bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic testing of landlocked Kildin cod (Gadus morhua kildinensis) for its ancestral state: stationary or migratory ecotype?
Authors: Teterina Anastasia A , Zhivotovsky Lev A
Published: January 2018

Kildin cod is a small landlocked population of Atlantic cod reproductively isolated from marine counterparts for around 1500-2000 years. The Kildin cod lives in a shallow meromictic lake in the five-meter intermediate layer of water with sharp gradients of oxygen and salinity. The cod had an effective population size of around one hundred individuals and evolved unique physiological, morphological and behavioral features. The marine Atlantic cod has two ecologically distinct forms: the stationary (coastal) and migratory (deep-water) ecotypes that differ in migratory behavior and habitat preferences (the depth, oxygen content, salinity and temperature). To understand the origin and genetic properties of Kildin cod, we scrutinized genomic regions associated with the cod ecotypes differentiation (LG1, LG2, and LG7) and found out that Kildin cod’s regions LG2 and LG7 were fixed with the migratory variants, whereas polymorphic LG1 had a higher frequency of the stationary variant, that could be explained by the possible strong genetic drift. The lake cod investigated had four times lesser genome diversity than marine population. Our finding suggests that Kildin cod originated from the migratory ecotype of the marine cod.
Fifteen novel microsatellites for the Louisiana Waterthrush (Aves: Parulidae: Parkesia motacilla) using MiSeq sequencing
Authors: Von Hagen R. Lynn , Khan Rafia A , Woltmann Stefan
Published: January 2018

The Louisiana Waterthrush (Parkesia motacilla) breeds along wooded streams throughout much of eastern North America, and winters in the Caribbean and Central America. Because of its dependence on stream macroinvertebrates—which are themselves dependent on high water quality—the Louisiana Waterthrush may serve as a useful bioindicator of both stream and landscape integrity. Perhaps unique among eastern North American songbirds, the Louisiana Waterthrush often maintains essentially linear territories along streams, and this provides a unique context in which to ask questions about the genetic (as opposed to social) mating system of this species. We developed 15 microsatellite loci for Louisiana Waterthrush using MiSeq sequencing. All loci presented here are polymorphic, with 3-15 alleles detected in a reference sample of 35-43 individuals. For parentage analyses, these loci have a combined non-exclusion probability of 0.0011 if neither parent is known a priori, and a non-exclusion probability of < 0.0001 if one parent is known. These 15 loci thus provide high discriminatory power to assign parentage to nestlings, and can also be used to examine population genetic structure within the species.
High non publication rate from publication professionals hinders evidence-based publication practices: a replication study in Europe
Authors: Marchington Jacqueline M
Published: January 2018

Background: Although publication professionals plan and facilitate the timely and high-quality reporting of clinical trial results, it has been previously shown that they are not as forthcoming when it comes to publishing their own professional research. The publication rate from abstracts presented at the Annual Meeting of the International Society for Medical Publication Professionals (ISMPP) has been shown to be 2.4%. We performed a replication study based on the European Meeting of ISMPP to determine the equivalent publication rate.

Methods: ISMPP European Meeting abstract lists (November 2011–January 2016), were searched in July 2016 and extracted into a copy of the original study spreadsheet. MEDLINE was searched in August 2016 to determine the publication rate.

Results: From 2011 to 2016, 76 abstracts were submitted of which 60 were accepted (78.9%). We found three corresponding publications (publication rate 5.0%). Most studies were observational (50/60; 83.3%) and most abstracts included employees of medical communications agencies as authors (50/60; 83.3%). Most researchers were based in Europe (165/222; 74.3%) or the US (53/222; 23.9%).

Discussion: This study confirms previous findings that the publication rate of member research from ISMPP meetings in the peer-reviewed literature is low. Members of ISMPP, and of other organizations who aspire to set professional standards, should be encouraged to conduct robust research and share it with the academic community.
Overexpression of 2-Cys Prx increased salt tolerance of photosystem Ⅱ(PSⅡ) in tobacco
Authors: Zhang Hui-hui , Xu Nan , Li Xin , Gu Si-yu
Published: January 2018

To explore the plant active oxygen scavenging and photosynthesis function of 2-Cys Prx, a newly discovered member of the antioxidant protease family, the tobacco 2-Cys Prx gene was cloned into the plant expression vector prok Ⅱ. This vector, which is controlled by the constitutive strong promoter CaMV35S, was introduced into tobacco by Agrobacteria-mediated transformation. The 816-bp open reading frame of tobacco 2-Cys Prx encodes 271 amino acids and showed high homology with 2-Cys Prx genes from Solanum lycopersicum, Vitis vinifera, and Populus trichocarpa, indicating 2-Cys Prx gene is highly conserved. The active oxygen metabolism and chlorophyll fluorescence response to salt stress were also studied. Under salt stress, superoxide dismutase (SOD) activity in tobacco leaves increased, while ascorbate peroxidase (APX) activity decreased. Additionally, the donor- and acceptor-side function of photosystem Ⅱ (PSⅡ) were affected by salt stress to different degrees, with the latter significantly more affected than the former. The H2O2 and malondialdehyde content of 2-Cys Prx-overexpression tobacco leaves under salt stress were all significantly lower than those of wild-type (CK) leaves. The PSⅡ maximum photochemical efficiency (Fv/Fm) and the performance index on absorption basis (PIABS) of 2-Cys Prx-overexpression leaves were significantly lower than those of CK leaves under salt stress. Various relative fluorescence intensities of the 2-Cys Prx-overexpression plants exhibited significantly lower increases in amplitude than those of CK plants. Thus, 2-Cys Prx increased the salt tolerance of PSⅡ function and lowered the PSⅡ light inhibition effect in plants under salt stress, suggesting that 2-Cys Prx gene overexpression can alleviate H2O2 buildup and lower the peroxide levels of cytomembrane lipids under salt stress. Thus, 2-Cys Prx gene overexpression can protect oxygen-evolving complex function at the donor side of PSⅡ under salt stress and also improve electron transfer at the acceptor side of PSⅡ.
The Australian science gateways ecosystem
Authors: Barker Michelle
Published: January 2018

This talk examines Australian government initiatives to facilitate the development of science gateways, and identifies the successes and challenges in this approach.

Since 2011 the Australian Government has funded the development of science gateways through the National eResearch Collaborative Tools and Resources ( NeCTAR ) program (www.nectar.org.au). NeCTAR has funded the development of twelve science gateways in diverse disciplines that provide highly collaborative, research-domain oriented, integrative research software infrastructure to meet researcher-defined needs. The virtual laboratories enable over 10,000 users to access data, models, analytical and workflow tools through a single online platform.

NeCTAR also funds the Research Cloud , which provides computing infrastructure, software and services to enable Australia’s research community to store, access, and run data, remotely, rapidly and autonomously. NeCTAR Cloud’s self-service structure allows over 7,500 users to access their own data at any time and collaborate with others from their desktop in a fast and efficient way. NeCTAR aims to enhance research collaboration through the development of eResearch infrastructure.

This paper explores the structure of the NeCTAR Virtual Laboratory program, its successes and challenges, and future plans. Key features of the program include creation of platforms where tools, models and data meeting, enabling automating and sharing of research methodologies and democratisation of access. As such, the Virtual Laboratories deliver transformative research impacts and are exemplars for sector adoption of capability. Virtual Laboratories exist in disciplines including climate and weather science, genomics, characterisation, biodiversity and climate change, astronomy, human communication science, marine studies, geophysics, endocrine disorders, and cultural studies.

Some of the enabling factors include governance structures that emphasise ownership of the Virtual Laboratories by the research community, strong user engagement in development and a support program that assists in enabling issues across the Virtual Laboratories. This has run project in areas such as provenance, authentication, security, data movement and user support. Challenges exist in sustaining a strategic approach to research software infrastructure, particularly strengthening the focus on shared research software services, improving research software quality, reliability and sustainability, and building capability within the research communities.

This paper will also provide opportunities for comparison and identification of potential alignment with other national/regional/disciplinary programs. Europe and USA have both initiated funding programs that have some similarities to the NeCTAR Virtual Laboratories program; however, these also take some different approaches on some issues.
Selective enhancement of attentional networks in college table tennis athletes: a preliminary investigation
Authors: Wang Biye , Guo Wei , Zhou Chenglin
Published: January 2018

The purpose of the study was to investigate the characteristics of the attentional network in college table tennis athletes. A total of 65 college students categorized as table tennis athlete group or non-athlete group participated in the study. All participants completed the attentional network test (ANT) which measured the alerting, orienting and executive control networks. The results showed a significant difference between the athlete and non-athlete group for executive control network (p <0.01), while no differences were observed for alerting (p>0.05) or orienting (p>0.05) networks. These results combined suggest that college table tennis athletes exhibited selectively enhanced executive control of attentional networks.
A microservice-based portal for X-ray transient and variable sources
Authors: D'Agostino Daniele , Roverelli Luca , Zereik Gabriele , De Luca Andrea , Salvaterra Ruben , Belfiore Andrea , Lisini Gianni , Novara Giovanni , Tiengo Andrea
Published: January 2018

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project is harvesting the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Imaging Camera (EPIC) instrument onboard the ESA XMM-Newton, in 16 years of observations. Part of this analysis is performed through a dedicated science gateway, the EXTraS portal, whose initial release is the subject of this paper. In particular the focus is on its light software architecture, based on the use of microservices, providing a better resilience and more decoupled development lifecycle with respect to the approaches followed by the most used science gateway toolkits.
Interoperability and FAIRness through a novel combination of Web technologies
Authors: Wilkinson Mark D , Verborgh Ruben , Bonino da Silva Santos Luiz Olavo , Clark Tim , Swertz Morris A , Kelpin Fleur D.L. , Gray Alasdair J. G. , Schultes Erik A. , van Mulligen Erik M. , Ciccarese Paolo , Thompson Mark , Kaliyaperumal Rajaram , Bolleman Jerven T. , Dumontier Michel
Published: January 2018

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, or EUDat). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved even to the level of an individual spreadsheet cell. We note that the behaviors of this architecture compare favorably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.
The effects of exercise-induced heat stress on cognitive function in firefighters
Authors: Williams-Bell F. Michael , McLellan Tom M , Murphy Bernadette A
Published: January 2018

Background. Firefighting requires tremendous cognitive demands including assessing emergency scenes, executing critical decisions, and situational awareness of their surroundings. The aim of this study was to determine the effects of differing rates of increasing core temperature on cognitive function during exercise-induced heat stress.

Methods. Nineteen male firefighters were exposed to repeated cognitive assessments, randomized and counter-balanced, in 30°C and 35°C and 50% humidity. Participants performed treadmill walking (4.5 km.h-1 and 2.5% grade) with cognitive function assessed before exercise (PRE), after mounting the treadmill (Cog 1), at core temperatures of 37.8°C (Cog 2), 38.5°C (Cog 3), and 39.0°C (Cog 4), after dismounting the treadmill (POST), and following an active cooling recovery to a core temperature of 37.8°C (REC). The cognitive tests implemented at PRE and POST were spatial working memory (SWM), rapid visual information processing (RVP), and reaction time (RTI) while paired associates learning (PAL) and spatial span (SSP) were assessed at Cog 1, Cog 2, Cog 3, and Cog 4. All five cognitive tests were assessed at REC.

Results. Planned contrasts revealed that SSP and PAL were impaired at Cog 3, with SSP also impaired at Cog 4 compared to Cog 1. REC revealed no difference compared to Cog 1, but increased errors compared to Cog 2 for PAL.

Conclusions. The decrements in cognitive function observed at a core temperature of 38.5°C are likely attributed to the cognitive resources required to maintain performance being overloaded due to increasing task complexity and external stimuli from exercise-induced heat stress. The addition of an active cooling recovery restored cognitive function to initial levels.
High-throughput sequencing identifies distinct fecal and mucosal gut microbiota correlating with different mucosal proteins
Authors: Dong Li-na , Wang Jun-ping , Liu Ping , Yang Yun-feng , Feng Jing , Han Yi
Published: January 2018

The intestinal microbiota is associated with human health. The luminal microbiota (LM) and mucosa-associated microbiota (MAM) are distinct ecosystems with different metabolic and immunological functions. Several studies have examined the correlations between the gut microbiota and clinical indices, but few have investigated the relationships between the microbiota and mucosal proteins. We characterized the intestinal LM and MAM in Chinese people and examined the association between these communities and the expression of mucosal proteins. Fresh fecal samples and distal colonic mucosal biopsies were collected from 32 subjects before (fecal) and during (mucosal) flexible sigmoidoscopy. We used high-throughput sequencing targeting the 16SrRNA gene V3–V4 region to analyze the samples and reverse transcription(RT)–PCR to detect the expression of colonic proteins BDNF, ZO1, TLR2, TLR4, AQP3, and AQP8. Differences in the stool and mucosal microbiota were identified and a correlation network analysis performed. The LM and MAM populations differed signiﬁcantly. In LM, the microbiota composition correlated significantly positively with host age, and Firmicutes (phylum) correlated positively with body mass index (BMI), but inversely with ZO1.At the genus level, systemic indices, such as age, BMI, and BDNF, correlated predominantly with LM, whereas systemic and local indices, such as TLR2, correlated with both MAM and LM. ZO1 and TLR4 which usually exert a local effect, mainly correlated with MAM. Different bacteria were associated with the expression of different proteins. Our data suggest that The microbial compositions of LM and MAM differed. Different gut bacteria may play different roles by regulating the expression of different proteins.
Endocrine disruption: Where are we now: Tier 2 testing
Authors: Ottinger Mary Ann , Flynn Kevin , Degitz Sigmund J , Verslycke Tim , Krueger Hank , Touart Leslie W , Olmstead Allen , Goumelon Anne
Published: January 2018

The focus of this session was on the proposed USEPA Endocrine Disruption Screening Program (EDSP) Tier 2 testing protocols. Tier 2 tests have been developed to evaluate the potential impacts of endocrine disrupting chemicals (EDCs) over the life cycle across organisms representing vertebrate and invertebrate classes. Key aspects of these Tier 2 testing protocols rely on selecting appropriate measurement end points to reveal differential sensitivity and adverse impacts across an organism’s life stages. To this end, certain Tier 2 tests utilize a multigenerational protocol, which detect both short- and long-term effects. However, multigenerational testing protocols can be time consuming and costly. As such, other testing protocols have also been considered, including partial life-cycle and extended one-generation tests. Regardless of the specifics of the multigenerational protocol, it is critical to identify key measurement end points that are responsive, reliable, and repeatable indicators of exposure to endocrine disrupting chemicals; these measures should also provide information to enable initial assessments of risk translated from individual to potential population level effects across a variety of living organisms. Presentations in Session three of the Society of Environmental Toxicology and Chemistry (SETAC) North America Focused Topic Meeting: Endocrine Disruption (February 4 – 6, 2014) focused on the current state of the science for EPA EDSP Tier 2 testing. Presentations in this session considered the strengths and weaknesses of the Tier 2 assays across several classes of organisms, and provided an industry perspective on Tier 2 testing. The interactive panel discussion provided an interesting perspective that balanced regulatory needs for reliable testing protocols that are highly repeatable and utilize consistent indices of exposure and adverse effect.
A comparison of models for interval-censored plant cover data, with applications to monitoring schemes
Authors: Pescott Oliver L , Jitlal Mark , Smart Simon M , Walker Kevin J , Roy David B , Freeman Stephen N
Published: January 2018

Plant cover data collected by monitoring schemes are often expressed on interval-censored scales to reduce field effort. Existing statistical approaches to such data may not make full use of available information, or may both induce bias and assume more precision than may be warranted, e.g. by analysing mid-points and disregarding the spread of observations within a class.

We compare four approaches to modelling such data: two established methods (the proportional odds model and generalised linear mixed models) and two novel methods that explicitly accommodate the interval-censored nature of much data on plant cover. Of the latter, the first is a maximum likelihood (ML) approach that incorporates knowledge of the metric interval in which each datum lies. The second uses a Bayesian approach to incorporate interval-censoring and random effects to account for variation in annual changes between sites. All four methods are compared using data simulated with parameter values derived from analysis of a long-term monitoring dataset.

We demonstrate that model choice can influence the quality of statistical inference, particularly between models that make simplifications for convenience of fitting, and those which combine realistic distributional assumptions with accommodation of imprecise observations. A comparison of three of the methods demonstrated that all provide good accuracy and increasing precision over time. A comparison of power across the three frequentist approaches showed higher power for the novel ML approach. This is likely to be due to this non-hierarchical method underestimating residual variance. The Bayesian model is not directly comparable, but the measure of belief in a negative trend considered here was generally high, providing gradual increases in the believability of a decline with increasing time, number of sites, initial abundance, and larger effect sizes.

Our results suggest that the use of hierarchical models for plant monitoring schemes, conveniently applied in a Bayesian context, will help to bring greater realism and sensitivity to assessments of population change, and allow the use of more of the underlying information contained within cover data. Interval-censored methods will also allow for the integration of long-term plant datasets collected according to different cover scales, as well as presence/absence data.
Technology to limit the available number of chosen-plaintext
Authors: Kazawa Ichiroh
Published: January 2018

This technology sets an upper limit on the number of available pairs for chosen-plaintext and ciphertext in any chosen-plaintext-attack (CPA).By applying the typical implementation of 128-bit encryption, all CPAs cannot use more than 16 chosen-plaintexts.It does not encrypt the plaintext directly with this technique.256 kinds of variations are created from the plaintext.

It then chooses one variation at random to encrypt.

Unless the encryption key is used in decryption, it is impossible to find out which of the 256 kinds of variations was used for the ciphertext.

A CPA when used for multiple chosen-plaintexts would need to repeat the comparison for the total amount of combinations of the chosen-plaintext.If the CPA increases the total amount of chosen-plaintexts by one, the number of generated encryption keys increased by 256 times.256^{16} (== 2^{128}) encryption keys will be generated from the 16 chosen-plaintexts.Since the the total key possibilities generated exceed the total number of encryption keys, it is not possible for CPA to win with a brute force attack.RC4 is no longer recommended.However, the compactness of RC4 in embedded devices (e.g. RF-ID) has a big advantage in regards to block ciphers such as AES.

Secret Key Size(bit length) / Variations Count(bit length) > Chosen Plaintexts Count(useable count)

** Industrial significance **

RC4 is no longer recommended.

However, the compactness of RC4 in embedded devices (e.g. RF-ID) has a big advantage in regards to block ciphers such as AES.

RC4 can regain its security with this technology.

Compacting embedded devices will lead mainly to the reduction of costs.

It is believed that this technology will contribute greatly to the IoT.

”XORveR”, is this technologies codename.
Gerbils (Meriones unguiculatus) as a new experimental model of obesity induced by diet
Authors: Ventura Luciana L A , Fortes Nathália C L , Santiago Helton C , Caliari Marcelo Vidigal , Gomes Maria A , Oliveira Dirce R
Published: January 2018

Background. Currently, the number of obese people in the world has reached alarming proportions. During the expansion of adipose tissue, a number of functions such as activation and release of cytokines and hormones may be affected. This causes the body to take a pro-inflammatory pattern, which may affect the proper functioning of many tissues. Thus, studying the mechanisms by which obesity induces physiological disorders is necessary, and may be facilitated by the use of animal models, in particular rodents. We sought to investigate whether the gerbil (Meriones unguiculatus) would be a good experimental model for the study of obesity and metabolic changes resulting from a diet rich in fats and sugars. Methods. 14 gerbils were divided according to weight into two experimental groups and received a a standard diet with 4,15kcal/g (CT; n = 7) or a diet rich in simple carbohydrates and fats with 5,86kcal/g (OB, n = 7) for 11 weeks. The animals had free access to water and food. The weight of each animal and food consumption of each cage were measured weekly and at the end of the experiment, blood, adipose tissue and liver were collected. The following parameters were determined: cholesterol (COL), triglycerides (TGL) and glycemia (GLI) in the plasma; cytokines (IL-6, IL-10 and TNF-α) and hormones (adiponectin and leptin) in adipose tissue; activity of superoxide dismutase (SOD) and catalase (CAT), extraction and differentiation of fat in the liver and liver histology. Results. The consumption of a diet rich in simple fats and carbohydrates led to an increase of total body weight, relative weights of liver and adipose tissue, glucose and triglycerides levels, and TNF-α concentration in adipose tissue. Animals of this group also showed a significant increase of total fat, cholesterol and triglyceride content in the liver, contributing to higher intensity of hepatic steatosis. On the other hand, depletion in the enzyme activity of SOD and CAT in the liver, as well as reduction of IL-10 and adiponectin levels were found in adipose tissue of these animals. Conclusion. Diet consumption consisting of an excess in saturated fat and simple carbohydrates establish the gerbil as an experimental model for the study of obesity and metabolic and liver abnormalities resulting from this disease.
Fast Access to Remote Objects 2.0 A renewed gateway to ENEAGRID distributed computing resources
Authors: Mariano Angelo , D'Amato Giulio , Ambrosino Fiorenzo , Aprea Giuseppe , Colavincenzo Antonio , Fina Marco , Funel Agostino , Guarnieri Guido , Palombi Filippo , Pierattini Samuele , Ponti Giovanni , Santomauro Giuseppe , Bracco Giovanni , Migliori Silvio
Published: January 2018

This paper introduces a renewed gateway to ENEAGRID distributed computing resources, named Fast Access to Remote Objects 2.0 (FARO 2.0). FARO 2.0 is a tool for application and desktop virtualization with a strong focus towards user experience (UX), providing trained as well as untrained users a collection of centralized services that can be seamlessly used on their client through a remote desktop protocol. FARO 2.0 is a JavaFX application whose graphical user interface (GUI) and whose main logics has been implemented through the well- known Web technologies (HTML5, CSS3, Javascript) for a easier maintainability and customizability, taking full advantage of the WebView component. Its framework has been deployed both as general purpose GUI for remote user access to ENEAGRID resources and as specialized application or workflow oriented GUI. They are applied in a set of applicative domains, ranging from material science to technologies for energy and industry, environmental modeling and nuclear fusion. Some examples and results are also presented.
A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
Authors: Redelings Benjamin D , Holder Mark T
Published: January 2018

We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree.

We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies.

This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project's "synthetic tree" starting at version 5. This software pipeline is called "propinquity". It relies heavily on "otcetera" - a set of C++ tools to perform most of the steps of the pipeline. All of the components are free software and are available on GitHub.
Virtual reconstruction of the brain and sinuses of the early Jurassic marine crocodylomorph Pelagosaurus typus (Thalattosuchia)
Authors: Pierce Stephanie E , Williams Megan , Benson Roger BJ
Published: January 2018

Thalattosuchians were highly specialised marine archosaurs of the Jurassic and Early Cretaceous, and represent a peak of aquatic adaptation among crocodylomorphs. Relatively little is known of their endocranial anatomy or its relevance for the evolution of sensory systems, physiology, and other aspects of biology. Nevertheless, such data have significance for two reasons: (1) thalattosuchians represent an important data point regarding adaptation to marine life in tetrapods; and (2) as early-diverging members of the crocodylian stem-lineage, thalattosuchians provide information on the evolutionary assembly of the brain and other endocranial structures in crocodylomorphs. Here we use µCT data to virtually reconstruct the brain and sinuses of Pelagosaurus typus, an early thalattosuchian with plesiomorphic traits of relevance to the split between the two major subgroups: Teleosauroidea and Metriorhynchoidea. Interpreted in a phylogenetic context, these data indicate several endocranial features as likely synapomorphies of Thalattosuchia, including: a pyramidal morphology of the semicircular canals, the presence of an elongate cochlear duct that may indicate enhanced hearing ability, the presence of large, paired canals extending anteriorly from an enlarged pituitary fossa, a relatively straight brain (possibly due to the presence of large, laterally placed orbits) and an enlarged dorsal longitudinal sinus that is confluent with the paratympanic sinus system. Notably, we document a large expansion of the nasal cavity anterior to the orbits in Pelagosaurus as an osteological correlate of an enlarged salt gland previously only documented in Late Jurassic metriorhynchoids. This is the first direct evidence of this structure in early thalattosuchians. Pelagosaurus also shares the presence of paired olfactory tracts with metriorhynchoids, and shows an enlarged cerebrum, which may also be present in teleosauroids. Taken together, our findings indicate that physiological and sensory adaptations to marine life occurred early in thalattosuchians evolution, predating the origins of flippers, tail flukes, and hydrodynamic body forms seen later in metriorhynchoids.
Relative toxicity of herbicide use in the United States 1990 to 2015
Authors: Kniss Andrew R
Published: January 2018

Herbicide use is among the most criticized aspects of modern farming operations, especially in response to widespread adoption of genetically-engineered (GE) herbicide-resistant crops. Many previous analyses of herbicide use have relied on flawed metrics in an attempt to evaluate trends in herbicide intensity and toxicity. Here, it is shown that herbicide use intensity has increased over the last 25 years in corn, cotton, rice, and wheat. Although GE glyphosate-resistant crops have been previously blamed for increasing herbicide use, herbicide use increased more rapidly in the non-GE crops rice and wheat. Even as herbicide use has increased, the chronic toxicity hazard associated with herbicide use decreased in 3 out of 6 crops, while acute toxicity hazard decreased in 5 out of 6 crops. In GE glyphosate-resistant crops, glyphosate accounted for 26% of corn, 43% of soybean, and 45% of cotton herbicide applications. However, due to it’s relatively low chronic toxicity, glyphosate contributed only 0.1%, 0.3%, and 3.5% of the chronic toxicity hazard in these same crops, respectively.
Genetic and morphological analyses indicate that the Australian endemic scorpion Urodacus yaschenkoi (Scorpiones: Urodacidae) is a species complex
Authors: Luna-Ramirez Karen , Miller Adam D , Rašić Gordana
Published: January 2018

Background. Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom. Methods. We employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual’s membership to a putative species. Results. Genetic and morphological data suggest that U. yaschenkoi is a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83–100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones. Discussion. Our results indicate that the taxonomic status of U. yaschenkoi requires revision, and we provide recommendations for such future efforts. A complex evolutionary history and extensive diversity highlights the importance of conserving U. yaschenkoi populations from different Australian arid zones in order to preserve patterns of endemism and evolutionary potential.
Mouse sperm delivery via cauda epididymis without transport medium
Authors: Jiang Man-Xi , Wang Mei-Shan , Ou Xiang-Hong , Chen Xue-Jin , Zhu Yan
Published: January 2018

This study was aimed to investigate the effects of room temperature (RT, 20-25 oC) and absence of medium during cauda epididymis transport on spermatozoa quality, fertility and embryo development. In the first experiment, fresh sperm from one side of cauda epididymis was used for in vitro fertilization, and another side was delivered at RT or 4-8 oC either with or without M2. In the second experiment, each side of cauda epididymis obtained from the same mouse was individually delivered at RT or 4 oC with or without M2. Finally, sperm motility, progressive motility scores and fertility of fresh spermatozoa or those from transported cauda epididymis, and IVF embryo development were evaluated. Progressive motility scores and fertilization rates were higher in fresh spermatozoa than transported sperm; sperm motility of transported cauda epididymis at 4-8 oC was comparable to fresh spermatozoa, but spermatozoa motility of transported cauda epididymis at RT was inferior to fresh spermatozoa. Spermatozoa motillty of transported cauda epididymis at 4-8 oC with transport medium was much higher than that without transport medium; absence of transport medium did not affect sperm motility of transported cauda epididymis at 4-8 oC but affected sperm motility of transported cauda epididymis at RT. Sperm quality from transported cauda epididymis can be efficiently kept at 4-8 oC, and cauda epididymis transport at 4-8 oC without M2 is more beneficial on keeping their fertility. Moreover cauda epididymis transport at RT without medium could sufficiently produce embryos for obtainning live offsprings.
Information extraction and transparency in big data processing
Authors: Clay Ieuan
Published: January 2018

Developing new endpoints for mobility is an important strategic aim for many groups both in industry and academia and the focus of a growing field. Bringing those novel endpoints to health authority acceptance for clinical decision making will require a concerted effort from this research community. This in turn will require openness and transparency; sharing data, methods and findings. Here we discuss challenges within the field to such an open approach and give examples of how they might be overcome.
Bax-inhibitor-1 loss of function phenotypes are suppressed by Buffy in Drosophila
Authors: M'Angale P Githure , Staveley Brian E
Published: January 2018

Background. Bax Inhibitor-1 (BI-1), an integral transmembrane protein, acts as a suppressor of Bax-induced apoptosis through regulation of endoplasmic reticulum (ER) stress-induced cell death. The gene is highly conserved being found in a diverse range of organisms that include yeast, Arabidopsis, Drosophila, mouse and humans. BI-1 is implicated in the regulation of calcium levels, reactive oxygen species, apoptosis, autophagy and ER stress signalling pathways. We inhibited the cytoprotective BI-1 in the dopa decarboxylase (Ddc) expressing neurons and in the developing eye of Drosophila melanogaster to investigate its neuroprotective functions. Methods. We assessed the longevity and locomotor ability of flies in response to altered BI-1 expression in the Ddc-Gal4-expressing neurons where we exploited two RNAi transgenic fly lines. A control that expressed the benign lacZ responding transgene was used to compare against the RNAi transgenic flies. In addition, we compared the effect of the loss of BI-1 expression in the developing eye, through biometric analysis of the number of ommatidia and extent of disruption of the ommatidial arrays. Finally, Buffy and α-synuclein were co-expressed to evaluate the potential for interactions. Results. The inhibition of BI-1 in these neurons resulted in a shortened lifespan and precocious loss of locomotor ability. The co-expression of Buffy, the sole anti-apoptotic Bcl-2 homologue in Drosophila, with BI-1-RNAi resulted in suppression of the reduced lifespan and impaired climbing ability. Expression of human α-synuclein in Drosophila dopaminergic neurons results in age-dependent loss in climbing ability. We exploited this neurotoxic system to investigate possible BI-1 neuroprotective function. The co-expression of α-synuclein with BI-1-RNAi results in decreased survival coupled with an impaired climbing ability. In supportive experiments, we employed the neuron-rich Drosophila compound eye to investigate subtle phenotypes that result from altered gene expression. The inhibition of BI-1 in the Drosophila developing eye under the direction of the GMR-Gal4 transgene results in reduced ommatidia number and increased disruption of the ommatidial array. Similarly, the co-expression of BI-1-RNAi with Buffy results in the suppression of the eye phenotypes. The expression of α-synuclein along with the inhibition of BI-1 results in reduction of ommatidia number and increased disruption of the ommatidial array. Conclusions. Inhibition of BI-1 in the dopaminergic neurons of Drosophila results in a shortened lifespan and premature loss in climbing ability, phenotypes that appear to be strongly associated with models of Parkinson disease in Drosophila. These are suppressed upon overexpression of Buffy and worsened by co-expression with α-synuclein. This suggests that BI-1 acts in neuroprotection and that its inhibition can be counteracted by the overexpression of the pro-survival Bcl-2 homologue, Buffy.
Testing the habituation assumption underlying models of parasitoid foraging behavior
Authors: Abram Paul K , Cusumano Antonino , Abram Katrina , Colazza Stefano , Peri Ezio
Published: January 2018

Habituation, a form of non-associative learning, has several well-defined characteristics that apply to a wide range of physiological and behavioral responses in many organisms. In classic patch time allocation models, habituation is considered to be a major mechanistic component of parasitoid behavioral strategies. However, parasitoid behavioral responses to host cues have not previously been tested for the known, specific characteristics of habituation. Here, we tested whether the foraging behavior of the egg parasitoid Trissolcus basalis shows specific characteristics of habituation in response to consecutive encounters with patches of host (Nezara viridula) chemical contact cues (footprints), in particular: (i) a training interval-dependent decline in response intensity, and (ii) a training interval dependent recovery of the response. As would be expected of a habituated response, wasps trained at higher frequencies decreased their behavioral response to host footprints more quickly and to a greater degree than those trained at low frequencies, and subsequently showed a more rapid, although partial, recovery of their behavioral response to host footprints. In contrast to previously studied forms of parasitoid memory (i.e., from associative learning), this putative habituation learning could not be blocked by cold anesthesia, ingestion of an ATPase inhibitor, or ingestion of a protein synthesis inhibitor. Our study provides support for the assumption that diminishing responses of parasitoids to chemical indicators of host presence constitutes habituation as opposed to sensory fatigue, and may indicate that the underlying mechanisms differ from other, better-studied forms of parasitoid learning.
Migrating bats cross top of Europe
Authors: Zingg Peter E , Bontadina Fabio
Published: January 2018

Bats have evolved migration to escape unfavourable climatic conditions. However, their migratory flyways and the way how they surmount geographical barriers are still unknown. The Jungfraujoch in the Swiss Alps is a mountain covered in permafrost (3460m ASL), known colloquially as the “Top of Europe”. Using broadband ultrasound recorders, we tested the occurrence of bats at the high altitude research station. In 36 nights, we recorded 268 bat call sequences of 8 species, including all European long-distance migrant bats. Since no feeding buzzes were recorded, we assume the bats were on transit. This is the first evidence to show that migrating bats can fly at unprecedented altitudes to cross the Alps. This feat outperforms the spectacular behaviour of the high altitude foraging bat Tadarida brasiliensis. Our findings shed light on the bats’ migratory flyways and demonstrate that the field of aeroecology can still uncover unexpected perspectives on the behaviour of bats.
Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas
Authors: Truelove Nathan K , Fai Ho Loong , Preziosi Richard F , Box Stephen J.
Published: January 2018

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.
A review and meta-analysis of the enemy release hypothesis in plant–herbivorous insect systems
Authors: Meijer Kim , Schilthuizen Menno , Beukeboom Leo , Smit Christian
Published: January 2018

A suggested mechanism for the success of introduced non-native species is the enemy release hypothesis (ERH). Many studies have tested the predictions of the ERH using the community approach (native and non-native species studied in the same habitat) or the biogeographical approach (species studied in their native and non-native range), but results are highly variable, possibly due to large variety of study systems incorporated. We therefore focused on one specific system: plants and their herbivorous insects. We performed a systematic review and compiled a large number (68) of datasets from studies comparing herbivorous insects on native and non-native plants using the community or biogeographical approach. We performed a meta-analysis to test the predictions from the ERH for insect diversity (number of species), insect load (number of individuals) and level of herbivory for both the community and biogeographical approach. For both the community and biogeographical approach insect diversity was significantly higher on native than on non-native plants. Insect load tended to be higher on native than non-native plants at the community approach only. Herbivory was not different between native and non-native plants at the community approach, while there was too little data available for testing the biogeographical approach. Our meta-analysis generally supports the predictions from the ERH for both the community and biogeographical approach, but also shows that the outcome is importantly determined by the response measured and approach applied. So far, very few studies apply both approaches simultaneously in a reciprocal manner while this is arguably the best way for testing the ERH.