate the MITF-high/pigmentation tumor molecular subtype in a large cohort (120) of melanoma cell lines. Interestingly, CITED1 overexpression significantly suppressed MITF promoter activation, mRNA and protein expression levels while MITF was transiently upregulated following siRNA mediated CITED1 silencing. Conversely, MITF siRNA silencing resulted in CITED1 downregulation indicating a reciprocal relationship. Whole genome expression analysis identified a phenotype shift induced by CITED1 silencing and driven mainly by expression of MITF and a cohort of MITF target genes that were significantly altered. Concomitantly, we found changes in the cell-cycle profile that manifest as transient G1 accumulation, increased expression of CDKN1A and a reduction in cell viability. Additionally, we could predict survival outcome by classifying primary melanoma tumors using our in vitro derived ‘CITED1-silenced’ gene expression signature. We hypothesize that CITED1 acts a regulator of MITF, functioning to maintain MITF levels in a range compatible with tumourigenesis.
Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success
Authors: Kashiwagi Tom , Maxwell Elisabeth A , Marshall Andrea D , Christensen Ana B
Published: January 2018

Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTATM Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing.