bluuebunny/crossref_metadata_2025 huggingface dataset:
Your wish is my command! Influence of symbolic modelling on preschool children’s delay of gratification
Authors: Scarf Damian , Kumst Sahlia
Published: January 2018

Children’s ability to delay gratification is correlated with a range of positive outcomes in adulthood, showing the potential impact of helping young children increase their competence in this area. This study investigated the influence of symbolic models on 3-year-old children’s self-control. Eighty-three children were randomly assigned to one of three modelling conditions: personal story-telling, impersonal story-telling, and control. Children were tested on the delay-of-gratification maintenance paradigm both before and after being exposed to a symbolic model or control condition. Repeated measures ANOVA revealed no significant differences between the two story-telling groups and the control group, indicating that the symbolic models did not influence children’s ability to delay gratification. A serendipitous finding showed a positive relationship between children’s ability to wait and their production and accurate use of temporal terms, which was more pronounced in girls than boys. This finding may be an indication that a higher temporal vocabulary is linked to a continuous representation of the self in time, facilitating children’s representation of the future-self receiving a larger reward than what the present-self could receive.
Understanding of emotions and cardiovascular related diseases
Authors: Vlachakis Dimitrios , Vlachakis Chrisanthy
Published: January 2018

The aim of the present study is to examine the relation between understanding of emotions and cardiovascular related diseases, namely coronary heart disease, diabetes mellitus and obesity. Coronary heart disease is a type of cardiovascular disease that usually coexists with other diseases, such as diabetes mellitus and obesity. The uniqueness of this study lies in the fact that examined the relationship between the cardiovascular related diseases named above and the understanding of emotions in the context of Emotional Intelligence (EI). The latter consists of a wide range of psychological factors that reflect many aspects of human thought and behavior, providing a very comprehensive picture of each person. The experimental design through the observed variables were approached, has not been applied in previous studies internationally. The study was conducted in 300 participants during a 3 year period. All participants completed a self-report questionnaire, assessing various aspects of EI, such as self-emotion appraisal, other emotion appraisal, emotion regulation and use of emotions. As hypothesized, coronary heart disease is a prognostic factor of regulation of emotions. The results of this study extend and reinforce the findings of previous studies, which emphasize on the relationship of cardiovascular related diseases and psychological characteristics, such as anxiety and anger, being aspects of EI. Additionally, this work fills a gap in the relevant Greek literature, as a first attempt to examine the correlation of EI with cardiovascular related diseases. New approaches are needed to improve primary prevention, early detection and clinical management of those diseases. Furthermore, this study focused on the need to cultivate and improve EI of patients, in order to eliminate the effects of the diseases.
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols
Authors: Combs Peter A , Eisen Michael B
Published: January 2018

Recently, a number of protocols extending RNA-sequencing to the single-cell regime have been published. However, we were concerned that the additional steps to deal with such minute quantities of input sample would introduce serious biases that would make analysis of the data using existing approaches invalid. In this study, we performed a critical evaluation of several of these low-volume RNA-seq protocols, and found that they performed slightly less well in metrics of interest to us than a more standard protocol, but with at least two orders of magnitude less sample required. We also explored a simple modification to one of these protocols that, for many samples, reduced the cost of library preparation to approximately $20/sample.
Efficient algorithms for sampling feasible sets of abundance distributions
Authors: Locey Kenneth J. , McGlinn Daniel J.
Published: January 2018

Ecological variables such as species richness (S) and total abundance (N) can strongly influence ecological patterns. For example, the general form of the species abundance distribution (SAD) can often be explained by the majority of possible forms having the same N and S, i.e. the SAD feasible set. The feasible set reveals how variables determine observable variation, whether empirical patterns are exceptional to the majority of possible forms, and provides a constraint-based explanation for the ubiquity of hollow-curve SADs in nature. However, use of the feasible set has been limited to inefficient sampling algorithms that prevent large ecological communities and ecologically realistic combinations of N and S from being examined. This is the primary hindrance to using this otherwise novel perspective and theoretical framework. We developed efficient computational algorithms to generate random samples of the feasible set for the SAD and similar discrete distributions of abundance, including those that allow for zero-values, e.g., absences. We provide Python and R based implementations of our algorithms and tools for testing and using them. Our algorithms are often several orders of magnitude faster than a long-standing and recently used approach. This greatly increases the size and diversity of communities that can be examined with the feasible set approach and thus advances progress using constraint-based approaches to decipher ecological patterns.
Anthropogenic stress alters community concordance at the river-riparian interface
Authors: Tonkin Jonathan D , Stoll Stefan , Jähnig Sonja C , Haase Peter
Published: January 2018

Organisms often respond in similar ways to environmental or spatial gradients, particularly at large spatial scales, but patterns at finer scales and across ecotones are less certain. It is important to understand these relationships at multiple spatial scales, as managers often need suitable surrogate taxa for conservation and monitoring purposes. We explored whether community concordance at the river-riparian interface was decoupled by increasing anthropogenic stress (a gradient of local land-use intensity) at 15 sites over three years within the LTER site, Rhine-Main Observatory, a low mountain river system in central Germany. We assessed concordance between four organism groups: riparian spiders and carabid beetles, benthic macroinvertebrates, and combined aquatic macrophytes and riparian plants. This represented three different linkages: (1) predator-prey, (2) direct competition, and (3) habitat associations. While there were no correlations in richness patterns, multivariate community structure was highly concordant between all groups. Anthropogenic stress strongly reduced links between riparian spiders and carabid beetles, likely resulting from their shared resource requirements. However, increasing concordance occurred between plants and other groups. We posit that patterns may be resulting from two processes: (1) linkages between directly competing species decouple with increasing anthropogenic stress, and (2) stronger coupling may occur between habitat providers and dependent species when overall habitat complexity is reduced. These results highlight the complex manner in which anthropogenic stress can influence ecosystems and the importance of considering community structure when exploring biodiversity patterns in basic and applied ecological research, particularly at small scales and for surrogate taxa development.
Amyloid domains in the cell nucleus controlled by nucleoskeletal protein lamin B1 reveal a new pathway of mercury neurotoxicity
Authors: Arnhold Florian , Guehrs Karl-Heinz , von Mikecz Anna
Published: January 2018

Mercury (Hg) is a bioaccumulating trace metal that globally circulates the atmosphere and waters in its elemental, inorganic and organic chemical forms. While Hg represents a notorious neurotoxicant, the underlying cellular pathways are insufficiently understood. We identify amyloid protein aggregation in the cell nucleus as a novel pathway of Hg-bio-interactions. By mass spectrometry of purified protein aggregates a subset of spliceosomal components and nucleoskeletal protein lamin B1 were detected as constituent parts of an Hg-induced nuclear aggregome network. The aggregome network was located by confocal imaging of amyloid-specific antibodies and dyes to amyloid cores within splicing-speckles that additionally recruit components of the ubiquitin-proteasome system. Hg significantly enhances global proteasomal activity in the nucleus suggesting that formation of amyloid speckles plays a role in maintenance of protein homeostasis. RNAi knock down showed that lamin B1 for its part regulates amyloid speckle formation and thus likewise participates in nuclear protein homeostasis. As the Hg-induced cascade of interactions between the nucleoskeleton and protein homeostasis reduces neuronal signalling, amyloid fibrillation in the cell nucleus is introduced as a feature of Hg-neurotoxicity that opens new avenues of future research. Similar to protein aggregation events in the cytoplasm that are controlled by the cytoskeleton, amyloid fibrillation of nuclear proteins may be driven by the nucleoskeleton.
Research groups: how big should they be?
Authors: Cook Isabelle , Grange Sam , Eyre-Walker Adam
Published: January 2018

We have investigated the relationship between research group size and productivity in the life sciences in the United Kingdom using data from 398 principle investigators (PIs). We show that the number of publications increases linearly with group size, but that the slope is modest relative to the intercept, and that the relationship explains little of the variance in productivity. A comparison of the slope and intercept suggests that PIs contribute on average 5-times more productivity than an average group member and using multiple regression we estimate that post-doctoral researchers are approximately 3–times more productive than PhD students. We also find that the impact factor and the number of citations are both non-linearly related to group size such that there is a maximum. However, the relationships explain little of the variance and the curvatures are shallow so the impact factor and the number of citations do not greatly depend upon group size. The intercept is large relative to curvature suggesting that the PI is largely responsible for the impact factor and the number of citations from their group. Surprisingly we find this non-linear relationship for post-docs, but for PhD students we observe a slight but significant decrease in the impact factor. The results have important implications for the funding of research. Given a set number of Pis there is no evidence of diminishing returns in terms of the number of papers published and only a very weak cost to very large groups in terms of where those papers are published and the number of citations they receive. However, the results do suggest that it might be more productive to invest in new permanent members of faculty rather than additional post-docs and PhD students.
Demographics and feeding ecology of whale sharks at Mafia Island, Tanzania
Authors: Cagua Edgar F , Cochran Jesse , Rohner Chris , Igulu Mathias M , Rubens Jason , Pierce Simon J , Berumen Michael L
Published: January 2018

Background. The Western Indian Ocean is a globally important region for the whale shark Rhincodon typus, with well-studied coastal aggregation sites in southern Mozambique, Seychelles and Djibouti. Here we present an overview of a new study at Mafia Island, Tanzania. Methods. We monitored whale shark abundances on 103 boat trips from October 2012–March 2013. We also used passive acoustic telemetry (VEMCO® V16 tags) and photographic identification to monitor the residency times and local movements of 29 tagged individuals. Shark sizes were estimated using laser photogrammetry. Results. In total we observed 87 individual sharks with a mean of 5.1 ± 5.2 (± SD) per trip and a peak in December of 8.2 ± 6.3. Total length ranged from 4.1 to 9.7 m and almost all sharks were immature. After boat-based visual observations dropped to zero in March 2013 (with the same ongoing sampling effort), the acoustic array still detected 75% of tagged sharks. Tagged individuals were detected by the acoustic array for 73 ± 40 days on average. They showed a strong site fidelity to a 15 km2 area in the inner part of the bay and then progressively moved offshore at the end of the season, matching a decrease in plankton abundance. Sharks were mostly observed feeding on dense patches of the pelagic shrimp Lucifer hanseni, often in association with planktivorous fishes. Photo IDs from 2007-09 and 2012-13 indicate that a large proportion of the juvenile individuals return to Mafia Island each spring-summer. Conclusion. The size range and gender distribution of whale sharks at Mafia Island is similar to other coastal aggregations in the Indian Ocean, but the relatively high site fidelity and residency time stands in contrast.
Isolation and identification of Yersinia and Pseudomonas sp. from Australian milk and salad using 16s rDNA
Authors: Nawaz Malik A , Bhattarai Rewati Raman
Published: January 2018

A systematic research was conducted for the isolation and identification of undesirable microorganisms in food products using molecular approach. The result revealed the presence of Yersinia aleksiciae and Pseudomonas fluorescens strains in Australian pasteurized milk and mixed salad respectively. Y. aleksiciae grouped as lacking virulence marker and is regarded non-pathogenic. P. fluorescens has been identified as a marker of spoilage of ready-to-eat vegetable salads. This study confirms the rapidity and sensitivity of 16s rDNA analysis in identifying strains which contribute in early monitoring, accurate analysis and control of microbial risks in food products. The described methodology has special relevance in food quality control and safety.
An ecological implication of glandular trichome-sequestered artemisinin: as a sink of biotic/abiotic stress-triggered singlet oxygen
Authors: He Jiang , Gao Qian , Liao Tao , Zeng Qing-Ping
Published: January 2018

Artemisinin is accumulated in wormwood (Artemisia annua) with uncertain ecological implications. Here, we suggest that artemisinin is generated in response to biotic/abiotic stress, during which dihydroartemisinic acid, a direct artemisinin precursor, quenches singlet oxygen (1O2), one kind of reactive oxygen species. Evidence supporting artemisinin as a sink of 1O2 emerges from that volatile isoprenoids protect plants from biotic/abiotic stress; biotic/abiotic stress induces artemisinin biosynthesis; and stress signaling pathways are involved in the biosynthesis of volatile isoprenoids among plants as well as the biosynthesis of artemisinin in A. annua. In this review, we address the ecological implication of glandular trichome-sequestered artemisinin as a sink sink of biotic/abiotic stress-triggered 1O2 , and also summarize the cumulating data on the transcriptomic and metabolic profiling of stress-enhanced artemisinin production upon eliciting 1O2 omission from chloroplasts and initiating retrograde 1O2 signaling from chloroplasts to nuclei.
The geographic scaling of biotic interactions
Authors: Araújo Miguel B , Rozenfeld Alejandro
Published: January 2018

A central tenet of ecology and biogeography is that the broad outlines of species ranges are determined by climate, whereas the effects of biotic interactions are manifested at local scales. While the first proposition is supported by ample evidence, the second is still a matter of controversy. To address this question, we develop a mathematical model that predicts the spatial overlap, i.e., co-occurrence, between pairs of species subject to all possible types of interactions. We then identify the scale in which predicted range overlaps are lost. We found that co-occurrence arising from positive interactions, such as mutualism (+/+) and commensalism (+/0), are manifested across scales of resolution. Negative interactions, such as competition (-/-) and amensalism (-/0), generate checkerboard-type co-occurrence patterns that are discernible at finer resolutions. Scale dependence in consumer-resource interactions (+/-) depends on the strength of positive dependencies between species. Our results challenge the widely held view that climate alone is sufficient to characterize species distributions at broad scales, but also demonstrate that the spatial signature of competition is unlikely to be discernible beyond local and regional scales.
Assessing the reproducibility of discriminant function analyses
Authors: Andrew Rose L , Albert Arianne YK , Renaut Sebastien , Rennison Diana J , Bock Dan G , Vines Tim
Published: January 2018

Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. While data files may be securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an excellent case study to test reproducibility. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA, used complex and unique data transformations, or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 16 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or incomplete data sets. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was high (20 of 25 and 43 of 59 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 36 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (66%) of 70 datasets. While our results are encouraging, they highlight the fact that science still has some way to go before we have the carefully curated and reproducible research that the public expects.
A new unsupervised binning method for metagenomic dataset with automated estimation of number of species
Authors: Liu Yun , Hou Tao , Fu Liu
Published: January 2018

One necessary step of metagenome analysis is to assign sequences to classes according to their taxonomic origins. Unsupervised binning method is one of the two binning categories. However existing unsupervised binning methods yield to estimate the species number automatically and accurately. In this paper, a new unsupervised binning method based on an improved fuzzy c-means method (iFCM) is presented for metagenomic dataset. First, a range of the number of bins is obtained by the relationship among sequencing depth, number of reads and average read length. Secondly, iFCM algorithm is implemented several times with the initial number of bins in this range. Finally, the number of bins is determined by a clustering validity, modified partition coefficient. Experimental results show that this method is an effective unsupervised binning method for metagenomic dataset and could estimate the species number more accurately than MetaCluster3.0 and AbundanceBin.
Exome sequencing and prediction of long-term kidney allograft function
Authors: Mesnard Laurent , Muthukumar Thangamani , Burbach Maren , Li Carol , Shang Huimin , Dadhania Darshana , Lee John R , Sharma Vijay K , Xiang Jenny , Suberbielle Caroline , Carmagnat Maryvonnick , Ouali Nacera , Rondeau Eric , Friedewald John J , Abecassis Michael M , Suthanthiran Manikkam , Campagne Fabien
Published: January 2018

Current strategies to improve graft outcome following kidney transplantation consider information at the HLA loci. Here, we used exome sequencing of DNA from ABO compatible kidney graft recipients and their living donors to determine recipient and donor mismatches at the amino acid level over entire exomes. We estimated the number of amino acid mismatches in transmembrane proteins, more likely to be seen as foreign by the recipient’s immune system, and designated this tally as the allogenomics mismatch score (AMS). The AMS can be measured prior to transplantation with DNA for potential donor and recipient pairs. We examined the degree of relationship between the AMS and post-transplantation kidney allograft function by linear regression. In a discovery cohort, we found a significant inverse correlation between the AMS and kidney graft function at 36 months post-transplantation (n=10 recipient/donor pairs; 20 exomes) (r2>=0.57, P<0.05). The predictive ability of the AMS persists when the score is restricted to regions outside of the HLA loci. This relationship was validated using an independent cohort of 24 recipient donor pairs (n=48 exomes) (r2>=0.39, P<0.005). In an additional cohort of living and mostly intra-familial recipient/donor pairs (n=19, 38 exomes), we validated the association after controlling for donor age at time of transplantation. Finally, a model that controls for donor age, HLA mismatches and time post-transplantation yields a consistent AMS effect across these three independent cohorts (P<0.05). Taken together, these results show that the AMS is a strong predictor of long-term graft function in kidney transplant recipients.
Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults
Authors: Paal Tunde , Carpenter Thomas , Nettle Daniel
Published: January 2018

There is evidence to suggest that impulsivity is predicted by socioeconomic background, with people from more deprived backgrounds tending to be more impulsive, and by current mood, with poorer mood associated with greater impulsivity. However, impulsivity is not a unitary construct, and previous research in this area has focused on measures of ‘waiting’ impulsivity rather than behavioural disinhibition. We administered a standard measure of behavioural disinhibition, the stop-signal task, to 58 adult participants from a community sample. We had measured socioeconomic background using participant postcode at age 16, and assigned participants to receive either a neutral or a negative mood induction. We found no effects of mood on behavioural disinhibition, but we found a significant effect of socioeconomic background. Participants with more deprived postcodes at age 16 showed longer stop-signal reaction times, and hence greater behavioural disinhibition. The pattern was independent of participant age and overall reaction time. Greater behavioural disinhibition may be a consequence of experiencing childhood socioeconomic deprivation, and could play a role in maintaining social gradients in outcomes such as addiction.
Colorless agar for enhanced color contrast between microbial colonies and solid medium
Authors: Ng Wenfa
Published: January 2018

Solid medium enables spatially resolved simultaneous cultivation of different microbes in a simple and relatively low cost format useful for preliminary screening of microbial diversity. Lack of color contrast between colonies and agar, however, hampers colony identification by automated image analysis, which is a challenge for phenotype screening experiments and viable cell counting. Since microbes secrete pigments of myriad hues, this research sought to develop a colorless agar, which when placed on colored paper of suitable hue, would enhance the color contrast between agar and colonies of any color. However, practical realization of the concept is hampered by heat-induced formation of colored compounds between medium components during autoclave sterilization, which in this study, was prevented by dissolving glucose and ammonium chloride in two separate solutions (each containing other medium components). Mixing the two sterilized solutions at 48 oC yielded a colorless agar, which remained colorless even after adding sterile yeast extract (max: 1 g/L) for providing essential vitamins to microbes unable to synthesize them. Culture experiments revealed good growth of Escherichia coli DH5α (ATCC 53868), Pseudomonas protegens Pf-5 (ATCC BAA-477), Pseudomonas aeruginosa (ATCC 15442), and Bacillus subtilis (ATCC 8473) with cell yield positively correlated with yeast extract concentration. Additionally, identical viable cell concentration and colonies of similar morphologies were observed on both the colorless and LB agar; thus, suggesting that no inhibitory compounds were formed during agar preparation. Collectively, using commonly used buffer components as well as salts and nutrients, a colorless agar was prepared by segregating chromogenic compounds during heat sterilization; thus, suggesting its use for enhancing color contrast between colonies and agar in revealing finer details of pure culture colonies, or more accurate automated colony identification and counting in screening and viable cell count assays.
A newly developed dispersal metric indicates the succession of benthic invertebrates in restored rivers
Authors: Li Fengqing , Sundermann Andrea , Stoll Stefan , Haase Peter
Published: January 2018

Dispersal capacity plays a fundamental role in the riverine benthic invertebrate colonization of new habitats that emerges following flash floods or restoration. However, an appropriate measure of dispersal capacity for benthic invertebrates is still lacking. The dispersal of benthic invertebrates occurs mainly during the aquatic (larval) and aerial (adult) life stages, and the dispersal of each stage can be further subdivided into active and passive modes. Based on these four possible dispersal modes, we first developed a metric (which is very similar to the well-known and widely used saprobic index) to estimate the dispersal capacity for 528 benthic invertebrate taxa by incorporating a weight for each mode. Second, we tested this metric using benthic invertebrate community data from a) 23 large restored river sites with improvements of river bottom habitats dating back 1 to 10 years, b) 23 unrestored sites, and c) 298 adjacent surrounding sites in the low mountain and lowland areas of Germany. We hypothesize that our metric will reflect the temporal succession process of benthic invertebrate communities colonizing the restored sites, whereas no temporal changes are expected in the unrestored and surrounding sites. By applying our metric to these three river treatment categories, we found that the average dispersal capacity of benthic invertebrate communities in the restored sites significantly decreased in the early years following restoration, whereas there were no changes in either the unrestored or the surrounding sites. After all taxa had been divided into quartiles representing weak to strong dispersers, this pattern became even more obvious; strong dispersers colonized the restored sites during the first year after restoration and then significantly decreased over time, whereas weak dispersers continued to increase. The successful application of our metric to river restoration might be promising in further applications of this metric, for example, in assessments of rivers or metacommunity structure.
A reappraisal of the Middle Triassic chirotheriid Chirotherium ibericus Navás, 1906 (Iberian Range NE Spain), with comments on the Triassic tetrapod track biochronology of the Iberian Peninsula
Authors: Díaz-Martínez Ignacio , Castanera Diego , Gasca José Manuel J.M. , Canudo José Ignacio
Published: January 2018

Triassic vertebrate tracks are known from the beginning of the 19th century and have a worldwide distribution. Several Triassic track ichnoassemblages and ichnotaxa have a restricted stratigraphic range and are useful in biochronology and biostratigraphy. The record of Triassic tracks in the Iberian Peninsula has gone almost unnoticed although more than 25 localities have been described since 1897. In one of these localities, the naturalist Longinos Navás described the ichnotaxon Chirotherium ibericus in 1906.The vertebrate tracks are in two sandy slabs from the Anisian (Middle Triassic) of the Moncayo massif (Zaragoza, Spain). In a recent revision, new, previously undescribed vertebrate tracks have been identified. The tracks considered to be C. ibericus as well as other tracks with the same morphology from both slabs have been classified as Chirotherium barthii. The rest of the tracks have been assigned to Chirotheriidae indet., Rhynchosauroides isp. and undetermined material. This new identification of C. barthii at the Navás site adds new data to the Iberian record of this ichnotaxon, which is characterized by the small size of the tracks when compared with the main occurrences of this ichnotaxon elsewhere. As at the Navás tracksite, the Anisian C. barthii-Rhynchosauroides ichnoassemblage has been found in other coeval localities in Iberia and worldwide. This ichnoassemblage belongs to the upper Olenekian-lower Anisian interval according to previous biochronological proposals. Analysis of the Triassic Iberian record of tetrapod tracks is uneven in terms of abundance over time. From the earliest Triassic to the latest Lower Triassic the record is very scarce, with Rhynchosauroides being the only known ichnotaxon. Rhynchosauroides covers a wide temporal range and gives poor information for biochronology. The record from the uppermost Lower Triassic to the Middle Triassic is abundant. The highest ichnodiversity has been reported for the Anisian with an assemblage composed of Dicynodontipus, Procolophonichnium, Rhynchosauroides, Rotodactylus, Chirotherium, Isochirotherium, Coelurosaurichnus and Paratrisauropus. The Iberian track record from the Anisian is coherent with the global biochronology proposed for Triassic tetrapod tracks. Nevertheless, the scarcity of track occurrences during the late Olenekian and Ladinian prevents analysis of the corresponding biochrons. Finally, although the Iberian record for the Upper Triassic is not abundant, the presence of Eubrontes, Anchisauripus and probably Brachychirotherium is coherent with the global track biochronology as well. Thus, the Triassic track record in the Iberian Peninsula matches the expected record for this age on the basis of a global biochronological approach, supporting the idea that vertebrate Triassic tracks are a useful tool in biochronology.
A(a)LS: Ammonia-induced amyotrophic lateral sclerosis
Authors: Parekh Bhavin K
Published: January 2018

Amyotrophic lateral sclerosis (ALS) is a dreadful, devastating and incurable motor neuron disease. Aetiologically, it is a multigenic, multifactorial and multiorgan disease. Despite intense research, ALS pathology remains unexplained. After the literature review, this paper posits a new integrative explanation. This framework proposes that ammonia neurotoxicity is a main player in ALS pathogenesis. According to this explanation, a combination of impaired ammonia removal— mainly because of impaired hepatic urea cycle dysfunction—and increased ammoniagenesis— mainly because of impaired glycolytic metabolism in fast twitch skeletal muscle—causes chronic hyperammonia in ALS. In the absence of neuroprotective calcium binding proteins (calbindin, calreticulin and parvalbumin), elevated ammonia—a neurotoxin—damages motor neurons. Ammonia-induced motor neuron damage occurs through multiple mechanisms such as macroautophagy-endolysosomal impairment, ER-stress, CDK5 activation, oxidative/nitrosative stress and neuroinflammation. Furthermore, the regional pattern of calcium binding proteins’ loss, owing to either ER stress and/or impaired oxidative metabolism, determines clinical viabilities of ALS. Most importantly, this new framework can be generalised to explain other neurodegenerative disorders such as Huntington’s disease.
Blood targeted proteomics: centrifugal filter sample preparation vs dilute-and-shoot
Authors: Vehus Tore , Brandtzaeg Ole Kristian , Lundanes Elsa , Wilson Steven Ray
Published: January 2018

Blood has a complex proteome with a huge span of protein abundances, and we are currently exploring sample preparation strategies addressing this potential challenge. We first evaluated the possibility to simply reduce complexity by fractionating blood samples (prior to targeted proteomics), using combinations of centrifugal filters that are promoted as having differing molar mass (M M ) selectivity. However, systematic fractionation was not possible, as the units had surprisingly unpredictable M M filtration profiles. Hence, labeling implying M M selectivity of centrifugal filters shouldn’t be taken literally. One filter combination (100+50K) however appeared to reduce human serum albumin (HSA) compared with much of the proteome (assessed using gel electrophoresis and staining). However, for our target protein beta-catenin, a “dilute-and-shoot” approach (without any attempt to remove high abundant proteins) was what enabled identification of beta-catenin in blood with nano liquid chromatography mass spectrometry (nano-LC-MS). Thus, minimal sample preparation can be an option in targeted blood proteomics. All blood samples prepared and analyzed (using ultrafast nano-LC-MS) were of considerable complexity, and we document the importance of using external standard spiking and minimum three MS/MS transitions to confirm the presence of target proteins.
An integrated phylogenetic analysis of turtles
Authors: Pereira Anieli , Schrago Carlos
Published: January 2018

Background. Testudines is a reptilian order with unique morphological features among vertebrates. This order is currently divided into two suborders: Pleurodira and Cryptodira; which comprises approimately 14 extant families with 95 genera, about 320 species. Phylogenetic affinities below the family level remain largely unresolved. The main discrepancies among previous studies concern the position of the superfamily Trionychoidea and the families Chelydridae and Platystenidae. The recent improvement in combined phylogenetic inference and divergence time estimates, as well as the increased taxon sampling available in databases, prompted us to investigate their evolutionary relationships. Methods. In order to clarify the phylogenetic relatioships of Testudines, we inferred phylogenies from two datasets: (1) molecular dataset based on 12 genes, including 294 species; and (2) total evidence based on 12 genes plus 235 morphologic caracteres from the matrix of Sterli et al. (2013), including 28 extant and 69 extinct taxa. Maximum likelihood phylogenetic inference was performed with the data set partitioned into: (1) molecular nuclear data under GTR model of substitution, and (2) morphological data under Mk model. Statistical support for clades was assessed with 2000 nonparametric bootstrap replicates (BT). Results. Our results supported a split between Pleurodira and Cryptodira (BT > 97). In Cryptodira, we inferred an early split between Trionychoidea and all other Cryptodira, known as Durocryptodira (BT = 100). The monophyly of all families and superfamilies were recovered with high support (BT=100), except for the family Podocnemididae (BT=59). In both analyses, Chelydridae was recovered as sister-group to the superfamily Kinosternoidae (BT=99). With regard to Platysternidae, this monotypic asian family would split from Emydidae in the molecular phylogeny (BT = 81), whereas in the total analysis this split was between Emydidae and all remaining Testudinoidea: Emydidae + Geomydidae + Testudinidae. Discussion. All 14 families were represented in both analyses, although the molecular analysis contains 294 species-level taxa and total-evidence one has only 29 genus-level taxa. Pleurodira and Cryptodira were recovered as monophyletic as in most previous works. Trionychoidea was recovered as a clade within Cryptodira, in contrast to previous hypotheses, which placed this superfamily either as sister to Pleurodira or Cryptodira, or as sister group of all Testudines altogether. Chelydridae was recovered as sister-group of Kinosternoidae, whereas Platysternidae, a monotypic Asian family, was recovered as a member of Testudinoidae; although his position within the group was conflicting. This position of Platysternidae was the only conflict between crown groups found between our datasets.
Age estimation for Asian Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) implying phylogeographic inference
Authors: Biswal Devendra K , Marbaniang Jean V , Tandon Pramod
Published: January 2018

Abstract: Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and bio-geographers. The focus had always been on woody land plants rather than on herbs. Orchidaceae is one such family belonging to angiosperms, with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and bio-geographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of Cymbidiums was reconstructed based on sequence analyses of internal transcribed spacer (ITS2) regions and maturaseK (matK) from the chloroplast region available on the public domain in GenBank at NCBI. Crassulacean acid metabolism (CAM) is one of the photosynthetic pathways regarded as adaptation to water stress in land plants. Hardly any information exists on correlations among the level of CAM activity, habitat, life form, and phylogenetic relationship of a plant group from an evolutionary perspective. This study examines a genus level analyses by integrating ITS and matK data to all fossil data available on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary plasticity of photosynthetic characters. Our study has enabled age estimations for the genus Cymbidum (12Ma) for the first time using BEAST by addition of previously analyzed two internal calibration points.
Megalochelys: gigantic tortoise from the Neogene of Myanmar
Authors: Hirayama Ren , Sonoda Teppei , Takai Masanaru , Htike Thaung , Maung Thein Zin Maung , Takahashi Akio
Published: January 2018

Background. The genus Megalochelys is the largest known testudinid (family Testudnidae) found from the upper Miocene to lower Pleistocene of India to Indonesian Islands. The maximum length of the shell in this genus has been estimated as up to about 2 m long based on a specimen from the lower Pleistocene of Java Island, Indonesia. Recently, joint paleontological expeditions of Japan and Myanmar led by M. Takai have unearthed abundant fossils of this genus from the Neogene since 2003. These materials shed new light on this unique gigantic tortoise. Methods. All materials of Megalochelys were found from the Lower Irrawaddy Beds in poor preservation except for one nearly complete shell. The shell lengths from the fragmentary materials were estimated by using those of medium to large–sized testudinids. Results. Postcranial materials, including twenty-five epiplastra, one cervical vertebra, appendicular skeletons, and one nearly complete shell (about 180 cm long) have been discovered from the Lower Irrawaddy Beds in narrow area near Pauk Township. They are associated with terrestrial mammals such as Stegodon, suggesting that the age of the fossil bearing beds are attributed to the late Miocene to the early Pliocene. Of these, the epiplastra in two morphological states appear to be derived from sexual dimorphism of this genus as seen in several testudinids and noted previously by second author on the relevant materials. A huge distal portion of the humerus (ca. 31 cm long) suggests that its original length was about 75 cm. Discussion. A nearly complete shell is about 180 cm long, although this seems a rather young male individual of Megalochelys based on its rather slender epiplastral morphology, which is nearly as large as given estimation of the maximum shell length from Java material. On the other hand, the largest humerus, estimated as 75 cm in original length, suggests its shell was about 270 cm long. This estimation seems to be supported by other isolated materials such as the nuchal plate, largest epiplastron, and the pectoral girdle. Hitherto, Stupendemys geographica (from the Pliocene of Venezuela) and Archelon ischyros (from the Lower Cretaceous of North America) were regarded as largest known turtles with about 220 cm long shell. However, Megalochelys from Myanmar involves much larger specimens, suggesting this is a true largest known turtle.
Three-taxon analysis can always successfully recognize groups based on putative reversals
Authors: Mavrodiev Evgeny V
Published: January 2018

Three-taxon analysis in it canonical form can always successfully recognize groups based on putative reversals if latter are coded as separate states before three-taxon permutations are derived from conventional matrices. This way of coding removes incongruence from either conventional multistate or three-taxon matrices and makes the discussions about symplesiomorphy as a putative homology unnecessary. The ability of conventional parsimony to recognize reversal-based clades is technically nothing more than grouping by plesiomorphic values. Therefore this solution cannot be accepted as a Cladistic approach to data and must be correctly classified as “post-Hennigian” or “phenetic”. The ability of three-taxon analysis to recognize groups based on the putative reversals may be viewed as a heuristic cladistics attempts to prevent this “phenetic” approach affecting the analysis of the data.
Tyrannosaurids didn't use their claws in combat
Authors: Yun Chan-gyu
Published: January 2018

Rothschild (2013) suggested that many of the facial and postcranial scars in tyrannosaurid specimens are in fact caused by claws of the other tyrannosaurids. However, the evidences suggested by Rothschild (2013) are very weak. Tooth marks can have very different shapes with real tooth sections or shapes, and multi-ton giants like tyrannosaurids would have been impossible to kick each others' faces. Also, the very short, range limited tyrannosaurid forelimbs would be impossible to hit the opponents' faces.
Assessment of Posidonia oceanica status along the north Croatian coast (Adriatic Sea)
Authors: Guala Ivan , Iveša Ljiljana , Krstinić Patrik , Jakl Zrinka , Šijan Milena , Prvan Mosor , Sertic Maya , Špika Matea , Nikolić Vedran , Žuljević Ante , Cvitković Ivan , Di Carlo Giuseppe , Rajković Željka
Published: January 2018

Monitoring of Posidonia oceanica was carried out in the framework of the MedMPAnet Project in eight meadows not formerly explored in an area along the north coast of Croatia (Primorje-Gorski Kotar County, Northern Adriatic Sea). The survey was aimed to collect preliminary data as a baseline for future surveillance cycles of the priority habitat 1120 "Posidonia beds" within the framework of the National Monitoring Programme, according to the requirements of the EU Habitats Directive. Fieldwork was carried out in 2013 and 2014 through direct SCUBA diving surveys. At each site, general information on coastal features and potential human pressures was recorded and the following descriptors of meadow conditions were assessed at three depth ranges: shoot density, percent coverage of Posidonia oceanica, dead matte and substrate type; depth and type of lower limits were also recorded for each meadow. Two meadows, located in the island of Rab (Uvala Planka and Frkanj), were investigated during both years of survey in order to test any differences due to the methodological approach we used. Overall, results indicated signs of distress for several meadows. Density ranged from 355±22 to 629±21 shoot per m2 at shallow stations (<10 m depth), from 141±8 to 324±23 shoot per m2 at intermediate depth (about 15 m), and from 79±5 to 157±10 shoot per m2 at the lower limit. Regression was also testified by high coverage of dead matte (locally >40%) especially at the lower limit, which was regressive in four meadows and in no case did it exceed 27 meters in depth. The temporal comparison provided consistent results between the two years for investigation of shoot density, at all sites and throughout the bathymetric range. However, some changes were detected in the deepest portions of both meadows in the coverage of Posidonia oceanica (lower than 50% in 2014). Further monitoring and research campaigns are recommended to improve the level of knowledge on the status of meadows in this area, to develop a baseline for assessing trends on a long-term temporal scale as requested by Habitats Directive, and to shed light on the relevance of both environmental and anthropogenic factors in determining the health status of the meadows. Intercalibration among operators is also suggested to ensure reliable data in implementing the National Monitoring Programme.
Wristwatches predict personality and punctuality
Authors: Ellis David A , Jenkins Rob
Published: January 2018

In exploratory (N>100) and confirmatory samples (N>600), we compared big-five personality traits between individuals who do or do not regularly wear a traditional wristwatch. Alongside lower levels of extraversion and openness, significantly higher levels of conscientiousness were observed in participants who wear a watch. In a third study (N=85), we observed that watch wearers arrive significantly earlier to appointments in comparison to controls. These results are discussed in relation to the rise of wearable technology including smartwatches.